From e890443185840604b4782dab4bbb948c673de456 Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Tue, 14 Jan 2025 21:59:17 -0800 Subject: [PATCH 01/30] revert: "correcting spelling of VEuPathDB (#202)" This reverts commit 5d050df0326805118f0bf915e18667c56e53843e. --- .../brc-analytics-catalog/common/entities.ts | 2 +- .../Organisms/content/organismsWarning.mdx | 2 +- .../Home/content/sectionSubHero.mdx | 2 +- app/components/content/sectionAbout.mdx | 2 +- app/components/content/sectionRoadmap.mdx | 20 +- .../common/viewModelBuilders.ts | 6 +- app/views/RoadmapView/roadmapView.tsx | 2 +- files/build-catalog.ts | 2 +- files/out/genomes.json | 1488 ++++++++--------- files/source/organisms-from-ncbi.tsv | 24 +- site-config/brc-analytics/category.ts | 2 +- .../local/index/genomeEntityConfig.ts | 2 +- 12 files changed, 777 insertions(+), 777 deletions(-) diff --git a/app/apis/catalog/brc-analytics-catalog/common/entities.ts b/app/apis/catalog/brc-analytics-catalog/common/entities.ts index ef046a1..6ec031a 100644 --- a/app/apis/catalog/brc-analytics-catalog/common/entities.ts +++ b/app/apis/catalog/brc-analytics-catalog/common/entities.ts @@ -20,7 +20,7 @@ export interface BRCDataCatalogGenome { strain: string; supercontigs: number; ucscBrowserUrl: string; - vEuPathDBProject: string; + vEuPathDbProject: string; } export interface EntitiesResponse { diff --git a/app/components/EntityList/components/Organisms/content/organismsWarning.mdx b/app/components/EntityList/components/Organisms/content/organismsWarning.mdx index f2da0ca..6645d3d 100644 --- a/app/components/EntityList/components/Organisms/content/organismsWarning.mdx +++ b/app/components/EntityList/components/Organisms/content/organismsWarning.mdx @@ -1,7 +1,7 @@ If you do not see your organism in this list: it will be there! We are in the process of ingesting sequences and annotations for all 785 taxa from - VEuPathDB. The table below is generated by comparing the list maintained by + VEuPathDb. The table below is generated by comparing the list maintained by VEuPathDB against official NCBI genome builds. The three buttons adjacent to each taxon direct you to a page listing available analytical workflows as well as direct links to genomic data (NCBI Datasets) and a genome browser (UCSC). A diff --git a/app/components/Home/content/sectionSubHero.mdx b/app/components/Home/content/sectionSubHero.mdx index de87de0..da94f3a 100644 --- a/app/components/Home/content/sectionSubHero.mdx +++ b/app/components/Home/content/sectionSubHero.mdx @@ -1,5 +1,5 @@ BRC Analytics is your new destination for analysis of biological -data related to pathogens. Building on the foundation of VEuPathDB +data related to pathogens. Building on the foundation of VEuPathDb the platform will provide access and analysis capabilities for [785 eukaryotic pathogens](/data/organisms), hosts, and vectors. The functionality will be developed and made available incrementally over the [following months](/roadmap). diff --git a/app/components/content/sectionAbout.mdx b/app/components/content/sectionAbout.mdx index 7f03fea..d1b0f9d 100644 --- a/app/components/content/sectionAbout.mdx +++ b/app/components/content/sectionAbout.mdx @@ -170,7 +170,7 @@ Biotechnology Information (NCBI) supplemented with custom annotations stored and distributed by the UCSC Table Browser. This data will include annotations that were previously available from - the VEuPathDB resource. Users will be able to view, download and + the VEuPathDb resource. Users will be able to view, download and visualize the data.{" "} diff --git a/app/components/content/sectionRoadmap.mdx b/app/components/content/sectionRoadmap.mdx index 60c56b6..2a8f336 100644 --- a/app/components/content/sectionRoadmap.mdx +++ b/app/components/content/sectionRoadmap.mdx @@ -10,28 +10,28 @@ - VEuPathDB database migration + VEuPathDb database migration - This set of tasks deals with transferring data from VEuPathDB + This set of tasks deals with transferring data from VEuPathDb infrastructure and creating a list of genomes that will be initially maintained within BRC Analytics. The number of taxa included in our system will - 1. Transferring databases and associated data from VEuPathDB servers to TACC infrastructure. - 1. Understanding the structure of VEuPathDB database and deciding which data will be ingested as custom + 1. Transferring databases and associated data from VEuPathDb servers to TACC infrastructure. + 1. Understanding the structure of VEuPathDb database and deciding which data will be ingested as custom tracks for the BRC Analytics instance of the UCSC Genome Browser. - 1. Uncovering how JBrowse instances were created within VEuPathDB gene pages and replicating this data at + 1. Uncovering how JBrowse instances were created within VEuPathDb gene pages and replicating this data at the BRC Analytics instance of the UCSC Genome Browser. Harmonization of genomic data for all taxa - This set of tasks ensures that BRC Analytics provides access to the latest versions of all 785 VEuPathDB + This set of tasks ensures that BRC Analytics provides access to the latest versions of all 785 VEuPathDb taxa and associated annotations. - 1. Build UCSC Genome Browsers for all 785 taxa by matching genomes found in VEuPathDB against NCBI Datasets. - 1. Add annotations that can be extracted from the VEuPathDB databases and JBrowse instances (related to 2 + 1. Build UCSC Genome Browsers for all 785 taxa by matching genomes found in VEuPathDb against NCBI Datasets. + 1. Add annotations that can be extracted from the VEuPathDb databases and JBrowse instances (related to 2 and 3 above) 1. Create links from UCSC Gene Pages to NCBI Gene pages 1. Work with NCBI on evolution of gene pages to contain information valuable for understanding the structure @@ -52,7 +52,7 @@ 1. Develop "simplified workflow" interface (see [Simplified workflow run interface galaxy#18883](https://github.com/galaxyproject/galaxy/issues/18883)) 1. Develop and polish workflows for variant discovery, epigenetics, transcriptomics, assembly, and protein - folding that were previously available to the users on VEuPathDB Galaxy instance. + folding that were previously available to the users on VEuPathDb Galaxy instance. @@ -60,7 +60,7 @@ 1. Create dedicated linkedin, mastodon, and bluesky accounts 1. Create a dedicated support channel using Discourse infrastructure. - 1. Try to connect with as many users of VEuPathDB as possible to solicit their feedback across multiple + 1. Try to connect with as many users of VEuPathDb as possible to solicit their feedback across multiple areas including: which features are needed, what genomes should be integrated, which key datasets need to be re-analyzed in put in the context of available genomic data. 1. Beginning on Oct 1st begin posting regular updates via social media channels. diff --git a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts index f2a6d1e..49a7e47 100644 --- a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts +++ b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts @@ -156,7 +156,7 @@ export const buildGenomeDetails = ( value: genome.genomeVersionAssemblyId, }) ); - keyValuePairs.set("VEuPathDB Project", genome.vEuPathDBProject); + keyValuePairs.set("VeUPathDB Project", genome.vEuPathDbProject); keyValuePairs.set("Contigs", genome.contigs); keyValuePairs.set("Super Contigs", genome.supercontigs); keyValuePairs.set("Chromosomes", genome.chromosomes); @@ -225,11 +225,11 @@ export const buildSupercontigs = ( * @param genome - Genome entity. * @returns Props to be used for the cell. */ -export const buildVEuPathDBProject = ( +export const buildVEuPathDbProject = ( genome: BRCDataCatalogGenome ): ComponentProps => { return { - value: genome.vEuPathDBProject, + value: genome.vEuPathDbProject, }; }; diff --git a/app/views/RoadmapView/roadmapView.tsx b/app/views/RoadmapView/roadmapView.tsx index 059bcd5..b17a17b 100644 --- a/app/views/RoadmapView/roadmapView.tsx +++ b/app/views/RoadmapView/roadmapView.tsx @@ -9,7 +9,7 @@ export const RoadmapView = (): JSX.Element => { diff --git a/files/build-catalog.ts b/files/build-catalog.ts index ef18cec..8573975 100644 --- a/files/build-catalog.ts +++ b/files/build-catalog.ts @@ -30,7 +30,7 @@ async function buildGenomes(): Promise { strain: row.Strain, supercontigs: parseNumber(row.Supercontigs), ucscBrowserUrl: row.ucscBrowser, - vEuPathDBProject: row["VEuPathDB Project"], + vEuPathDbProject: row["VEuPathDB Project"], }) ); return mappedRows.sort((a, b) => diff --git a/files/out/genomes.json b/files/out/genomes.json index 4c56cf9..1030336 100644 --- a/files/out/genomes.json +++ b/files/out/genomes.json @@ -10,7 +10,7 @@ "strain": "iso-1", "supercontigs": 1862, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000001215.4", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -23,7 +23,7 @@ "strain": "ATCC 18224", "supercontigs": 452, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000001985.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 14, @@ -36,7 +36,7 @@ "strain": "Sal-1", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002415.2", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 5, @@ -49,7 +49,7 @@ "strain": "isolate WB 2019", "supercontigs": 30, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002435.2", - "vEuPathDBProject": "GiardiaDB" + "vEuPathDbProject": "GiardiaDB" }, { "chromosomes": 16, @@ -62,7 +62,7 @@ "strain": "brucei TREU927", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002445.2", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 7, @@ -75,7 +75,7 @@ "strain": "70-15", "supercontigs": 46, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002495.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 6, @@ -88,7 +88,7 @@ "strain": "NRRL Y-1140", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002515.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 6, @@ -101,7 +101,7 @@ "strain": "CLIB122", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002525.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 13, @@ -114,7 +114,7 @@ "strain": "CBS 138", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002545.3", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 8, @@ -127,7 +127,7 @@ "strain": "Af293", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002655.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -140,7 +140,7 @@ "strain": "NRRL 1", "supercontigs": 143, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002715.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 36, @@ -153,7 +153,7 @@ "strain": "strain Friedlin", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002725.2", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 14, @@ -166,7 +166,7 @@ "strain": "3D7", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002765.5", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 0, @@ -179,7 +179,7 @@ "strain": "G3", "supercontigs": 64764, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002825.2", - "vEuPathDBProject": "TrichDB" + "vEuPathDbProject": "TrichDB" }, { "chromosomes": 36, @@ -192,7 +192,7 @@ "strain": "MHOM/BR/75/M2904", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002845.2", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -205,7 +205,7 @@ "strain": "CBS 513.88", "supercontigs": 19, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002855.4", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -218,7 +218,7 @@ "strain": "yoelii 17XNL", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000003085.2", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 0, @@ -231,7 +231,7 @@ "strain": "ATCC 10500", "supercontigs": 820, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000003125.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 4, @@ -244,7 +244,7 @@ "strain": "strain Ankara", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000003225.1", - "vEuPathDBProject": "PiroplasmaDB" + "vEuPathDbProject": "PiroplasmaDB" }, { "chromosomes": 0, @@ -257,7 +257,7 @@ "strain": "1704", "supercontigs": 44, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000003515.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -270,7 +270,7 @@ "strain": "ER-3", "supercontigs": 25, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000003525.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -283,7 +283,7 @@ "strain": "ATCC 42720", "supercontigs": 9, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000003835.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -296,7 +296,7 @@ "strain": "SLH14081", "supercontigs": 100, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000003855.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -309,7 +309,7 @@ "strain": "strain NEG-M", "supercontigs": 784, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000004985.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -322,7 +322,7 @@ "strain": "NRRL3357", "supercontigs": 282, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000006275.3", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -335,7 +335,7 @@ "strain": "USDA", "supercontigs": 1882, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000006295.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -348,7 +348,7 @@ "strain": "MYA-3404", "supercontigs": 23, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000006335.3", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 14, @@ -361,7 +361,7 @@ "strain": "strain H", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000006355.2", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 0, @@ -374,7 +374,7 @@ "strain": "TU502", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000006425.1", - "vEuPathDBProject": "CryptoDB" + "vEuPathDbProject": "CryptoDB" }, { "chromosomes": 7, @@ -387,7 +387,7 @@ "strain": "CBS767", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000006445.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 8, @@ -400,7 +400,7 @@ "strain": "CD36", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000026945.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 14, @@ -413,7 +413,7 @@ "strain": "var. neoformans JEC21", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000091045.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 11, @@ -426,7 +426,7 @@ "strain": "GB-M1", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000091225.2", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -439,7 +439,7 @@ "strain": "T30-4", "supercontigs": 4921, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000142945.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -452,7 +452,7 @@ "strain": "DAOM BR144", "supercontigs": 975, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000143045.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -465,7 +465,7 @@ "strain": "H4-8", "supercontigs": 25, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000143185.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -478,7 +478,7 @@ "strain": "CBS 148.51", "supercontigs": 21, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000143365.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 18, @@ -491,7 +491,7 @@ "strain": "B05.10", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000143535.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -504,7 +504,7 @@ "strain": "R3-111a-1", "supercontigs": 513, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000145635.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 16, @@ -517,7 +517,7 @@ "strain": "S288C", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000146045.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 11, @@ -530,7 +530,7 @@ "strain": "ATCC 50506", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000146465.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -543,7 +543,7 @@ "strain": "M1.001", "supercontigs": 653, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000149035.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 8, @@ -556,7 +556,7 @@ "strain": "FGSC A4", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000149205.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 14, @@ -569,7 +569,7 @@ "strain": "var. grubii H99", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000149245.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -582,7 +582,7 @@ "strain": "RA 99-880", "supercontigs": 81, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000149305.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -595,7 +595,7 @@ "strain": "RS", "supercontigs": 6, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000149335.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 14, @@ -608,7 +608,7 @@ "strain": "var. neoformans B-3501A", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000149385.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -621,7 +621,7 @@ "strain": "ATCC 6260", "supercontigs": 9, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000149425.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -634,7 +634,7 @@ "strain": "WO-1", "supercontigs": 16, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000149445.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 11, @@ -647,7 +647,7 @@ "strain": "7600", "supercontigs": 10, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000149555.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -660,7 +660,7 @@ "strain": "NAm1", "supercontigs": 276, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000149585.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -673,7 +673,7 @@ "strain": "NIH2624", "supercontigs": 26, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000149615.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -686,7 +686,7 @@ "strain": "NRRL 181", "supercontigs": 163, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000149645.3", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -699,7 +699,7 @@ "strain": "NRRL YB-4239", "supercontigs": 27, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000149685.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 14, @@ -712,7 +712,7 @@ "strain": "GT1", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000149715.2", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -725,7 +725,7 @@ "strain": "strain P6497", "supercontigs": 82, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000149755.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -738,7 +738,7 @@ "strain": "H538.4", "supercontigs": 553, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000149815.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -751,7 +751,7 @@ "strain": "yFS275", "supercontigs": 32, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000149845.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -764,7 +764,7 @@ "strain": "JEL423", "supercontigs": 69, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000149865.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -777,7 +777,7 @@ "strain": "RMSCC 2394", "supercontigs": 23, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000149895.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -790,7 +790,7 @@ "strain": "f. sp. tritici CRL 75-36-700-3", "supercontigs": 392, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000149925.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 15, @@ -803,7 +803,7 @@ "strain": "f. sp. lycopersici 4287", "supercontigs": 70, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000149955.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 14, @@ -816,7 +816,7 @@ "strain": "VEG", "supercontigs": 1290, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000150015.2", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -829,7 +829,7 @@ "strain": "RMSCC 3488", "supercontigs": 6, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000150055.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -842,7 +842,7 @@ "strain": "RMSCC 3703", "supercontigs": 286, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000150085.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -855,7 +855,7 @@ "strain": "A1163", "supercontigs": 55, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000150145.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -868,7 +868,7 @@ "strain": "RMSCC 2133", "supercontigs": 53, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000150185.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -881,7 +881,7 @@ "strain": "RMSCC 3700", "supercontigs": 241, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000150215.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -894,7 +894,7 @@ "strain": "CPA 0001", "supercontigs": 255, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000150245.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -907,7 +907,7 @@ "strain": "Pb03", "supercontigs": 65, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000150475.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -920,7 +920,7 @@ "strain": "yFS286", "supercontigs": 5, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000150505.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -933,7 +933,7 @@ "strain": "RMSCC 1037", "supercontigs": 633, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000150555.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -946,7 +946,7 @@ "strain": "RMSCC 1038", "supercontigs": 551, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000150585.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -959,7 +959,7 @@ "strain": "CPA 0020", "supercontigs": 620, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000150615.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -972,7 +972,7 @@ "strain": "CPA 0066", "supercontigs": 473, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000150645.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -985,7 +985,7 @@ "strain": "Pb01", "supercontigs": 110, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000150705.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -998,7 +998,7 @@ "strain": "Pb18", "supercontigs": 57, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000150735.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1011,7 +1011,7 @@ "strain": "Mali-NIH", "supercontigs": 10521, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000150765.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -1024,7 +1024,7 @@ "strain": "Pimperena", "supercontigs": 13042, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000150785.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -1037,7 +1037,7 @@ "strain": "CBS 118893", "supercontigs": 18, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000150975.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1050,7 +1050,7 @@ "strain": "H143", "supercontigs": 48, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000151035.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1063,7 +1063,7 @@ "strain": "CBS 113480", "supercontigs": 16, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000151145.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1076,7 +1076,7 @@ "strain": "CBS 127.97", "supercontigs": 123, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000151175.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1089,7 +1089,7 @@ "strain": "ATCC 38327", "supercontigs": 101, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000151295.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1102,7 +1102,7 @@ "strain": "C735 delta SOWgp", "supercontigs": 55, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000151335.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1115,7 +1115,7 @@ "strain": "77-13-4", "supercontigs": 209, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000151355.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1128,7 +1128,7 @@ "strain": "CBS 118892", "supercontigs": 35, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000151425.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1141,7 +1141,7 @@ "strain": "CBS 112818", "supercontigs": 110, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000151455.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1154,7 +1154,7 @@ "strain": "1-1 BBBD Race 1", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000151525.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1167,7 +1167,7 @@ "strain": "CBS 223.65", "supercontigs": 1442, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000151545.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1180,7 +1180,7 @@ "strain": "2N", "supercontigs": 3143, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000151735.1", - "vEuPathDBProject": "HostDB" + "vEuPathDbProject": "HostDB" }, { "chromosomes": 8, @@ -1193,7 +1193,7 @@ "strain": "Iowa II", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000165345.1", - "vEuPathDBProject": "CryptoDB" + "vEuPathDbProject": "CryptoDB" }, { "chromosomes": 2, @@ -1206,7 +1206,7 @@ "strain": "strain Muguga", "supercontigs": 6, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000165365.1", - "vEuPathDBProject": "PiroplasmaDB" + "vEuPathDbProject": "PiroplasmaDB" }, { "chromosomes": 3, @@ -1219,7 +1219,7 @@ "strain": "T2Bo", "supercontigs": 3, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000165395.2", - "vEuPathDBProject": "PiroplasmaDB" + "vEuPathDbProject": "PiroplasmaDB" }, { "chromosomes": 0, @@ -1232,7 +1232,7 @@ "strain": "ATCC 26199", "supercontigs": 3282, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000166155.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1245,7 +1245,7 @@ "strain": "RP-78", "supercontigs": 232, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000167175.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1258,7 +1258,7 @@ "strain": "QM6a", "supercontigs": 77, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000167675.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1271,7 +1271,7 @@ "strain": "str. Silveira", "supercontigs": 54, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000170175.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1284,7 +1284,7 @@ "strain": "Gv29-8", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000170995.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1297,7 +1297,7 @@ "strain": "Emoy2", "supercontigs": 3044, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000173235.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1310,7 +1310,7 @@ "strain": "CDC", "supercontigs": 16537, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000181055.3", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -1323,7 +1323,7 @@ "strain": "isolate GS", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000182405.1", - "vEuPathDBProject": "GiardiaDB" + "vEuPathDbProject": "GiardiaDB" }, { "chromosomes": 0, @@ -1336,7 +1336,7 @@ "strain": "DAOM BR117", "supercontigs": 38, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000182565.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1349,7 +1349,7 @@ "strain": "isolate P15", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000182665.1", - "vEuPathDBProject": "GiardiaDB" + "vEuPathDbProject": "GiardiaDB" }, { "chromosomes": 8, @@ -1362,7 +1362,7 @@ "strain": "CDC317", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000182765.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1375,7 +1375,7 @@ "strain": "okayama7#130", "supercontigs": 67, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000182895.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 7, @@ -1388,7 +1388,7 @@ "strain": "OR74A", "supercontigs": 13, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000182925.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 8, @@ -1401,7 +1401,7 @@ "strain": "SC5314", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000182965.3", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1414,7 +1414,7 @@ "strain": "BRL01", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000182985.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -1427,7 +1427,7 @@ "strain": "20631-21", "supercontigs": 1846, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000184105.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 8, @@ -1440,7 +1440,7 @@ "strain": "RIB40", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000184455.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 14, @@ -1453,7 +1453,7 @@ "strain": "WM276", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000185945.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1466,7 +1466,7 @@ "strain": "Sylvio X10/1-2012", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000188675.2", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -1479,7 +1479,7 @@ "strain": "ERTm3", "supercontigs": 53, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000190615.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -1492,7 +1492,7 @@ "strain": "subsp. floridensis", "supercontigs": 379, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000192795.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -1505,7 +1505,7 @@ "strain": "ATCC 64411", "supercontigs": 205, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000193285.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1518,7 +1518,7 @@ "strain": "98AG31", "supercontigs": 462, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000204055.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1531,7 +1531,7 @@ "strain": "Wikel", "supercontigs": 369492, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000208615.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 14, @@ -1544,7 +1544,7 @@ "strain": "Liverpool", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000208865.1", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -1557,7 +1557,7 @@ "strain": "HM-1:IMSS", "supercontigs": 1496, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000208925.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -1570,7 +1570,7 @@ "strain": "strain CL Brener", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000209065.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -1583,7 +1583,7 @@ "strain": "SAW760", "supercontigs": 3312, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000209125.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -1596,7 +1596,7 @@ "strain": "Johannesburg", "supercontigs": 3171, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000209185.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -1609,7 +1609,7 @@ "strain": "H348", "supercontigs": 3, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000209485.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 11, @@ -1622,7 +1622,7 @@ "strain": "gambiense DAL972", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000210295.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -1635,7 +1635,7 @@ "strain": "Coari", "supercontigs": 2220, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000211455.3", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -1648,7 +1648,7 @@ "strain": "FGSC 2508", "supercontigs": 81, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000213175.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 21, @@ -1661,7 +1661,7 @@ "strain": "IPO323", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000219625.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 15, @@ -1674,7 +1674,7 @@ "strain": "EC3", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000221245.2", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 16, @@ -1687,7 +1687,7 @@ "strain": "EC2", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000221265.2", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 12, @@ -1700,7 +1700,7 @@ "strain": "EC1", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000221285.2", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -1713,7 +1713,7 @@ "strain": "Unknown strain", "supercontigs": 469, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000223845.1", - "vEuPathDBProject": "CryptoDB" + "vEuPathDbProject": "CryptoDB" }, { "chromosomes": 0, @@ -1726,7 +1726,7 @@ "strain": "RUB", "supercontigs": 2424, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000224805.2", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -1739,7 +1739,7 @@ "strain": "TgCATBr9", "supercontigs": 2452, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000224825.2", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -1752,7 +1752,7 @@ "strain": "VAND", "supercontigs": 2137, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000224845.2", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -1765,7 +1765,7 @@ "strain": "MAS", "supercontigs": 2180, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000224865.2", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -1778,7 +1778,7 @@ "strain": "p89", "supercontigs": 2150, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000224885.2", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -1791,7 +1791,7 @@ "strain": "FOU", "supercontigs": 2869, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000224905.2", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -1804,7 +1804,7 @@ "strain": "E277", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000225285.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1817,7 +1817,7 @@ "strain": "CM01", "supercontigs": 32, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000225605.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 7, @@ -1830,7 +1830,7 @@ "strain": "ATCC 42464", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000226095.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1843,7 +1843,7 @@ "strain": "Wisconsin 54-1255", "supercontigs": 49, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000226395.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1856,7 +1856,7 @@ "strain": "S mat+", "supercontigs": 33, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000226545.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 36, @@ -1869,7 +1869,7 @@ "strain": "BPK282A1", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000227135.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 11, @@ -1882,7 +1882,7 @@ "strain": "Y486", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000227375.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 11, @@ -1895,7 +1895,7 @@ "strain": "IL3000", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000227395.2", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 23, @@ -1908,7 +1908,7 @@ "strain": "SRZ2", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000230245.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1921,7 +1921,7 @@ "strain": "JN3", "supercontigs": 76, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000230375.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1934,7 +1934,7 @@ "strain": "ATCC 1015", "supercontigs": 24, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000230395.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1947,7 +1947,7 @@ "strain": "USNM 41457", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000230595.3", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -1960,7 +1960,7 @@ "strain": "NIH/UT8656", "supercontigs": 10, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000230625.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -1973,7 +1973,7 @@ "strain": "ATCC 50505", "supercontigs": 220, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000231115.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 34, @@ -1986,7 +1986,7 @@ "strain": "MHOM/GT/2001/U1103", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000234665.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -1999,7 +1999,7 @@ "strain": "IFO 4308", "supercontigs": 146, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000239835.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -2012,7 +2012,7 @@ "strain": "INRA-310", "supercontigs": 708, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000247585.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -2025,7 +2025,7 @@ "strain": "ERTm2", "supercontigs": 202, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000250695.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -2038,7 +2038,7 @@ "strain": "strain SD 75.1", "supercontigs": 36, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000250755.2", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -2051,7 +2051,7 @@ "strain": "ARI", "supercontigs": 2723, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000250965.2", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -2064,7 +2064,7 @@ "strain": "ERTm1", "supercontigs": 65, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000250985.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -2077,7 +2077,7 @@ "strain": "CAST", "supercontigs": 2656, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000256705.2", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -2090,7 +2090,7 @@ "strain": "TgCatPRC2", "supercontigs": 3060, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000256725.2", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -2103,7 +2103,7 @@ "strain": "strain H.H.34", "supercontigs": 14860, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000258005.1", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -2116,7 +2116,7 @@ "strain": "TgCATBr5", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000259835.1", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -2129,7 +2129,7 @@ "strain": "NRRL 54006", "supercontigs": 418, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000260195.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -2142,7 +2142,7 @@ "strain": "f. sp. melonis 26406", "supercontigs": 1146, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000260495.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -2155,7 +2155,7 @@ "strain": "Israel", "supercontigs": 106826, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000262795.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -2168,7 +2168,7 @@ "strain": "Jacobina", "supercontigs": 11532, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000265325.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -2181,7 +2181,7 @@ "strain": "DSM 1558", "supercontigs": 45, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000271645.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -2194,7 +2194,7 @@ "strain": "Fo47", "supercontigs": 124, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000271705.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -2207,7 +2207,7 @@ "strain": "NRRL 32931", "supercontigs": 168, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000271745.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 12, @@ -2220,7 +2220,7 @@ "strain": "ATCC 50504", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000277815.2", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -2233,7 +2233,7 @@ "strain": "CtCo5", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000278365.1", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 13, @@ -2246,7 +2246,7 @@ "strain": "SJ-2008", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000280035.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -2259,7 +2259,7 @@ "strain": "VS20", "supercontigs": 390, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000281045.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -2272,7 +2272,7 @@ "strain": "var. asahii CBS 2479", "supercontigs": 77, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000293215.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -2285,7 +2285,7 @@ "strain": "marinkellei strain B7", "supercontigs": 16783, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000300495.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -2298,7 +2298,7 @@ "strain": "Indian", "supercontigs": 23371, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000300775.2", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -2311,7 +2311,7 @@ "strain": "MS6", "supercontigs": 1506, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000302655.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -2324,7 +2324,7 @@ "strain": "PYCC 5710", "supercontigs": 394, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000312925.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -2337,7 +2337,7 @@ "strain": "str. Neff", "supercontigs": 384, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000313135.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -2350,7 +2350,7 @@ "strain": "Undeen", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000313815.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -2363,7 +2363,7 @@ "strain": "Unknown strain", "supercontigs": 310, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000316135.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 14, @@ -2376,7 +2376,7 @@ "strain": "strain B", "supercontigs": 1649, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000321355.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 0, @@ -2389,7 +2389,7 @@ "strain": "GAB2-2007-GAL-DOM2", "supercontigs": 2481, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000325525.2", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -2402,7 +2402,7 @@ "strain": "strain Esmeraldo", "supercontigs": 796, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000327425.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 23, @@ -2415,7 +2415,7 @@ "strain": "521", "supercontigs": 4, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000328475.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -2428,7 +2428,7 @@ "strain": "IP1", "supercontigs": 1144, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000330505.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 30, @@ -2441,7 +2441,7 @@ "strain": "strain Cf-Cl", "supercontigs": 427, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000331325.2", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 36, @@ -2454,7 +2454,7 @@ "strain": "strain LV39c5", "supercontigs": 773, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000331345.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -2467,7 +2467,7 @@ "strain": "JR cl. 4", "supercontigs": 560, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000331405.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 36, @@ -2480,7 +2480,7 @@ "strain": "strain LV88", "supercontigs": 1925, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000333855.2", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -2493,7 +2493,7 @@ "strain": "SE8", "supercontigs": 328, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000333975.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -2506,7 +2506,7 @@ "strain": "COUG", "supercontigs": 105, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000338675.2", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -2519,7 +2519,7 @@ "strain": "KU27", "supercontigs": 1796, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000338855.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -2532,7 +2532,7 @@ "strain": "CIRAD86", "supercontigs": 56, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000340215.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 35, @@ -2545,7 +2545,7 @@ "strain": "MHOM/BR/75/M2903", "supercontigs": 709, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000340355.2", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 36, @@ -2558,7 +2558,7 @@ "strain": "MHOM/COL/81/L13", "supercontigs": 820, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000340495.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 2, @@ -2571,7 +2571,7 @@ "strain": "strain WA", "supercontigs": 8, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000342415.1", - "vEuPathDBProject": "PiroplasmaDB" + "vEuPathDbProject": "PiroplasmaDB" }, { "chromosomes": 0, @@ -2584,7 +2584,7 @@ "strain": "HM-1:IMSS-B", "supercontigs": 1938, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000344925.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -2597,7 +2597,7 @@ "strain": "HM-3:IMSS", "supercontigs": 1880, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000346345.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -2610,7 +2610,7 @@ "strain": "20.1", "supercontigs": 191, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000347355.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -2623,7 +2623,7 @@ "strain": "B123", "supercontigs": 20, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000349005.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -2636,7 +2636,7 @@ "strain": "MINIMUS1", "supercontigs": 678, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000349025.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -2649,7 +2649,7 @@ "strain": "SDA-500", "supercontigs": 1110, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000349045.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -2662,7 +2662,7 @@ "strain": "SANGWE", "supercontigs": 2823, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000349065.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -2675,7 +2675,7 @@ "strain": "Epiroticus2", "supercontigs": 2673, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000349105.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 5, @@ -2688,7 +2688,7 @@ "strain": "STECLA", "supercontigs": 196, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000349125.2", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -2701,7 +2701,7 @@ "strain": "WRAIR2", "supercontigs": 1266, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000349145.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -2714,7 +2714,7 @@ "strain": "ACHKN1017", "supercontigs": 30369, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000349165.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -2727,7 +2727,7 @@ "strain": "Dongola", "supercontigs": 1214, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000349185.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -2740,7 +2740,7 @@ "strain": "f. sp. cubense race 1", "supercontigs": 1341, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000350345.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -2753,7 +2753,7 @@ "strain": "strain race 4", "supercontigs": 840, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000350365.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -2766,7 +2766,7 @@ "strain": "CBS 101466", "supercontigs": 19, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000365145.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -2779,7 +2779,7 @@ "strain": "CBS 160.54", "supercontigs": 19, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000365165.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -2792,7 +2792,7 @@ "strain": "Tula cl2", "supercontigs": 1780, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000365225.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -2805,7 +2805,7 @@ "strain": "HM-1:IMSS-A", "supercontigs": 1685, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000365475.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -2818,7 +2818,7 @@ "strain": "aabys", "supercontigs": 20487, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000371365.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -2831,7 +2831,7 @@ "strain": "CQ1", "supercontigs": 1607, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000383075.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -2844,7 +2844,7 @@ "strain": "PRA109", "supercontigs": 7113, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000385855.2", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -2857,7 +2857,7 @@ "strain": "PRA339", "supercontigs": 431, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000385875.2", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -2870,7 +2870,7 @@ "strain": "DAOM BR486", "supercontigs": 5887, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000387425.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -2883,7 +2883,7 @@ "strain": "DAOM BR444", "supercontigs": 1774, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000387445.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -2896,7 +2896,7 @@ "strain": "DAOM BR242034", "supercontigs": 11542, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000387465.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -2909,7 +2909,7 @@ "strain": "ATCC 12531", "supercontigs": 10972, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000387505.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -2922,7 +2922,7 @@ "strain": "var. sporangiiferum BR650", "supercontigs": 5482, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000387525.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -2935,7 +2935,7 @@ "strain": "DAOM BR484", "supercontigs": 3685, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000387545.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 8, @@ -2948,7 +2948,7 @@ "strain": "JR2", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000400815.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -2961,7 +2961,7 @@ "strain": "1006PhL", "supercontigs": 470, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000401635.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 36, @@ -2974,7 +2974,7 @@ "strain": "LEM2494", "supercontigs": 215, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000409445.2", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 36, @@ -2987,7 +2987,7 @@ "strain": "strain LEM1108", "supercontigs": 132, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000410695.2", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 36, @@ -3000,7 +3000,7 @@ "strain": "L590", "supercontigs": 124, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000410715.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -3013,7 +3013,7 @@ "strain": "UAMH 11346", "supercontigs": 45, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000410735.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 36, @@ -3026,7 +3026,7 @@ "strain": "strain LEM3045", "supercontigs": 459, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000410755.2", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -3039,7 +3039,7 @@ "strain": "42_110", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000430065.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -3052,7 +3052,7 @@ "strain": "MHOM/BR/71973/M2269", "supercontigs": 2627, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000438535.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -3065,7 +3065,7 @@ "strain": "China", "supercontigs": 9592, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000441895.2", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 36, @@ -3078,7 +3078,7 @@ "strain": "strain LEM423", "supercontigs": 183, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000441995.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 36, @@ -3091,7 +3091,7 @@ "strain": "strain LEM452", "supercontigs": 106, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000443025.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 36, @@ -3104,7 +3104,7 @@ "strain": "L147", "supercontigs": 124, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000444285.2", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -3117,7 +3117,7 @@ "strain": "BRL 01", "supercontigs": 554, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000447185.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 36, @@ -3130,7 +3130,7 @@ "strain": "strain BHU 1220", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000470725.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -3143,7 +3143,7 @@ "strain": "SINENSIS", "supercontigs": 10448, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000472065.2", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -3156,7 +3156,7 @@ "strain": "maculatus3", "supercontigs": 47797, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000473185.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -3169,7 +3169,7 @@ "strain": "A-37", "supercontigs": 16162, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000473375.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -3182,7 +3182,7 @@ "strain": "FAR1", "supercontigs": 310, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000473445.2", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 5, @@ -3195,7 +3195,7 @@ "strain": "EBRO", "supercontigs": 1315, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000473505.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -3208,7 +3208,7 @@ "strain": "CM1001059_A", "supercontigs": 20229, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000473525.2", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -3221,7 +3221,7 @@ "strain": "MAF", "supercontigs": 2027, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000473845.2", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -3234,7 +3234,7 @@ "strain": "SC58", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000492115.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -3247,7 +3247,7 @@ "strain": "Dm28c 2014", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000496795.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -3260,7 +3260,7 @@ "strain": "2 isolate DH", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000498715.1", - "vEuPathDBProject": "GiardiaDB" + "vEuPathDbProject": "GiardiaDB" }, { "chromosomes": 0, @@ -3273,7 +3273,7 @@ "strain": "isolate GS_B", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000498735.1", - "vEuPathDBProject": "GiardiaDB" + "vEuPathDbProject": "GiardiaDB" }, { "chromosomes": 0, @@ -3286,7 +3286,7 @@ "strain": "ATCC 30863", "supercontigs": 1124, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000499105.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -3299,7 +3299,7 @@ "strain": "Houghton", "supercontigs": 3707, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000499385.1", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -3312,7 +3312,7 @@ "strain": "Houghton", "supercontigs": 3415, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000499425.1", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -3325,7 +3325,7 @@ "strain": "Houghton", "supercontigs": 21348, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000499445.1", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -3338,7 +3338,7 @@ "strain": "strain Houghton", "supercontigs": 4664, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000499545.1", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -3351,7 +3351,7 @@ "strain": "Weybridge", "supercontigs": 3564, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000499605.1", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -3364,7 +3364,7 @@ "strain": "Houghton", "supercontigs": 8575, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000499725.1", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -3377,7 +3377,7 @@ "strain": "Houghton", "supercontigs": 15978, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000499745.2", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -3390,7 +3390,7 @@ "strain": "CBS 569", "supercontigs": 242, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000507425.3", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -3403,7 +3403,7 @@ "strain": "strain APO3", "supercontigs": 835, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000520075.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -3416,7 +3416,7 @@ "strain": "NJM9701", "supercontigs": 481, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000520115.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -3429,7 +3429,7 @@ "strain": "San Antonio 1", "supercontigs": 323, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000524495.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 0, @@ -3442,7 +3442,7 @@ "strain": "petteri strain CR", "supercontigs": 66, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000524515.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 0, @@ -3455,7 +3455,7 @@ "strain": "CBS 114405", "supercontigs": 8, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000585515.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -3468,7 +3468,7 @@ "strain": "CBS 110553", "supercontigs": 123, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000585535.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -3481,7 +3481,7 @@ "strain": "Harlan", "supercontigs": 417, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000648675.2", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -3494,7 +3494,7 @@ "strain": "IAEA", "supercontigs": 2395, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000671735.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -3507,7 +3507,7 @@ "strain": "IAEA", "supercontigs": 1651, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000671755.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -3520,7 +3520,7 @@ "strain": "IAEA", "supercontigs": 1726, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000688715.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -3533,7 +3533,7 @@ "strain": "TTRI", "supercontigs": 2205, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000688735.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -3546,7 +3546,7 @@ "strain": "ANR4", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000691245.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 4, @@ -3559,7 +3559,7 @@ "strain": "strain RI", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000691945.2", - "vEuPathDBProject": "PiroplasmaDB" + "vEuPathDbProject": "PiroplasmaDB" }, { "chromosomes": 0, @@ -3572,7 +3572,7 @@ "strain": "PC15", "supercontigs": 12, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000697685.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -3585,7 +3585,7 @@ "strain": "vinckei strain vinckei", "supercontigs": 49, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000709005.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 0, @@ -3598,7 +3598,7 @@ "strain": "CBS 119918", "supercontigs": 151, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000709125.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 5, @@ -3611,7 +3611,7 @@ "strain": "strain BOND", "supercontigs": 478, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000723445.1", - "vEuPathDBProject": "PiroplasmaDB" + "vEuPathDbProject": "PiroplasmaDB" }, { "chromosomes": 0, @@ -3624,7 +3624,7 @@ "strain": "JMRC:FSU:9682", "supercontigs": 209, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000723665.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 14, @@ -3637,7 +3637,7 @@ "strain": "CDC", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000723685.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 0, @@ -3650,7 +3650,7 @@ "strain": "SN3", "supercontigs": 171, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000727475.1", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -3663,7 +3663,7 @@ "strain": "IHEM 14462", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000732125.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -3676,7 +3676,7 @@ "strain": "IBT 40293", "supercontigs": 2342, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000732565.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -3689,7 +3689,7 @@ "strain": "ERTm6", "supercontigs": 22, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000738915.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 4, @@ -3702,7 +3702,7 @@ "strain": "strain Shintoku", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000740895.1", - "vEuPathDBProject": "PiroplasmaDB" + "vEuPathDbProject": "PiroplasmaDB" }, { "chromosomes": 35, @@ -3715,7 +3715,7 @@ "strain": "strain MHOM/PA/94/PSC-1", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000755165.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -3728,7 +3728,7 @@ "strain": "UGP3", "supercontigs": 610, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000760515.2", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -3741,7 +3741,7 @@ "strain": "strain CHN_HEN01", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000769155.1", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -3754,7 +3754,7 @@ "strain": "d1", "supercontigs": 270, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000769735.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -3767,7 +3767,7 @@ "strain": "OC4", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000803265.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -3780,7 +3780,7 @@ "strain": "37999", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000804495.1", - "vEuPathDBProject": "CryptoDB" + "vEuPathDbProject": "CryptoDB" }, { "chromosomes": 0, @@ -3793,7 +3793,7 @@ "strain": "ARSEF 549", "supercontigs": 74, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000814975.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -3806,7 +3806,7 @@ "strain": "IAEA", "supercontigs": 3926, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000818775.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -3819,7 +3819,7 @@ "strain": "5110", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000820605.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -3832,7 +3832,7 @@ "strain": "Unknown", "supercontigs": 98248, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000826245.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -3845,7 +3845,7 @@ "strain": "A1", "supercontigs": 72411, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000826265.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -3858,7 +3858,7 @@ "strain": "PD2S", "supercontigs": 79048, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000826285.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -3871,7 +3871,7 @@ "strain": "Reich", "supercontigs": 26188, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000826305.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -3884,7 +3884,7 @@ "strain": "SH621", "supercontigs": 56742, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000826325.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -3897,7 +3897,7 @@ "strain": "T4B-type", "supercontigs": 224482, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000826345.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -3910,7 +3910,7 @@ "strain": "Incertae_sedis", "supercontigs": 24098, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000826365.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -3923,7 +3923,7 @@ "strain": "Singh", "supercontigs": 62836, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000826385.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -3936,7 +3936,7 @@ "strain": "L3a", "supercontigs": 67459, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000826425.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -3949,7 +3949,7 @@ "strain": "Vil3", "supercontigs": 60490, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000826445.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -3962,7 +3962,7 @@ "strain": "1652", "supercontigs": 67233, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000826465.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -3975,7 +3975,7 @@ "strain": "Ma", "supercontigs": 221748, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000826485.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -3988,7 +3988,7 @@ "strain": "Galka", "supercontigs": 224137, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000826505.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -4001,7 +4001,7 @@ "strain": "Arlian", "supercontigs": 18859, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000828355.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -4014,7 +4014,7 @@ "strain": "chipmunk LX-2015", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000831705.1", - "vEuPathDBProject": "CryptoDB" + "vEuPathDbProject": "CryptoDB" }, { "chromosomes": 0, @@ -4027,7 +4027,7 @@ "strain": "CBS 271.37", "supercontigs": 11, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000835455.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4040,7 +4040,7 @@ "strain": "CBS 173.52", "supercontigs": 60, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000835475.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4053,7 +4053,7 @@ "strain": "strain CBS 83496", "supercontigs": 277, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000835495.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4066,7 +4066,7 @@ "strain": "strain CBS 72588", "supercontigs": 143, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000835515.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4079,7 +4079,7 @@ "strain": "CBS 650.93", "supercontigs": 17, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000835555.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4092,7 +4092,7 @@ "strain": "EJB2", "supercontigs": 282, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000835745.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4105,7 +4105,7 @@ "strain": "CBS 89968", "supercontigs": 28, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000836115.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4118,7 +4118,7 @@ "strain": "strain CBS 40295", "supercontigs": 9, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000836275.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4131,7 +4131,7 @@ "strain": "strain CBS 43764", "supercontigs": 367, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000836295.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4144,7 +4144,7 @@ "strain": "CBS 102226", "supercontigs": 67, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000836435.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4157,7 +4157,7 @@ "strain": "CA1873", "supercontigs": 33, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000855695.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4170,7 +4170,7 @@ "strain": "SO SN1", "supercontigs": 3066, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000875885.1", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -4183,7 +4183,7 @@ "strain": "NT10", "supercontigs": 226, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000935105.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4196,7 +4196,7 @@ "strain": "strain nilgiri", "supercontigs": 247, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000956335.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 0, @@ -4209,7 +4209,7 @@ "strain": "1099-18", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000961545.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4222,7 +4222,7 @@ "strain": "DAOM 233423", "supercontigs": 869, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000966635.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4235,7 +4235,7 @@ "strain": "Charles River", "supercontigs": 204516, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000973045.2", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -4248,7 +4248,7 @@ "strain": "strain PA08_1199", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000988165.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -4261,7 +4261,7 @@ "strain": "UAMH 3008", "supercontigs": 1734, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001008285.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4274,7 +4274,7 @@ "strain": "USDA", "supercontigs": 12042, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_001015335.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -4287,7 +4287,7 @@ "strain": "Yale", "supercontigs": 13807, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001077435.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -4300,7 +4300,7 @@ "strain": "strain Rouen 1987", "supercontigs": 141, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001077455.2", - "vEuPathDBProject": "PiroplasmaDB" + "vEuPathDbProject": "PiroplasmaDB" }, { "chromosomes": 15, @@ -4313,7 +4313,7 @@ "strain": "EcunIII-L", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001078035.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -4326,7 +4326,7 @@ "strain": "CCMP3155", "supercontigs": 1064, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001179505.1", - "vEuPathDBProject": "CryptoDB" + "vEuPathDbProject": "CryptoDB" }, { "chromosomes": 0, @@ -4339,7 +4339,7 @@ "strain": "CDC-V039", "supercontigs": 1604, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001185145.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -4352,7 +4352,7 @@ "strain": "6684", "supercontigs": 99, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_001189475.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4365,7 +4365,7 @@ "strain": "strain 2046", "supercontigs": 14699, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001262475.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -4378,7 +4378,7 @@ "strain": "strain RO10H11247", "supercontigs": 15715, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001263375.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4391,7 +4391,7 @@ "strain": "mm55", "supercontigs": 804, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001275765.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4404,7 +4404,7 @@ "strain": "CBS 1879", "supercontigs": 91, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_001278385.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 35, @@ -4417,7 +4417,7 @@ "strain": "H10", "supercontigs": 25, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_001293395.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -4430,7 +4430,7 @@ "strain": "ATCC 30220", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001299535.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -4443,7 +4443,7 @@ "strain": "isolate UAMH 5669", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001430925.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4456,7 +4456,7 @@ "strain": "isolate UAMH 3576", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001430935.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4469,7 +4469,7 @@ "strain": "isolate UAMH 3544", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001430945.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4482,7 +4482,7 @@ "strain": "isolate CBS 280.77", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001430955.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4495,7 +4495,7 @@ "strain": "strain MK1", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001432165.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -4508,7 +4508,7 @@ "strain": "NRRL Y-1402", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001444555.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4521,7 +4521,7 @@ "strain": "strain IFM 54703", "supercontigs": 12, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001445615.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4534,7 +4534,7 @@ "strain": "CBS 789", "supercontigs": 534, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_001447935.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4547,7 +4547,7 @@ "strain": "OVI", "supercontigs": 2026, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_001457755.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -4560,7 +4560,7 @@ "strain": "strain Lake Konstanz", "supercontigs": 2256, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001460835.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -4573,7 +4573,7 @@ "strain": "RU7", "supercontigs": 70, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_001477535.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4586,7 +4586,7 @@ "strain": "isolate 30976", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001483515.1", - "vEuPathDBProject": "CryptoDB" + "vEuPathDbProject": "CryptoDB" }, { "chromosomes": 0, @@ -4599,7 +4599,7 @@ "strain": "AS175", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001493575.1", - "vEuPathDBProject": "GiardiaDB" + "vEuPathDbProject": "GiardiaDB" }, { "chromosomes": 0, @@ -4612,7 +4612,7 @@ "strain": "isolate BAH15c1", "supercontigs": 508, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001543975.1", - "vEuPathDBProject": "GiardiaDB" + "vEuPathDbProject": "GiardiaDB" }, { "chromosomes": 0, @@ -4625,7 +4625,7 @@ "strain": "A1 (DAOM-664342)", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001593125.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4638,7 +4638,7 @@ "strain": "RH 2016", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001593265.1", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -4651,7 +4651,7 @@ "strain": "strain UKMEL1", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001593445.1", - "vEuPathDBProject": "CryptoDB" + "vEuPathDbProject": "CryptoDB" }, { "chromosomes": 0, @@ -4664,7 +4664,7 @@ "strain": "TAMU-09Q1", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001593455.1", - "vEuPathDBProject": "CryptoDB" + "vEuPathDbProject": "CryptoDB" }, { "chromosomes": 0, @@ -4677,7 +4677,7 @@ "strain": "isolate TU502_2012", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001593465.1", - "vEuPathDBProject": "CryptoDB" + "vEuPathDbProject": "CryptoDB" }, { "chromosomes": 0, @@ -4690,7 +4690,7 @@ "strain": "UKH1", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001593475.1", - "vEuPathDBProject": "CryptoDB" + "vEuPathDbProject": "CryptoDB" }, { "chromosomes": 0, @@ -4703,7 +4703,7 @@ "strain": "JCM 9937", "supercontigs": 61, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001598995.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4716,7 +4716,7 @@ "strain": "strain JCM 9410", "supercontigs": 23, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001599035.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4729,7 +4729,7 @@ "strain": "JCM2334", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001599735.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 14, @@ -4742,7 +4742,7 @@ "strain": "strain SY75", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_001602025.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 0, @@ -4755,7 +4755,7 @@ "strain": "strain SISKIN1", "supercontigs": 2982, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001625125.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 0, @@ -4768,7 +4768,7 @@ "strain": "ARSEF 7405", "supercontigs": 82, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001636715.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4781,7 +4781,7 @@ "strain": "CBS 277.49", "supercontigs": 21, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001638945.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4794,7 +4794,7 @@ "strain": "NRRL 1555(-)", "supercontigs": 80, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_001638985.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4807,7 +4807,7 @@ "strain": "SRC1lrK2f", "supercontigs": 79, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_001642055.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4820,7 +4820,7 @@ "strain": "strain JUm2807", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001642395.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -4833,7 +4833,7 @@ "strain": "ERTm5", "supercontigs": 186, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001642415.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -4846,7 +4846,7 @@ "strain": "PA203", "supercontigs": 101, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001643675.2", - "vEuPathDBProject": "GiardiaDB" + "vEuPathDbProject": "GiardiaDB" }, { "chromosomes": 0, @@ -4859,7 +4859,7 @@ "strain": "strain ATCC 30222", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001650055.1", - "vEuPathDBProject": "PiroplasmaDB" + "vEuPathDbProject": "PiroplasmaDB" }, { "chromosomes": 0, @@ -4872,7 +4872,7 @@ "strain": "strain ATCC PRA-99", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001650065.1", - "vEuPathDBProject": "PiroplasmaDB" + "vEuPathDbProject": "PiroplasmaDB" }, { "chromosomes": 0, @@ -4885,7 +4885,7 @@ "strain": "strain GreenwichYale_Lab_strain_1", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001650075.1", - "vEuPathDBProject": "PiroplasmaDB" + "vEuPathDbProject": "PiroplasmaDB" }, { "chromosomes": 0, @@ -4898,7 +4898,7 @@ "strain": "strain GI", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001650105.1", - "vEuPathDBProject": "PiroplasmaDB" + "vEuPathDbProject": "PiroplasmaDB" }, { "chromosomes": 0, @@ -4911,7 +4911,7 @@ "strain": "strain Naushon", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001650135.1", - "vEuPathDBProject": "PiroplasmaDB" + "vEuPathDbProject": "PiroplasmaDB" }, { "chromosomes": 0, @@ -4924,7 +4924,7 @@ "strain": "Nan_Hs_2011_N11-50", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001650145.1", - "vEuPathDBProject": "PiroplasmaDB" + "vEuPathDbProject": "PiroplasmaDB" }, { "chromosomes": 0, @@ -4937,7 +4937,7 @@ "strain": "CBS 136260", "supercontigs": 4444, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001660665.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 11, @@ -4950,7 +4950,7 @@ "strain": "IMI 349063", "supercontigs": 14, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_001672515.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 14, @@ -4963,7 +4963,7 @@ "strain": "Hackeri", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_001680005.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 0, @@ -4976,7 +4976,7 @@ "strain": "1.58", "supercontigs": 268, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001692895.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -4989,7 +4989,7 @@ "strain": "KSF", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001700775.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5002,7 +5002,7 @@ "strain": "GZAAS20.1005", "supercontigs": 68, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001717485.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5015,7 +5015,7 @@ "strain": "strain AWRI3580", "supercontigs": 18, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001747055.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 6, @@ -5028,7 +5028,7 @@ "strain": "CLIB89 (W29)", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001761485.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 16, @@ -5041,7 +5041,7 @@ "strain": "1980 UF-70", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001857865.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5054,7 +5054,7 @@ "strain": "isolate 39726", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_001865345.1", - "vEuPathDBProject": "CryptoDB" + "vEuPathDbProject": "CryptoDB" }, { "chromosomes": 0, @@ -5067,7 +5067,7 @@ "strain": "isolate 30847", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_001865355.1", - "vEuPathDBProject": "CryptoDB" + "vEuPathDbProject": "CryptoDB" }, { "chromosomes": 0, @@ -5080,7 +5080,7 @@ "strain": "WSBS2006", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001875675.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -5093,7 +5093,7 @@ "strain": "strain EI222", "supercontigs": 3868, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001883805.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5106,7 +5106,7 @@ "strain": "Ep9510", "supercontigs": 1643, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001883825.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5119,7 +5119,7 @@ "strain": "CBS 101740", "supercontigs": 103, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001889945.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5132,7 +5132,7 @@ "strain": "CBS 506.65", "supercontigs": 246, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_001890105.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5145,7 +5145,7 @@ "strain": "CBS 583.65", "supercontigs": 51, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_001890125.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5158,7 +5158,7 @@ "strain": "CBS 106.47", "supercontigs": 100, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001890685.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5171,7 +5171,7 @@ "strain": "CBS 593.65", "supercontigs": 97, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_001890705.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5184,7 +5184,7 @@ "strain": "DTO 134E9", "supercontigs": 27, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_001890725.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5197,7 +5197,7 @@ "strain": "CBS 134.48", "supercontigs": 33, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001890745.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5210,7 +5210,7 @@ "strain": "CBS 516.65", "supercontigs": 82, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_001890805.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5223,7 +5223,7 @@ "strain": "ATCC 16872", "supercontigs": 660, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_001890905.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5236,7 +5236,7 @@ "strain": "65", "supercontigs": 25, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001983305.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5249,7 +5249,7 @@ "strain": "ITEM 5010", "supercontigs": 829, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_001990825.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 7, @@ -5262,7 +5262,7 @@ "strain": "QM6a 2017", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_002006585.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 16, @@ -5275,7 +5275,7 @@ "strain": "CBS432", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_002079055.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5288,7 +5288,7 @@ "strain": "strain TH1", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_002081675.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -5301,7 +5301,7 @@ "strain": "var. microsporus ATCC 52814", "supercontigs": 560, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_002083745.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5314,7 +5314,7 @@ "strain": "isolate Edinburgh", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_002087225.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -5327,7 +5327,7 @@ "strain": "strain canceri", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_002087875.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -5340,7 +5340,7 @@ "strain": "strain GB1", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_002087885.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -5353,7 +5353,7 @@ "strain": "strain GB1", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_002087915.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -5366,7 +5366,7 @@ "strain": "Xinjiang", "supercontigs": 215, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_002095265.1", - "vEuPathDBProject": "PiroplasmaDB" + "vEuPathDbProject": "PiroplasmaDB" }, { "chromosomes": 0, @@ -5379,7 +5379,7 @@ "strain": "5z489", "supercontigs": 108, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_002110485.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5392,7 +5392,7 @@ "strain": "EXF-2000", "supercontigs": 628, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_002127715.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5405,7 +5405,7 @@ "strain": "strain Malayan Strain Pk1 A", "supercontigs": 28, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_002140095.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 3, @@ -5418,7 +5418,7 @@ "strain": "LVP_AGWG", "supercontigs": 2306, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_002204515.2", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 5, @@ -5431,7 +5431,7 @@ "strain": "var. neoformans XL280", "supercontigs": 32, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_002216205.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 14, @@ -5444,7 +5444,7 @@ "strain": "var. grubii KN99", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_002216725.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5457,7 +5457,7 @@ "strain": "Dm28c 2017", "supercontigs": 1029, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_002219105.2", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 13, @@ -5470,7 +5470,7 @@ "strain": "DSY562", "supercontigs": 5, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_002219185.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 8, @@ -5483,7 +5483,7 @@ "strain": "UdeA01", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_002223825.1", - "vEuPathDBProject": "CryptoDB" + "vEuPathDbProject": "CryptoDB" }, { "chromosomes": 0, @@ -5496,7 +5496,7 @@ "strain": "strain HMR AF 39", "supercontigs": 647, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_002237265.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5509,7 +5509,7 @@ "strain": "AV1007", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_002247145.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5522,7 +5522,7 @@ "strain": "Bayer Haberkorn 1970", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_002271815.1", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -5535,7 +5535,7 @@ "strain": "JHH-5317", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_002276285.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5548,7 +5548,7 @@ "strain": "Tc1/148", "supercontigs": 536, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_002287245.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 13, @@ -5561,7 +5561,7 @@ "strain": "strain Bb-Ger1", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_002563875.1", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -5574,7 +5574,7 @@ "strain": "strain Wien I", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_002600585.1", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -5587,7 +5587,7 @@ "strain": "Bug2148", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_002749415.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -5600,7 +5600,7 @@ "strain": "strain Y", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_002749425.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -5613,7 +5613,7 @@ "strain": "NCCPF 102052", "supercontigs": 411, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_002749535.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5626,7 +5626,7 @@ "strain": "B11221", "supercontigs": 20, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_002775015.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5639,7 +5639,7 @@ "strain": "IBT 24754", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_002846915.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5652,7 +5652,7 @@ "strain": "IBT 16806", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_002847465.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5665,7 +5665,7 @@ "strain": "IBT 28561", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_002847485.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5678,7 +5678,7 @@ "strain": "IBT 23096", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_002849105.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5691,7 +5691,7 @@ "strain": "ISE6", "supercontigs": 6476, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_002892825.2", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -5704,7 +5704,7 @@ "strain": "strain Miyake", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_002897235.1", - "vEuPathDBProject": "PiroplasmaDB" + "vEuPathDbProject": "PiroplasmaDB" }, { "chromosomes": 0, @@ -5717,7 +5717,7 @@ "strain": "var. palmivora strain sbr112.9", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_002911725.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5730,7 +5730,7 @@ "strain": "Laredo", "supercontigs": 1147, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_002914575.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -5743,7 +5743,7 @@ "strain": "strain 93-210", "supercontigs": 492, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_002920065.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5756,7 +5756,7 @@ "strain": "93TX-2", "supercontigs": 561, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_002920205.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5769,7 +5769,7 @@ "strain": "CUL13", "supercontigs": 266, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_002921335.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -5782,7 +5782,7 @@ "strain": "B11899", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_002926055.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5795,7 +5795,7 @@ "strain": "B09383", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_002926085.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 14, @@ -5808,7 +5808,7 @@ "strain": "R265", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_002954075.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5821,7 +5821,7 @@ "strain": "var. grubii H99 2018", "supercontigs": 14, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003011985.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 11, @@ -5834,7 +5834,7 @@ "strain": "IL3000 2019", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003013265.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 7, @@ -5847,7 +5847,7 @@ "strain": "B11220", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_003013715.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5860,7 +5860,7 @@ "strain": "B12108", "supercontigs": 36, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_003013735.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5873,7 +5873,7 @@ "strain": "B11243", "supercontigs": 238, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003014415.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 5, @@ -5886,7 +5886,7 @@ "strain": "strain CBS5147", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003054405.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 5, @@ -5899,7 +5899,7 @@ "strain": "strain CBS573", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_003054445.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5912,7 +5912,7 @@ "strain": "TIMM 2789", "supercontigs": 16543, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003118255.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5925,7 +5925,7 @@ "strain": "TCC", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003177095.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -5938,7 +5938,7 @@ "strain": "Dm28c 2018", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003177105.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -5951,7 +5951,7 @@ "strain": "CBS 122712", "supercontigs": 131, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_003184535.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5964,7 +5964,7 @@ "strain": "CBS 117.55", "supercontigs": 205, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_003184545.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5977,7 +5977,7 @@ "strain": "CBS 121057", "supercontigs": 166, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003184635.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -5990,7 +5990,7 @@ "strain": "CBS 707.79", "supercontigs": 518, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003184645.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -6003,7 +6003,7 @@ "strain": "CBS 121591", "supercontigs": 172, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_003184745.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -6016,7 +6016,7 @@ "strain": "CBS 313.89", "supercontigs": 149, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_003184825.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -6029,7 +6029,7 @@ "strain": "CBS 121593", "supercontigs": 116, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_003184845.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -6042,7 +6042,7 @@ "strain": "CBS 101889", "supercontigs": 152, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_003184865.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -6055,7 +6055,7 @@ "strain": "10300", "supercontigs": 4623, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003287315.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 9, @@ -6068,7 +6068,7 @@ "strain": "KCTC 27527", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_003290485.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -6081,7 +6081,7 @@ "strain": "strain ATCC 30569", "supercontigs": 109, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_003324165.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 22, @@ -6094,7 +6094,7 @@ "strain": "isolate AG07107", "supercontigs": 2916, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_003339765.1", - "vEuPathDBProject": "HostDB" + "vEuPathDbProject": "HostDB" }, { "chromosomes": 0, @@ -6107,7 +6107,7 @@ "strain": "ATCC 13496", "supercontigs": 133, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003344705.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -6120,7 +6120,7 @@ "strain": "PvSY56", "supercontigs": 14, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003402215.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 0, @@ -6133,7 +6133,7 @@ "strain": "strain S11", "supercontigs": 7855, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003594385.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -6146,7 +6146,7 @@ "strain": "strain Ycl4", "supercontigs": 6664, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003594405.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -6159,7 +6159,7 @@ "strain": "strain S23b", "supercontigs": 7145, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003594425.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -6172,7 +6172,7 @@ "strain": "strain S92a", "supercontigs": 7134, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003594445.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -6185,7 +6185,7 @@ "strain": "strain Ycl6", "supercontigs": 6967, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003594465.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -6198,7 +6198,7 @@ "strain": "strain Ycl2", "supercontigs": 6884, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003594485.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -6211,7 +6211,7 @@ "strain": "strain S15", "supercontigs": 9197, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003594585.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -6224,7 +6224,7 @@ "strain": "strain S162a", "supercontigs": 8588, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003594605.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -6237,7 +6237,7 @@ "strain": "strain S44a", "supercontigs": 4971, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003594705.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -6250,7 +6250,7 @@ "strain": "strain S154a", "supercontigs": 6946, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003594715.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 9, @@ -6263,7 +6263,7 @@ "strain": "CBS 7877", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003691605.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -6276,7 +6276,7 @@ "strain": "EHP-ID16", "supercontigs": 162, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003709115.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -6289,7 +6289,7 @@ "strain": "CBS 132003", "supercontigs": 118, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003709865.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -6302,7 +6302,7 @@ "strain": "strain CL", "supercontigs": 7764, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003719155.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -6315,7 +6315,7 @@ "strain": "strain G", "supercontigs": 1450, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003719455.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 36, @@ -6328,7 +6328,7 @@ "strain": "CL-SL", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003719575.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -6341,7 +6341,7 @@ "strain": "ALCF2SS1-7", "supercontigs": 207, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003813185.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 7, @@ -6354,7 +6354,7 @@ "strain": "Fl1", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003814445.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -6367,7 +6367,7 @@ "strain": "R13", "supercontigs": 784, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003843895.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 3, @@ -6380,7 +6380,7 @@ "strain": "FUMOZ", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003951495.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 8, @@ -6393,7 +6393,7 @@ "strain": "TM4", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_003971505.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -6406,7 +6406,7 @@ "strain": "CBS H-5679", "supercontigs": 14, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_004000055.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -6419,7 +6419,7 @@ "strain": "Franzen", "supercontigs": 952, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_004000155.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -6432,7 +6432,7 @@ "strain": "WA_211", "supercontigs": 62, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_004115165.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -6445,7 +6445,7 @@ "strain": "Race XXXIII", "supercontigs": 116756, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_004125335.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -6458,7 +6458,7 @@ "strain": "Ngousso", "supercontigs": 205, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_004136515.2", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -6471,7 +6471,7 @@ "strain": "GB-EP-1", "supercontigs": 18, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_004324935.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -6484,7 +6484,7 @@ "strain": "NO-V-7", "supercontigs": 21, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_004324945.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -6497,7 +6497,7 @@ "strain": "IL-BN-2", "supercontigs": 3833, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_004325035.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -6510,7 +6510,7 @@ "strain": "FI-OER-3-3", "supercontigs": 2915, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_004325045.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -6523,7 +6523,7 @@ "strain": "FI-SK-17-1", "supercontigs": 26, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_004325055.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -6536,7 +6536,7 @@ "strain": "BE-OM-2", "supercontigs": 3550, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_004325065.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -6549,7 +6549,7 @@ "strain": "IL-G-3", "supercontigs": 2738, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_004325075.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 5, @@ -6562,7 +6562,7 @@ "strain": "Br36", "supercontigs": 103, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_004337985.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -6575,7 +6575,7 @@ "strain": "Ricmel1", "supercontigs": 848, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_004355085.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 19, @@ -6588,7 +6588,7 @@ "strain": "strain SF5", "supercontigs": 201, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_004359215.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -6601,7 +6601,7 @@ "strain": "NIH1004", "supercontigs": 1715, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_004798825.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -6614,7 +6614,7 @@ "strain": "BRL", "supercontigs": 110, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_004919615.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -6627,7 +6627,7 @@ "strain": "strain 37763", "supercontigs": 50, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_004936735.2", - "vEuPathDBProject": "CryptoDB" + "vEuPathDbProject": "CryptoDB" }, { "chromosomes": 5, @@ -6640,7 +6640,7 @@ "strain": "strain Roberts-Thomson", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_006247105.1", - "vEuPathDBProject": "GiardiaDB" + "vEuPathDbProject": "GiardiaDB" }, { "chromosomes": 0, @@ -6653,7 +6653,7 @@ "strain": "Foshan FPA", "supercontigs": 2196, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_006496715.2", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -6666,7 +6666,7 @@ "strain": "MB42", "supercontigs": 786, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_006535955.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 8, @@ -6679,7 +6679,7 @@ "strain": "isolate UGA55", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_007210665.1", - "vEuPathDBProject": "CryptoDB" + "vEuPathDbProject": "CryptoDB" }, { "chromosomes": 17, @@ -6692,7 +6692,7 @@ "strain": "CLX", "supercontigs": 1, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_007674295.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 7, @@ -6705,7 +6705,7 @@ "strain": "ATCC 34164", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_008080495.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 7, @@ -6718,7 +6718,7 @@ "strain": "B11245", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_008275145.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -6731,7 +6731,7 @@ "strain": "strain ATCC 30894", "supercontigs": 81, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_008403515.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -6744,7 +6744,7 @@ "strain": "CBS 613", "supercontigs": 169, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_008704595.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -6757,7 +6757,7 @@ "strain": "CBS 4856", "supercontigs": 583, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_008704605.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 10, @@ -6770,7 +6770,7 @@ "strain": "KPH11", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_008728235.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 8, @@ -6783,7 +6783,7 @@ "strain": "NRRL3357 2020", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_009017415.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -6796,7 +6796,7 @@ "strain": "CBS 117618", "supercontigs": 270, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_009176385.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 13, @@ -6809,7 +6809,7 @@ "strain": "MF34", "supercontigs": 2, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_009650685.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -6822,7 +6822,7 @@ "strain": "Parrot Tar II 2019", "supercontigs": 179, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_009731335.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -6835,7 +6835,7 @@ "strain": "NF135.C10", "supercontigs": 21, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_009761425.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 0, @@ -6848,7 +6848,7 @@ "strain": "NF54", "supercontigs": 28, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_009761475.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 0, @@ -6861,7 +6861,7 @@ "strain": "NF166", "supercontigs": 30, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_009761515.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 0, @@ -6874,7 +6874,7 @@ "strain": "7G8 2019", "supercontigs": 20, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_009761555.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 0, @@ -6887,7 +6887,7 @@ "strain": "isolate 45015", "supercontigs": 55, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_009768925.1", - "vEuPathDBProject": "CryptoDB" + "vEuPathDbProject": "CryptoDB" }, { "chromosomes": 0, @@ -6900,7 +6900,7 @@ "strain": "45019", "supercontigs": 93, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_009792415.1", - "vEuPathDBProject": "CryptoDB" + "vEuPathDbProject": "CryptoDB" }, { "chromosomes": 0, @@ -6913,7 +6913,7 @@ "strain": "strain LDM3", "supercontigs": 14, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_009812365.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 13, @@ -6926,7 +6926,7 @@ "strain": "CBS138 2020", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_010111755.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -6939,7 +6939,7 @@ "strain": "isolate FIOC_28", "supercontigs": 14951, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_011037195.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -6952,7 +6952,7 @@ "strain": "isolate WB Calgary", "supercontigs": 37, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_011634545.1", - "vEuPathDBProject": "GiardiaDB" + "vEuPathDbProject": "GiardiaDB" }, { "chromosomes": 0, @@ -6965,7 +6965,7 @@ "strain": "Beaver", "supercontigs": 8, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_011634555.1", - "vEuPathDBProject": "GiardiaDB" + "vEuPathDbProject": "GiardiaDB" }, { "chromosomes": 0, @@ -6978,7 +6978,7 @@ "strain": "isolate GS Calgary", "supercontigs": 19, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_011634595.1", - "vEuPathDBProject": "GiardiaDB" + "vEuPathDbProject": "GiardiaDB" }, { "chromosomes": 13, @@ -6991,7 +6991,7 @@ "strain": "RH-88", "supercontigs": 183, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_013099955.1", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 7, @@ -7004,7 +7004,7 @@ "strain": "MYA-3404 2020", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_013177555.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 11, @@ -7017,7 +7017,7 @@ "strain": "Hyas-2018", "supercontigs": 6308, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_013339685.2", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 11, @@ -7030,7 +7030,7 @@ "strain": "Rmic-2018", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_013339725.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 11, @@ -7043,7 +7043,7 @@ "strain": "Dsil-2018", "supercontigs": 1653, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_013339745.2", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 11, @@ -7056,7 +7056,7 @@ "strain": "HaeL-2018", "supercontigs": 3874, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_013339765.2", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -7069,7 +7069,7 @@ "strain": "Berenice", "supercontigs": 923, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_013358655.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -7082,7 +7082,7 @@ "strain": "Iper-2018", "supercontigs": 11596, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_013358835.2", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -7095,7 +7095,7 @@ "strain": "NRRL 25331", "supercontigs": 1222, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_013396185.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -7108,7 +7108,7 @@ "strain": "KleinGrass", "supercontigs": 16339, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_013436015.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 15, @@ -7121,7 +7121,7 @@ "strain": "f. sp. conglutinans Fo5176", "supercontigs": 4, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_014154955.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -7134,7 +7134,7 @@ "strain": "RL4", "supercontigs": 169, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_014183025.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 13, @@ -7147,7 +7147,7 @@ "strain": "BG2", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_014217725.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 40, @@ -7160,7 +7160,7 @@ "strain": "familiaris isolate SID07034", "supercontigs": 336, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_014441545.1", - "vEuPathDBProject": "HostDB" + "vEuPathDbProject": "HostDB" }, { "chromosomes": 12, @@ -7173,7 +7173,7 @@ "strain": "HN6", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_014607475.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -7186,7 +7186,7 @@ "strain": "T1", "supercontigs": 1391, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_014805555.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -7199,7 +7199,7 @@ "strain": "IAEA 2018", "supercontigs": 7986, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_014805625.2", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -7212,7 +7212,7 @@ "strain": "Dv6", "supercontigs": 7783, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_014805705.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 37, @@ -7225,7 +7225,7 @@ "strain": "strain Ty", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_014843625.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -7238,7 +7238,7 @@ "strain": "strain ME49xCTG F1 S27", "supercontigs": 48, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_014898695.1", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 43, @@ -7251,7 +7251,7 @@ "strain": "Brazil A4", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_015033625.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 40, @@ -7264,7 +7264,7 @@ "strain": "Y C6", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_015033655.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 22, @@ -7277,7 +7277,7 @@ "strain": "BN/NHsdMcwi", "supercontigs": 153, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_015227675.2", - "vEuPathDBProject": "HostDB" + "vEuPathDbProject": "HostDB" }, { "chromosomes": 8, @@ -7290,7 +7290,7 @@ "strain": "IOWA-ATCC", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_015245375.1", - "vEuPathDBProject": "CryptoDB" + "vEuPathDbProject": "CryptoDB" }, { "chromosomes": 3, @@ -7303,7 +7303,7 @@ "strain": "JHB 2020", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_015732765.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -7316,7 +7316,7 @@ "strain": "Ou3-Ou53", "supercontigs": 1754, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_015832245.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 13, @@ -7329,7 +7329,7 @@ "strain": "Liverpool 2019", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_016097395.1", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -7342,7 +7342,7 @@ "strain": "Ou19", "supercontigs": 1033, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_016255985.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -7355,7 +7355,7 @@ "strain": "Ou54", "supercontigs": 11522, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_016256075.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -7368,7 +7368,7 @@ "strain": "LT1534", "supercontigs": 782, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_016618375.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -7381,7 +7381,7 @@ "strain": "#326", "supercontigs": 31, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_016772295.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 23, @@ -7394,7 +7394,7 @@ "strain": "SN15", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_016801405.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -7407,7 +7407,7 @@ "strain": "CPMC6", "supercontigs": 99, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_016906325.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 17, @@ -7420,7 +7420,7 @@ "strain": "2A", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_017301755.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 7, @@ -7433,7 +7433,7 @@ "strain": "WU24", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_017310585.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 6, @@ -7446,7 +7446,7 @@ "strain": "H88", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_017310615.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -7459,7 +7459,7 @@ "strain": "CS1", "supercontigs": 38, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_017311285.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 6, @@ -7472,7 +7472,7 @@ "strain": "G186AR", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_017355575.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -7485,7 +7485,7 @@ "strain": "G217B", "supercontigs": 11, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_017607445.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -7498,7 +7498,7 @@ "strain": "G184AR", "supercontigs": 11, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_017607465.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -7511,7 +7511,7 @@ "strain": "BP57", "supercontigs": 9, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_017655625.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -7524,7 +7524,7 @@ "strain": "CanA", "supercontigs": 33, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_017788925.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 36, @@ -7537,7 +7537,7 @@ "strain": "MCAV/BR/2001/CUR178", "supercontigs": 18, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_017916305.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 36, @@ -7550,7 +7550,7 @@ "strain": "MHOM/TH/2012/LSCM1", "supercontigs": 6, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_017916325.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 36, @@ -7563,7 +7563,7 @@ "strain": "MHOM/TH/2014/LSCM4", "supercontigs": 62, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_017916335.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 36, @@ -7576,7 +7576,7 @@ "strain": "MHOM/GH/2012/GH5", "supercontigs": 80, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_017918215.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 36, @@ -7589,7 +7589,7 @@ "strain": "MPRO/NA/1975/252/LV425", "supercontigs": 31, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_017918225.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 36, @@ -7602,7 +7602,7 @@ "strain": "MCOE/PA/1965/C119", "supercontigs": 38, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_017918235.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 16, @@ -7615,7 +7615,7 @@ "strain": "P2C", "supercontigs": 3, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_018127085.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -7628,7 +7628,7 @@ "strain": "Swiss", "supercontigs": 32, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_018342045.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -7641,7 +7641,7 @@ "strain": "strain 1802A", "supercontigs": 79, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_018398725.1", - "vEuPathDBProject": "PiroplasmaDB" + "vEuPathDbProject": "PiroplasmaDB" }, { "chromosomes": 0, @@ -7654,7 +7654,7 @@ "strain": "CCMP2878", "supercontigs": 5963, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_018398765.1", - "vEuPathDBProject": "CryptoDB" + "vEuPathDbProject": "CryptoDB" }, { "chromosomes": 8, @@ -7667,7 +7667,7 @@ "strain": "strain Silveira 2022", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_018416015.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -7680,7 +7680,7 @@ "strain": "DS4-868", "supercontigs": 1177, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_018466815.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -7693,7 +7693,7 @@ "strain": "GKB4", "supercontigs": 133, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_018691715.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -7706,7 +7706,7 @@ "strain": "KU48", "supercontigs": 1168, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_019059535.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 11, @@ -7719,7 +7719,7 @@ "strain": "EATRO1125", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_019096175.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 8, @@ -7732,7 +7732,7 @@ "strain": "2022", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_019844115.2", - "vEuPathDBProject": "CryptoDB" + "vEuPathDbProject": "CryptoDB" }, { "chromosomes": 0, @@ -7745,7 +7745,7 @@ "strain": "A", "supercontigs": 787, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_019968955.1", - "vEuPathDBProject": "CryptoDB" + "vEuPathDbProject": "CryptoDB" }, { "chromosomes": 0, @@ -7758,7 +7758,7 @@ "strain": "2922-C6/04-290x", "supercontigs": 281, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_020184695.1", - "vEuPathDBProject": "TrichDB" + "vEuPathDbProject": "TrichDB" }, { "chromosomes": 0, @@ -7771,7 +7771,7 @@ "strain": "2922-C6/04-10x", "supercontigs": 187, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_020186115.1", - "vEuPathDBProject": "TrichDB" + "vEuPathDbProject": "TrichDB" }, { "chromosomes": 0, @@ -7784,7 +7784,7 @@ "strain": "KU50", "supercontigs": 1063, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_020283535.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -7797,7 +7797,7 @@ "strain": "strain Winnie", "supercontigs": 358, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_020283715.1", - "vEuPathDBProject": "PiroplasmaDB" + "vEuPathDbProject": "PiroplasmaDB" }, { "chromosomes": 13, @@ -7810,7 +7810,7 @@ "strain": "BG3993", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_020450195.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -7823,7 +7823,7 @@ "strain": "B08-376", "supercontigs": 545, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_020509355.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 33, @@ -7836,7 +7836,7 @@ "strain": "DAOM 181602=DAOM 197198", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_020716725.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 33, @@ -7849,7 +7849,7 @@ "strain": "C2", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_020716745.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -7862,7 +7862,7 @@ "strain": "strain Pr102", "supercontigs": 28, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_020800215.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -7875,7 +7875,7 @@ "strain": "14567", "supercontigs": 27, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_020800235.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 14, @@ -7888,7 +7888,7 @@ "strain": "yoelii 17XNL 2023", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_020844765.3", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 0, @@ -7901,7 +7901,7 @@ "strain": "C3", "supercontigs": 174, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_021020595.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -7914,7 +7914,7 @@ "strain": "str. Neff 2021", "supercontigs": 111, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_021020605.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -7927,7 +7927,7 @@ "strain": "MF1", "supercontigs": 7789, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_021527665.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -7940,7 +7940,7 @@ "strain": "JUm2507", "supercontigs": 111, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_021653875.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -7953,7 +7953,7 @@ "strain": "Aag2", "supercontigs": 3752, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_021653915.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -7966,7 +7966,7 @@ "strain": "FI-F-10", "supercontigs": 22, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_021821965.1", - "vEuPathDBProject": "MicrosporidiaDB" + "vEuPathDbProject": "MicrosporidiaDB" }, { "chromosomes": 0, @@ -7979,7 +7979,7 @@ "strain": "St. Kilda", "supercontigs": 64, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_022059095.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -7992,7 +7992,7 @@ "strain": "CBS 124340", "supercontigs": 89, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_022385695.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -8005,7 +8005,7 @@ "strain": "NL_76_15_250", "supercontigs": 199, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_022530875.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -8018,7 +8018,7 @@ "strain": "DRCT72020", "supercontigs": 12702, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_022627015.2", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 14, @@ -8031,7 +8031,7 @@ "strain": "strain:VNII", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_022832995.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -8044,7 +8044,7 @@ "strain": "isolate CIA", "supercontigs": 93, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_022985015.1", - "vEuPathDBProject": "GiardiaDB" + "vEuPathDbProject": "GiardiaDB" }, { "chromosomes": 0, @@ -8057,7 +8057,7 @@ "strain": "isolate DID", "supercontigs": 260, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_022985025.1", - "vEuPathDBProject": "GiardiaDB" + "vEuPathDbProject": "GiardiaDB" }, { "chromosomes": 0, @@ -8070,7 +8070,7 @@ "strain": "qqDerAnde1.1", "supercontigs": 8198, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_023375915.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 8, @@ -8083,7 +8083,7 @@ "strain": "yc1106", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_023920165.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -8096,7 +8096,7 @@ "strain": "SK-2019", "supercontigs": 125877, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_023969395.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 14, @@ -8109,7 +8109,7 @@ "strain": "strain Bolivian I", "supercontigs": 29, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_023973825.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 0, @@ -8122,7 +8122,7 @@ "strain": "CBS 100304", "supercontigs": 260, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_024516155.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -8135,7 +8135,7 @@ "strain": "strain WA1", "supercontigs": 7, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_024586265.1", - "vEuPathDBProject": "PiroplasmaDB" + "vEuPathDbProject": "PiroplasmaDB" }, { "chromosomes": 0, @@ -8148,7 +8148,7 @@ "strain": "USDA-D6B2", "supercontigs": 7, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_024862765.1", - "vEuPathDBProject": "PiroplasmaDB" + "vEuPathDbProject": "PiroplasmaDB" }, { "chromosomes": 34, @@ -8161,7 +8161,7 @@ "strain": "strain PH8", "supercontigs": 42, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_025688915.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 6, @@ -8174,7 +8174,7 @@ "strain": "G3 2022", "supercontigs": 212, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_026262505.1", - "vEuPathDBProject": "TrichDB" + "vEuPathDbProject": "TrichDB" }, { "chromosomes": 0, @@ -8187,7 +8187,7 @@ "strain": "SK_2022b", "supercontigs": 1790, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_027943245.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -8200,7 +8200,7 @@ "strain": "SK_2022a", "supercontigs": 2108, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_027943295.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -8213,7 +8213,7 @@ "strain": "SK_2022c", "supercontigs": 20778, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_027944975.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -8226,7 +8226,7 @@ "strain": "P57", "supercontigs": 77, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_028554745.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 5, @@ -8239,7 +8239,7 @@ "strain": "strain WA1 2023", "supercontigs": 160, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_028658345.1", - "vEuPathDBProject": "PiroplasmaDB" + "vEuPathDbProject": "PiroplasmaDB" }, { "chromosomes": 14, @@ -8252,7 +8252,7 @@ "strain": "chabaudi", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_900002335.3", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 14, @@ -8265,7 +8265,7 @@ "strain": "ANKA", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_900002375.2", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 14, @@ -8278,7 +8278,7 @@ "strain": "yoelii 17X", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_900002385.2", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 14, @@ -8291,7 +8291,7 @@ "strain": "yoelii YM", "supercontigs": 181, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900002395.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 14, @@ -8304,7 +8304,7 @@ "strain": "SGS1-like", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_900005765.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 0, @@ -8317,7 +8317,7 @@ "strain": "8A", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_900005855.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 0, @@ -8330,7 +8330,7 @@ "strain": "strain NRRL62905", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900029915.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -8343,7 +8343,7 @@ "strain": "MRC7560", "supercontigs": 254, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_900044065.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 4, @@ -8356,7 +8356,7 @@ "strain": "PH-1", "supercontigs": 1, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900044135.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -8369,7 +8369,7 @@ "strain": "ET1", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_900067095.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 12, @@ -8382,7 +8382,7 @@ "strain": "IMI 58289", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_900079805.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 14, @@ -8395,7 +8395,7 @@ "strain": "wallikeri PowCR01", "supercontigs": 763, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900090025.2", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 14, @@ -8408,7 +8408,7 @@ "strain": "curtisi GH01", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900090035.2", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 14, @@ -8421,7 +8421,7 @@ "strain": "UG01", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_900090045.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 14, @@ -8434,7 +8434,7 @@ "strain": "P01", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900093555.2", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 14, @@ -8447,7 +8447,7 @@ "strain": "strain G01", "supercontigs": 39, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900095595.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 14, @@ -8460,7 +8460,7 @@ "strain": "G01", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_900097015.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 14, @@ -8473,7 +8473,7 @@ "strain": "G01", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900097025.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 14, @@ -8486,7 +8486,7 @@ "strain": "G01", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900097035.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 14, @@ -8499,7 +8499,7 @@ "strain": "strain G01", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900097045.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 0, @@ -8512,7 +8512,7 @@ "strain": "strain UTAD222", "supercontigs": 208, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900119595.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 8, @@ -8525,7 +8525,7 @@ "strain": "ATCC 42132", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900149145.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 14, @@ -8538,7 +8538,7 @@ "strain": "strain A1H1", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900162085.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 14, @@ -8551,7 +8551,7 @@ "strain": "strain M", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900180395.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 21, @@ -8564,7 +8564,7 @@ "strain": "ST99CH_3D1", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900184105.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -8577,7 +8577,7 @@ "strain": "strain NIH4 ATCC 30207", "supercontigs": 4161, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900231805.1", - "vEuPathDBProject": "TrichDB" + "vEuPathDbProject": "TrichDB" }, { "chromosomes": 0, @@ -8590,7 +8590,7 @@ "strain": "strain RACE1", "supercontigs": 99, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900237765.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -8603,7 +8603,7 @@ "strain": "strain N402 (ATCC64974)", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900248155.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -8616,7 +8616,7 @@ "strain": "strain 231", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900252365.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 14, @@ -8629,7 +8629,7 @@ "strain": "G01", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900257145.2", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 7, @@ -8642,7 +8642,7 @@ "strain": "strain T mat+", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900290415.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -8655,7 +8655,7 @@ "strain": "UTAD17", "supercontigs": 1360, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900491785.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 44, @@ -8668,7 +8668,7 @@ "strain": "Lister strain 427 2018", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900497135.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 36, @@ -8681,7 +8681,7 @@ "strain": "JPCM5", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900500625.2", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 12, @@ -8694,7 +8694,7 @@ "strain": "f. sp. tritici 96224", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900519115.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 14, @@ -8707,7 +8707,7 @@ "strain": "CD01", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900617135.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 14, @@ -8720,7 +8720,7 @@ "strain": "KE01", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900631975.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 14, @@ -8733,7 +8733,7 @@ "strain": "HB3", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900631985.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 14, @@ -8746,7 +8746,7 @@ "strain": "GN01", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900631995.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 14, @@ -8759,7 +8759,7 @@ "strain": "GA01", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900632005.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 14, @@ -8772,7 +8772,7 @@ "strain": "KH02", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900632015.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 14, @@ -8785,7 +8785,7 @@ "strain": "KH01", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900632025.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 14, @@ -8798,7 +8798,7 @@ "strain": "GB4", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900632035.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 14, @@ -8811,7 +8811,7 @@ "strain": "Dd2", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900632045.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 14, @@ -8824,7 +8824,7 @@ "strain": "IT", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900632055.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 14, @@ -8837,7 +8837,7 @@ "strain": "TG01", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900632065.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 14, @@ -8850,7 +8850,7 @@ "strain": "SN01", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900632075.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 14, @@ -8863,7 +8863,7 @@ "strain": "ML01", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900632085.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 13, @@ -8876,7 +8876,7 @@ "strain": "SD01", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900632095.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 36, @@ -8889,7 +8889,7 @@ "strain": "HU3", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_900635355.2", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 14, @@ -8902,7 +8902,7 @@ "strain": "vinckei CY", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_900681995.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 0, @@ -8915,7 +8915,7 @@ "strain": "2019", "supercontigs": 2439, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_902459845.2", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 0, @@ -8928,7 +8928,7 @@ "strain": "ATCC 30984", "supercontigs": 1925, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_902651635.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 14, @@ -8941,7 +8941,7 @@ "strain": "brucechwatti DA", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_903994205.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 14, @@ -8954,7 +8954,7 @@ "strain": "lentum DE", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_903994225.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 14, @@ -8967,7 +8967,7 @@ "strain": "petteri CR 2020", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_903994235.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 14, @@ -8980,7 +8980,7 @@ "strain": "Cameroon EL", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_903994265.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 29, @@ -8993,7 +8993,7 @@ "strain": "strain Cavalho ATCC PRA-265", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_903995115.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 11, @@ -9006,7 +9006,7 @@ "strain": "f. sp. triticale THUN-12", "supercontigs": 25, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_905067625.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 15, @@ -9019,7 +9019,7 @@ "strain": "Houghton 2021", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_905310635.1", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -9032,7 +9032,7 @@ "strain": "PvW1", "supercontigs": 19, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_914969965.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 36, @@ -9045,7 +9045,7 @@ "strain": "Friedlin 2021", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_916722125.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -9058,7 +9058,7 @@ "strain": "Rahman", "supercontigs": 18523, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_917563895.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 13, @@ -9071,7 +9071,7 @@ "strain": "strain STIB 805", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_917563935.1", - "vEuPathDBProject": "TriTrypDB" + "vEuPathDbProject": "TriTrypDB" }, { "chromosomes": 0, @@ -9084,7 +9084,7 @@ "strain": "PAM", "supercontigs": 28, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_949152365.1", - "vEuPathDBProject": "PlasmoDB" + "vEuPathDbProject": "PlasmoDB" }, { "chromosomes": 7, @@ -9097,7 +9097,7 @@ "strain": "AX4", "supercontigs": 33, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000004695.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -9110,7 +9110,7 @@ "strain": "RN66", "supercontigs": 84, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000006515.1", - "vEuPathDBProject": "CryptoDB" + "vEuPathDbProject": "CryptoDB" }, { "chromosomes": 14, @@ -9123,7 +9123,7 @@ "strain": "ME49", "supercontigs": 2248, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000006565.2", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -9136,7 +9136,7 @@ "strain": "k-hell", "supercontigs": 1212, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000182805.3", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -9149,7 +9149,7 @@ "strain": "QSDP1", "supercontigs": 799, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000190715.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -9162,7 +9162,7 @@ "strain": "P19", "supercontigs": 5233, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_000257125.1", - "vEuPathDBProject": "AmoebaDB" + "vEuPathDbProject": "AmoebaDB" }, { "chromosomes": 0, @@ -9175,7 +9175,7 @@ "strain": "Pd1", "supercontigs": 53, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000315645.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 21, @@ -9188,7 +9188,7 @@ "strain": "REF", "supercontigs": 7579, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000364345.1", - "vEuPathDBProject": "HostDB" + "vEuPathDbProject": "HostDB" }, { "chromosomes": 0, @@ -9201,7 +9201,7 @@ "strain": "CBS 131958", "supercontigs": 131, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_001299255.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 8, @@ -9214,7 +9214,7 @@ "strain": "DMKU3-1042", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_001417885.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -9227,7 +9227,7 @@ "strain": "B80", "supercontigs": 62, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_001477545.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -9240,7 +9240,7 @@ "strain": "C6/36 cell line", "supercontigs": 2434, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_001876365.2", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -9253,7 +9253,7 @@ "strain": "isolate NF1_C8", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_002999335.1", - "vEuPathDBProject": "ToxoDB" + "vEuPathDbProject": "ToxoDB" }, { "chromosomes": 0, @@ -9266,7 +9266,7 @@ "strain": "CBS 101075", "supercontigs": 86, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_004022145.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 3, @@ -9279,7 +9279,7 @@ "strain": "UCISS2018", "supercontigs": 491, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_013141755.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 11, @@ -9292,7 +9292,7 @@ "strain": "Rsan-2018", "supercontigs": 2316, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_013339695.2", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 3, @@ -9305,7 +9305,7 @@ "strain": "STECLA 2020", "supercontigs": 4, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_013758885.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -9318,7 +9318,7 @@ "strain": "mMyoMyo1", "supercontigs": 92, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_014108235.1", - "vEuPathDBProject": "HostDB" + "vEuPathDbProject": "HostDB" }, { "chromosomes": 0, @@ -9331,7 +9331,7 @@ "strain": "PC9", "supercontigs": 16, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_014466165.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 41, @@ -9344,7 +9344,7 @@ "strain": "isolate bGalGal1", "supercontigs": 172, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_016699485.2", - "vEuPathDBProject": "HostDB" + "vEuPathDbProject": "HostDB" }, { "chromosomes": 3, @@ -9357,7 +9357,7 @@ "strain": "MOPTI", "supercontigs": 196, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_016920705.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 3, @@ -9370,7 +9370,7 @@ "strain": "DONGOLA 2021", "supercontigs": 98, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_016920715.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -9383,7 +9383,7 @@ "strain": "PalLabHiFi", "supercontigs": 648, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_016920785.2", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 5, @@ -9396,7 +9396,7 @@ "strain": "MAF 2021", "supercontigs": 1322, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_017562075.2", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -9409,7 +9409,7 @@ "strain": "FSSC 5 MPI-SDFR-AT-0091", "supercontigs": 74, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_020744495.1", - "vEuPathDBProject": "FungiDB" + "vEuPathDbProject": "FungiDB" }, { "chromosomes": 0, @@ -9422,7 +9422,7 @@ "strain": "qqDerAnde1.2", "supercontigs": 3118, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_023375885.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 4, @@ -9435,7 +9435,7 @@ "strain": "M1", "supercontigs": 0, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_024334085.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 5, @@ -9448,7 +9448,7 @@ "strain": "M1", "supercontigs": 640, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_024763615.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -9461,7 +9461,7 @@ "strain": "aabys 2023", "supercontigs": 339, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_030504385.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 3, @@ -9474,7 +9474,7 @@ "strain": "AcruBR1", "supercontigs": 5085, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943734635.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 3, @@ -9487,7 +9487,7 @@ "strain": "ScyaPA1", "supercontigs": 5, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943734655.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 4, @@ -9500,7 +9500,7 @@ "strain": "AaquGF1", "supercontigs": 86, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943734665.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 3, @@ -9513,7 +9513,7 @@ "strain": "AcolN3", "supercontigs": 125, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943734685.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 3, @@ -9526,7 +9526,7 @@ "strain": "AmacGA1", "supercontigs": 167, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943734695.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 3, @@ -9539,7 +9539,7 @@ "strain": "AcouGA1", "supercontigs": 416, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943734705.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 3, @@ -9552,7 +9552,7 @@ "strain": "AmarGA1", "supercontigs": 285, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943734725.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 3, @@ -9565,7 +9565,7 @@ "strain": "Ifakara", "supercontigs": 187, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943734735.2", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 3, @@ -9578,7 +9578,7 @@ "strain": "AdarGF1", "supercontigs": 62, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943734745.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 3, @@ -9591,7 +9591,7 @@ "strain": "AmouCM1", "supercontigs": 342, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943734755.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 3, @@ -9604,7 +9604,7 @@ "strain": "AzieGA1", "supercontigs": 416, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943734765.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 3, @@ -9617,7 +9617,7 @@ "strain": "AfunGA1", "supercontigs": 326, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943734845.2", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 3, @@ -9630,7 +9630,7 @@ "strain": "AbelBR1", "supercontigs": 2982, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943735745.2", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 3, @@ -9643,7 +9643,7 @@ "strain": "AnilCM1", "supercontigs": 153, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943737925.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 0, @@ -9656,7 +9656,7 @@ "strain": "India", "supercontigs": 64, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_947086385.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" }, { "chromosomes": 18, @@ -9669,6 +9669,6 @@ "strain": "XG47", "supercontigs": 25, "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_947242115.1", - "vEuPathDBProject": "VectorBase" + "vEuPathDbProject": "VectorBase" } ] diff --git a/files/source/organisms-from-ncbi.tsv b/files/source/organisms-from-ncbi.tsv index af7aec6..83237cd 100644 --- a/files/source/organisms-from-ncbi.tsv +++ b/files/source/organisms-from-ncbi.tsv @@ -1,18 +1,18 @@ taxon taxonomyId assemblyCount CustomTags -Anopheles gambiae 7165 7 VEuPathDB +Anopheles gambiae 7165 7 VEuPathDb Coccidioides immitis 5501 5 Coccidioides posadasii 199306 13 -Culex pipiens 7175 5 VEuPathDB -Leishmania braziliensis 5660 11 VEuPathDB -Leishmania donovani 5661 12 VEuPathDB -Leishmania major 5664 7 VEuPathDB +Culex pipiens 7175 5 VEuPathDb +Leishmania braziliensis 5660 11 VEuPathDb +Leishmania donovani 5661 12 VEuPathDb +Leishmania major 5664 7 VEuPathDb Monkeypox virus 10244 6911 Virus Mycobacterium tuberculosis 1773 7823 Bact -Plasmodium falciparum 5833 67 VEuPathDB -Plasmodium vinckei 5860 10 VEuPathDB -Plasmodium vivax 5855 19 VEuPathDB -Plasmodium yoelii 5861 15 VEuPathDB +Plasmodium falciparum 5833 67 VEuPathDb +Plasmodium vinckei 5860 10 VEuPathDb +Plasmodium vivax 5855 19 VEuPathDb +Plasmodium yoelii 5861 15 VEuPathDb Severe acute respiratory syndrome coronavirus 2 2697049 92 Virus -Toxoplasma gondii 5811 29 VEuPathDB -Trypanosoma brucei 5691 5 VEuPathDB -Trypanosoma cruzi 5693 45 VEuPathDB +Toxoplasma gondii 5811 29 VEuPathDb +Trypanosoma brucei 5691 5 VEuPathDb +Trypanosoma cruzi 5693 45 VEuPathDb diff --git a/site-config/brc-analytics/category.ts b/site-config/brc-analytics/category.ts index 3b30ee2..825f5d8 100644 --- a/site-config/brc-analytics/category.ts +++ b/site-config/brc-analytics/category.ts @@ -7,7 +7,7 @@ export const BRC_DATA_CATALOG_CATEGORY_KEY = { STRAIN: "strain", SUPERCONTIGS: "supercontigs", UCSC_BROWSER_URL: "ucscBrowserUrl", - VEUPATHDB_PROJECT: "vEuPathDBProject", + VEUPATHDB_PROJECT: "vEuPathDbProject", }; export const BRC_DATA_CATALOG_CATEGORY_LABEL = { diff --git a/site-config/brc-analytics/local/index/genomeEntityConfig.ts b/site-config/brc-analytics/local/index/genomeEntityConfig.ts index 01e1d8d..5ae373c 100644 --- a/site-config/brc-analytics/local/index/genomeEntityConfig.ts +++ b/site-config/brc-analytics/local/index/genomeEntityConfig.ts @@ -111,7 +111,7 @@ export const genomeEntityConfig: BRCEntityConfig = { { componentConfig: { component: C.BasicCell, - viewBuilder: V.buildVEuPathDBProject, + viewBuilder: V.buildVEuPathDbProject, } as ComponentConfig, header: BRC_DATA_CATALOG_CATEGORY_LABEL.VEUPATHDB_PROJECT, id: BRC_DATA_CATALOG_CATEGORY_KEY.VEUPATHDB_PROJECT, From 73ed726c62aeff5423f4fcd4d204c5e35e80dca2 Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Sat, 16 Nov 2024 15:54:18 -0800 Subject: [PATCH 02/30] feat: update genome list to use data from ncbi (#177) --- .../brc-analytics-catalog/common/entities.ts | 21 +- .../brc-analytics-catalog/common/utils.ts | 4 +- .../common/viewModelBuilders.ts | 258 +- files/build-catalog.ts | 44 +- files/entities.ts | 31 +- files/out/genomes.json | 9916 +---------------- site-config/brc-analytics/category.ts | 36 +- .../local/index/genomeEntityConfig.ts | 138 +- 8 files changed, 634 insertions(+), 9814 deletions(-) diff --git a/app/apis/catalog/brc-analytics-catalog/common/entities.ts b/app/apis/catalog/brc-analytics-catalog/common/entities.ts index 6ec031a..8e69429 100644 --- a/app/apis/catalog/brc-analytics-catalog/common/entities.ts +++ b/app/apis/catalog/brc-analytics-catalog/common/entities.ts @@ -10,17 +10,20 @@ export enum ANALYSIS_METHOD { export type BRCCatalog = BRCDataCatalogGenome; export interface BRCDataCatalogGenome { - chromosomes: number; - contigs: number; - geneModelUrl: string; - genomeVersionAssemblyId: string; + accession: string; + annotationStatus: string | null; + chromosomes: number | null; + coverage: string | null; + gcPercent: number; + isRef: boolean; + length: number; + level: string; ncbiTaxonomyId: string; organism: string; - species: string; - strain: string; - supercontigs: number; - ucscBrowserUrl: string; - vEuPathDbProject: string; + scaffoldCount: number; + scaffoldL50: number; + scaffoldN50: number; + ucscBrowserUrl: string | null; } export interface EntitiesResponse { diff --git a/app/apis/catalog/brc-analytics-catalog/common/utils.ts b/app/apis/catalog/brc-analytics-catalog/common/utils.ts index 8146c3b..935fde0 100644 --- a/app/apis/catalog/brc-analytics-catalog/common/utils.ts +++ b/app/apis/catalog/brc-analytics-catalog/common/utils.ts @@ -1,12 +1,12 @@ import { BRCDataCatalogGenome } from "./entities"; export function getGenomeId(genome: BRCDataCatalogGenome): string { - return sanitizeEntityId(genome.genomeVersionAssemblyId); + return sanitizeEntityId(genome.accession); } export function getGenomeTitle(genome?: BRCDataCatalogGenome): string { if (!genome) return ""; - return `${genome.species} - ${genome.strain}`; + return `${genome.organism}`; } export function sanitizeEntityId(entityId?: string): string { diff --git a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts index 49a7e47..022a1a2 100644 --- a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts +++ b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts @@ -10,6 +10,19 @@ import { BRCDataCatalogGenome } from "../../../../apis/catalog/brc-analytics-cat import * as C from "../../../../components"; import { GENOME_BROWSER, NCBI_DATASETS_URL } from "./constants"; +/** + * Build props for the accession cell. + * @param genome - Genome entity. + * @returns Props to be used for the cell. + */ +export const buildAccession = ( + genome: BRCDataCatalogGenome +): ComponentProps => { + return { + value: genome.accession, + }; +}; + /** * Build props for the genome analysis cell. * @param genome - Genome entity. @@ -20,7 +33,7 @@ export const buildAnalyzeGenome = ( genome: BRCDataCatalogGenome, viewContext: ViewContext ): ComponentProps => { - const { genomeVersionAssemblyId, ncbiTaxonomyId, ucscBrowserUrl } = genome; + const { accession, ncbiTaxonomyId, ucscBrowserUrl } = genome; const rowId = viewContext.cellContext?.row?.id; return { analyze: { @@ -28,10 +41,12 @@ export const buildAnalyzeGenome = ( url: rowId ? `${ROUTES.ORGANISMS}/${rowId}` : "", }, views: [ - { label: "UCSC Genome Browser", url: ucscBrowserUrl }, + ...(ucscBrowserUrl + ? [{ label: "UCSC Genome Browser", url: ucscBrowserUrl }] + : []), { label: "NCBI Genome Assembly", - url: `${NCBI_DATASETS_URL}/genome/${genomeVersionAssemblyId}`, + url: `${NCBI_DATASETS_URL}/genome/${accession}`, }, { label: "NCBI Taxonomy", @@ -43,6 +58,19 @@ export const buildAnalyzeGenome = ( }; }; +/** + * Build props for the annotation status cell. + * @param genome - Genome entity. + * @returns Props to be used for the cell. + */ +export const buildAnnotationStatus = ( + genome: BRCDataCatalogGenome +): ComponentProps => { + return { + value: genome.annotationStatus, + }; +}; + /** * Build props for the chromosomes cell. * @param genome - Genome entity. @@ -57,179 +85,229 @@ export const buildChromosomes = ( }; /** - * Build props for the contigs cell. + * Build props for the coverage cell. * @param genome - Genome entity. * @returns Props to be used for the cell. */ -export const buildContigs = ( +export const buildCoverage = ( genome: BRCDataCatalogGenome ): ComponentProps => { return { - value: genome.contigs, + value: genome.coverage, }; }; /** - * Build props for the genome AnalysisMethod component. + * Build props for the GC% cell. * @param genome - Genome entity. - * @param analysisMethodProps - Analysis Method properties. - * @param analysisMethodProps.analysisMethod - Analysis method. - * @param analysisMethodProps.content - Content to be displayed. - * @returns Props to be used for the AnalysisMethod component. + * @returns Props to be used for the cell. */ -export const buildGenomeAnalysisMethod = ( - genome: BRCDataCatalogGenome, - analysisMethodProps: Pick< - ComponentProps, - "analysisMethod" | "content" - > -): ComponentProps => { +export const buildGcPercent = ( + genome: BRCDataCatalogGenome +): ComponentProps => { return { - ...analysisMethodProps, - geneModelUrl: genome.geneModelUrl, - genomeVersionAssemblyId: genome.genomeVersionAssemblyId, + value: genome.gcPercent, }; }; /** - * Build props for the genome AnalysisPortals component. + * Build props for the "is ref" cell. * @param genome - Genome entity. - * @returns Props to be used for the AnalysisPortals component. + * @returns Props to be used for the cell. */ -export const buildGenomeAnalysisPortals = ( +export const buildIsRef = ( genome: BRCDataCatalogGenome -): ComponentProps => { +): ComponentProps => { return { - portals: [ - { - imageProps: { - alt: GENOME_BROWSER, - src: "/analysis-portals/ucsc-genome.png", - width: 20, - }, - label: GENOME_BROWSER, - url: genome.ucscBrowserUrl, - }, - ], + value: genome.isRef ? "Yes" : "No", }; }; /** - * Build props for the genome DetailViewHero component. + * Build props for the length cell. * @param genome - Genome entity. - * @returns Props to be used for the DetailViewHero component. + * @returns Props to be used for the cell. */ -export const buildGenomeChooseAnalysisMethodDetailViewHero = ( +export const buildLength = ( genome: BRCDataCatalogGenome -): ComponentProps => { +): ComponentProps => { return { - breadcrumbs: C.Breadcrumbs({ - breadcrumbs: getGenomeEntityChooseAnalysisMethodBreadcrumbs(genome), - }), - title: "Choose Analysis Methods", + value: genome.length, }; }; /** - * Build props for the genome detail KeyValuePairs component. + * Build props for the level cell. * @param genome - Genome entity. - * @returns Props to be used for the KeyValuePairs component. + * @returns Props to be used for the cell. */ -export const buildGenomeDetails = ( +export const buildLevel = ( genome: BRCDataCatalogGenome -): ComponentProps => { - const keyValuePairs = new Map(); - keyValuePairs.set( - "Species", - C.Link({ - label: genome.species, - url: `https://www.ncbi.nlm.nih.gov/datasets/taxonomy/${encodeURIComponent( - genome.ncbiTaxonomyId - )}/`, - }) - ); - keyValuePairs.set("Strain", genome.strain); - keyValuePairs.set( - "Assembly Version ID", - C.CopyText({ - children: genome.genomeVersionAssemblyId, - value: genome.genomeVersionAssemblyId, - }) - ); - keyValuePairs.set("VeUPathDB Project", genome.vEuPathDbProject); - keyValuePairs.set("Contigs", genome.contigs); - keyValuePairs.set("Super Contigs", genome.supercontigs); - keyValuePairs.set("Chromosomes", genome.chromosomes); +): ComponentProps => { return { - KeyElType: C.KeyElType, - KeyValuesElType: (props) => C.Stack({ gap: 4, ...props }), - ValueElType: C.ValueElType, - keyValuePairs, + value: genome.level, }; }; /** - * Build props for the genome version/assembly ID cell. + * Build props for the organism cell. * @param genome - Genome entity. * @returns Props to be used for the cell. */ -export const buildGenomeVersionAssemblyId = ( +export const buildOrganism = ( genome: BRCDataCatalogGenome ): ComponentProps => { return { - value: genome.genomeVersionAssemblyId, + value: genome.organism, }; }; /** - * Build props for the species cell. + * Build props for the scaffold count cell. * @param genome - Genome entity. * @returns Props to be used for the cell. */ -export const buildSpecies = ( +export const buildScaffoldCount = ( genome: BRCDataCatalogGenome ): ComponentProps => { return { - value: genome.species, + value: genome.scaffoldCount, }; }; /** - * Build props for the strain cell. + * Build props for the scaffold L50 cell. * @param genome - Genome entity. * @returns Props to be used for the cell. */ -export const buildStrain = ( +export const buildScaffoldL50 = ( genome: BRCDataCatalogGenome ): ComponentProps => { return { - value: genome.strain, + value: genome.scaffoldL50, }; }; /** - * Build props for the supercontigs cell. + * Build props for the scaffold N50 cell. * @param genome - Genome entity. * @returns Props to be used for the cell. */ -export const buildSupercontigs = ( +export const buildScaffoldN50 = ( genome: BRCDataCatalogGenome ): ComponentProps => { return { - value: genome.supercontigs, + value: genome.scaffoldN50, }; }; /** - * Build props for the VEuPathDB project cell. + * Build props for the taxonomy ID cell. * @param genome - Genome entity. * @returns Props to be used for the cell. */ -export const buildVEuPathDbProject = ( +export const buildTaxonomyId = ( genome: BRCDataCatalogGenome ): ComponentProps => { return { - value: genome.vEuPathDbProject, + value: genome.ncbiTaxonomyId, + }; +}; + +/** + * Build props for the genome AnalysisMethod component. + * @param genome - Genome entity. + * @param analysisMethodProps - Analysis Method properties. + * @param analysisMethodProps.analysisMethod - Analysis method. + * @param analysisMethodProps.content - Content to be displayed. + * @returns Props to be used for the AnalysisMethod component. + */ +export const buildGenomeAnalysisMethod = ( + genome: BRCDataCatalogGenome, + analysisMethodProps: Pick< + ComponentProps, + "analysisMethod" | "content" + > +): ComponentProps => { + return { + ...analysisMethodProps, + geneModelUrl: "", + genomeVersionAssemblyId: genome.accession, + }; +}; + +/** + * Build props for the genome AnalysisPortals component. + * @param genome - Genome entity. + * @returns Props to be used for the AnalysisPortals component. + */ +export const buildGenomeAnalysisPortals = ( + genome: BRCDataCatalogGenome +): ComponentProps => { + return { + portals: genome.ucscBrowserUrl + ? [ + { + imageProps: { + alt: GENOME_BROWSER, + src: "/analysis-portals/ucsc-genome.png", + width: 20, + }, + label: GENOME_BROWSER, + url: genome.ucscBrowserUrl, + }, + ] + : [], + }; +}; + +/** + * Build props for the genome DetailViewHero component. + * @param genome - Genome entity. + * @returns Props to be used for the DetailViewHero component. + */ +export const buildGenomeChooseAnalysisMethodDetailViewHero = ( + genome: BRCDataCatalogGenome +): ComponentProps => { + return { + breadcrumbs: C.Breadcrumbs({ + breadcrumbs: getGenomeEntityChooseAnalysisMethodBreadcrumbs(genome), + }), + title: "Choose Analysis Methods", + }; +}; + +/** + * Build props for the genome detail KeyValuePairs component. + * @param genome - Genome entity. + * @returns Props to be used for the KeyValuePairs component. + */ +export const buildGenomeDetails = ( + genome: BRCDataCatalogGenome +): ComponentProps => { + const keyValuePairs = new Map(); + keyValuePairs.set( + "Taxon", + C.Link({ + label: genome.organism, + url: `https://www.ncbi.nlm.nih.gov/datasets/taxonomy/${encodeURIComponent( + genome.ncbiTaxonomyId + )}/`, + }) + ); + keyValuePairs.set( + "Accession", + C.CopyText({ + children: genome.accession, + value: genome.accession, + }) + ); + keyValuePairs.set("Chromosomes", genome.chromosomes); + return { + KeyElType: C.KeyElType, + KeyValuesElType: (props) => C.Stack({ gap: 4, ...props }), + ValueElType: C.ValueElType, + keyValuePairs, }; }; @@ -243,7 +321,7 @@ function getGenomeEntityChooseAnalysisMethodBreadcrumbs( ): Breadcrumb[] { return [ { path: ROUTES.ORGANISMS, text: "Organisms" }, - { path: "", text: `${genome.species} - ${genome.strain}` }, + { path: "", text: `${genome.organism}` }, { path: "", text: "Choose Analysis Methods" }, ]; } diff --git a/files/build-catalog.ts b/files/build-catalog.ts index 8573975..49229d0 100644 --- a/files/build-catalog.ts +++ b/files/build-catalog.ts @@ -3,7 +3,7 @@ import fsp from "fs/promises"; import { BRCDataCatalogGenome } from "../app/apis/catalog/brc-analytics-catalog/common/entities"; import { SourceGenome } from "./entities"; -const SOURCE_PATH_GENOMES = "files/source/genomes.tsv"; +const SOURCE_PATH_GENOMES = "files/source/genomes-from-ncbi.tsv"; buildCatalog(); @@ -20,22 +20,23 @@ async function buildGenomes(): Promise { const sourceRows = await readValuesFile(SOURCE_PATH_GENOMES); const mappedRows = sourceRows.map( (row): BRCDataCatalogGenome => ({ - chromosomes: parseNumber(row.Chromosomes), - contigs: parseNumber(row.Contigs), - geneModelUrl: row.geneModelUrl, - genomeVersionAssemblyId: row["Genome Version/Assembly ID"], - ncbiTaxonomyId: row.taxId, - organism: row.Organism, - species: row.Species, - strain: row.Strain, - supercontigs: parseNumber(row.Supercontigs), - ucscBrowserUrl: row.ucscBrowser, - vEuPathDbProject: row["VEuPathDB Project"], + accession: row.accession, + annotationStatus: parseStringOrNull(row.annotationStatus), + chromosomes: parseNumberOrNull(row.chromosomeCount), + coverage: parseStringOrNull(row.coverage), + gcPercent: parseNumber(row.gcPercent), + isRef: parseBoolean(row.isRef), + length: parseNumber(row.length), + level: row.level, + ncbiTaxonomyId: row.taxonomyId, + organism: row.taxon, + scaffoldCount: parseNumber(row.scaffoldCount), + scaffoldL50: parseNumber(row.scaffoldL50), + scaffoldN50: parseNumber(row.scaffoldN50), + ucscBrowserUrl: parseStringOrNull(row.ucscBrowser), }) ); - return mappedRows.sort((a, b) => - a.genomeVersionAssemblyId.localeCompare(b.genomeVersionAssemblyId) - ); + return mappedRows.sort((a, b) => a.accession.localeCompare(b.accession)); } async function readValuesFile( @@ -54,6 +55,15 @@ async function saveJson(filePath: string, data: unknown): Promise { await fsp.writeFile(filePath, JSON.stringify(data, undefined, 2) + "\n"); } +function parseStringOrNull(value: string): string | null { + return value || null; +} + +function parseNumberOrNull(value: string): number | null { + if (!value) return null; + return parseNumber(value); +} + function parseNumber(value: string): number { value = value.trim(); const n = Number(value); @@ -61,3 +71,7 @@ function parseNumber(value: string): number { throw new Error(`Invalid number value: ${JSON.stringify(value)}`); return n; } + +function parseBoolean(value: string): boolean { + return value[0].toLowerCase() === "t"; +} diff --git a/files/entities.ts b/files/entities.ts index dad7cc1..6f5b6f6 100644 --- a/files/entities.ts +++ b/files/entities.ts @@ -1,21 +1,16 @@ export interface SourceGenome { - asmId: string; - Chromosomes: string; - comName: string; - Contigs: string; - genBank: string; - geneModelUrl: string; - "Genome Source": string; - "Genome Version/Assembly ID": string; - identical: string; - "Is Reference Strain": string; - Organism: string; - refSeq: string; - sciName: string; - Species: string; - Strain: string; - Supercontigs: string; - taxId: string; + accession: string; + annotationStatus: string; + chromosomeCount: string; + coverage: string; + gcPercent: string; + isRef: string; + length: string; + level: string; + scaffoldCount: string; + scaffoldL50: string; + scaffoldN50: string; + taxon: string; + taxonomyId: string; ucscBrowser: string; - "VEuPathDB Project": string; } diff --git a/files/out/genomes.json b/files/out/genomes.json index 1030336..abbeba6 100644 --- a/files/out/genomes.json +++ b/files/out/genomes.json @@ -1,9674 +1,322 @@ [ { - "chromosomes": 7, - "contigs": 0, - "geneModelUrl": "", - "genomeVersionAssemblyId": "GCA_000001215.4", - "ncbiTaxonomyId": "7227", - "organism": "Drosophila melanogaster iso-1", - "species": "Drosophila melanogaster", - "strain": "iso-1", - "supercontigs": 1862, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000001215.4", - "vEuPathDbProject": "VectorBase" - }, - { - "chromosomes": 0, - "contigs": 0, - "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCA/000/001/985/GCA_000001985.1/genes/GCA_000001985.1_JCVI-PMFA1-2.0.augustus.gtf.gz", - "genomeVersionAssemblyId": "GCA_000001985.1", - "ncbiTaxonomyId": "441960", - "organism": "Talaromyces marneffei ATCC 18224", - "species": "Talaromyces marneffei", - "strain": "ATCC 18224", - "supercontigs": 452, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000001985.1", - "vEuPathDbProject": "FungiDB" - }, - { - "chromosomes": 14, - "contigs": 2733, - "geneModelUrl": "", - "genomeVersionAssemblyId": "GCA_000002415.2", + "accession": "GCF_000002415.2", + "annotationStatus": "Full annotation", + "chromosomes": 14, + "coverage": null, + "gcPercent": 42.5, + "isRef": true, + "length": 27007701, + "level": "Chromosome", "ncbiTaxonomyId": "5855", - "organism": "Plasmodium vivax Sal-1", - "species": "Plasmodium vivax", - "strain": "Sal-1", - "supercontigs": 0, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002415.2", - "vEuPathDbProject": "PlasmoDB" - }, - { - "chromosomes": 5, - "contigs": 0, - "geneModelUrl": "", - "genomeVersionAssemblyId": "GCA_000002435.2", - "ncbiTaxonomyId": "5741", - "organism": "Giardia Assemblage A isolate WB 2019", - "species": "Giardia Assemblage A", - "strain": "isolate WB 2019", - "supercontigs": 30, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002435.2", - "vEuPathDbProject": "GiardiaDB" + "organism": "Plasmodium vivax", + "scaffoldCount": 2747, + "scaffoldL50": 6, + "scaffoldN50": 1678596, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002415.2" }, { - "chromosomes": 16, - "contigs": 115, - "geneModelUrl": "", - "genomeVersionAssemblyId": "GCA_000002445.1", + "accession": "GCF_000002445.2", + "annotationStatus": "Full annotation", + "chromosomes": 11, + "coverage": null, + "gcPercent": 46.5, + "isRef": true, + "length": 26075494, + "level": "Chromosome", "ncbiTaxonomyId": "185431", "organism": "Trypanosoma brucei brucei TREU927", - "species": "Trypanosoma brucei", - "strain": "brucei TREU927", - "supercontigs": 0, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002445.2", - "vEuPathDbProject": "TriTrypDB" - }, - { - "chromosomes": 7, - "contigs": 0, - "geneModelUrl": "", - "genomeVersionAssemblyId": "GCA_000002495.2", - "ncbiTaxonomyId": "242507", - "organism": "Pyricularia oryzae 70-15", - "species": "Pyricularia oryzae", - "strain": "70-15", - "supercontigs": 46, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002495.2", - "vEuPathDbProject": "FungiDB" - }, - { - "chromosomes": 6, - "contigs": 0, - "geneModelUrl": "", - "genomeVersionAssemblyId": "GCA_000002515.1", - "ncbiTaxonomyId": "28985", - "organism": "Kluyveromyces lactis NRRL Y-1140", - "species": "Kluyveromyces lactis", - "strain": "NRRL Y-1140", - "supercontigs": 0, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002515.2", - "vEuPathDbProject": "FungiDB" - }, - { - "chromosomes": 6, - "contigs": 0, - "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCA/000/002/525/GCA_000002525.1/genes/GCA_000002525.1_ASM252v1.augustus.gtf.gz", - 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"ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943734755.1", - "vEuPathDbProject": "VectorBase" - }, - { - "chromosomes": 3, - "contigs": 0, - "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/943/734/765/GCF_943734765.1/genes/GCF_943734765.1_idAnoZiCoDA_A2_x.2.ncbiRefSeq.gtf.gz", - "genomeVersionAssemblyId": "GCF_943734765.1", - "ncbiTaxonomyId": "345580", - "organism": "Anopheles ziemanni AzieGA1", - "species": "Anopheles ziemanni", - "strain": "AzieGA1", - "supercontigs": 416, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943734765.1", - "vEuPathDbProject": "VectorBase" - }, - { - "chromosomes": 3, - "contigs": 0, - "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/943/734/845/GCF_943734845.2/genes/GCF_943734845.2_idAnoFuneDA-416_04.ncbiRefSeq.gtf.gz", - "genomeVersionAssemblyId": "GCF_943734845.2", - "ncbiTaxonomyId": "62324", - "organism": "Anopheles funestus AfunGA1", - "species": "Anopheles funestus", - "strain": "AfunGA1", - "supercontigs": 326, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943734845.2", - "vEuPathDbProject": "VectorBase" - }, - { - "chromosomes": 3, - "contigs": 0, - "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/943/735/745/GCF_943735745.2/genes/GCF_943735745.2_idAnoBellAS_SP24_06.2.ncbiRefSeq.gtf.gz", - "genomeVersionAssemblyId": "GCF_943735745.2", - "ncbiTaxonomyId": "139047", - "organism": "Anopheles bellator AbelBR1", - "species": "Anopheles bellator", - "strain": "AbelBR1", - "supercontigs": 2982, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943735745.2", - "vEuPathDbProject": "VectorBase" - }, - { - "chromosomes": 3, - "contigs": 0, - "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/943/737/925/GCF_943737925.1/genes/GCF_943737925.1_idAnoNiliSN_F5_01.ncbiRefSeq.gtf.gz", - "genomeVersionAssemblyId": "GCF_943737925.1", - "ncbiTaxonomyId": "185578", - "organism": "Anopheles nili AnilCM1", - "species": "Anopheles nili", - "strain": "AnilCM1", - "supercontigs": 153, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943737925.1", - "vEuPathDbProject": "VectorBase" - }, - { - "chromosomes": 0, - "contigs": 0, - "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/947/086/385/GCF_947086385.1/genes/GCF_947086385.1_Phlebotomus_argentipes_genome_assembly.ncbiRefSeq.gtf.gz", - "genomeVersionAssemblyId": "GCF_947086385.1", - "ncbiTaxonomyId": "94469", - "organism": "Phlebotomus argentipes India", - "species": "Phlebotomus argentipes", - "strain": "India", - "supercontigs": 64, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_947086385.1", - "vEuPathDbProject": "VectorBase" - }, - { - "chromosomes": 18, - "contigs": 0, - "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/947/242/115/GCF_947242115.1/genes/GCF_947242115.1_xgBioGlab47.1.ncbiRefSeq.gtf.gz", - "genomeVersionAssemblyId": "GCF_947242115.1", - "ncbiTaxonomyId": "6526", - "organism": "Biomphalaria glabrata XG47", - "species": "Biomphalaria glabrata", - "strain": "XG47", - "supercontigs": 25, - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_947242115.1", - "vEuPathDbProject": "VectorBase" + "organism": "Anopheles gambiae", + "scaffoldCount": 190, + "scaffoldL50": 2, + "scaffoldN50": 99149756, + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943734735.2" + }, + { + "accession": "GCF_963525475.1", + "annotationStatus": null, + "chromosomes": 1, + "coverage": "100.0x", + "gcPercent": 65.5, + "isRef": false, + "length": 4469156, + "level": "Complete Genome", + "ncbiTaxonomyId": "1773", + "organism": "Mycobacterium tuberculosis", + "scaffoldCount": 1, + "scaffoldL50": 1, + "scaffoldN50": 4469156, + "ucscBrowserUrl": null } ] diff --git a/site-config/brc-analytics/category.ts b/site-config/brc-analytics/category.ts index 825f5d8..7a4519f 100644 --- a/site-config/brc-analytics/category.ts +++ b/site-config/brc-analytics/category.ts @@ -1,23 +1,35 @@ export const BRC_DATA_CATALOG_CATEGORY_KEY = { + ACCESSION: "accession", ANALYZE_GENOME: "analyzeGenome", + ANNOTATION_STATUS: "annotationStatus", CHROMOSOMES: "chromosomes", - CONTIGS: "contigs", - GENOME_VERSION_ASSEMBLY_ID: "genomeVersionAssemblyId", - SPECIES: "species", - STRAIN: "strain", - SUPERCONTIGS: "supercontigs", + COVERAGE: "coverage", + GC_PERCENT: "gcPercent", + IS_REF: "isRef", + LENGTH: "length", + LEVEL: "level", + ORGANISM: "organism", + SCAFFOLD_COUNT: "scaffoldCount", + SCAFFOLD_L50: "scaffoldL50", + SCAFFOLD_N50: "scaffoldN50", + TAXONOMY_ID: "ncbiTaxonomyId", UCSC_BROWSER_URL: "ucscBrowserUrl", - VEUPATHDB_PROJECT: "vEuPathDbProject", }; export const BRC_DATA_CATALOG_CATEGORY_LABEL = { + ACCESSION: "Accession", ANALYZE_GENOME: "Action", + ANNOTATION_STATUS: "Annotation Status", CHROMOSOMES: "Chromosomes", - CONTIGS: "Contigs", - GENOME_VERSION_ASSEMBLY_ID: "Assembly Version ID", - SPECIES: "Species", - STRAIN: "Strain", - SUPERCONTIGS: "Supercontigs", + COVERAGE: "Coverage", + GC_PERCENT: "GC%", + IS_REF: "Is Reference", + LENGTH: "Length", + LEVEL: "Level", + ORGANISM: "Organism", + SCAFFOLD_COUNT: "Scaffolds", + SCAFFOLD_L50: "Scaffold L50", + SCAFFOLD_N50: "Scaffold N50", + TAXONOMY_ID: "Taxonomy ID", UCSC_BROWSER_URL: "UCSC Browser", - VEUPATHDB_PROJECT: "VEuPathDB Project", }; diff --git a/site-config/brc-analytics/local/index/genomeEntityConfig.ts b/site-config/brc-analytics/local/index/genomeEntityConfig.ts index 5ae373c..cca7cad 100644 --- a/site-config/brc-analytics/local/index/genomeEntityConfig.ts +++ b/site-config/brc-analytics/local/index/genomeEntityConfig.ts @@ -30,20 +30,36 @@ export const genomeEntityConfig: BRCEntityConfig = { { categoryConfigs: [ { - key: BRC_DATA_CATALOG_CATEGORY_KEY.SPECIES, - label: BRC_DATA_CATALOG_CATEGORY_LABEL.SPECIES, + key: BRC_DATA_CATALOG_CATEGORY_KEY.ORGANISM, + label: BRC_DATA_CATALOG_CATEGORY_LABEL.ORGANISM, }, { - key: BRC_DATA_CATALOG_CATEGORY_KEY.STRAIN, - label: BRC_DATA_CATALOG_CATEGORY_LABEL.STRAIN, + key: BRC_DATA_CATALOG_CATEGORY_KEY.TAXONOMY_ID, + label: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXONOMY_ID, }, { - key: BRC_DATA_CATALOG_CATEGORY_KEY.GENOME_VERSION_ASSEMBLY_ID, - label: BRC_DATA_CATALOG_CATEGORY_LABEL.GENOME_VERSION_ASSEMBLY_ID, + key: BRC_DATA_CATALOG_CATEGORY_KEY.ACCESSION, + label: BRC_DATA_CATALOG_CATEGORY_LABEL.ACCESSION, }, { - key: BRC_DATA_CATALOG_CATEGORY_KEY.VEUPATHDB_PROJECT, - label: BRC_DATA_CATALOG_CATEGORY_LABEL.VEUPATHDB_PROJECT, + key: BRC_DATA_CATALOG_CATEGORY_KEY.IS_REF, + label: BRC_DATA_CATALOG_CATEGORY_LABEL.IS_REF, + mapSelectCategoryValue: (value) => ({ + ...value, + label: value.label ? "Yes" : "No", + }), + }, + { + key: BRC_DATA_CATALOG_CATEGORY_KEY.LEVEL, + label: BRC_DATA_CATALOG_CATEGORY_LABEL.LEVEL, + }, + { + key: BRC_DATA_CATALOG_CATEGORY_KEY.COVERAGE, + label: BRC_DATA_CATALOG_CATEGORY_LABEL.COVERAGE, + }, + { + key: BRC_DATA_CATALOG_CATEGORY_KEY.ANNOTATION_STATUS, + label: BRC_DATA_CATALOG_CATEGORY_LABEL.ANNOTATION_STATUS, }, ], }, @@ -83,65 +99,119 @@ export const genomeEntityConfig: BRCEntityConfig = { { componentConfig: { component: C.BasicCell, - viewBuilder: V.buildSpecies, + viewBuilder: V.buildOrganism, } as ComponentConfig, - header: BRC_DATA_CATALOG_CATEGORY_LABEL.SPECIES, - id: BRC_DATA_CATALOG_CATEGORY_KEY.SPECIES, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.ORGANISM, + id: BRC_DATA_CATALOG_CATEGORY_KEY.ORGANISM, width: { max: "1fr", min: "284px" }, }, { componentConfig: { component: C.BasicCell, - viewBuilder: V.buildStrain, + viewBuilder: V.buildTaxonomyId, } as ComponentConfig, - header: BRC_DATA_CATALOG_CATEGORY_LABEL.STRAIN, - id: BRC_DATA_CATALOG_CATEGORY_KEY.STRAIN, - width: { max: "1fr", min: "124px" }, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXONOMY_ID, + id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXONOMY_ID, + width: { max: "0.5fr", min: "100px" }, }, { columnPinned: true, componentConfig: { component: C.BasicCell, - viewBuilder: V.buildGenomeVersionAssemblyId, + viewBuilder: V.buildAccession, } as ComponentConfig, - header: BRC_DATA_CATALOG_CATEGORY_LABEL.GENOME_VERSION_ASSEMBLY_ID, - id: BRC_DATA_CATALOG_CATEGORY_KEY.GENOME_VERSION_ASSEMBLY_ID, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.ACCESSION, + id: BRC_DATA_CATALOG_CATEGORY_KEY.ACCESSION, width: { max: "1fr", min: "164px" }, }, { componentConfig: { component: C.BasicCell, - viewBuilder: V.buildVEuPathDbProject, + viewBuilder: V.buildIsRef, } as ComponentConfig, - header: BRC_DATA_CATALOG_CATEGORY_LABEL.VEUPATHDB_PROJECT, - id: BRC_DATA_CATALOG_CATEGORY_KEY.VEUPATHDB_PROJECT, - width: { max: "1fr", min: "140px" }, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.IS_REF, + id: BRC_DATA_CATALOG_CATEGORY_KEY.IS_REF, + width: { max: "0.5fr", min: "100px" }, }, { componentConfig: { component: C.BasicCell, - viewBuilder: V.buildContigs, + viewBuilder: V.buildLevel, } as ComponentConfig, - header: BRC_DATA_CATALOG_CATEGORY_LABEL.CONTIGS, - id: BRC_DATA_CATALOG_CATEGORY_KEY.CONTIGS, - width: { max: "0.5fr", min: "100px" }, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.LEVEL, + id: BRC_DATA_CATALOG_CATEGORY_KEY.LEVEL, + width: { max: "0.5fr", min: "142px" }, + }, + { + componentConfig: { + component: C.BasicCell, + viewBuilder: V.buildChromosomes, + } as ComponentConfig, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.CHROMOSOMES, + id: BRC_DATA_CATALOG_CATEGORY_KEY.CHROMOSOMES, + width: { max: "0.5fr", min: "142px" }, }, { componentConfig: { component: C.BasicCell, - viewBuilder: V.buildSupercontigs, + viewBuilder: V.buildLength, } as ComponentConfig, - header: BRC_DATA_CATALOG_CATEGORY_LABEL.SUPERCONTIGS, - id: BRC_DATA_CATALOG_CATEGORY_KEY.SUPERCONTIGS, - width: { max: "0.5fr", min: "140px" }, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.LENGTH, + id: BRC_DATA_CATALOG_CATEGORY_KEY.LENGTH, + width: { max: "0.5fr", min: "120px" }, }, { componentConfig: { component: C.BasicCell, - viewBuilder: V.buildChromosomes, + viewBuilder: V.buildScaffoldCount, } as ComponentConfig, - header: BRC_DATA_CATALOG_CATEGORY_LABEL.CHROMOSOMES, - id: BRC_DATA_CATALOG_CATEGORY_KEY.CHROMOSOMES, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.SCAFFOLD_COUNT, + id: BRC_DATA_CATALOG_CATEGORY_KEY.SCAFFOLD_COUNT, + width: { max: "0.5fr", min: "80px" }, + }, + { + componentConfig: { + component: C.BasicCell, + viewBuilder: V.buildScaffoldN50, + } as ComponentConfig, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.SCAFFOLD_N50, + id: BRC_DATA_CATALOG_CATEGORY_KEY.SCAFFOLD_N50, + width: { max: "0.5fr", min: "142px" }, + }, + { + componentConfig: { + component: C.BasicCell, + viewBuilder: V.buildScaffoldL50, + } as ComponentConfig, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.SCAFFOLD_L50, + id: BRC_DATA_CATALOG_CATEGORY_KEY.SCAFFOLD_L50, + width: { max: "0.5fr", min: "80px" }, + }, + { + componentConfig: { + component: C.BasicCell, + viewBuilder: V.buildCoverage, + } as ComponentConfig, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.COVERAGE, + id: BRC_DATA_CATALOG_CATEGORY_KEY.COVERAGE, + width: { max: "0.5fr", min: "80px" }, + }, + { + componentConfig: { + component: C.BasicCell, + viewBuilder: V.buildGcPercent, + } as ComponentConfig, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.GC_PERCENT, + id: BRC_DATA_CATALOG_CATEGORY_KEY.GC_PERCENT, + width: { max: "0.5fr", min: "80px" }, + }, + { + componentConfig: { + component: C.BasicCell, + viewBuilder: V.buildAnnotationStatus, + } as ComponentConfig, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.ANNOTATION_STATUS, + id: BRC_DATA_CATALOG_CATEGORY_KEY.ANNOTATION_STATUS, width: { max: "0.5fr", min: "142px" }, }, ], @@ -151,7 +221,7 @@ export const genomeEntityConfig: BRCEntityConfig = { sorting: [ { desc: SORT_DIRECTION.ASCENDING, - id: BRC_DATA_CATALOG_CATEGORY_KEY.SPECIES, + id: BRC_DATA_CATALOG_CATEGORY_KEY.ORGANISM, }, ], }, From 1f06c6273e3d388c67e39b3a9fd45f19e9cd49bb Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Sat, 16 Nov 2024 16:39:54 -0800 Subject: [PATCH 03/30] feat: restore gene model url (#177) --- .../brc-analytics-catalog/common/entities.ts | 1 + .../Entity/components/AnalysisMethod/types.ts | 2 +- app/utils/galaxy-api.ts | 4 +- .../common/viewModelBuilders.ts | 2 +- files/build-catalog.ts | 1 + files/build-files-from-ncbi.py | 39 +++++++++++++++-- files/entities.ts | 1 + files/out/genomes.json | 20 +++++++++ files/source/genomes-from-ncbi.tsv | 42 +++++++++---------- files/source/organisms-from-ncbi.tsv | 4 +- 10 files changed, 86 insertions(+), 30 deletions(-) diff --git a/app/apis/catalog/brc-analytics-catalog/common/entities.ts b/app/apis/catalog/brc-analytics-catalog/common/entities.ts index 8e69429..3087c32 100644 --- a/app/apis/catalog/brc-analytics-catalog/common/entities.ts +++ b/app/apis/catalog/brc-analytics-catalog/common/entities.ts @@ -15,6 +15,7 @@ export interface BRCDataCatalogGenome { chromosomes: number | null; coverage: string | null; gcPercent: number; + geneModelUrl: string | null; isRef: boolean; length: number; level: string; diff --git a/app/components/Entity/components/AnalysisMethod/types.ts b/app/components/Entity/components/AnalysisMethod/types.ts index 3c8fb1a..852c04a 100644 --- a/app/components/Entity/components/AnalysisMethod/types.ts +++ b/app/components/Entity/components/AnalysisMethod/types.ts @@ -4,6 +4,6 @@ import { ANALYSIS_METHOD } from "../../../../apis/catalog/brc-analytics-catalog/ export interface Props { analysisMethod: ANALYSIS_METHOD; content: ReactNode; - geneModelUrl: string; + geneModelUrl: string | null; genomeVersionAssemblyId: string; } diff --git a/app/utils/galaxy-api.ts b/app/utils/galaxy-api.ts index 4063b9d..be3705f 100644 --- a/app/utils/galaxy-api.ts +++ b/app/utils/galaxy-api.ts @@ -32,7 +32,7 @@ const WORKFLOW_LANDING_URL_PREFIX = export async function getWorkflowLandingUrl( workflowId: WORKFLOW_ID, referenceGenome: string, - geneModelUrl: string + geneModelUrl: string | null ): Promise { const body: WorkflowLandingsBody = { public: true, @@ -74,7 +74,7 @@ function buildFastaUrl(identifier: string): string { function getWorkflowLandingsRequestState( workflowId: WORKFLOW_ID, referenceGenome: string, - geneModelUrl: string + geneModelUrl: string | null ): WorkflowLandingsBodyRequestState { if (workflowId === WORKFLOW_ID.VARIANT_CALLING && geneModelUrl) { return { diff --git a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts index 022a1a2..d45adc9 100644 --- a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts +++ b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts @@ -231,7 +231,7 @@ export const buildGenomeAnalysisMethod = ( ): ComponentProps => { return { ...analysisMethodProps, - geneModelUrl: "", + geneModelUrl: genome.geneModelUrl, genomeVersionAssemblyId: genome.accession, }; }; diff --git a/files/build-catalog.ts b/files/build-catalog.ts index 49229d0..3576b9b 100644 --- a/files/build-catalog.ts +++ b/files/build-catalog.ts @@ -25,6 +25,7 @@ async function buildGenomes(): Promise { chromosomes: parseNumberOrNull(row.chromosomeCount), coverage: parseStringOrNull(row.coverage), gcPercent: parseNumber(row.gcPercent), + geneModelUrl: parseStringOrNull(row.geneModelUrl), isRef: parseBoolean(row.isRef), length: parseNumber(row.length), level: row.level, diff --git a/files/build-files-from-ncbi.py b/files/build-files-from-ncbi.py index 8a0717b..0690d18 100644 --- a/files/build-files-from-ncbi.py +++ b/files/build-files-from-ncbi.py @@ -1,6 +1,7 @@ -from urllib.parse import quote as url_quote import pandas as pd import requests +import urllib.parse +import re TAXA_URL = "https://docs.google.com/spreadsheets/d/1Gg9sw2Qw765tOx2To53XkTAn-RAMiBtqYrfItlLXXrc/gviz/tq?tqx=out:csv&sheet=Sheet1.csv" @@ -28,7 +29,7 @@ def get_tax_ids(organisms_df): return list(organisms_df["taxonomyId"]) def build_genomes_url(tax_ids): - return f"https://api.ncbi.nlm.nih.gov/datasets/v2/genome/taxon/{url_quote(",".join([str(id) for id in tax_ids]))}/dataset_report?filters.assembly_source=refseq&filters.has_annotation=true&filters.exclude_paired_reports=true&filters.exclude_atypical=true&filters.assembly_level=scaffold&filters.assembly_level=chromosome&filters.assembly_level=complete_genome" + return f"https://api.ncbi.nlm.nih.gov/datasets/v2/genome/taxon/{urllib.parse.quote(",".join([str(id) for id in tax_ids]))}/dataset_report?filters.assembly_source=refseq&filters.has_annotation=true&filters.exclude_paired_reports=true&filters.exclude_atypical=true&filters.assembly_level=scaffold&filters.assembly_level=chromosome&filters.assembly_level=complete_genome" def get_genome_row(genome_info): refseq_category = genome_info["assembly_info"].get("refseq_category") @@ -52,6 +53,38 @@ def get_genome_row(genome_info): def get_genomes_df(tax_ids): return pd.DataFrame(data=[get_genome_row(genome_info) for genome_info in requests.get(build_genomes_url(tax_ids)).json()["reports"]]) +def _id_to_gene_model_url(asm_id): + hubs_url = "https://hgdownload.soe.ucsc.edu/hubs/" + components = [asm_id[0:3], asm_id[4:7], asm_id[7:10], asm_id[10:13], asm_id, "genes"] + url = urllib.parse.urljoin(hubs_url, "/".join(components)) + # url looks something like https://hgdownload.soe.ucsc.edu/hubs/GCF/030/504/385/GCF_030504385.1/genes/ + # and contains html content with links to gene models. + # we need to scrape this to get the gtf + print(f"fetching url {url}") + response = requests.get(url) + try: + response.raise_for_status() + except Exception: + # FIXME?: Some accessions don't have a gene folder + return None + # find link to gtf, should ideally be ncbiRefSeq, but augustus will do + html_content = response.text + pattern = rf"{asm_id.replace('.', r'\.')}.*?\.gtf\.gz" + augustus_file = None + for match in re.findall(pattern, html_content): + if "ncbiRefSeq" in match: + return urllib.parse.urljoin(f"{url}/", match) + elif "augustus" in match: + augustus_file = match + if augustus_file: + return urllib.parse.urljoin(f"{url}/", augustus_file) + # No match, I guess that's OK ? + return None + + +def add_gene_model_url(genomes_df: pd.DataFrame): + return pd.concat([genomes_df, genomes_df["accession"].apply(_id_to_gene_model_url).rename("geneModelUrl")], axis="columns") + def build_files(): print("Building files") @@ -71,7 +104,7 @@ def build_files(): gen_bank_merge_df = genomes_source_df.merge(assemblies_df, how="left", left_on="pairedAccession", right_on="genBank") ref_seq_merge_df = genomes_source_df.merge(assemblies_df, how="left", left_on="accession", right_on="refSeq") - genomes_df = gen_bank_merge_df.combine_first(ref_seq_merge_df) + genomes_df = add_gene_model_url(gen_bank_merge_df.combine_first(ref_seq_merge_df)) genomes_df.to_csv(GENOMES_OUTPUT_PATH, index=False, sep="\t") diff --git a/files/entities.ts b/files/entities.ts index 6f5b6f6..3aa6edd 100644 --- a/files/entities.ts +++ b/files/entities.ts @@ -4,6 +4,7 @@ export interface SourceGenome { chromosomeCount: string; coverage: string; gcPercent: string; + geneModelUrl: string; isRef: string; length: string; level: string; diff --git a/files/out/genomes.json b/files/out/genomes.json index abbeba6..203502b 100644 --- a/files/out/genomes.json +++ b/files/out/genomes.json @@ -5,6 +5,7 @@ "chromosomes": 14, "coverage": null, "gcPercent": 42.5, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/415/GCF_000002415.2/genes/GCF_000002415.2_ASM241v2.ncbiRefSeq.gtf.gz", "isRef": true, "length": 27007701, "level": "Chromosome", @@ -21,6 +22,7 @@ "chromosomes": 11, "coverage": null, "gcPercent": 46.5, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/445/GCF_000002445.2/genes/GCF_000002445.2_ASM244v1.ncbiRefSeq.gtf.gz", "isRef": true, "length": 26075494, "level": "Chromosome", @@ -37,6 +39,7 @@ "chromosomes": 36, "coverage": null, "gcPercent": 59.5, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/725/GCF_000002725.2/genes/GCF_000002725.2_ASM272v2.ncbiRefSeq.gtf.gz", "isRef": true, "length": 32855089, "level": "Complete Genome", @@ -53,6 +56,7 @@ "chromosomes": 14, "coverage": "100.0x", "gcPercent": 19.5, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/765/GCF_000002765.6/genes/GCF_000002765.6_GCA_000002765.ncbiRefSeq.gtf.gz", "isRef": true, "length": 23292622, "level": "Complete Genome", @@ -69,6 +73,7 @@ "chromosomes": 35, "coverage": null, "gcPercent": 58, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/845/GCF_000002845.2/genes/GCF_000002845.2_ASM284v2.ncbiRefSeq.gtf.gz", "isRef": true, "length": 32068771, "level": "Chromosome", @@ -85,6 +90,7 @@ "chromosomes": 14, "coverage": "26.5x", "gcPercent": 52.5, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/006/565/GCF_000006565.2/genes/GCF_000006565.2_TGA4.ncbiRefSeq.gtf.gz", "isRef": true, "length": 65633124, "level": "Chromosome", @@ -101,6 +107,7 @@ "chromosomes": null, "coverage": null, "gcPercent": 46, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/149/335/GCF_000149335.2/genes/GCF_000149335.2_ASM14933v2.ncbiRefSeq.gtf.gz", "isRef": true, "length": 28947925, "level": "Scaffold", @@ -117,6 +124,7 @@ "chromosomes": 1, "coverage": null, "gcPercent": 65.5, + "geneModelUrl": null, "isRef": true, "length": 4411532, "level": "Complete Genome", @@ -133,6 +141,7 @@ "chromosomes": null, "coverage": null, "gcPercent": 51.5, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/209/065/GCF_000209065.1/genes/GCF_000209065.1_ASM20906v1.ncbiRefSeq.gtf.gz", "isRef": true, "length": 89937456, "level": "Scaffold", @@ -149,6 +158,7 @@ "chromosomes": 36, "coverage": null, "gcPercent": 59.5, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/227/135/GCF_000227135.1/genes/GCF_000227135.1_ASM22713v2.ncbiRefSeq.gtf.gz", "isRef": true, "length": 32444968, "level": "Chromosome", @@ -165,6 +175,7 @@ "chromosomes": 1, "coverage": null, "gcPercent": 65.5, + "geneModelUrl": null, "isRef": false, "length": 4411709, "level": "Complete Genome", @@ -181,6 +192,7 @@ "chromosomes": 1, "coverage": null, "gcPercent": 33, + "geneModelUrl": null, "isRef": false, "length": 196858, "level": "Complete Genome", @@ -197,6 +209,7 @@ "chromosomes": 1, "coverage": null, "gcPercent": 38, + "geneModelUrl": null, "isRef": false, "length": 29903, "level": "Complete Genome", @@ -213,6 +226,7 @@ "chromosomes": 3, "coverage": "250.0x", "gcPercent": 37, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/016/801/865/GCF_016801865.2/genes/GCF_016801865.2_TS_CPP_V2.ncbiRefSeq.gtf.gz", "isRef": true, "length": 566339288, "level": "Chromosome", @@ -229,6 +243,7 @@ "chromosomes": 9, "coverage": "475.0x", "gcPercent": 46.5, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/018/416/015/GCF_018416015.2/genes/GCF_018416015.2_ASM1841601v2.ncbiRefSeq.gtf.gz", "isRef": true, "length": 28193268, "level": "Complete Genome", @@ -245,6 +260,7 @@ "chromosomes": 1, "coverage": "20.0x", "gcPercent": 65.5, + "geneModelUrl": null, "isRef": false, "length": 4516435, "level": "Complete Genome", @@ -261,6 +277,7 @@ "chromosomes": 14, "coverage": "100.0x", "gcPercent": 21.5, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/900/002/385/GCF_900002385.2/genes/GCF_900002385.2_GCA_900002385.ncbiRefSeq.gtf.gz", "isRef": true, "length": 23043114, "level": "Complete Genome", @@ -277,6 +294,7 @@ "chromosomes": 14, "coverage": "155.0x", "gcPercent": 23, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/900/681/995/GCF_900681995.1/genes/GCF_900681995.1_PVVCY_v1.ncbiRefSeq.gtf.gz", "isRef": true, "length": 18338688, "level": "Complete Genome", @@ -293,6 +311,7 @@ "chromosomes": 3, "coverage": "54.0x", "gcPercent": 44.5, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/943/734/735/GCF_943734735.2/genes/GCF_943734735.2_idAnoGambNW_F1_1.ncbiRefSeq.gtf.gz", "isRef": true, "length": 264451381, "level": "Chromosome", @@ -309,6 +328,7 @@ "chromosomes": 1, "coverage": "100.0x", "gcPercent": 65.5, + "geneModelUrl": null, "isRef": false, "length": 4469156, "level": "Complete Genome", diff --git a/files/source/genomes-from-ncbi.tsv b/files/source/genomes-from-ncbi.tsv index 8876bf3..79d5b1b 100644 --- a/files/source/genomes-from-ncbi.tsv +++ b/files/source/genomes-from-ncbi.tsv @@ -1,21 +1,21 @@ -taxon taxonomyId accession isRef level chromosomeCount length scaffoldCount scaffoldN50 scaffoldL50 coverage gcPercent annotationStatus pairedAccession ucscBrowser genBank refSeq -Mycobacterium tuberculosis H37Rv 83332 GCF_000195955.2 True Complete Genome 1.0 4411532 1 4411532 1 65.5 GCA_000195955.2 -Plasmodium falciparum 3D7 36329 GCF_000002765.6 True Complete Genome 14.0 23292622 14 1687656 5 100.0x 19.5 Full annotation GCA_000002765.3 https://genome.ucsc.edu/h/GCF_000002765.5 GCA_000002765.3 GCF_000002765.5 -Leishmania major strain Friedlin 347515 GCF_000002725.2 True Complete Genome 36.0 32855089 36 1091540 11 59.5 Full annotation GCA_000002725.2 https://genome.ucsc.edu/h/GCF_000002725.2 GCA_000002725.2 GCF_000002725.2 -Plasmodium yoelii 5861 GCF_900002385.2 True Complete Genome 14.0 23043114 14 2046250 5 100.0x 21.5 Full annotation GCA_900002385.2 https://genome.ucsc.edu/h/GCF_900002385.2 GCA_900002385.2 GCF_900002385.2 -Coccidioides posadasii str. Silveira 443226 GCF_018416015.2 True Complete Genome 9.0 28193268 9 8079863 2 475.0x 46.5 Full annotation GCA_018416015.2 https://genome.ucsc.edu/h/GCA_018416015.2 GCA_018416015.2 GCF_018416015.1 -Plasmodium vinckei vinckei 54757 GCF_900681995.1 True Complete Genome 14.0 18338688 14 1692345 5 155.0x 23.0 Full annotation GCA_900681995.1 https://genome.ucsc.edu/h/GCF_900681995.1 GCA_900681995.1 GCF_900681995.1 -Leishmania donovani 5661 GCF_000227135.1 True Chromosome 36.0 32444968 36 1024085 11 59.5 Full annotation GCA_000227135.2 https://genome.ucsc.edu/h/GCF_000227135.1 GCA_000227135.2 GCF_000227135.1 -Toxoplasma gondii ME49 508771 GCF_000006565.2 True Chromosome 14.0 65633124 2276 4973582 6 26.5x 52.5 GCA_000006565.2 https://genome.ucsc.edu/h/GCF_000006565.2 GCA_000006565.2 GCF_000006565.2 -Trypanosoma brucei brucei TREU927 185431 GCF_000002445.2 True Chromosome 11.0 26075494 12 2481190 4 46.5 Full annotation GCA_000002445.1 https://genome.ucsc.edu/h/GCF_000002445.2 GCA_000002445.1 GCF_000002445.2 -Anopheles gambiae 7165 GCF_943734735.2 True Chromosome 3.0 264451381 190 99149756 2 54.0x 44.5 Full annotation GCA_943734735.2 https://genome.ucsc.edu/h/GCF_943734735.2 GCA_943734735.2 GCF_943734735.2 -Plasmodium vivax 5855 GCF_000002415.2 True Chromosome 14.0 27007701 2747 1678596 6 42.5 Full annotation GCA_000002415.2 https://genome.ucsc.edu/h/GCF_000002415.2 GCA_000002415.2 GCF_000002415.2 -Culex pipiens pallens 42434 GCF_016801865.2 True Chromosome 3.0 566339288 289 186194774 2 250.0x 37.0 Full annotation GCA_016801865.2 -Leishmania braziliensis MHOM/BR/75/M2904 420245 GCF_000002845.2 True Chromosome 35.0 32068771 138 992961 11 58.0 GCA_000002845.2 https://genome.ucsc.edu/h/GCF_000002845.2 GCA_000002845.2 GCF_000002845.2 -Trypanosoma cruzi 5693 GCF_000209065.1 True Scaffold 89937456 29495 88624 212 51.5 Full annotation GCA_000209065.1 https://genome.ucsc.edu/h/GCF_000209065.1 GCA_000209065.1 GCF_000209065.1 -Coccidioides immitis RS 246410 GCF_000149335.2 True Scaffold 28947925 6 4323945 3 46.0 Full annotation GCA_000149335.2 https://genome.ucsc.edu/h/GCF_000149335.2 GCA_000149335.2 GCF_000149335.2 -Mycobacterium tuberculosis H37Rv 83332 GCF_000277735.2 False Complete Genome 1.0 4411709 1 4411709 1 65.5 GCA_000277735.2 -Severe acute respiratory syndrome coronavirus 2 2697049 GCF_009858895.2 False Complete Genome 1.0 29903 1 29903 1 38.0 GCA_009858895.3 -Monkeypox virus 10244 GCF_000857045.1 False Complete Genome 1.0 196858 1 196858 1 33.0 GCA_000857045.1 -Mycobacterium tuberculosis 1773 GCF_030566675.1 False Complete Genome 1.0 4516435 1 4516435 1 20.0x 65.5 GCA_030566675.1 -Mycobacterium tuberculosis 1773 GCF_963525475.1 False Complete Genome 1.0 4469156 1 4469156 1 100.0x 65.5 GCA_963525475.1 +taxon taxonomyId accession isRef level chromosomeCount length scaffoldCount scaffoldN50 scaffoldL50 coverage gcPercent annotationStatus pairedAccession ucscBrowser genBank refSeq geneModelUrl +Mycobacterium tuberculosis H37Rv 83332 GCF_000195955.2 True Complete Genome 1.0 4411532 1 4411532 1 65.5 GCA_000195955.2 +Plasmodium falciparum 3D7 36329 GCF_000002765.6 True Complete Genome 14.0 23292622 14 1687656 5 100.0x 19.5 Full annotation GCA_000002765.3 https://genome.ucsc.edu/h/GCF_000002765.5 GCA_000002765.3 GCF_000002765.5 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/765/GCF_000002765.6/genes/GCF_000002765.6_GCA_000002765.ncbiRefSeq.gtf.gz +Leishmania major strain Friedlin 347515 GCF_000002725.2 True Complete Genome 36.0 32855089 36 1091540 11 59.5 Full annotation GCA_000002725.2 https://genome.ucsc.edu/h/GCF_000002725.2 GCA_000002725.2 GCF_000002725.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/725/GCF_000002725.2/genes/GCF_000002725.2_ASM272v2.ncbiRefSeq.gtf.gz +Plasmodium yoelii 5861 GCF_900002385.2 True Complete Genome 14.0 23043114 14 2046250 5 100.0x 21.5 Full annotation GCA_900002385.2 https://genome.ucsc.edu/h/GCF_900002385.2 GCA_900002385.2 GCF_900002385.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/900/002/385/GCF_900002385.2/genes/GCF_900002385.2_GCA_900002385.ncbiRefSeq.gtf.gz +Coccidioides posadasii str. Silveira 443226 GCF_018416015.2 True Complete Genome 9.0 28193268 9 8079863 2 475.0x 46.5 Full annotation GCA_018416015.2 https://genome.ucsc.edu/h/GCA_018416015.2 GCA_018416015.2 GCF_018416015.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/018/416/015/GCF_018416015.2/genes/GCF_018416015.2_ASM1841601v2.ncbiRefSeq.gtf.gz +Plasmodium vinckei vinckei 54757 GCF_900681995.1 True Complete Genome 14.0 18338688 14 1692345 5 155.0x 23.0 Full annotation GCA_900681995.1 https://genome.ucsc.edu/h/GCF_900681995.1 GCA_900681995.1 GCF_900681995.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/900/681/995/GCF_900681995.1/genes/GCF_900681995.1_PVVCY_v1.ncbiRefSeq.gtf.gz +Leishmania donovani 5661 GCF_000227135.1 True Chromosome 36.0 32444968 36 1024085 11 59.5 Full annotation GCA_000227135.2 https://genome.ucsc.edu/h/GCF_000227135.1 GCA_000227135.2 GCF_000227135.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/227/135/GCF_000227135.1/genes/GCF_000227135.1_ASM22713v2.ncbiRefSeq.gtf.gz +Toxoplasma gondii ME49 508771 GCF_000006565.2 True Chromosome 14.0 65633124 2276 4973582 6 26.5x 52.5 GCA_000006565.2 https://genome.ucsc.edu/h/GCF_000006565.2 GCA_000006565.2 GCF_000006565.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/006/565/GCF_000006565.2/genes/GCF_000006565.2_TGA4.ncbiRefSeq.gtf.gz +Trypanosoma brucei brucei TREU927 185431 GCF_000002445.2 True Chromosome 11.0 26075494 12 2481190 4 46.5 Full annotation GCA_000002445.1 https://genome.ucsc.edu/h/GCF_000002445.2 GCA_000002445.1 GCF_000002445.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/445/GCF_000002445.2/genes/GCF_000002445.2_ASM244v1.ncbiRefSeq.gtf.gz +Anopheles gambiae 7165 GCF_943734735.2 True Chromosome 3.0 264451381 190 99149756 2 54.0x 44.5 Full annotation GCA_943734735.2 https://genome.ucsc.edu/h/GCF_943734735.2 GCA_943734735.2 GCF_943734735.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/943/734/735/GCF_943734735.2/genes/GCF_943734735.2_idAnoGambNW_F1_1.ncbiRefSeq.gtf.gz +Plasmodium vivax 5855 GCF_000002415.2 True Chromosome 14.0 27007701 2747 1678596 6 42.5 Full annotation GCA_000002415.2 https://genome.ucsc.edu/h/GCF_000002415.2 GCA_000002415.2 GCF_000002415.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/415/GCF_000002415.2/genes/GCF_000002415.2_ASM241v2.ncbiRefSeq.gtf.gz +Culex pipiens pallens 42434 GCF_016801865.2 True Chromosome 3.0 566339288 289 186194774 2 250.0x 37.0 Full annotation GCA_016801865.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/016/801/865/GCF_016801865.2/genes/GCF_016801865.2_TS_CPP_V2.ncbiRefSeq.gtf.gz +Leishmania braziliensis MHOM/BR/75/M2904 420245 GCF_000002845.2 True Chromosome 35.0 32068771 138 992961 11 58.0 GCA_000002845.2 https://genome.ucsc.edu/h/GCF_000002845.2 GCA_000002845.2 GCF_000002845.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/845/GCF_000002845.2/genes/GCF_000002845.2_ASM284v2.ncbiRefSeq.gtf.gz +Trypanosoma cruzi 5693 GCF_000209065.1 True Scaffold 89937456 29495 88624 212 51.5 Full annotation GCA_000209065.1 https://genome.ucsc.edu/h/GCF_000209065.1 GCA_000209065.1 GCF_000209065.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/209/065/GCF_000209065.1/genes/GCF_000209065.1_ASM20906v1.ncbiRefSeq.gtf.gz +Coccidioides immitis RS 246410 GCF_000149335.2 True Scaffold 28947925 6 4323945 3 46.0 Full annotation GCA_000149335.2 https://genome.ucsc.edu/h/GCF_000149335.2 GCA_000149335.2 GCF_000149335.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/149/335/GCF_000149335.2/genes/GCF_000149335.2_ASM14933v2.ncbiRefSeq.gtf.gz +Mycobacterium tuberculosis H37Rv 83332 GCF_000277735.2 False Complete Genome 1.0 4411709 1 4411709 1 65.5 GCA_000277735.2 +Severe acute respiratory syndrome coronavirus 2 2697049 GCF_009858895.2 False Complete Genome 1.0 29903 1 29903 1 38.0 GCA_009858895.3 +Monkeypox virus 10244 GCF_000857045.1 False Complete Genome 1.0 196858 1 196858 1 33.0 GCA_000857045.1 +Mycobacterium tuberculosis 1773 GCF_030566675.1 False Complete Genome 1.0 4516435 1 4516435 1 20.0x 65.5 GCA_030566675.1 +Mycobacterium tuberculosis 1773 GCF_963525475.1 False Complete Genome 1.0 4469156 1 4469156 1 100.0x 65.5 GCA_963525475.1 diff --git a/files/source/organisms-from-ncbi.tsv b/files/source/organisms-from-ncbi.tsv index 83237cd..6686f92 100644 --- a/files/source/organisms-from-ncbi.tsv +++ b/files/source/organisms-from-ncbi.tsv @@ -1,7 +1,7 @@ taxon taxonomyId assemblyCount CustomTags Anopheles gambiae 7165 7 VEuPathDb Coccidioides immitis 5501 5 -Coccidioides posadasii 199306 13 +Coccidioides posadasii 199306 13 VEuPathDb Culex pipiens 7175 5 VEuPathDb Leishmania braziliensis 5660 11 VEuPathDb Leishmania donovani 5661 12 VEuPathDb @@ -15,4 +15,4 @@ Plasmodium yoelii 5861 15 VEuPathDb Severe acute respiratory syndrome coronavirus 2 2697049 92 Virus Toxoplasma gondii 5811 29 VEuPathDb Trypanosoma brucei 5691 5 VEuPathDb -Trypanosoma cruzi 5693 45 VEuPathDb +Trypanosoma cruzi 5693 44 VEuPathDb From 1fa83738c14034e014299599d1558bdad3ab1ad4 Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Sat, 16 Nov 2024 17:24:58 -0800 Subject: [PATCH 04/30] feat: relabel "organisms" to "genomes" (#177) --- .../Section/components/SectionHero/sectionHero.tsx | 2 +- app/components/Home/content/sectionSubHero.mdx | 2 +- .../brc-analytics-catalog/common/viewModelBuilders.ts | 4 ++-- pages/_app.tsx | 2 +- routes/constants.ts | 2 +- site-config/brc-analytics/local/config.ts | 2 +- site-config/brc-analytics/local/index/genomeEntityConfig.ts | 6 +++--- 7 files changed, 10 insertions(+), 10 deletions(-) diff --git a/app/components/Home/components/Section/components/SectionHero/sectionHero.tsx b/app/components/Home/components/Section/components/SectionHero/sectionHero.tsx index 0069043..21faa17 100644 --- a/app/components/Home/components/Section/components/SectionHero/sectionHero.tsx +++ b/app/components/Home/components/Section/components/SectionHero/sectionHero.tsx @@ -32,7 +32,7 @@ export const SectionHero = (): JSX.Element => { annotations and functional insights into disease-causing organisms and their carriers - diff --git a/app/components/Home/content/sectionSubHero.mdx b/app/components/Home/content/sectionSubHero.mdx index da94f3a..0512771 100644 --- a/app/components/Home/content/sectionSubHero.mdx +++ b/app/components/Home/content/sectionSubHero.mdx @@ -1,5 +1,5 @@ BRC Analytics is your new destination for analysis of biological data related to pathogens. Building on the foundation of VEuPathDb the platform will provide access and analysis capabilities for -[785 eukaryotic pathogens](/data/organisms), hosts, and vectors. The functionality will +[785 eukaryotic pathogens](/data/genomes), hosts, and vectors. The functionality will be developed and made available incrementally over the [following months](/roadmap). diff --git a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts index d45adc9..c364d2c 100644 --- a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts +++ b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts @@ -38,7 +38,7 @@ export const buildAnalyzeGenome = ( return { analyze: { label: "Analyze", - url: rowId ? `${ROUTES.ORGANISMS}/${rowId}` : "", + url: rowId ? `${ROUTES.GENOMES}/${rowId}` : "", }, views: [ ...(ucscBrowserUrl @@ -320,7 +320,7 @@ function getGenomeEntityChooseAnalysisMethodBreadcrumbs( genome: BRCDataCatalogGenome ): Breadcrumb[] { return [ - { path: ROUTES.ORGANISMS, text: "Organisms" }, + { path: ROUTES.GENOMES, text: "Genomes" }, { path: "", text: `${genome.organism}` }, { path: "", text: "Choose Analysis Methods" }, ]; diff --git a/pages/_app.tsx b/pages/_app.tsx index b22a50f..799c6e6 100644 --- a/pages/_app.tsx +++ b/pages/_app.tsx @@ -21,7 +21,7 @@ import { config } from "../app/config/config"; import { mergeAppTheme } from "../app/theme/theme"; import { GoogleSignInAuthenticationProvider } from "@databiosphere/findable-ui/lib/providers/googleSignInAuthentication/provider"; -const DEFAULT_ENTITY_LIST_TYPE = "organisms"; +const DEFAULT_ENTITY_LIST_TYPE = "genomes"; export interface PageProps extends AzulEntitiesStaticResponse { pageTitle?: string; diff --git a/routes/constants.ts b/routes/constants.ts index c44740a..05eb80a 100644 --- a/routes/constants.ts +++ b/routes/constants.ts @@ -1,5 +1,5 @@ export const ROUTES = { ABOUT: "/about", - ORGANISMS: "/data/organisms", + GENOMES: "/data/genomes", ROADMAP: "/roadmap", }; diff --git a/site-config/brc-analytics/local/config.ts b/site-config/brc-analytics/local/config.ts index 5d6e907..781a54a 100644 --- a/site-config/brc-analytics/local/config.ts +++ b/site-config/brc-analytics/local/config.ts @@ -68,7 +68,7 @@ export function makeConfig(browserUrl: string, gitHubUrl: string): SiteConfig { undefined, [ { label: "About", url: ROUTES.ABOUT }, - { label: "Datasets", url: ROUTES.ORGANISMS }, + { label: "Datasets", url: ROUTES.GENOMES }, { label: "Roadmap", url: ROUTES.ROADMAP }, ], undefined, diff --git a/site-config/brc-analytics/local/index/genomeEntityConfig.ts b/site-config/brc-analytics/local/index/genomeEntityConfig.ts index cca7cad..f0039da 100644 --- a/site-config/brc-analytics/local/index/genomeEntityConfig.ts +++ b/site-config/brc-analytics/local/index/genomeEntityConfig.ts @@ -80,10 +80,10 @@ export const genomeEntityConfig: BRCEntityConfig = { ], }, exploreMode: EXPLORE_MODE.CS_FETCH_CS_FILTERING, - explorerTitle: "Organisms", + explorerTitle: "Genomes", getId: getGenomeId, getTitle: getGenomeTitle, - label: "Organisms", + label: "Genomes", list: { columns: [ { @@ -233,6 +233,6 @@ export const genomeEntityConfig: BRCEntityConfig = { enableTab: false, listHero, }, - route: "organisms", + route: "genomes", staticLoadFile: "files/out/genomes.json", }; From d2695a1e7dabe08f753defe8c71f4f80f769b8ad Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Sat, 16 Nov 2024 17:35:55 -0800 Subject: [PATCH 05/30] feat: rename "organism" to "taxon" (#177) --- .../brc-analytics-catalog/common/entities.ts | 2 +- .../brc-analytics-catalog/common/utils.ts | 2 +- .../common/viewModelBuilders.ts | 10 ++--- files/build-catalog.ts | 2 +- files/out/genomes.json | 40 +++++++++---------- site-config/brc-analytics/category.ts | 4 +- .../local/index/genomeEntityConfig.ts | 12 +++--- 7 files changed, 36 insertions(+), 36 deletions(-) diff --git a/app/apis/catalog/brc-analytics-catalog/common/entities.ts b/app/apis/catalog/brc-analytics-catalog/common/entities.ts index 3087c32..28d0b20 100644 --- a/app/apis/catalog/brc-analytics-catalog/common/entities.ts +++ b/app/apis/catalog/brc-analytics-catalog/common/entities.ts @@ -20,10 +20,10 @@ export interface BRCDataCatalogGenome { length: number; level: string; ncbiTaxonomyId: string; - organism: string; scaffoldCount: number; scaffoldL50: number; scaffoldN50: number; + taxon: string; ucscBrowserUrl: string | null; } diff --git a/app/apis/catalog/brc-analytics-catalog/common/utils.ts b/app/apis/catalog/brc-analytics-catalog/common/utils.ts index 935fde0..0baded0 100644 --- a/app/apis/catalog/brc-analytics-catalog/common/utils.ts +++ b/app/apis/catalog/brc-analytics-catalog/common/utils.ts @@ -6,7 +6,7 @@ export function getGenomeId(genome: BRCDataCatalogGenome): string { export function getGenomeTitle(genome?: BRCDataCatalogGenome): string { if (!genome) return ""; - return `${genome.organism}`; + return `${genome.taxon}`; } export function sanitizeEntityId(entityId?: string): string { diff --git a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts index c364d2c..d960147 100644 --- a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts +++ b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts @@ -150,15 +150,15 @@ export const buildLevel = ( }; /** - * Build props for the organism cell. + * Build props for the taxon cell. * @param genome - Genome entity. * @returns Props to be used for the cell. */ -export const buildOrganism = ( +export const buildTaxon = ( genome: BRCDataCatalogGenome ): ComponentProps => { return { - value: genome.organism, + value: genome.taxon, }; }; @@ -289,7 +289,7 @@ export const buildGenomeDetails = ( keyValuePairs.set( "Taxon", C.Link({ - label: genome.organism, + label: genome.taxon, url: `https://www.ncbi.nlm.nih.gov/datasets/taxonomy/${encodeURIComponent( genome.ncbiTaxonomyId )}/`, @@ -321,7 +321,7 @@ function getGenomeEntityChooseAnalysisMethodBreadcrumbs( ): Breadcrumb[] { return [ { path: ROUTES.GENOMES, text: "Genomes" }, - { path: "", text: `${genome.organism}` }, + { path: "", text: `${genome.taxon}` }, { path: "", text: "Choose Analysis Methods" }, ]; } diff --git a/files/build-catalog.ts b/files/build-catalog.ts index 3576b9b..ff24ba7 100644 --- a/files/build-catalog.ts +++ b/files/build-catalog.ts @@ -30,10 +30,10 @@ async function buildGenomes(): Promise { length: parseNumber(row.length), level: row.level, ncbiTaxonomyId: row.taxonomyId, - organism: row.taxon, scaffoldCount: parseNumber(row.scaffoldCount), scaffoldL50: parseNumber(row.scaffoldL50), scaffoldN50: parseNumber(row.scaffoldN50), + taxon: row.taxon, ucscBrowserUrl: parseStringOrNull(row.ucscBrowser), }) ); diff --git a/files/out/genomes.json b/files/out/genomes.json index 203502b..771cac1 100644 --- a/files/out/genomes.json +++ b/files/out/genomes.json @@ -10,10 +10,10 @@ "length": 27007701, "level": "Chromosome", "ncbiTaxonomyId": "5855", - "organism": "Plasmodium vivax", "scaffoldCount": 2747, "scaffoldL50": 6, "scaffoldN50": 1678596, + "taxon": "Plasmodium vivax", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002415.2" }, { @@ -27,10 +27,10 @@ "length": 26075494, "level": "Chromosome", "ncbiTaxonomyId": "185431", - "organism": "Trypanosoma brucei brucei TREU927", "scaffoldCount": 12, "scaffoldL50": 4, "scaffoldN50": 2481190, + "taxon": "Trypanosoma brucei brucei TREU927", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002445.2" }, { @@ -44,10 +44,10 @@ "length": 32855089, "level": "Complete Genome", "ncbiTaxonomyId": "347515", - "organism": "Leishmania major strain Friedlin", "scaffoldCount": 36, "scaffoldL50": 11, "scaffoldN50": 1091540, + "taxon": "Leishmania major strain Friedlin", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002725.2" }, { @@ -61,10 +61,10 @@ "length": 23292622, "level": "Complete Genome", "ncbiTaxonomyId": "36329", - "organism": "Plasmodium falciparum 3D7", "scaffoldCount": 14, "scaffoldL50": 5, "scaffoldN50": 1687656, + "taxon": "Plasmodium falciparum 3D7", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002765.5" }, { @@ -78,10 +78,10 @@ "length": 32068771, "level": "Chromosome", "ncbiTaxonomyId": "420245", - "organism": "Leishmania braziliensis MHOM/BR/75/M2904", "scaffoldCount": 138, "scaffoldL50": 11, "scaffoldN50": 992961, + "taxon": "Leishmania braziliensis MHOM/BR/75/M2904", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002845.2" }, { @@ -95,10 +95,10 @@ "length": 65633124, "level": "Chromosome", "ncbiTaxonomyId": "508771", - "organism": "Toxoplasma gondii ME49", "scaffoldCount": 2276, "scaffoldL50": 6, "scaffoldN50": 4973582, + "taxon": "Toxoplasma gondii ME49", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000006565.2" }, { @@ -112,10 +112,10 @@ "length": 28947925, "level": "Scaffold", "ncbiTaxonomyId": "246410", - "organism": "Coccidioides immitis RS", "scaffoldCount": 6, "scaffoldL50": 3, "scaffoldN50": 4323945, + "taxon": "Coccidioides immitis RS", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000149335.2" }, { @@ -129,10 +129,10 @@ "length": 4411532, "level": "Complete Genome", "ncbiTaxonomyId": "83332", - "organism": "Mycobacterium tuberculosis H37Rv", "scaffoldCount": 1, "scaffoldL50": 1, "scaffoldN50": 4411532, + "taxon": "Mycobacterium tuberculosis H37Rv", "ucscBrowserUrl": null }, { @@ -146,10 +146,10 @@ "length": 89937456, "level": "Scaffold", "ncbiTaxonomyId": "5693", - "organism": "Trypanosoma cruzi", "scaffoldCount": 29495, "scaffoldL50": 212, "scaffoldN50": 88624, + "taxon": "Trypanosoma cruzi", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000209065.1" }, { @@ -163,10 +163,10 @@ "length": 32444968, "level": "Chromosome", "ncbiTaxonomyId": "5661", - "organism": "Leishmania donovani", "scaffoldCount": 36, "scaffoldL50": 11, "scaffoldN50": 1024085, + "taxon": "Leishmania donovani", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000227135.1" }, { @@ -180,10 +180,10 @@ "length": 4411709, "level": "Complete Genome", "ncbiTaxonomyId": "83332", - "organism": "Mycobacterium tuberculosis H37Rv", "scaffoldCount": 1, "scaffoldL50": 1, "scaffoldN50": 4411709, + "taxon": "Mycobacterium tuberculosis H37Rv", "ucscBrowserUrl": null }, { @@ -197,10 +197,10 @@ "length": 196858, "level": "Complete Genome", "ncbiTaxonomyId": "10244", - "organism": "Monkeypox virus", "scaffoldCount": 1, "scaffoldL50": 1, "scaffoldN50": 196858, + "taxon": "Monkeypox virus", "ucscBrowserUrl": null }, { @@ -214,10 +214,10 @@ "length": 29903, "level": "Complete Genome", "ncbiTaxonomyId": "2697049", - "organism": "Severe acute respiratory syndrome coronavirus 2", "scaffoldCount": 1, "scaffoldL50": 1, "scaffoldN50": 29903, + "taxon": "Severe acute respiratory syndrome coronavirus 2", "ucscBrowserUrl": null }, { @@ -231,10 +231,10 @@ "length": 566339288, "level": "Chromosome", "ncbiTaxonomyId": "42434", - "organism": "Culex pipiens pallens", "scaffoldCount": 289, "scaffoldL50": 2, "scaffoldN50": 186194774, + "taxon": "Culex pipiens pallens", "ucscBrowserUrl": null }, { @@ -248,10 +248,10 @@ "length": 28193268, "level": "Complete Genome", "ncbiTaxonomyId": "443226", - "organism": "Coccidioides posadasii str. Silveira", "scaffoldCount": 9, "scaffoldL50": 2, "scaffoldN50": 8079863, + "taxon": "Coccidioides posadasii str. Silveira", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_018416015.2" }, { @@ -265,10 +265,10 @@ "length": 4516435, "level": "Complete Genome", "ncbiTaxonomyId": "1773", - "organism": "Mycobacterium tuberculosis", "scaffoldCount": 1, "scaffoldL50": 1, "scaffoldN50": 4516435, + "taxon": "Mycobacterium tuberculosis", "ucscBrowserUrl": null }, { @@ -282,10 +282,10 @@ "length": 23043114, "level": "Complete Genome", "ncbiTaxonomyId": "5861", - "organism": "Plasmodium yoelii", "scaffoldCount": 14, "scaffoldL50": 5, "scaffoldN50": 2046250, + "taxon": "Plasmodium yoelii", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_900002385.2" }, { @@ -299,10 +299,10 @@ "length": 18338688, "level": "Complete Genome", "ncbiTaxonomyId": "54757", - "organism": "Plasmodium vinckei vinckei", "scaffoldCount": 14, "scaffoldL50": 5, "scaffoldN50": 1692345, + "taxon": "Plasmodium vinckei vinckei", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_900681995.1" }, { @@ -316,10 +316,10 @@ "length": 264451381, "level": "Chromosome", "ncbiTaxonomyId": "7165", - "organism": "Anopheles gambiae", "scaffoldCount": 190, "scaffoldL50": 2, "scaffoldN50": 99149756, + "taxon": "Anopheles gambiae", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943734735.2" }, { @@ -333,10 +333,10 @@ "length": 4469156, "level": "Complete Genome", "ncbiTaxonomyId": "1773", - "organism": "Mycobacterium tuberculosis", "scaffoldCount": 1, "scaffoldL50": 1, "scaffoldN50": 4469156, + "taxon": "Mycobacterium tuberculosis", "ucscBrowserUrl": null } ] diff --git a/site-config/brc-analytics/category.ts b/site-config/brc-analytics/category.ts index 7a4519f..92fc0f1 100644 --- a/site-config/brc-analytics/category.ts +++ b/site-config/brc-analytics/category.ts @@ -8,10 +8,10 @@ export const BRC_DATA_CATALOG_CATEGORY_KEY = { IS_REF: "isRef", LENGTH: "length", LEVEL: "level", - ORGANISM: "organism", SCAFFOLD_COUNT: "scaffoldCount", SCAFFOLD_L50: "scaffoldL50", SCAFFOLD_N50: "scaffoldN50", + TAXON: "taxon", TAXONOMY_ID: "ncbiTaxonomyId", UCSC_BROWSER_URL: "ucscBrowserUrl", }; @@ -26,10 +26,10 @@ export const BRC_DATA_CATALOG_CATEGORY_LABEL = { IS_REF: "Is Reference", LENGTH: "Length", LEVEL: "Level", - ORGANISM: "Organism", SCAFFOLD_COUNT: "Scaffolds", SCAFFOLD_L50: "Scaffold L50", SCAFFOLD_N50: "Scaffold N50", + TAXON: "Taxon", TAXONOMY_ID: "Taxonomy ID", UCSC_BROWSER_URL: "UCSC Browser", }; diff --git a/site-config/brc-analytics/local/index/genomeEntityConfig.ts b/site-config/brc-analytics/local/index/genomeEntityConfig.ts index f0039da..29763e1 100644 --- a/site-config/brc-analytics/local/index/genomeEntityConfig.ts +++ b/site-config/brc-analytics/local/index/genomeEntityConfig.ts @@ -30,8 +30,8 @@ export const genomeEntityConfig: BRCEntityConfig = { { categoryConfigs: [ { - key: BRC_DATA_CATALOG_CATEGORY_KEY.ORGANISM, - label: BRC_DATA_CATALOG_CATEGORY_LABEL.ORGANISM, + key: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON, + label: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXON, }, { key: BRC_DATA_CATALOG_CATEGORY_KEY.TAXONOMY_ID, @@ -99,10 +99,10 @@ export const genomeEntityConfig: BRCEntityConfig = { { componentConfig: { component: C.BasicCell, - viewBuilder: V.buildOrganism, + viewBuilder: V.buildTaxon, } as ComponentConfig, - header: BRC_DATA_CATALOG_CATEGORY_LABEL.ORGANISM, - id: BRC_DATA_CATALOG_CATEGORY_KEY.ORGANISM, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXON, + id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON, width: { max: "1fr", min: "284px" }, }, { @@ -221,7 +221,7 @@ export const genomeEntityConfig: BRCEntityConfig = { sorting: [ { desc: SORT_DIRECTION.ASCENDING, - id: BRC_DATA_CATALOG_CATEGORY_KEY.ORGANISM, + id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON, }, ], }, From e43026f7251fb0764b00eec499858a054b6af5c9 Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Sun, 17 Nov 2024 18:33:14 -0800 Subject: [PATCH 06/30] feat: add tags to genome list (#177) --- .../brc-analytics-catalog/common/entities.ts | 1 + app/components/index.ts | 1 + .../common/viewModelBuilders.ts | 14 +++++++ files/build-catalog.ts | 19 +++++++--- files/entities.ts | 7 ++++ files/out/genomes.json | 38 +++++++++++++++++++ site-config/brc-analytics/category.ts | 2 + .../local/index/genomeEntityConfig.ts | 13 +++++++ 8 files changed, 90 insertions(+), 5 deletions(-) diff --git a/app/apis/catalog/brc-analytics-catalog/common/entities.ts b/app/apis/catalog/brc-analytics-catalog/common/entities.ts index 28d0b20..e61b319 100644 --- a/app/apis/catalog/brc-analytics-catalog/common/entities.ts +++ b/app/apis/catalog/brc-analytics-catalog/common/entities.ts @@ -23,6 +23,7 @@ export interface BRCDataCatalogGenome { scaffoldCount: number; scaffoldL50: number; scaffoldN50: number; + tags: string[]; taxon: string; ucscBrowserUrl: string | null; } diff --git a/app/components/index.ts b/app/components/index.ts index 53ec783..4a868b3 100644 --- a/app/components/index.ts +++ b/app/components/index.ts @@ -22,6 +22,7 @@ export { export { Logo } from "@databiosphere/findable-ui/lib/components/Layout/components/Header/components/Content/components/Logo/logo"; export { Link } from "@databiosphere/findable-ui/lib/components/Links/components/Link/link"; export { BasicCell } from "@databiosphere/findable-ui/lib/components/Table/components/TableCell/components/BasicCell/basicCell"; +export { NTagCell } from "@databiosphere/findable-ui/lib/components/Table/components/TableCell/components/NTagCell/nTagCell"; export { CopyText } from "./common/CopyText/copyText"; export { AnalysisMethod } from "./Entity/components/AnalysisMethod/analysisMethod"; export { AnalysisMethods } from "./Entity/components/AnalysisMethods/analysisMethods"; diff --git a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts index d960147..72b346f 100644 --- a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts +++ b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts @@ -201,6 +201,20 @@ export const buildScaffoldN50 = ( }; }; +/** + * Build props for the tags cell. + * @param genome - Genome entity. + * @returns Props to be used for the cell. + */ +export const buildTags = ( + genome: BRCDataCatalogGenome +): ComponentProps => { + return { + label: "Tags", + values: genome.tags, + }; +}; + /** * Build props for the taxonomy ID cell. * @param genome - Genome entity. diff --git a/files/build-catalog.ts b/files/build-catalog.ts index ff24ba7..4c8a323 100644 --- a/files/build-catalog.ts +++ b/files/build-catalog.ts @@ -1,8 +1,9 @@ import { parse as parseCsv } from "csv-parse/sync"; import fsp from "fs/promises"; import { BRCDataCatalogGenome } from "../app/apis/catalog/brc-analytics-catalog/common/entities"; -import { SourceGenome } from "./entities"; +import { SourceGenome, SourceOrganism } from "./entities"; +const SOURCE_PATH_ORGANISMS = "files/source/organisms-from-ncbi.tsv"; const SOURCE_PATH_GENOMES = "files/source/genomes-from-ncbi.tsv"; buildCatalog(); @@ -17,9 +18,16 @@ async function buildCatalog(): Promise { } async function buildGenomes(): Promise { + const sourceOrganismRows = await readValuesFile( + SOURCE_PATH_ORGANISMS + ); + const sourceOrganismsByTaxon = new Map( + sourceOrganismRows.map((row) => [row.taxon, row]) + ); const sourceRows = await readValuesFile(SOURCE_PATH_GENOMES); - const mappedRows = sourceRows.map( - (row): BRCDataCatalogGenome => ({ + const mappedRows = sourceRows.map((row): BRCDataCatalogGenome => { + const tagsString = sourceOrganismsByTaxon.get(row.taxon)?.CustomTags; + return { accession: row.accession, annotationStatus: parseStringOrNull(row.annotationStatus), chromosomes: parseNumberOrNull(row.chromosomeCount), @@ -33,10 +41,11 @@ async function buildGenomes(): Promise { scaffoldCount: parseNumber(row.scaffoldCount), scaffoldL50: parseNumber(row.scaffoldL50), scaffoldN50: parseNumber(row.scaffoldN50), + tags: tagsString ? [tagsString] : [], taxon: row.taxon, ucscBrowserUrl: parseStringOrNull(row.ucscBrowser), - }) - ); + }; + }); return mappedRows.sort((a, b) => a.accession.localeCompare(b.accession)); } diff --git a/files/entities.ts b/files/entities.ts index 3aa6edd..40c1774 100644 --- a/files/entities.ts +++ b/files/entities.ts @@ -15,3 +15,10 @@ export interface SourceGenome { taxonomyId: string; ucscBrowser: string; } + +export interface SourceOrganism { + assemblyCount: string; + CustomTags: string; + taxon: string; + taxonomyId: string; +} diff --git a/files/out/genomes.json b/files/out/genomes.json index 771cac1..b8c9c76 100644 --- a/files/out/genomes.json +++ b/files/out/genomes.json @@ -13,6 +13,9 @@ "scaffoldCount": 2747, "scaffoldL50": 6, "scaffoldN50": 1678596, + "tags": [ + "VEuPathDb" + ], "taxon": "Plasmodium vivax", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002415.2" }, @@ -30,6 +33,7 @@ "scaffoldCount": 12, "scaffoldL50": 4, "scaffoldN50": 2481190, + "tags": [], "taxon": "Trypanosoma brucei brucei TREU927", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002445.2" }, @@ -47,6 +51,7 @@ "scaffoldCount": 36, "scaffoldL50": 11, "scaffoldN50": 1091540, + "tags": [], "taxon": "Leishmania major strain Friedlin", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002725.2" }, @@ -64,6 +69,7 @@ "scaffoldCount": 14, "scaffoldL50": 5, "scaffoldN50": 1687656, + "tags": [], "taxon": "Plasmodium falciparum 3D7", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002765.5" }, @@ -81,6 +87,7 @@ "scaffoldCount": 138, "scaffoldL50": 11, "scaffoldN50": 992961, + "tags": [], "taxon": "Leishmania braziliensis MHOM/BR/75/M2904", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002845.2" }, @@ -98,6 +105,7 @@ "scaffoldCount": 2276, "scaffoldL50": 6, "scaffoldN50": 4973582, + "tags": [], "taxon": "Toxoplasma gondii ME49", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000006565.2" }, @@ -115,6 +123,7 @@ "scaffoldCount": 6, "scaffoldL50": 3, "scaffoldN50": 4323945, + "tags": [], "taxon": "Coccidioides immitis RS", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000149335.2" }, @@ -132,6 +141,7 @@ "scaffoldCount": 1, "scaffoldL50": 1, "scaffoldN50": 4411532, + "tags": [], "taxon": "Mycobacterium tuberculosis H37Rv", "ucscBrowserUrl": null }, @@ -149,6 +159,9 @@ "scaffoldCount": 29495, "scaffoldL50": 212, "scaffoldN50": 88624, + "tags": [ + "VEuPathDb" + ], "taxon": "Trypanosoma cruzi", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000209065.1" }, @@ -166,6 +179,9 @@ "scaffoldCount": 36, "scaffoldL50": 11, "scaffoldN50": 1024085, + "tags": [ + "VEuPathDb" + ], "taxon": "Leishmania donovani", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000227135.1" }, @@ -183,6 +199,7 @@ "scaffoldCount": 1, "scaffoldL50": 1, "scaffoldN50": 4411709, + "tags": [], "taxon": "Mycobacterium tuberculosis H37Rv", "ucscBrowserUrl": null }, @@ -200,6 +217,9 @@ "scaffoldCount": 1, "scaffoldL50": 1, "scaffoldN50": 196858, + "tags": [ + "Virus" + ], "taxon": "Monkeypox virus", "ucscBrowserUrl": null }, @@ -217,6 +237,9 @@ "scaffoldCount": 1, "scaffoldL50": 1, "scaffoldN50": 29903, + "tags": [ + "Virus" + ], "taxon": "Severe acute respiratory syndrome coronavirus 2", "ucscBrowserUrl": null }, @@ -234,6 +257,7 @@ "scaffoldCount": 289, "scaffoldL50": 2, "scaffoldN50": 186194774, + "tags": [], "taxon": "Culex pipiens pallens", "ucscBrowserUrl": null }, @@ -251,6 +275,7 @@ "scaffoldCount": 9, "scaffoldL50": 2, "scaffoldN50": 8079863, + "tags": [], "taxon": "Coccidioides posadasii str. Silveira", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_018416015.2" }, @@ -268,6 +293,9 @@ "scaffoldCount": 1, "scaffoldL50": 1, "scaffoldN50": 4516435, + "tags": [ + "Bact" + ], "taxon": "Mycobacterium tuberculosis", "ucscBrowserUrl": null }, @@ -285,6 +313,9 @@ "scaffoldCount": 14, "scaffoldL50": 5, "scaffoldN50": 2046250, + "tags": [ + "VEuPathDb" + ], "taxon": "Plasmodium yoelii", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_900002385.2" }, @@ -302,6 +333,7 @@ "scaffoldCount": 14, "scaffoldL50": 5, "scaffoldN50": 1692345, + "tags": [], "taxon": "Plasmodium vinckei vinckei", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_900681995.1" }, @@ -319,6 +351,9 @@ "scaffoldCount": 190, "scaffoldL50": 2, "scaffoldN50": 99149756, + "tags": [ + "VEuPathDb" + ], "taxon": "Anopheles gambiae", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943734735.2" }, @@ -336,6 +371,9 @@ "scaffoldCount": 1, "scaffoldL50": 1, "scaffoldN50": 4469156, + "tags": [ + "Bact" + ], "taxon": "Mycobacterium tuberculosis", "ucscBrowserUrl": null } diff --git a/site-config/brc-analytics/category.ts b/site-config/brc-analytics/category.ts index 92fc0f1..edca097 100644 --- a/site-config/brc-analytics/category.ts +++ b/site-config/brc-analytics/category.ts @@ -11,6 +11,7 @@ export const BRC_DATA_CATALOG_CATEGORY_KEY = { SCAFFOLD_COUNT: "scaffoldCount", SCAFFOLD_L50: "scaffoldL50", SCAFFOLD_N50: "scaffoldN50", + TAGS: "tags", TAXON: "taxon", TAXONOMY_ID: "ncbiTaxonomyId", UCSC_BROWSER_URL: "ucscBrowserUrl", @@ -29,6 +30,7 @@ export const BRC_DATA_CATALOG_CATEGORY_LABEL = { SCAFFOLD_COUNT: "Scaffolds", SCAFFOLD_L50: "Scaffold L50", SCAFFOLD_N50: "Scaffold N50", + TAGS: "Tags", TAXON: "Taxon", TAXONOMY_ID: "Taxonomy ID", UCSC_BROWSER_URL: "UCSC Browser", diff --git a/site-config/brc-analytics/local/index/genomeEntityConfig.ts b/site-config/brc-analytics/local/index/genomeEntityConfig.ts index 29763e1..f7ab369 100644 --- a/site-config/brc-analytics/local/index/genomeEntityConfig.ts +++ b/site-config/brc-analytics/local/index/genomeEntityConfig.ts @@ -61,6 +61,10 @@ export const genomeEntityConfig: BRCEntityConfig = { key: BRC_DATA_CATALOG_CATEGORY_KEY.ANNOTATION_STATUS, label: BRC_DATA_CATALOG_CATEGORY_LABEL.ANNOTATION_STATUS, }, + { + key: BRC_DATA_CATALOG_CATEGORY_KEY.TAGS, + label: BRC_DATA_CATALOG_CATEGORY_LABEL.TAGS, + }, ], }, ], @@ -214,6 +218,15 @@ export const genomeEntityConfig: BRCEntityConfig = { id: BRC_DATA_CATALOG_CATEGORY_KEY.ANNOTATION_STATUS, width: { max: "0.5fr", min: "142px" }, }, + { + componentConfig: { + component: C.NTagCell, + viewBuilder: V.buildTags, + } as ComponentConfig, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAGS, + id: BRC_DATA_CATALOG_CATEGORY_KEY.TAGS, + width: { max: "0.5fr", min: "142px" }, + }, ], tableOptions: { initialState: { From 20fba07844333ffde4830cab18aba887d76b47f3 Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Mon, 18 Nov 2024 18:15:31 -0800 Subject: [PATCH 07/30] feat: add organism list (#177) --- .../brc-analytics-catalog/common/entities.ts | 7 + .../brc-analytics-catalog/common/utils.ts | 6 +- .../common/viewModelBuilders.ts | 24 +++- files/build-catalog.ts | 40 ++++-- files/out/organisms.json | 136 ++++++++++++++++++ routes/constants.ts | 1 + site-config/brc-analytics/category.ts | 2 + site-config/brc-analytics/local/config.ts | 14 +- .../local/index/organismEntityConfig.ts | 102 +++++++++++++ 9 files changed, 316 insertions(+), 16 deletions(-) create mode 100644 files/out/organisms.json create mode 100644 site-config/brc-analytics/local/index/organismEntityConfig.ts diff --git a/app/apis/catalog/brc-analytics-catalog/common/entities.ts b/app/apis/catalog/brc-analytics-catalog/common/entities.ts index e61b319..7e713f5 100644 --- a/app/apis/catalog/brc-analytics-catalog/common/entities.ts +++ b/app/apis/catalog/brc-analytics-catalog/common/entities.ts @@ -28,6 +28,13 @@ export interface BRCDataCatalogGenome { ucscBrowserUrl: string | null; } +export interface BRCDataCatalogOrganism { + assemblyCount: number; + ncbiTaxonomyId: string; + tags: string[]; + taxon: string; +} + export interface EntitiesResponse { hits: R[]; pagination: EntitiesResponsePagination; diff --git a/app/apis/catalog/brc-analytics-catalog/common/utils.ts b/app/apis/catalog/brc-analytics-catalog/common/utils.ts index 0baded0..45fc474 100644 --- a/app/apis/catalog/brc-analytics-catalog/common/utils.ts +++ b/app/apis/catalog/brc-analytics-catalog/common/utils.ts @@ -1,4 +1,4 @@ -import { BRCDataCatalogGenome } from "./entities"; +import { BRCDataCatalogGenome, BRCDataCatalogOrganism } from "./entities"; export function getGenomeId(genome: BRCDataCatalogGenome): string { return sanitizeEntityId(genome.accession); @@ -9,6 +9,10 @@ export function getGenomeTitle(genome?: BRCDataCatalogGenome): string { return `${genome.taxon}`; } +export function getOrganismId(organism: BRCDataCatalogOrganism): string { + return sanitizeEntityId(organism.ncbiTaxonomyId); +} + export function sanitizeEntityId(entityId?: string): string { if (!entityId) return ""; return entityId.replace(/\./g, "_"); diff --git a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts index 72b346f..b7f6e85 100644 --- a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts +++ b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts @@ -6,7 +6,10 @@ import { import { ViewContext } from "@databiosphere/findable-ui/lib/config/entities"; import { ComponentProps } from "react"; import { ROUTES } from "../../../../../routes/constants"; -import { BRCDataCatalogGenome } from "../../../../apis/catalog/brc-analytics-catalog/common/entities"; +import { + BRCDataCatalogGenome, + BRCDataCatalogOrganism, +} from "../../../../apis/catalog/brc-analytics-catalog/common/entities"; import * as C from "../../../../components"; import { GENOME_BROWSER, NCBI_DATASETS_URL } from "./constants"; @@ -71,6 +74,19 @@ export const buildAnnotationStatus = ( }; }; +/** + * Build props for the assemblies cell. + * @param organism - Genome entity. + * @returns Props to be used for the cell. + */ +export const buildAssemblyCount = ( + organism: BRCDataCatalogOrganism +): ComponentProps => { + return { + value: organism.assemblyCount, + }; +}; + /** * Build props for the chromosomes cell. * @param genome - Genome entity. @@ -155,7 +171,7 @@ export const buildLevel = ( * @returns Props to be used for the cell. */ export const buildTaxon = ( - genome: BRCDataCatalogGenome + genome: BRCDataCatalogOrganism | BRCDataCatalogGenome ): ComponentProps => { return { value: genome.taxon, @@ -207,7 +223,7 @@ export const buildScaffoldN50 = ( * @returns Props to be used for the cell. */ export const buildTags = ( - genome: BRCDataCatalogGenome + genome: BRCDataCatalogOrganism | BRCDataCatalogGenome ): ComponentProps => { return { label: "Tags", @@ -221,7 +237,7 @@ export const buildTags = ( * @returns Props to be used for the cell. */ export const buildTaxonomyId = ( - genome: BRCDataCatalogGenome + genome: BRCDataCatalogOrganism | BRCDataCatalogGenome ): ComponentProps => { return { value: genome.ncbiTaxonomyId, diff --git a/files/build-catalog.ts b/files/build-catalog.ts index 4c8a323..6c881f2 100644 --- a/files/build-catalog.ts +++ b/files/build-catalog.ts @@ -1,6 +1,9 @@ import { parse as parseCsv } from "csv-parse/sync"; import fsp from "fs/promises"; -import { BRCDataCatalogGenome } from "../app/apis/catalog/brc-analytics-catalog/common/entities"; +import { + BRCDataCatalogGenome, + BRCDataCatalogOrganism, +} from "../app/apis/catalog/brc-analytics-catalog/common/entities"; import { SourceGenome, SourceOrganism } from "./entities"; const SOURCE_PATH_ORGANISMS = "files/source/organisms-from-ncbi.tsv"; @@ -9,7 +12,16 @@ const SOURCE_PATH_GENOMES = "files/source/genomes-from-ncbi.tsv"; buildCatalog(); async function buildCatalog(): Promise { - const genomes = await buildGenomes(); + const organisms = await buildOrganisms(); + + const organismsByTaxon = new Map( + organisms.map((organism) => [organism.taxon, organism]) + ); + + const genomes = await buildGenomes(organismsByTaxon); + + console.log("Organisms:", genomes.length); + await saveJson("files/out/organisms.json", organisms); console.log("Genomes:", genomes.length); await saveJson("files/out/genomes.json", genomes); @@ -17,16 +29,28 @@ async function buildCatalog(): Promise { console.log("Done"); } -async function buildGenomes(): Promise { - const sourceOrganismRows = await readValuesFile( +async function buildOrganisms(): Promise { + const sourceRows = await readValuesFile( SOURCE_PATH_ORGANISMS ); - const sourceOrganismsByTaxon = new Map( - sourceOrganismRows.map((row) => [row.taxon, row]) + const mappedRows = sourceRows.map((row): BRCDataCatalogOrganism => { + return { + assemblyCount: parseNumber(row.assemblyCount), + ncbiTaxonomyId: row.taxonomyId, + tags: row.CustomTags ? [row.CustomTags] : [], + taxon: row.taxon, + }; + }); + return mappedRows.sort((a, b) => + a.ncbiTaxonomyId.localeCompare(b.ncbiTaxonomyId) ); +} + +async function buildGenomes( + organismsByTaxon: Map +): Promise { const sourceRows = await readValuesFile(SOURCE_PATH_GENOMES); const mappedRows = sourceRows.map((row): BRCDataCatalogGenome => { - const tagsString = sourceOrganismsByTaxon.get(row.taxon)?.CustomTags; return { accession: row.accession, annotationStatus: parseStringOrNull(row.annotationStatus), @@ -41,7 +65,7 @@ async function buildGenomes(): Promise { scaffoldCount: parseNumber(row.scaffoldCount), scaffoldL50: parseNumber(row.scaffoldL50), scaffoldN50: parseNumber(row.scaffoldN50), - tags: tagsString ? [tagsString] : [], + tags: organismsByTaxon.get(row.taxon)?.tags ?? [], taxon: row.taxon, ucscBrowserUrl: parseStringOrNull(row.ucscBrowser), }; diff --git a/files/out/organisms.json b/files/out/organisms.json new file mode 100644 index 0000000..4ceb6ba --- /dev/null +++ b/files/out/organisms.json @@ -0,0 +1,136 @@ +[ + { + "assemblyCount": 6911, + "ncbiTaxonomyId": "10244", + "tags": [ + "Virus" + ], + "taxon": "Monkeypox virus" + }, + { + "assemblyCount": 7823, + "ncbiTaxonomyId": "1773", + "tags": [ + "Bact" + ], + "taxon": "Mycobacterium tuberculosis" + }, + { + "assemblyCount": 13, + "ncbiTaxonomyId": "199306", + "tags": [ + "VEuPathDb" + ], + "taxon": "Coccidioides posadasii" + }, + { + "assemblyCount": 92, + "ncbiTaxonomyId": "2697049", + "tags": [ + "Virus" + ], + "taxon": "Severe acute respiratory syndrome coronavirus 2" + }, + { + "assemblyCount": 5, + "ncbiTaxonomyId": "5501", + "tags": [], + "taxon": "Coccidioides immitis" + }, + { + "assemblyCount": 11, + "ncbiTaxonomyId": "5660", + "tags": [ + "VEuPathDb" + ], + "taxon": "Leishmania braziliensis" + }, + { + "assemblyCount": 12, + "ncbiTaxonomyId": "5661", + "tags": [ + "VEuPathDb" + ], + "taxon": "Leishmania donovani" + }, + { + "assemblyCount": 7, + "ncbiTaxonomyId": "5664", + "tags": [ + "VEuPathDb" + ], + "taxon": "Leishmania major" + }, + { + "assemblyCount": 5, + "ncbiTaxonomyId": "5691", + "tags": [ + "VEuPathDb" + ], + "taxon": "Trypanosoma brucei" + }, + { + "assemblyCount": 44, + "ncbiTaxonomyId": "5693", + "tags": [ + "VEuPathDb" + ], + "taxon": "Trypanosoma cruzi" + }, + { + "assemblyCount": 29, + "ncbiTaxonomyId": "5811", + "tags": [ + "VEuPathDb" + ], + "taxon": "Toxoplasma gondii" + }, + { + "assemblyCount": 67, + "ncbiTaxonomyId": "5833", + "tags": [ + "VEuPathDb" + ], + "taxon": "Plasmodium falciparum" + }, + { + "assemblyCount": 19, + "ncbiTaxonomyId": "5855", + "tags": [ + "VEuPathDb" + ], + "taxon": "Plasmodium vivax" + }, + { + "assemblyCount": 10, + "ncbiTaxonomyId": "5860", + "tags": [ + "VEuPathDb" + ], + "taxon": "Plasmodium vinckei" + }, + { + "assemblyCount": 15, + "ncbiTaxonomyId": "5861", + "tags": [ + "VEuPathDb" + ], + "taxon": "Plasmodium yoelii" + }, + { + "assemblyCount": 7, + "ncbiTaxonomyId": "7165", + "tags": [ + "VEuPathDb" + ], + "taxon": "Anopheles gambiae" + }, + { + "assemblyCount": 5, + "ncbiTaxonomyId": "7175", + "tags": [ + "VEuPathDb" + ], + "taxon": "Culex pipiens" + } +] diff --git a/routes/constants.ts b/routes/constants.ts index 05eb80a..b1f6088 100644 --- a/routes/constants.ts +++ b/routes/constants.ts @@ -1,5 +1,6 @@ export const ROUTES = { ABOUT: "/about", GENOMES: "/data/genomes", + ORGANISMS: "/data/organisms", ROADMAP: "/roadmap", }; diff --git a/site-config/brc-analytics/category.ts b/site-config/brc-analytics/category.ts index edca097..122bf19 100644 --- a/site-config/brc-analytics/category.ts +++ b/site-config/brc-analytics/category.ts @@ -2,6 +2,7 @@ export const BRC_DATA_CATALOG_CATEGORY_KEY = { ACCESSION: "accession", ANALYZE_GENOME: "analyzeGenome", ANNOTATION_STATUS: "annotationStatus", + ASSEMBLY_COUNT: "assemblyCount", CHROMOSOMES: "chromosomes", COVERAGE: "coverage", GC_PERCENT: "gcPercent", @@ -21,6 +22,7 @@ export const BRC_DATA_CATALOG_CATEGORY_LABEL = { ACCESSION: "Accession", ANALYZE_GENOME: "Action", ANNOTATION_STATUS: "Annotation Status", + ASSEMBLY_COUNT: "Assemblies", CHROMOSOMES: "Chromosomes", COVERAGE: "Coverage", GC_PERCENT: "GC%", diff --git a/site-config/brc-analytics/local/config.ts b/site-config/brc-analytics/local/config.ts index 781a54a..627af71 100644 --- a/site-config/brc-analytics/local/config.ts +++ b/site-config/brc-analytics/local/config.ts @@ -1,11 +1,15 @@ import { ANCHOR_TARGET } from "@databiosphere/findable-ui/lib/components/Links/common/entities"; import { SiteConfig } from "@databiosphere/findable-ui/lib/config/entities"; import { EntityConfig } from "@databiosphere/findable-ui/src/config/entities"; -import { BRCDataCatalogGenome } from "../../../app/apis/catalog/brc-analytics-catalog/common/entities"; +import { + BRCDataCatalogGenome, + BRCDataCatalogOrganism, +} from "../../../app/apis/catalog/brc-analytics-catalog/common/entities"; import * as C from "../../../app/components"; import { ROUTES } from "../../../routes/constants"; import { floating } from "./floating/floating"; import { genomeEntityConfig } from "./index/genomeEntityConfig"; +import { organismEntityConfig } from "./index/organismEntityConfig"; import { socialMedia } from "./socialMedia"; const LOCALHOST = "http://localhost:3000"; @@ -35,7 +39,10 @@ export function makeConfig(browserUrl: string, gitHubUrl: string): SiteConfig { dataSource: { url: "", }, - entities: [genomeEntityConfig as EntityConfig], + entities: [ + organismEntityConfig as EntityConfig, + genomeEntityConfig as EntityConfig, + ], explorerTitle: APP_TITLE, gitHubUrl, layout: { @@ -68,7 +75,8 @@ export function makeConfig(browserUrl: string, gitHubUrl: string): SiteConfig { undefined, [ { label: "About", url: ROUTES.ABOUT }, - { label: "Datasets", url: ROUTES.GENOMES }, + { label: "Organisms", url: ROUTES.ORGANISMS }, + { label: "Genomes", url: ROUTES.GENOMES }, { label: "Roadmap", url: ROUTES.ROADMAP }, ], undefined, diff --git a/site-config/brc-analytics/local/index/organismEntityConfig.ts b/site-config/brc-analytics/local/index/organismEntityConfig.ts new file mode 100644 index 0000000..1a39944 --- /dev/null +++ b/site-config/brc-analytics/local/index/organismEntityConfig.ts @@ -0,0 +1,102 @@ +import { + ComponentConfig, + ListConfig, + SORT_DIRECTION, +} from "@databiosphere/findable-ui/lib/config/entities"; +import { EXPLORE_MODE } from "@databiosphere/findable-ui/lib/hooks/useExploreMode"; +import { BRCDataCatalogOrganism } from "../../../../app/apis/catalog/brc-analytics-catalog/common/entities"; +import { getOrganismId } from "../../../../app/apis/catalog/brc-analytics-catalog/common/utils"; +import * as C from "../../../../app/components"; +import * as V from "../../../../app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders"; +import { BRCEntityConfig } from "../../../common/entities"; +import { + BRC_DATA_CATALOG_CATEGORY_KEY, + BRC_DATA_CATALOG_CATEGORY_LABEL, +} from "../../category"; + +/** + * Entity config object responsible to config anything related to the /genomes route. + */ +export const organismEntityConfig: BRCEntityConfig = { + categoryGroupConfig: { + categoryGroups: [ + { + categoryConfigs: [ + { + key: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON, + label: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXON, + }, + { + key: BRC_DATA_CATALOG_CATEGORY_KEY.TAXONOMY_ID, + label: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXONOMY_ID, + }, + { + key: BRC_DATA_CATALOG_CATEGORY_KEY.TAGS, + label: BRC_DATA_CATALOG_CATEGORY_LABEL.TAGS, + }, + ], + }, + ], + key: "organisms", + }, + detail: { + detailOverviews: [], + staticLoad: true, + tabs: [], + }, + exploreMode: EXPLORE_MODE.CS_FETCH_CS_FILTERING, + explorerTitle: "Organisms", + getId: getOrganismId, + label: "Organisms", + list: { + columns: [ + { + componentConfig: { + component: C.BasicCell, + viewBuilder: V.buildTaxon, + } as ComponentConfig, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXON, + id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON, + width: "auto", + }, + { + componentConfig: { + component: C.BasicCell, + viewBuilder: V.buildTaxonomyId, + } as ComponentConfig, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXONOMY_ID, + id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXONOMY_ID, + width: { max: "0.5fr", min: "164px" }, + }, + { + componentConfig: { + component: C.BasicCell, + viewBuilder: V.buildAssemblyCount, + } as ComponentConfig, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.ASSEMBLY_COUNT, + id: BRC_DATA_CATALOG_CATEGORY_KEY.ASSEMBLY_COUNT, + width: { max: "0.5fr", min: "164px" }, + }, + { + componentConfig: { + component: C.NTagCell, + viewBuilder: V.buildTags, + } as ComponentConfig, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAGS, + id: BRC_DATA_CATALOG_CATEGORY_KEY.TAGS, + width: { max: "0.5fr", min: "142px" }, + }, + ], + defaultSort: { + desc: SORT_DIRECTION.ASCENDING, + id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON, + }, + } as ListConfig, + listView: { + disablePagination: true, + enableDownload: true, + enableTab: false, + }, + route: "organisms", + staticLoadFile: "files/out/organisms.json", +}; From fed6a792ab963f2ce8fece414833de7a0e2bcf9b Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Thu, 5 Dec 2024 00:36:40 -0800 Subject: [PATCH 08/30] fix: make `isRef` a string to avoid error when searching filters (#177) --- .../brc-analytics-catalog/common/entities.ts | 2 +- .../common/viewModelBuilders.ts | 2 +- files/build-catalog.ts | 4 +- files/out/genomes.json | 40 +++++++++---------- 4 files changed, 24 insertions(+), 24 deletions(-) diff --git a/app/apis/catalog/brc-analytics-catalog/common/entities.ts b/app/apis/catalog/brc-analytics-catalog/common/entities.ts index 7e713f5..1998a66 100644 --- a/app/apis/catalog/brc-analytics-catalog/common/entities.ts +++ b/app/apis/catalog/brc-analytics-catalog/common/entities.ts @@ -16,7 +16,7 @@ export interface BRCDataCatalogGenome { coverage: string | null; gcPercent: number; geneModelUrl: string | null; - isRef: boolean; + isRef: string; length: number; level: string; ncbiTaxonomyId: string; diff --git a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts index b7f6e85..6968b98 100644 --- a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts +++ b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts @@ -135,7 +135,7 @@ export const buildIsRef = ( genome: BRCDataCatalogGenome ): ComponentProps => { return { - value: genome.isRef ? "Yes" : "No", + value: genome.isRef, }; }; diff --git a/files/build-catalog.ts b/files/build-catalog.ts index 6c881f2..ee6029e 100644 --- a/files/build-catalog.ts +++ b/files/build-catalog.ts @@ -106,6 +106,6 @@ function parseNumber(value: string): number { return n; } -function parseBoolean(value: string): boolean { - return value[0].toLowerCase() === "t"; +function parseBoolean(value: string): string { + return value[0].toLowerCase() === "t" ? "Yes" : "No"; } diff --git a/files/out/genomes.json b/files/out/genomes.json index b8c9c76..474a330 100644 --- a/files/out/genomes.json +++ b/files/out/genomes.json @@ -6,7 +6,7 @@ "coverage": null, "gcPercent": 42.5, "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/415/GCF_000002415.2/genes/GCF_000002415.2_ASM241v2.ncbiRefSeq.gtf.gz", - "isRef": true, + "isRef": "Yes", "length": 27007701, "level": "Chromosome", "ncbiTaxonomyId": "5855", @@ -26,7 +26,7 @@ "coverage": null, "gcPercent": 46.5, "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/445/GCF_000002445.2/genes/GCF_000002445.2_ASM244v1.ncbiRefSeq.gtf.gz", - "isRef": true, + "isRef": "Yes", "length": 26075494, "level": "Chromosome", "ncbiTaxonomyId": "185431", @@ -44,7 +44,7 @@ "coverage": null, "gcPercent": 59.5, "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/725/GCF_000002725.2/genes/GCF_000002725.2_ASM272v2.ncbiRefSeq.gtf.gz", - "isRef": true, + "isRef": "Yes", "length": 32855089, "level": "Complete Genome", "ncbiTaxonomyId": "347515", @@ -62,7 +62,7 @@ "coverage": "100.0x", "gcPercent": 19.5, "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/765/GCF_000002765.6/genes/GCF_000002765.6_GCA_000002765.ncbiRefSeq.gtf.gz", - "isRef": true, + "isRef": "Yes", "length": 23292622, "level": "Complete Genome", "ncbiTaxonomyId": "36329", @@ -80,7 +80,7 @@ "coverage": null, "gcPercent": 58, "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/845/GCF_000002845.2/genes/GCF_000002845.2_ASM284v2.ncbiRefSeq.gtf.gz", - "isRef": true, + "isRef": "Yes", "length": 32068771, "level": "Chromosome", "ncbiTaxonomyId": "420245", @@ -98,7 +98,7 @@ "coverage": "26.5x", "gcPercent": 52.5, "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/006/565/GCF_000006565.2/genes/GCF_000006565.2_TGA4.ncbiRefSeq.gtf.gz", - "isRef": true, + "isRef": "Yes", "length": 65633124, "level": "Chromosome", "ncbiTaxonomyId": "508771", @@ -116,7 +116,7 @@ "coverage": null, "gcPercent": 46, "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/149/335/GCF_000149335.2/genes/GCF_000149335.2_ASM14933v2.ncbiRefSeq.gtf.gz", - "isRef": true, + "isRef": "Yes", "length": 28947925, "level": "Scaffold", "ncbiTaxonomyId": "246410", @@ -134,7 +134,7 @@ "coverage": null, "gcPercent": 65.5, "geneModelUrl": null, - "isRef": true, + "isRef": "Yes", "length": 4411532, "level": "Complete Genome", "ncbiTaxonomyId": "83332", @@ -152,7 +152,7 @@ "coverage": null, "gcPercent": 51.5, "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/209/065/GCF_000209065.1/genes/GCF_000209065.1_ASM20906v1.ncbiRefSeq.gtf.gz", - "isRef": true, + "isRef": "Yes", "length": 89937456, "level": "Scaffold", "ncbiTaxonomyId": "5693", @@ -172,7 +172,7 @@ "coverage": null, "gcPercent": 59.5, "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/227/135/GCF_000227135.1/genes/GCF_000227135.1_ASM22713v2.ncbiRefSeq.gtf.gz", - "isRef": true, + "isRef": "Yes", "length": 32444968, "level": "Chromosome", "ncbiTaxonomyId": "5661", @@ -192,7 +192,7 @@ "coverage": null, "gcPercent": 65.5, "geneModelUrl": null, - "isRef": false, + "isRef": "No", "length": 4411709, "level": "Complete Genome", "ncbiTaxonomyId": "83332", @@ -210,7 +210,7 @@ "coverage": null, "gcPercent": 33, "geneModelUrl": null, - "isRef": false, + "isRef": "No", "length": 196858, "level": "Complete Genome", "ncbiTaxonomyId": "10244", @@ -230,7 +230,7 @@ "coverage": null, "gcPercent": 38, "geneModelUrl": null, - "isRef": false, + "isRef": "No", "length": 29903, "level": "Complete Genome", "ncbiTaxonomyId": "2697049", @@ -250,7 +250,7 @@ "coverage": "250.0x", "gcPercent": 37, "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/016/801/865/GCF_016801865.2/genes/GCF_016801865.2_TS_CPP_V2.ncbiRefSeq.gtf.gz", - "isRef": true, + "isRef": "Yes", "length": 566339288, "level": "Chromosome", "ncbiTaxonomyId": "42434", @@ -268,7 +268,7 @@ "coverage": "475.0x", "gcPercent": 46.5, "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/018/416/015/GCF_018416015.2/genes/GCF_018416015.2_ASM1841601v2.ncbiRefSeq.gtf.gz", - "isRef": true, + "isRef": "Yes", "length": 28193268, "level": "Complete Genome", "ncbiTaxonomyId": "443226", @@ -286,7 +286,7 @@ "coverage": "20.0x", "gcPercent": 65.5, "geneModelUrl": null, - "isRef": false, + "isRef": "No", "length": 4516435, "level": "Complete Genome", "ncbiTaxonomyId": "1773", @@ -306,7 +306,7 @@ "coverage": "100.0x", "gcPercent": 21.5, "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/900/002/385/GCF_900002385.2/genes/GCF_900002385.2_GCA_900002385.ncbiRefSeq.gtf.gz", - "isRef": true, + "isRef": "Yes", "length": 23043114, "level": "Complete Genome", "ncbiTaxonomyId": "5861", @@ -326,7 +326,7 @@ "coverage": "155.0x", "gcPercent": 23, "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/900/681/995/GCF_900681995.1/genes/GCF_900681995.1_PVVCY_v1.ncbiRefSeq.gtf.gz", - "isRef": true, + "isRef": "Yes", "length": 18338688, "level": "Complete Genome", "ncbiTaxonomyId": "54757", @@ -344,7 +344,7 @@ "coverage": "54.0x", "gcPercent": 44.5, "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/943/734/735/GCF_943734735.2/genes/GCF_943734735.2_idAnoGambNW_F1_1.ncbiRefSeq.gtf.gz", - "isRef": true, + "isRef": "Yes", "length": 264451381, "level": "Chromosome", "ncbiTaxonomyId": "7165", @@ -364,7 +364,7 @@ "coverage": "100.0x", "gcPercent": 65.5, "geneModelUrl": null, - "isRef": false, + "isRef": "No", "length": 4469156, "level": "Complete Genome", "ncbiTaxonomyId": "1773", From 42ff576bd6e132407d7ce3bd3e2b29292ddefaf1 Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Thu, 5 Dec 2024 15:32:53 -0800 Subject: [PATCH 09/30] feat: fix build from ncbi and report on accession matches (#177) --- files/build-files-from-ncbi.py | 33 +++++++++++++++++++++++----- files/source/genomes-from-ncbi.tsv | 24 ++++++++++---------- files/source/organisms-from-ncbi.tsv | 6 ++--- 3 files changed, 44 insertions(+), 19 deletions(-) diff --git a/files/build-files-from-ncbi.py b/files/build-files-from-ncbi.py index 0690d18..0c2c112 100644 --- a/files/build-files-from-ncbi.py +++ b/files/build-files-from-ncbi.py @@ -15,15 +15,21 @@ def build_taxonomy_request_body(taxa): return {"taxons": taxa, "children": False, "ranks": ["genus"]} -def get_organism_row(organism_taxonomy): +def get_organism_row(organism_info): + if len(organism_info.get("errors", [])) > 0: + raise Exception(organism_info) + + organism_taxonomy = organism_info["taxonomy"] + return { "taxon": organism_taxonomy["current_scientific_name"]["name"], - "taxonomyId": organism_taxonomy["tax_id"], + "taxonomyId": str(organism_taxonomy["tax_id"]), "assemblyCount": next(count["count"] for count in organism_taxonomy["counts"] if count["type"] == "COUNT_TYPE_ASSEMBLY"), } def get_organisms_df(taxa): - return pd.DataFrame([get_organism_row(organism_info["taxonomy"]) for organism_info in requests.post(TAXONOMY_URL, json=build_taxonomy_request_body(taxa)).json()["reports"]]) + organisms_info = requests.post(TAXONOMY_URL, json=build_taxonomy_request_body(taxa)).json()["reports"] + return pd.DataFrame([get_organism_row(organism_info) for organism_info in organisms_info]) def get_tax_ids(organisms_df): return list(organisms_df["taxonomyId"]) @@ -53,6 +59,22 @@ def get_genome_row(genome_info): def get_genomes_df(tax_ids): return pd.DataFrame(data=[get_genome_row(genome_info) for genome_info in requests.get(build_genomes_url(tax_ids)).json()["reports"]]) +def print_column_match_summary(from_df, in_df, from_column, in_column, important=True): + unmatched_values = from_df[from_column][~(from_df[from_column].isin(in_df[in_column]))] + message = ( + f"No values from {from_column} absent in {in_column}" if len(unmatched_values) == 0 + else f"{len(unmatched_values)} values from {from_column} absent in {in_column}: {", ".join(unmatched_values)}" + ) + if not important: + message = "(" + message + ")" + print(message) + +def print_accession_match_summaries(genomes_source_df, assemblies_df): + print_column_match_summary(genomes_source_df, assemblies_df, "pairedAccession", "genBank") + print_column_match_summary(genomes_source_df, assemblies_df, "pairedAccession", "refSeq", False) + print_column_match_summary(genomes_source_df, assemblies_df, "accession", "genBank", False) + print_column_match_summary(genomes_source_df, assemblies_df, "accession", "refSeq") + def _id_to_gene_model_url(asm_id): hubs_url = "https://hgdownload.soe.ucsc.edu/hubs/" components = [asm_id[0:3], asm_id[4:7], asm_id[7:10], asm_id[10:13], asm_id, "genes"] @@ -81,7 +103,6 @@ def _id_to_gene_model_url(asm_id): # No match, I guess that's OK ? return None - def add_gene_model_url(genomes_df: pd.DataFrame): return pd.concat([genomes_df, genomes_df["accession"].apply(_id_to_gene_model_url).rename("geneModelUrl")], axis="columns") @@ -90,7 +111,7 @@ def build_files(): taxa_df = pd.read_csv(TAXA_URL, keep_default_na=False) - organisms_source_df = get_organisms_df(list(taxa_df["Name"])) + organisms_source_df = get_organisms_df([taxon for taxon in taxa_df["Name"] if taxon]) organisms_df = organisms_source_df.merge(taxa_df[["TaxId", "CustomTags"]], how="left", left_on="taxonomyId", right_on="TaxId").drop(columns=["TaxId"]) @@ -104,6 +125,8 @@ def build_files(): gen_bank_merge_df = genomes_source_df.merge(assemblies_df, how="left", left_on="pairedAccession", right_on="genBank") ref_seq_merge_df = genomes_source_df.merge(assemblies_df, how="left", left_on="accession", right_on="refSeq") + print_accession_match_summaries(genomes_source_df, assemblies_df) + genomes_df = add_gene_model_url(gen_bank_merge_df.combine_first(ref_seq_merge_df)) genomes_df.to_csv(GENOMES_OUTPUT_PATH, index=False, sep="\t") diff --git a/files/source/genomes-from-ncbi.tsv b/files/source/genomes-from-ncbi.tsv index 79d5b1b..24926e2 100644 --- a/files/source/genomes-from-ncbi.tsv +++ b/files/source/genomes-from-ncbi.tsv @@ -1,21 +1,23 @@ taxon taxonomyId accession isRef level chromosomeCount length scaffoldCount scaffoldN50 scaffoldL50 coverage gcPercent annotationStatus pairedAccession ucscBrowser genBank refSeq geneModelUrl -Mycobacterium tuberculosis H37Rv 83332 GCF_000195955.2 True Complete Genome 1.0 4411532 1 4411532 1 65.5 GCA_000195955.2 +Mycobacterium tuberculosis H37Rv 83332 GCF_000195955.2 True Complete Genome 1.0 4411532 1 4411532 1 65.5 GCA_000195955.2 https://genome.ucsc.edu/h/GCF_000195955.2 GCA_000195955.2 GCF_000195955.2 Plasmodium falciparum 3D7 36329 GCF_000002765.6 True Complete Genome 14.0 23292622 14 1687656 5 100.0x 19.5 Full annotation GCA_000002765.3 https://genome.ucsc.edu/h/GCF_000002765.5 GCA_000002765.3 GCF_000002765.5 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/765/GCF_000002765.6/genes/GCF_000002765.6_GCA_000002765.ncbiRefSeq.gtf.gz -Leishmania major strain Friedlin 347515 GCF_000002725.2 True Complete Genome 36.0 32855089 36 1091540 11 59.5 Full annotation GCA_000002725.2 https://genome.ucsc.edu/h/GCF_000002725.2 GCA_000002725.2 GCF_000002725.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/725/GCF_000002725.2/genes/GCF_000002725.2_ASM272v2.ncbiRefSeq.gtf.gz +Plasmodium falciparum 3D7 36329 GCF_000002765.6 True Complete Genome 14.0 23292622 14 1687656 5 100.0x 19.5 Full annotation GCA_000002765.3 https://genome.ucsc.edu/h/GCF_000002765.6 GCA_000002765.3 GCF_000002765.6 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/765/GCF_000002765.6/genes/GCF_000002765.6_GCA_000002765.ncbiRefSeq.gtf.gz +Leishmania major strain Friedlin 347515 GCF_000002725.2 True Complete Genome 36.0 32855089 36 1091540 11 100.0x 59.5 Full annotation GCA_000002725.2 https://genome.ucsc.edu/h/GCF_000002725.2 GCA_000002725.2 GCF_000002725.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/725/GCF_000002725.2/genes/GCF_000002725.2_ASM272v2.ncbiRefSeq.gtf.gz Plasmodium yoelii 5861 GCF_900002385.2 True Complete Genome 14.0 23043114 14 2046250 5 100.0x 21.5 Full annotation GCA_900002385.2 https://genome.ucsc.edu/h/GCF_900002385.2 GCA_900002385.2 GCF_900002385.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/900/002/385/GCF_900002385.2/genes/GCF_900002385.2_GCA_900002385.ncbiRefSeq.gtf.gz Coccidioides posadasii str. Silveira 443226 GCF_018416015.2 True Complete Genome 9.0 28193268 9 8079863 2 475.0x 46.5 Full annotation GCA_018416015.2 https://genome.ucsc.edu/h/GCA_018416015.2 GCA_018416015.2 GCF_018416015.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/018/416/015/GCF_018416015.2/genes/GCF_018416015.2_ASM1841601v2.ncbiRefSeq.gtf.gz -Plasmodium vinckei vinckei 54757 GCF_900681995.1 True Complete Genome 14.0 18338688 14 1692345 5 155.0x 23.0 Full annotation GCA_900681995.1 https://genome.ucsc.edu/h/GCF_900681995.1 GCA_900681995.1 GCF_900681995.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/900/681/995/GCF_900681995.1/genes/GCF_900681995.1_PVVCY_v1.ncbiRefSeq.gtf.gz +Coccidioides posadasii str. Silveira 443226 GCF_018416015.2 True Complete Genome 9.0 28193268 9 8079863 2 475.0x 46.5 Full annotation GCA_018416015.2 https://genome.ucsc.edu/h/GCF_018416015.2 GCA_018416015.2 GCF_018416015.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/018/416/015/GCF_018416015.2/genes/GCF_018416015.2_ASM1841601v2.ncbiRefSeq.gtf.gz +Plasmodium vinckei vinckei 54757 GCF_900681995.1 True Chromosome 14.0 18338688 14 1692345 5 155.0x 23.0 Full annotation GCA_900681995.1 https://genome.ucsc.edu/h/GCF_900681995.1 GCA_900681995.1 GCF_900681995.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/900/681/995/GCF_900681995.1/genes/GCF_900681995.1_PVVCY_v1.ncbiRefSeq.gtf.gz Leishmania donovani 5661 GCF_000227135.1 True Chromosome 36.0 32444968 36 1024085 11 59.5 Full annotation GCA_000227135.2 https://genome.ucsc.edu/h/GCF_000227135.1 GCA_000227135.2 GCF_000227135.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/227/135/GCF_000227135.1/genes/GCF_000227135.1_ASM22713v2.ncbiRefSeq.gtf.gz -Toxoplasma gondii ME49 508771 GCF_000006565.2 True Chromosome 14.0 65633124 2276 4973582 6 26.5x 52.5 GCA_000006565.2 https://genome.ucsc.edu/h/GCF_000006565.2 GCA_000006565.2 GCF_000006565.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/006/565/GCF_000006565.2/genes/GCF_000006565.2_TGA4.ncbiRefSeq.gtf.gz +Toxoplasma gondii ME49 508771 GCF_000006565.2 True Chromosome 14.0 65633124 2276 4973582 6 26.5x 52.5 Full annotation GCA_000006565.2 https://genome.ucsc.edu/h/GCF_000006565.2 GCA_000006565.2 GCF_000006565.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/006/565/GCF_000006565.2/genes/GCF_000006565.2_TGA4.ncbiRefSeq.gtf.gz Trypanosoma brucei brucei TREU927 185431 GCF_000002445.2 True Chromosome 11.0 26075494 12 2481190 4 46.5 Full annotation GCA_000002445.1 https://genome.ucsc.edu/h/GCF_000002445.2 GCA_000002445.1 GCF_000002445.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/445/GCF_000002445.2/genes/GCF_000002445.2_ASM244v1.ncbiRefSeq.gtf.gz Anopheles gambiae 7165 GCF_943734735.2 True Chromosome 3.0 264451381 190 99149756 2 54.0x 44.5 Full annotation GCA_943734735.2 https://genome.ucsc.edu/h/GCF_943734735.2 GCA_943734735.2 GCF_943734735.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/943/734/735/GCF_943734735.2/genes/GCF_943734735.2_idAnoGambNW_F1_1.ncbiRefSeq.gtf.gz Plasmodium vivax 5855 GCF_000002415.2 True Chromosome 14.0 27007701 2747 1678596 6 42.5 Full annotation GCA_000002415.2 https://genome.ucsc.edu/h/GCF_000002415.2 GCA_000002415.2 GCF_000002415.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/415/GCF_000002415.2/genes/GCF_000002415.2_ASM241v2.ncbiRefSeq.gtf.gz -Culex pipiens pallens 42434 GCF_016801865.2 True Chromosome 3.0 566339288 289 186194774 2 250.0x 37.0 Full annotation GCA_016801865.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/016/801/865/GCF_016801865.2/genes/GCF_016801865.2_TS_CPP_V2.ncbiRefSeq.gtf.gz -Leishmania braziliensis MHOM/BR/75/M2904 420245 GCF_000002845.2 True Chromosome 35.0 32068771 138 992961 11 58.0 GCA_000002845.2 https://genome.ucsc.edu/h/GCF_000002845.2 GCA_000002845.2 GCF_000002845.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/845/GCF_000002845.2/genes/GCF_000002845.2_ASM284v2.ncbiRefSeq.gtf.gz -Trypanosoma cruzi 5693 GCF_000209065.1 True Scaffold 89937456 29495 88624 212 51.5 Full annotation GCA_000209065.1 https://genome.ucsc.edu/h/GCF_000209065.1 GCA_000209065.1 GCF_000209065.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/209/065/GCF_000209065.1/genes/GCF_000209065.1_ASM20906v1.ncbiRefSeq.gtf.gz -Coccidioides immitis RS 246410 GCF_000149335.2 True Scaffold 28947925 6 4323945 3 46.0 Full annotation GCA_000149335.2 https://genome.ucsc.edu/h/GCF_000149335.2 GCA_000149335.2 GCF_000149335.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/149/335/GCF_000149335.2/genes/GCF_000149335.2_ASM14933v2.ncbiRefSeq.gtf.gz -Mycobacterium tuberculosis H37Rv 83332 GCF_000277735.2 False Complete Genome 1.0 4411709 1 4411709 1 65.5 GCA_000277735.2 -Severe acute respiratory syndrome coronavirus 2 2697049 GCF_009858895.2 False Complete Genome 1.0 29903 1 29903 1 38.0 GCA_009858895.3 -Monkeypox virus 10244 GCF_000857045.1 False Complete Genome 1.0 196858 1 196858 1 33.0 GCA_000857045.1 +Culex pipiens pallens 42434 GCF_016801865.2 True Chromosome 3.0 566339288 289 186194774 2 250.0x 37.0 Full annotation GCA_016801865.2 https://genome.ucsc.edu/h/GCF_016801865.2 GCA_016801865.2 GCF_016801865.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/016/801/865/GCF_016801865.2/genes/GCF_016801865.2_TS_CPP_V2.ncbiRefSeq.gtf.gz +Leishmania braziliensis MHOM/BR/75/M2904 420245 GCF_000002845.2 True Chromosome 35.0 32068771 138 992961 11 58.0 Full annotation GCA_000002845.2 https://genome.ucsc.edu/h/GCF_000002845.2 GCA_000002845.2 GCF_000002845.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/845/GCF_000002845.2/genes/GCF_000002845.2_ASM284v2.ncbiRefSeq.gtf.gz +Trypanosoma cruzi 5693 GCF_000209065.1 True Scaffold 1.0 89937456 29495 88624 212 51.5 Full annotation GCA_000209065.1 https://genome.ucsc.edu/h/GCF_000209065.1 GCA_000209065.1 GCF_000209065.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/209/065/GCF_000209065.1/genes/GCF_000209065.1_ASM20906v1.ncbiRefSeq.gtf.gz +Coccidioides immitis RS 246410 GCF_000149335.2 True Scaffold 1.0 28947925 6 4323945 3 46.0 Full annotation GCA_000149335.2 https://genome.ucsc.edu/h/GCF_000149335.2 GCA_000149335.2 GCF_000149335.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/149/335/GCF_000149335.2/genes/GCF_000149335.2_ASM14933v2.ncbiRefSeq.gtf.gz +Mycobacterium tuberculosis H37Rv 83332 GCF_000277735.2 False Complete Genome 1.0 4411709 1 4411709 1 65.5 GCA_000277735.2 https://genome.ucsc.edu/h/GCF_000857045.1 GCA_000857045.1 GCF_000857045.1 +Severe acute respiratory syndrome coronavirus 2 2697049 GCF_009858895.2 False Complete Genome 1.0 29903 1 29903 1 20.0x 38.0 GCA_009858895.3 https://genome.ucsc.edu/h/GCF_009858895.2 GCA_009858895.3 GCF_009858895.2 +Monkeypox virus 10244 GCF_000857045.1 False Complete Genome 1.0 196858 1 196858 1 100.0x 33.0 GCA_000857045.1 https://genome.ucsc.edu/h/GCF_000857045.1 GCA_000857045.1 GCF_000857045.1 Mycobacterium tuberculosis 1773 GCF_030566675.1 False Complete Genome 1.0 4516435 1 4516435 1 20.0x 65.5 GCA_030566675.1 Mycobacterium tuberculosis 1773 GCF_963525475.1 False Complete Genome 1.0 4469156 1 4469156 1 100.0x 65.5 GCA_963525475.1 diff --git a/files/source/organisms-from-ncbi.tsv b/files/source/organisms-from-ncbi.tsv index 6686f92..499eae1 100644 --- a/files/source/organisms-from-ncbi.tsv +++ b/files/source/organisms-from-ncbi.tsv @@ -7,12 +7,12 @@ Leishmania braziliensis 5660 11 VEuPathDb Leishmania donovani 5661 12 VEuPathDb Leishmania major 5664 7 VEuPathDb Monkeypox virus 10244 6911 Virus -Mycobacterium tuberculosis 1773 7823 Bact +Mycobacterium tuberculosis 1773 7829 Bact Plasmodium falciparum 5833 67 VEuPathDb Plasmodium vinckei 5860 10 VEuPathDb Plasmodium vivax 5855 19 VEuPathDb Plasmodium yoelii 5861 15 VEuPathDb -Severe acute respiratory syndrome coronavirus 2 2697049 92 Virus +Severe acute respiratory syndrome coronavirus 2 2697049 12408 Virus Toxoplasma gondii 5811 29 VEuPathDb -Trypanosoma brucei 5691 5 VEuPathDb +Trypanosoma brucei 5691 6 VEuPathDb Trypanosoma cruzi 5693 44 VEuPathDb From 065c8413154701ea6b926f22666d7ed838a5dcf8 Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Thu, 5 Dec 2024 15:33:07 -0800 Subject: [PATCH 10/30] feat: build catalog (#177) --- files/out/genomes.json | 62 +++++++++++++++++++++++++++++++--------- files/out/organisms.json | 6 ++-- 2 files changed, 52 insertions(+), 16 deletions(-) diff --git a/files/out/genomes.json b/files/out/genomes.json index 474a330..d7bec9c 100644 --- a/files/out/genomes.json +++ b/files/out/genomes.json @@ -41,7 +41,7 @@ "accession": "GCF_000002725.2", "annotationStatus": "Full annotation", "chromosomes": 36, - "coverage": null, + "coverage": "100.0x", "gcPercent": 59.5, "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/725/GCF_000002725.2/genes/GCF_000002725.2_ASM272v2.ncbiRefSeq.gtf.gz", "isRef": "Yes", @@ -73,9 +73,27 @@ "taxon": "Plasmodium falciparum 3D7", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002765.5" }, + { + "accession": "GCF_000002765.6", + "annotationStatus": "Full annotation", + "chromosomes": 14, + "coverage": "100.0x", + "gcPercent": 19.5, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/765/GCF_000002765.6/genes/GCF_000002765.6_GCA_000002765.ncbiRefSeq.gtf.gz", + "isRef": "Yes", + "length": 23292622, + "level": "Complete Genome", + "ncbiTaxonomyId": "36329", + "scaffoldCount": 14, + "scaffoldL50": 5, + "scaffoldN50": 1687656, + "tags": [], + "taxon": "Plasmodium falciparum 3D7", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002765.6" + }, { "accession": "GCF_000002845.2", - "annotationStatus": null, + "annotationStatus": "Full annotation", "chromosomes": 35, "coverage": null, "gcPercent": 58, @@ -93,7 +111,7 @@ }, { "accession": "GCF_000006565.2", - "annotationStatus": null, + "annotationStatus": "Full annotation", "chromosomes": 14, "coverage": "26.5x", "gcPercent": 52.5, @@ -112,7 +130,7 @@ { "accession": "GCF_000149335.2", "annotationStatus": "Full annotation", - "chromosomes": null, + "chromosomes": 1, "coverage": null, "gcPercent": 46, "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/149/335/GCF_000149335.2/genes/GCF_000149335.2_ASM14933v2.ncbiRefSeq.gtf.gz", @@ -143,12 +161,12 @@ "scaffoldN50": 4411532, "tags": [], "taxon": "Mycobacterium tuberculosis H37Rv", - "ucscBrowserUrl": null + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000195955.2" }, { "accession": "GCF_000209065.1", "annotationStatus": "Full annotation", - "chromosomes": null, + "chromosomes": 1, "coverage": null, "gcPercent": 51.5, "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/209/065/GCF_000209065.1/genes/GCF_000209065.1_ASM20906v1.ncbiRefSeq.gtf.gz", @@ -201,13 +219,13 @@ "scaffoldN50": 4411709, "tags": [], "taxon": "Mycobacterium tuberculosis H37Rv", - "ucscBrowserUrl": null + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000857045.1" }, { "accession": "GCF_000857045.1", "annotationStatus": null, "chromosomes": 1, - "coverage": null, + "coverage": "100.0x", "gcPercent": 33, "geneModelUrl": null, "isRef": "No", @@ -221,13 +239,13 @@ "Virus" ], "taxon": "Monkeypox virus", - "ucscBrowserUrl": null + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000857045.1" }, { "accession": "GCF_009858895.2", "annotationStatus": null, "chromosomes": 1, - "coverage": null, + "coverage": "20.0x", "gcPercent": 38, "geneModelUrl": null, "isRef": "No", @@ -241,7 +259,7 @@ "Virus" ], "taxon": "Severe acute respiratory syndrome coronavirus 2", - "ucscBrowserUrl": null + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_009858895.2" }, { "accession": "GCF_016801865.2", @@ -259,7 +277,7 @@ "scaffoldN50": 186194774, "tags": [], "taxon": "Culex pipiens pallens", - "ucscBrowserUrl": null + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_016801865.2" }, { "accession": "GCF_018416015.2", @@ -279,6 +297,24 @@ "taxon": "Coccidioides posadasii str. Silveira", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_018416015.2" }, + { + "accession": "GCF_018416015.2", + "annotationStatus": "Full annotation", + "chromosomes": 9, + "coverage": "475.0x", + "gcPercent": 46.5, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/018/416/015/GCF_018416015.2/genes/GCF_018416015.2_ASM1841601v2.ncbiRefSeq.gtf.gz", + "isRef": "Yes", + "length": 28193268, + "level": "Complete Genome", + "ncbiTaxonomyId": "443226", + "scaffoldCount": 9, + "scaffoldL50": 2, + "scaffoldN50": 8079863, + "tags": [], + "taxon": "Coccidioides posadasii str. Silveira", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_018416015.2" + }, { "accession": "GCF_030566675.1", "annotationStatus": null, @@ -328,7 +364,7 @@ "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/900/681/995/GCF_900681995.1/genes/GCF_900681995.1_PVVCY_v1.ncbiRefSeq.gtf.gz", "isRef": "Yes", "length": 18338688, - "level": "Complete Genome", + "level": "Chromosome", "ncbiTaxonomyId": "54757", "scaffoldCount": 14, "scaffoldL50": 5, diff --git a/files/out/organisms.json b/files/out/organisms.json index 4ceb6ba..54db9de 100644 --- a/files/out/organisms.json +++ b/files/out/organisms.json @@ -8,7 +8,7 @@ "taxon": "Monkeypox virus" }, { - "assemblyCount": 7823, + "assemblyCount": 7829, "ncbiTaxonomyId": "1773", "tags": [ "Bact" @@ -24,7 +24,7 @@ "taxon": "Coccidioides posadasii" }, { - "assemblyCount": 92, + "assemblyCount": 12408, "ncbiTaxonomyId": "2697049", "tags": [ "Virus" @@ -62,7 +62,7 @@ "taxon": "Leishmania major" }, { - "assemblyCount": 5, + "assemblyCount": 6, "ncbiTaxonomyId": "5691", "tags": [ "VEuPathDb" From f29bad999b78d2cd9800b628b05a149509c0cfde Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Thu, 5 Dec 2024 23:11:05 -0800 Subject: [PATCH 11/30] feat: match only `accession` with both `genBank` and `refSeq` (#177) --- files/build-files-from-ncbi.py | 22 +++---------- files/out/genomes.json | 52 +++++------------------------- files/source/genomes-from-ncbi.tsv | 18 +++++------ 3 files changed, 20 insertions(+), 72 deletions(-) diff --git a/files/build-files-from-ncbi.py b/files/build-files-from-ncbi.py index 0c2c112..1b8da76 100644 --- a/files/build-files-from-ncbi.py +++ b/files/build-files-from-ncbi.py @@ -59,22 +59,6 @@ def get_genome_row(genome_info): def get_genomes_df(tax_ids): return pd.DataFrame(data=[get_genome_row(genome_info) for genome_info in requests.get(build_genomes_url(tax_ids)).json()["reports"]]) -def print_column_match_summary(from_df, in_df, from_column, in_column, important=True): - unmatched_values = from_df[from_column][~(from_df[from_column].isin(in_df[in_column]))] - message = ( - f"No values from {from_column} absent in {in_column}" if len(unmatched_values) == 0 - else f"{len(unmatched_values)} values from {from_column} absent in {in_column}: {", ".join(unmatched_values)}" - ) - if not important: - message = "(" + message + ")" - print(message) - -def print_accession_match_summaries(genomes_source_df, assemblies_df): - print_column_match_summary(genomes_source_df, assemblies_df, "pairedAccession", "genBank") - print_column_match_summary(genomes_source_df, assemblies_df, "pairedAccession", "refSeq", False) - print_column_match_summary(genomes_source_df, assemblies_df, "accession", "genBank", False) - print_column_match_summary(genomes_source_df, assemblies_df, "accession", "refSeq") - def _id_to_gene_model_url(asm_id): hubs_url = "https://hgdownload.soe.ucsc.edu/hubs/" components = [asm_id[0:3], asm_id[4:7], asm_id[7:10], asm_id[10:13], asm_id, "genes"] @@ -122,10 +106,12 @@ def build_files(): genomes_source_df = get_genomes_df(get_tax_ids(organisms_df)) assemblies_df = pd.DataFrame(requests.get(ASSEMBLIES_URL).json()["data"])[["ucscBrowser", "genBank", "refSeq"]] - gen_bank_merge_df = genomes_source_df.merge(assemblies_df, how="left", left_on="pairedAccession", right_on="genBank") + gen_bank_merge_df = genomes_source_df.merge(assemblies_df, how="left", left_on="accession", right_on="genBank") ref_seq_merge_df = genomes_source_df.merge(assemblies_df, how="left", left_on="accession", right_on="refSeq") - print_accession_match_summaries(genomes_source_df, assemblies_df) + unmatched_accessions = genomes_source_df["accession"][~(genomes_source_df["accession"].isin(assemblies_df["genBank"]) | genomes_source_df["accession"].isin(assemblies_df["refSeq"]))] + if len(unmatched_accessions) > 0: + print(f"{len(unmatched_accessions)} accessions had no match in assembly list: {", ".join(unmatched_accessions)}") genomes_df = add_gene_model_url(gen_bank_merge_df.combine_first(ref_seq_merge_df)) diff --git a/files/out/genomes.json b/files/out/genomes.json index d7bec9c..be5dfaf 100644 --- a/files/out/genomes.json +++ b/files/out/genomes.json @@ -41,7 +41,7 @@ "accession": "GCF_000002725.2", "annotationStatus": "Full annotation", "chromosomes": 36, - "coverage": "100.0x", + "coverage": null, "gcPercent": 59.5, "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/725/GCF_000002725.2/genes/GCF_000002725.2_ASM272v2.ncbiRefSeq.gtf.gz", "isRef": "Yes", @@ -55,24 +55,6 @@ "taxon": "Leishmania major strain Friedlin", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002725.2" }, - { - "accession": "GCF_000002765.6", - "annotationStatus": "Full annotation", - "chromosomes": 14, - "coverage": "100.0x", - "gcPercent": 19.5, - "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/765/GCF_000002765.6/genes/GCF_000002765.6_GCA_000002765.ncbiRefSeq.gtf.gz", - "isRef": "Yes", - "length": 23292622, - "level": "Complete Genome", - "ncbiTaxonomyId": "36329", - "scaffoldCount": 14, - "scaffoldL50": 5, - "scaffoldN50": 1687656, - "tags": [], - "taxon": "Plasmodium falciparum 3D7", - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002765.5" - }, { "accession": "GCF_000002765.6", "annotationStatus": "Full annotation", @@ -93,7 +75,7 @@ }, { "accession": "GCF_000002845.2", - "annotationStatus": "Full annotation", + "annotationStatus": null, "chromosomes": 35, "coverage": null, "gcPercent": 58, @@ -111,7 +93,7 @@ }, { "accession": "GCF_000006565.2", - "annotationStatus": "Full annotation", + "annotationStatus": null, "chromosomes": 14, "coverage": "26.5x", "gcPercent": 52.5, @@ -130,7 +112,7 @@ { "accession": "GCF_000149335.2", "annotationStatus": "Full annotation", - "chromosomes": 1, + "chromosomes": null, "coverage": null, "gcPercent": 46, "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/149/335/GCF_000149335.2/genes/GCF_000149335.2_ASM14933v2.ncbiRefSeq.gtf.gz", @@ -166,7 +148,7 @@ { "accession": "GCF_000209065.1", "annotationStatus": "Full annotation", - "chromosomes": 1, + "chromosomes": null, "coverage": null, "gcPercent": 51.5, "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/209/065/GCF_000209065.1/genes/GCF_000209065.1_ASM20906v1.ncbiRefSeq.gtf.gz", @@ -219,13 +201,13 @@ "scaffoldN50": 4411709, "tags": [], "taxon": "Mycobacterium tuberculosis H37Rv", - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000857045.1" + "ucscBrowserUrl": null }, { "accession": "GCF_000857045.1", "annotationStatus": null, "chromosomes": 1, - "coverage": "100.0x", + "coverage": null, "gcPercent": 33, "geneModelUrl": null, "isRef": "No", @@ -245,7 +227,7 @@ "accession": "GCF_009858895.2", "annotationStatus": null, "chromosomes": 1, - "coverage": "20.0x", + "coverage": null, "gcPercent": 38, "geneModelUrl": null, "isRef": "No", @@ -279,24 +261,6 @@ "taxon": "Culex pipiens pallens", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_016801865.2" }, - { - "accession": "GCF_018416015.2", - "annotationStatus": "Full annotation", - "chromosomes": 9, - "coverage": "475.0x", - "gcPercent": 46.5, - "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/018/416/015/GCF_018416015.2/genes/GCF_018416015.2_ASM1841601v2.ncbiRefSeq.gtf.gz", - "isRef": "Yes", - "length": 28193268, - "level": "Complete Genome", - "ncbiTaxonomyId": "443226", - "scaffoldCount": 9, - "scaffoldL50": 2, - "scaffoldN50": 8079863, - "tags": [], - "taxon": "Coccidioides posadasii str. Silveira", - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_018416015.2" - }, { "accession": "GCF_018416015.2", "annotationStatus": "Full annotation", diff --git a/files/source/genomes-from-ncbi.tsv b/files/source/genomes-from-ncbi.tsv index 24926e2..a0f918b 100644 --- a/files/source/genomes-from-ncbi.tsv +++ b/files/source/genomes-from-ncbi.tsv @@ -1,23 +1,21 @@ taxon taxonomyId accession isRef level chromosomeCount length scaffoldCount scaffoldN50 scaffoldL50 coverage gcPercent annotationStatus pairedAccession ucscBrowser genBank refSeq geneModelUrl Mycobacterium tuberculosis H37Rv 83332 GCF_000195955.2 True Complete Genome 1.0 4411532 1 4411532 1 65.5 GCA_000195955.2 https://genome.ucsc.edu/h/GCF_000195955.2 GCA_000195955.2 GCF_000195955.2 -Plasmodium falciparum 3D7 36329 GCF_000002765.6 True Complete Genome 14.0 23292622 14 1687656 5 100.0x 19.5 Full annotation GCA_000002765.3 https://genome.ucsc.edu/h/GCF_000002765.5 GCA_000002765.3 GCF_000002765.5 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/765/GCF_000002765.6/genes/GCF_000002765.6_GCA_000002765.ncbiRefSeq.gtf.gz Plasmodium falciparum 3D7 36329 GCF_000002765.6 True Complete Genome 14.0 23292622 14 1687656 5 100.0x 19.5 Full annotation GCA_000002765.3 https://genome.ucsc.edu/h/GCF_000002765.6 GCA_000002765.3 GCF_000002765.6 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/765/GCF_000002765.6/genes/GCF_000002765.6_GCA_000002765.ncbiRefSeq.gtf.gz -Leishmania major strain Friedlin 347515 GCF_000002725.2 True Complete Genome 36.0 32855089 36 1091540 11 100.0x 59.5 Full annotation GCA_000002725.2 https://genome.ucsc.edu/h/GCF_000002725.2 GCA_000002725.2 GCF_000002725.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/725/GCF_000002725.2/genes/GCF_000002725.2_ASM272v2.ncbiRefSeq.gtf.gz +Leishmania major strain Friedlin 347515 GCF_000002725.2 True Complete Genome 36.0 32855089 36 1091540 11 59.5 Full annotation GCA_000002725.2 https://genome.ucsc.edu/h/GCF_000002725.2 GCA_000002725.2 GCF_000002725.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/725/GCF_000002725.2/genes/GCF_000002725.2_ASM272v2.ncbiRefSeq.gtf.gz Plasmodium yoelii 5861 GCF_900002385.2 True Complete Genome 14.0 23043114 14 2046250 5 100.0x 21.5 Full annotation GCA_900002385.2 https://genome.ucsc.edu/h/GCF_900002385.2 GCA_900002385.2 GCF_900002385.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/900/002/385/GCF_900002385.2/genes/GCF_900002385.2_GCA_900002385.ncbiRefSeq.gtf.gz -Coccidioides posadasii str. Silveira 443226 GCF_018416015.2 True Complete Genome 9.0 28193268 9 8079863 2 475.0x 46.5 Full annotation GCA_018416015.2 https://genome.ucsc.edu/h/GCA_018416015.2 GCA_018416015.2 GCF_018416015.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/018/416/015/GCF_018416015.2/genes/GCF_018416015.2_ASM1841601v2.ncbiRefSeq.gtf.gz Coccidioides posadasii str. Silveira 443226 GCF_018416015.2 True Complete Genome 9.0 28193268 9 8079863 2 475.0x 46.5 Full annotation GCA_018416015.2 https://genome.ucsc.edu/h/GCF_018416015.2 GCA_018416015.2 GCF_018416015.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/018/416/015/GCF_018416015.2/genes/GCF_018416015.2_ASM1841601v2.ncbiRefSeq.gtf.gz Plasmodium vinckei vinckei 54757 GCF_900681995.1 True Chromosome 14.0 18338688 14 1692345 5 155.0x 23.0 Full annotation GCA_900681995.1 https://genome.ucsc.edu/h/GCF_900681995.1 GCA_900681995.1 GCF_900681995.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/900/681/995/GCF_900681995.1/genes/GCF_900681995.1_PVVCY_v1.ncbiRefSeq.gtf.gz Leishmania donovani 5661 GCF_000227135.1 True Chromosome 36.0 32444968 36 1024085 11 59.5 Full annotation GCA_000227135.2 https://genome.ucsc.edu/h/GCF_000227135.1 GCA_000227135.2 GCF_000227135.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/227/135/GCF_000227135.1/genes/GCF_000227135.1_ASM22713v2.ncbiRefSeq.gtf.gz -Toxoplasma gondii ME49 508771 GCF_000006565.2 True Chromosome 14.0 65633124 2276 4973582 6 26.5x 52.5 Full annotation GCA_000006565.2 https://genome.ucsc.edu/h/GCF_000006565.2 GCA_000006565.2 GCF_000006565.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/006/565/GCF_000006565.2/genes/GCF_000006565.2_TGA4.ncbiRefSeq.gtf.gz +Toxoplasma gondii ME49 508771 GCF_000006565.2 True Chromosome 14.0 65633124 2276 4973582 6 26.5x 52.5 GCA_000006565.2 https://genome.ucsc.edu/h/GCF_000006565.2 GCA_000006565.2 GCF_000006565.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/006/565/GCF_000006565.2/genes/GCF_000006565.2_TGA4.ncbiRefSeq.gtf.gz Trypanosoma brucei brucei TREU927 185431 GCF_000002445.2 True Chromosome 11.0 26075494 12 2481190 4 46.5 Full annotation GCA_000002445.1 https://genome.ucsc.edu/h/GCF_000002445.2 GCA_000002445.1 GCF_000002445.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/445/GCF_000002445.2/genes/GCF_000002445.2_ASM244v1.ncbiRefSeq.gtf.gz Anopheles gambiae 7165 GCF_943734735.2 True Chromosome 3.0 264451381 190 99149756 2 54.0x 44.5 Full annotation GCA_943734735.2 https://genome.ucsc.edu/h/GCF_943734735.2 GCA_943734735.2 GCF_943734735.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/943/734/735/GCF_943734735.2/genes/GCF_943734735.2_idAnoGambNW_F1_1.ncbiRefSeq.gtf.gz Plasmodium vivax 5855 GCF_000002415.2 True Chromosome 14.0 27007701 2747 1678596 6 42.5 Full annotation GCA_000002415.2 https://genome.ucsc.edu/h/GCF_000002415.2 GCA_000002415.2 GCF_000002415.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/415/GCF_000002415.2/genes/GCF_000002415.2_ASM241v2.ncbiRefSeq.gtf.gz Culex pipiens pallens 42434 GCF_016801865.2 True Chromosome 3.0 566339288 289 186194774 2 250.0x 37.0 Full annotation GCA_016801865.2 https://genome.ucsc.edu/h/GCF_016801865.2 GCA_016801865.2 GCF_016801865.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/016/801/865/GCF_016801865.2/genes/GCF_016801865.2_TS_CPP_V2.ncbiRefSeq.gtf.gz -Leishmania braziliensis MHOM/BR/75/M2904 420245 GCF_000002845.2 True Chromosome 35.0 32068771 138 992961 11 58.0 Full annotation GCA_000002845.2 https://genome.ucsc.edu/h/GCF_000002845.2 GCA_000002845.2 GCF_000002845.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/845/GCF_000002845.2/genes/GCF_000002845.2_ASM284v2.ncbiRefSeq.gtf.gz -Trypanosoma cruzi 5693 GCF_000209065.1 True Scaffold 1.0 89937456 29495 88624 212 51.5 Full annotation GCA_000209065.1 https://genome.ucsc.edu/h/GCF_000209065.1 GCA_000209065.1 GCF_000209065.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/209/065/GCF_000209065.1/genes/GCF_000209065.1_ASM20906v1.ncbiRefSeq.gtf.gz -Coccidioides immitis RS 246410 GCF_000149335.2 True Scaffold 1.0 28947925 6 4323945 3 46.0 Full annotation GCA_000149335.2 https://genome.ucsc.edu/h/GCF_000149335.2 GCA_000149335.2 GCF_000149335.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/149/335/GCF_000149335.2/genes/GCF_000149335.2_ASM14933v2.ncbiRefSeq.gtf.gz -Mycobacterium tuberculosis H37Rv 83332 GCF_000277735.2 False Complete Genome 1.0 4411709 1 4411709 1 65.5 GCA_000277735.2 https://genome.ucsc.edu/h/GCF_000857045.1 GCA_000857045.1 GCF_000857045.1 -Severe acute respiratory syndrome coronavirus 2 2697049 GCF_009858895.2 False Complete Genome 1.0 29903 1 29903 1 20.0x 38.0 GCA_009858895.3 https://genome.ucsc.edu/h/GCF_009858895.2 GCA_009858895.3 GCF_009858895.2 -Monkeypox virus 10244 GCF_000857045.1 False Complete Genome 1.0 196858 1 196858 1 100.0x 33.0 GCA_000857045.1 https://genome.ucsc.edu/h/GCF_000857045.1 GCA_000857045.1 GCF_000857045.1 +Leishmania braziliensis MHOM/BR/75/M2904 420245 GCF_000002845.2 True Chromosome 35.0 32068771 138 992961 11 58.0 GCA_000002845.2 https://genome.ucsc.edu/h/GCF_000002845.2 GCA_000002845.2 GCF_000002845.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/845/GCF_000002845.2/genes/GCF_000002845.2_ASM284v2.ncbiRefSeq.gtf.gz +Trypanosoma cruzi 5693 GCF_000209065.1 True Scaffold 89937456 29495 88624 212 51.5 Full annotation GCA_000209065.1 https://genome.ucsc.edu/h/GCF_000209065.1 GCA_000209065.1 GCF_000209065.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/209/065/GCF_000209065.1/genes/GCF_000209065.1_ASM20906v1.ncbiRefSeq.gtf.gz +Coccidioides immitis RS 246410 GCF_000149335.2 True Scaffold 28947925 6 4323945 3 46.0 Full annotation GCA_000149335.2 https://genome.ucsc.edu/h/GCF_000149335.2 GCA_000149335.2 GCF_000149335.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/149/335/GCF_000149335.2/genes/GCF_000149335.2_ASM14933v2.ncbiRefSeq.gtf.gz +Mycobacterium tuberculosis H37Rv 83332 GCF_000277735.2 False Complete Genome 1.0 4411709 1 4411709 1 65.5 GCA_000277735.2 +Severe acute respiratory syndrome coronavirus 2 2697049 GCF_009858895.2 False Complete Genome 1.0 29903 1 29903 1 38.0 GCA_009858895.3 https://genome.ucsc.edu/h/GCF_009858895.2 GCA_009858895.3 GCF_009858895.2 +Monkeypox virus 10244 GCF_000857045.1 False Complete Genome 1.0 196858 1 196858 1 33.0 GCA_000857045.1 https://genome.ucsc.edu/h/GCF_000857045.1 GCA_000857045.1 GCF_000857045.1 Mycobacterium tuberculosis 1773 GCF_030566675.1 False Complete Genome 1.0 4516435 1 4516435 1 20.0x 65.5 GCA_030566675.1 Mycobacterium tuberculosis 1773 GCF_963525475.1 False Complete Genome 1.0 4469156 1 4469156 1 100.0x 65.5 GCA_963525475.1 From b749959e3ee88a36ff6dd262027a44be1d0ac65c Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Fri, 6 Dec 2024 15:08:39 -0800 Subject: [PATCH 12/30] fix: "is ref" filter labels (#177) --- site-config/brc-analytics/local/index/genomeEntityConfig.ts | 4 ---- 1 file changed, 4 deletions(-) diff --git a/site-config/brc-analytics/local/index/genomeEntityConfig.ts b/site-config/brc-analytics/local/index/genomeEntityConfig.ts index f7ab369..de0f495 100644 --- a/site-config/brc-analytics/local/index/genomeEntityConfig.ts +++ b/site-config/brc-analytics/local/index/genomeEntityConfig.ts @@ -44,10 +44,6 @@ export const genomeEntityConfig: BRCEntityConfig = { { key: BRC_DATA_CATALOG_CATEGORY_KEY.IS_REF, label: BRC_DATA_CATALOG_CATEGORY_LABEL.IS_REF, - mapSelectCategoryValue: (value) => ({ - ...value, - label: value.label ? "Yes" : "No", - }), }, { key: BRC_DATA_CATALOG_CATEGORY_KEY.LEVEL, From 9da90212e4e909e5a52930d3c4c86246dfd94a68 Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Tue, 10 Dec 2024 23:49:29 -0800 Subject: [PATCH 13/30] chore: build catalog (#177) --- files/build-files-from-ncbi.py | 2 +- files/out/genomes.json | 158 +++++++++++++-------------- files/out/organisms.json | 56 +++++++--- files/source/genomes-from-ncbi.tsv | 10 +- files/source/organisms-from-ncbi.tsv | 30 ++--- 5 files changed, 139 insertions(+), 117 deletions(-) diff --git a/files/build-files-from-ncbi.py b/files/build-files-from-ncbi.py index 1b8da76..3cb9562 100644 --- a/files/build-files-from-ncbi.py +++ b/files/build-files-from-ncbi.py @@ -95,7 +95,7 @@ def build_files(): taxa_df = pd.read_csv(TAXA_URL, keep_default_na=False) - organisms_source_df = get_organisms_df([taxon for taxon in taxa_df["Name"] if taxon]) + organisms_source_df = get_organisms_df([taxon.strip() for taxon in taxa_df["Name"] if taxon]) organisms_df = organisms_source_df.merge(taxa_df[["TaxId", "CustomTags"]], how="left", left_on="taxonomyId", right_on="TaxId").drop(columns=["TaxId"]) diff --git a/files/out/genomes.json b/files/out/genomes.json index be5dfaf..e8ab3b0 100644 --- a/files/out/genomes.json +++ b/files/out/genomes.json @@ -14,7 +14,7 @@ "scaffoldL50": 6, "scaffoldN50": 1678596, "tags": [ - "VEuPathDb" + "VEuPathDB" ], "taxon": "Plasmodium vivax", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002415.2" @@ -37,6 +37,24 @@ "taxon": "Trypanosoma brucei brucei TREU927", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002445.2" }, + { + "accession": "GCF_000002655.1", + "annotationStatus": "Full annotation", + "chromosomes": 8, + "coverage": null, + "gcPercent": 50, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/655/GCF_000002655.1/genes/GCF_000002655.1_ASM265v1.ncbiRefSeq.gtf.gz", + "isRef": "Yes", + "length": 29384958, + "level": "Chromosome", + "ncbiTaxonomyId": "330879", + "scaffoldCount": 8, + "scaffoldL50": 4, + "scaffoldN50": 3948441, + "tags": [], + "taxon": "Aspergillus fumigatus Af293", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002655.1" + }, { "accession": "GCF_000002725.2", "annotationStatus": "Full annotation", @@ -109,6 +127,24 @@ "taxon": "Toxoplasma gondii ME49", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000006565.2" }, + { + "accession": "GCF_000091045.1", + "annotationStatus": "Full annotation", + "chromosomes": 14, + "coverage": null, + "gcPercent": 48.5, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/091/045/GCF_000091045.1/genes/GCF_000091045.1_ASM9104v1.ncbiRefSeq.gtf.gz", + "isRef": "Yes", + "length": 19051922, + "level": "Chromosome", + "ncbiTaxonomyId": "214684", + "scaffoldCount": 14, + "scaffoldL50": 6, + "scaffoldN50": 1438950, + "tags": [], + "taxon": "Cryptococcus neoformans var. neoformans JEC21", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000091045.1" + }, { "accession": "GCF_000149335.2", "annotationStatus": "Full annotation", @@ -127,6 +163,24 @@ "taxon": "Coccidioides immitis RS", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000149335.2" }, + { + "accession": "GCF_000182965.3", + "annotationStatus": "Full annotation", + "chromosomes": 8, + "coverage": "700.0x", + "gcPercent": 33.5, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/182/965/GCF_000182965.3/genes/GCF_000182965.3_ASM18296v3.ncbiRefSeq.gtf.gz", + "isRef": "Yes", + "length": 14282666, + "level": "Chromosome", + "ncbiTaxonomyId": "237561", + "scaffoldCount": 8, + "scaffoldL50": 3, + "scaffoldN50": 2231883, + "tags": [], + "taxon": "Candida albicans SC5314", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000182965.3" + }, { "accession": "GCF_000195955.2", "annotationStatus": null, @@ -160,7 +214,7 @@ "scaffoldL50": 212, "scaffoldN50": 88624, "tags": [ - "VEuPathDb" + "VEuPathDB" ], "taxon": "Trypanosoma cruzi", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000209065.1" @@ -180,7 +234,7 @@ "scaffoldL50": 11, "scaffoldN50": 1024085, "tags": [ - "VEuPathDb" + "VEuPathDB" ], "taxon": "Leishmania donovani", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000227135.1" @@ -201,47 +255,27 @@ "scaffoldN50": 4411709, "tags": [], "taxon": "Mycobacterium tuberculosis H37Rv", - "ucscBrowserUrl": null + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000277735.2" }, { - "accession": "GCF_000857045.1", - "annotationStatus": null, - "chromosomes": 1, - "coverage": null, - "gcPercent": 33, - "geneModelUrl": null, - "isRef": "No", - "length": 196858, - "level": "Complete Genome", - "ncbiTaxonomyId": "10244", - "scaffoldCount": 1, - "scaffoldL50": 1, - "scaffoldN50": 196858, - "tags": [ - "Virus" - ], - "taxon": "Monkeypox virus", - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000857045.1" - }, - { - "accession": "GCF_009858895.2", - "annotationStatus": null, - "chromosomes": 1, - "coverage": null, - "gcPercent": 38, - "geneModelUrl": null, - "isRef": "No", - "length": 29903, - "level": "Complete Genome", - "ncbiTaxonomyId": "2697049", - "scaffoldCount": 1, - "scaffoldL50": 1, - "scaffoldN50": 29903, + "accession": "GCF_015732765.1", + "annotationStatus": "Full annotation", + "chromosomes": 3, + "coverage": "76.0x", + "gcPercent": 37, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/015/732/765/GCF_015732765.1/genes/GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal.ncbiRefSeq.gtf.gz", + "isRef": "Yes", + "length": 573214445, + "level": "Chromosome", + "ncbiTaxonomyId": "7176", + "scaffoldCount": 56, + "scaffoldL50": 2, + "scaffoldN50": 201550677, "tags": [ - "Virus" + "VEuPathDB" ], - "taxon": "Severe acute respiratory syndrome coronavirus 2", - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_009858895.2" + "taxon": "Culex quinquefasciatus", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_015732765.1" }, { "accession": "GCF_016801865.2", @@ -279,26 +313,6 @@ "taxon": "Coccidioides posadasii str. Silveira", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_018416015.2" }, - { - "accession": "GCF_030566675.1", - "annotationStatus": null, - "chromosomes": 1, - "coverage": "20.0x", - "gcPercent": 65.5, - "geneModelUrl": null, - "isRef": "No", - "length": 4516435, - "level": "Complete Genome", - "ncbiTaxonomyId": "1773", - "scaffoldCount": 1, - "scaffoldL50": 1, - "scaffoldN50": 4516435, - "tags": [ - "Bact" - ], - "taxon": "Mycobacterium tuberculosis", - "ucscBrowserUrl": null - }, { "accession": "GCF_900002385.2", "annotationStatus": "Full annotation", @@ -314,7 +328,7 @@ "scaffoldL50": 5, "scaffoldN50": 2046250, "tags": [ - "VEuPathDb" + "VEuPathDB" ], "taxon": "Plasmodium yoelii", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_900002385.2" @@ -352,29 +366,9 @@ "scaffoldL50": 2, "scaffoldN50": 99149756, "tags": [ - "VEuPathDb" + "VEuPathDB" ], "taxon": "Anopheles gambiae", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943734735.2" - }, - { - "accession": "GCF_963525475.1", - "annotationStatus": null, - "chromosomes": 1, - "coverage": "100.0x", - "gcPercent": 65.5, - "geneModelUrl": null, - "isRef": "No", - "length": 4469156, - "level": "Complete Genome", - "ncbiTaxonomyId": "1773", - "scaffoldCount": 1, - "scaffoldL50": 1, - "scaffoldN50": 4469156, - "tags": [ - "Bact" - ], - "taxon": "Mycobacterium tuberculosis", - "ucscBrowserUrl": null } ] diff --git a/files/out/organisms.json b/files/out/organisms.json index 54db9de..1bf4697 100644 --- a/files/out/organisms.json +++ b/files/out/organisms.json @@ -19,7 +19,7 @@ "assemblyCount": 13, "ncbiTaxonomyId": "199306", "tags": [ - "VEuPathDb" + "VEuPathDB" ], "taxon": "Coccidioides posadasii" }, @@ -31,6 +31,24 @@ ], "taxon": "Severe acute respiratory syndrome coronavirus 2" }, + { + "assemblyCount": 1, + "ncbiTaxonomyId": "42434", + "tags": [], + "taxon": "Culex pipiens pallens" + }, + { + "assemblyCount": 183, + "ncbiTaxonomyId": "5207", + "tags": [], + "taxon": "Cryptococcus neoformans" + }, + { + "assemblyCount": 117, + "ncbiTaxonomyId": "5476", + "tags": [], + "taxon": "Candida albicans" + }, { "assemblyCount": 5, "ncbiTaxonomyId": "5501", @@ -41,7 +59,7 @@ "assemblyCount": 11, "ncbiTaxonomyId": "5660", "tags": [ - "VEuPathDb" + "VEuPathDB" ], "taxon": "Leishmania braziliensis" }, @@ -49,7 +67,7 @@ "assemblyCount": 12, "ncbiTaxonomyId": "5661", "tags": [ - "VEuPathDb" + "VEuPathDB" ], "taxon": "Leishmania donovani" }, @@ -57,7 +75,7 @@ "assemblyCount": 7, "ncbiTaxonomyId": "5664", "tags": [ - "VEuPathDb" + "VEuPathDB" ], "taxon": "Leishmania major" }, @@ -65,7 +83,7 @@ "assemblyCount": 6, "ncbiTaxonomyId": "5691", "tags": [ - "VEuPathDb" + "VEuPathDB" ], "taxon": "Trypanosoma brucei" }, @@ -73,7 +91,7 @@ "assemblyCount": 44, "ncbiTaxonomyId": "5693", "tags": [ - "VEuPathDb" + "VEuPathDB" ], "taxon": "Trypanosoma cruzi" }, @@ -81,7 +99,7 @@ "assemblyCount": 29, "ncbiTaxonomyId": "5811", "tags": [ - "VEuPathDb" + "VEuPathDB" ], "taxon": "Toxoplasma gondii" }, @@ -89,7 +107,7 @@ "assemblyCount": 67, "ncbiTaxonomyId": "5833", "tags": [ - "VEuPathDb" + "VEuPathDB" ], "taxon": "Plasmodium falciparum" }, @@ -97,7 +115,7 @@ "assemblyCount": 19, "ncbiTaxonomyId": "5855", "tags": [ - "VEuPathDb" + "VEuPathDB" ], "taxon": "Plasmodium vivax" }, @@ -105,7 +123,7 @@ "assemblyCount": 10, "ncbiTaxonomyId": "5860", "tags": [ - "VEuPathDb" + "VEuPathDB" ], "taxon": "Plasmodium vinckei" }, @@ -113,7 +131,7 @@ "assemblyCount": 15, "ncbiTaxonomyId": "5861", "tags": [ - "VEuPathDb" + "VEuPathDB" ], "taxon": "Plasmodium yoelii" }, @@ -121,16 +139,22 @@ "assemblyCount": 7, "ncbiTaxonomyId": "7165", "tags": [ - "VEuPathDb" + "VEuPathDB" ], "taxon": "Anopheles gambiae" }, { - "assemblyCount": 5, - "ncbiTaxonomyId": "7175", + "assemblyCount": 3, + "ncbiTaxonomyId": "7176", "tags": [ - "VEuPathDb" + "VEuPathDB" ], - "taxon": "Culex pipiens" + "taxon": "Culex quinquefasciatus" + }, + { + "assemblyCount": 352, + "ncbiTaxonomyId": "746128", + "tags": [], + "taxon": "Aspergillus fumigatus" } ] diff --git a/files/source/genomes-from-ncbi.tsv b/files/source/genomes-from-ncbi.tsv index a0f918b..468f878 100644 --- a/files/source/genomes-from-ncbi.tsv +++ b/files/source/genomes-from-ncbi.tsv @@ -5,17 +5,17 @@ Leishmania major strain Friedlin 347515 GCF_000002725.2 True Complete Genome 36. Plasmodium yoelii 5861 GCF_900002385.2 True Complete Genome 14.0 23043114 14 2046250 5 100.0x 21.5 Full annotation GCA_900002385.2 https://genome.ucsc.edu/h/GCF_900002385.2 GCA_900002385.2 GCF_900002385.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/900/002/385/GCF_900002385.2/genes/GCF_900002385.2_GCA_900002385.ncbiRefSeq.gtf.gz Coccidioides posadasii str. Silveira 443226 GCF_018416015.2 True Complete Genome 9.0 28193268 9 8079863 2 475.0x 46.5 Full annotation GCA_018416015.2 https://genome.ucsc.edu/h/GCF_018416015.2 GCA_018416015.2 GCF_018416015.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/018/416/015/GCF_018416015.2/genes/GCF_018416015.2_ASM1841601v2.ncbiRefSeq.gtf.gz Plasmodium vinckei vinckei 54757 GCF_900681995.1 True Chromosome 14.0 18338688 14 1692345 5 155.0x 23.0 Full annotation GCA_900681995.1 https://genome.ucsc.edu/h/GCF_900681995.1 GCA_900681995.1 GCF_900681995.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/900/681/995/GCF_900681995.1/genes/GCF_900681995.1_PVVCY_v1.ncbiRefSeq.gtf.gz +Candida albicans SC5314 237561 GCF_000182965.3 True Chromosome 8.0 14282666 8 2231883 3 700.0x 33.5 Full annotation GCA_000182965.3 https://genome.ucsc.edu/h/GCF_000182965.3 GCA_000182965.3 GCF_000182965.3 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/182/965/GCF_000182965.3/genes/GCF_000182965.3_ASM18296v3.ncbiRefSeq.gtf.gz +Cryptococcus neoformans var. neoformans JEC21 214684 GCF_000091045.1 True Chromosome 14.0 19051922 14 1438950 6 48.5 Full annotation GCA_000091045.1 https://genome.ucsc.edu/h/GCF_000091045.1 GCA_000091045.1 GCF_000091045.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/091/045/GCF_000091045.1/genes/GCF_000091045.1_ASM9104v1.ncbiRefSeq.gtf.gz Leishmania donovani 5661 GCF_000227135.1 True Chromosome 36.0 32444968 36 1024085 11 59.5 Full annotation GCA_000227135.2 https://genome.ucsc.edu/h/GCF_000227135.1 GCA_000227135.2 GCF_000227135.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/227/135/GCF_000227135.1/genes/GCF_000227135.1_ASM22713v2.ncbiRefSeq.gtf.gz +Aspergillus fumigatus Af293 330879 GCF_000002655.1 True Chromosome 8.0 29384958 8 3948441 4 50.0 Full annotation GCA_000002655.1 https://genome.ucsc.edu/h/GCF_000002655.1 GCA_000002655.1 GCF_000002655.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/655/GCF_000002655.1/genes/GCF_000002655.1_ASM265v1.ncbiRefSeq.gtf.gz Toxoplasma gondii ME49 508771 GCF_000006565.2 True Chromosome 14.0 65633124 2276 4973582 6 26.5x 52.5 GCA_000006565.2 https://genome.ucsc.edu/h/GCF_000006565.2 GCA_000006565.2 GCF_000006565.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/006/565/GCF_000006565.2/genes/GCF_000006565.2_TGA4.ncbiRefSeq.gtf.gz Trypanosoma brucei brucei TREU927 185431 GCF_000002445.2 True Chromosome 11.0 26075494 12 2481190 4 46.5 Full annotation GCA_000002445.1 https://genome.ucsc.edu/h/GCF_000002445.2 GCA_000002445.1 GCF_000002445.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/445/GCF_000002445.2/genes/GCF_000002445.2_ASM244v1.ncbiRefSeq.gtf.gz Anopheles gambiae 7165 GCF_943734735.2 True Chromosome 3.0 264451381 190 99149756 2 54.0x 44.5 Full annotation GCA_943734735.2 https://genome.ucsc.edu/h/GCF_943734735.2 GCA_943734735.2 GCF_943734735.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/943/734/735/GCF_943734735.2/genes/GCF_943734735.2_idAnoGambNW_F1_1.ncbiRefSeq.gtf.gz Plasmodium vivax 5855 GCF_000002415.2 True Chromosome 14.0 27007701 2747 1678596 6 42.5 Full annotation GCA_000002415.2 https://genome.ucsc.edu/h/GCF_000002415.2 GCA_000002415.2 GCF_000002415.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/415/GCF_000002415.2/genes/GCF_000002415.2_ASM241v2.ncbiRefSeq.gtf.gz +Culex quinquefasciatus 7176 GCF_015732765.1 True Chromosome 3.0 573214445 56 201550677 2 76.0x 37.0 Full annotation GCA_015732765.1 https://genome.ucsc.edu/h/GCF_015732765.1 GCA_015732765.1 GCF_015732765.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/015/732/765/GCF_015732765.1/genes/GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal.ncbiRefSeq.gtf.gz Culex pipiens pallens 42434 GCF_016801865.2 True Chromosome 3.0 566339288 289 186194774 2 250.0x 37.0 Full annotation GCA_016801865.2 https://genome.ucsc.edu/h/GCF_016801865.2 GCA_016801865.2 GCF_016801865.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/016/801/865/GCF_016801865.2/genes/GCF_016801865.2_TS_CPP_V2.ncbiRefSeq.gtf.gz Leishmania braziliensis MHOM/BR/75/M2904 420245 GCF_000002845.2 True Chromosome 35.0 32068771 138 992961 11 58.0 GCA_000002845.2 https://genome.ucsc.edu/h/GCF_000002845.2 GCA_000002845.2 GCF_000002845.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/845/GCF_000002845.2/genes/GCF_000002845.2_ASM284v2.ncbiRefSeq.gtf.gz Trypanosoma cruzi 5693 GCF_000209065.1 True Scaffold 89937456 29495 88624 212 51.5 Full annotation GCA_000209065.1 https://genome.ucsc.edu/h/GCF_000209065.1 GCA_000209065.1 GCF_000209065.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/209/065/GCF_000209065.1/genes/GCF_000209065.1_ASM20906v1.ncbiRefSeq.gtf.gz Coccidioides immitis RS 246410 GCF_000149335.2 True Scaffold 28947925 6 4323945 3 46.0 Full annotation GCA_000149335.2 https://genome.ucsc.edu/h/GCF_000149335.2 GCA_000149335.2 GCF_000149335.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/149/335/GCF_000149335.2/genes/GCF_000149335.2_ASM14933v2.ncbiRefSeq.gtf.gz -Mycobacterium tuberculosis H37Rv 83332 GCF_000277735.2 False Complete Genome 1.0 4411709 1 4411709 1 65.5 GCA_000277735.2 -Severe acute respiratory syndrome coronavirus 2 2697049 GCF_009858895.2 False Complete Genome 1.0 29903 1 29903 1 38.0 GCA_009858895.3 https://genome.ucsc.edu/h/GCF_009858895.2 GCA_009858895.3 GCF_009858895.2 -Monkeypox virus 10244 GCF_000857045.1 False Complete Genome 1.0 196858 1 196858 1 33.0 GCA_000857045.1 https://genome.ucsc.edu/h/GCF_000857045.1 GCA_000857045.1 GCF_000857045.1 -Mycobacterium tuberculosis 1773 GCF_030566675.1 False Complete Genome 1.0 4516435 1 4516435 1 20.0x 65.5 GCA_030566675.1 -Mycobacterium tuberculosis 1773 GCF_963525475.1 False Complete Genome 1.0 4469156 1 4469156 1 100.0x 65.5 GCA_963525475.1 +Mycobacterium tuberculosis H37Rv 83332 GCF_000277735.2 False Complete Genome 1.0 4411709 1 4411709 1 65.5 GCA_000277735.2 https://genome.ucsc.edu/h/GCF_000277735.2 GCA_000277735.2 GCF_000277735.2 diff --git a/files/source/organisms-from-ncbi.tsv b/files/source/organisms-from-ncbi.tsv index 499eae1..eb42060 100644 --- a/files/source/organisms-from-ncbi.tsv +++ b/files/source/organisms-from-ncbi.tsv @@ -1,18 +1,22 @@ taxon taxonomyId assemblyCount CustomTags -Anopheles gambiae 7165 7 VEuPathDb +Anopheles gambiae 7165 7 VEuPathDB +Aspergillus fumigatus 746128 352 +Candida albicans 5476 117 Coccidioides immitis 5501 5 -Coccidioides posadasii 199306 13 VEuPathDb -Culex pipiens 7175 5 VEuPathDb -Leishmania braziliensis 5660 11 VEuPathDb -Leishmania donovani 5661 12 VEuPathDb -Leishmania major 5664 7 VEuPathDb +Coccidioides posadasii 199306 13 VEuPathDB +Cryptococcus neoformans 5207 183 +Culex pipiens pallens 42434 1 +Culex quinquefasciatus 7176 3 VEuPathDB +Leishmania braziliensis 5660 11 VEuPathDB +Leishmania donovani 5661 12 VEuPathDB +Leishmania major 5664 7 VEuPathDB Monkeypox virus 10244 6911 Virus Mycobacterium tuberculosis 1773 7829 Bact -Plasmodium falciparum 5833 67 VEuPathDb -Plasmodium vinckei 5860 10 VEuPathDb -Plasmodium vivax 5855 19 VEuPathDb -Plasmodium yoelii 5861 15 VEuPathDb +Plasmodium falciparum 5833 67 VEuPathDB +Plasmodium vinckei 5860 10 VEuPathDB +Plasmodium vivax 5855 19 VEuPathDB +Plasmodium yoelii 5861 15 VEuPathDB Severe acute respiratory syndrome coronavirus 2 2697049 12408 Virus -Toxoplasma gondii 5811 29 VEuPathDb -Trypanosoma brucei 5691 6 VEuPathDb -Trypanosoma cruzi 5693 44 VEuPathDb +Toxoplasma gondii 5811 29 VEuPathDB +Trypanosoma brucei 5691 6 VEuPathDB +Trypanosoma cruzi 5693 44 VEuPathDB From 9aa5874811f6e5fbcce745bd790e06ccf7c11857 Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Wed, 11 Dec 2024 22:32:58 -0800 Subject: [PATCH 14/30] feat: make genome taxa the same as organism taxa and add strain field (#177) --- .../brc-analytics-catalog/common/entities.ts | 1 + files/build-catalog.ts | 1 + files/build-files-from-ncbi.py | 26 ++-- files/entities.ts | 1 + files/out/genomes.json | 115 +++++++++++++----- files/source/genomes-from-ncbi.tsv | 43 +++---- files/source/organisms-from-ncbi.tsv | 44 +++---- 7 files changed, 150 insertions(+), 81 deletions(-) diff --git a/app/apis/catalog/brc-analytics-catalog/common/entities.ts b/app/apis/catalog/brc-analytics-catalog/common/entities.ts index 1998a66..fb529c2 100644 --- a/app/apis/catalog/brc-analytics-catalog/common/entities.ts +++ b/app/apis/catalog/brc-analytics-catalog/common/entities.ts @@ -23,6 +23,7 @@ export interface BRCDataCatalogGenome { scaffoldCount: number; scaffoldL50: number; scaffoldN50: number; + strain: string | null; tags: string[]; taxon: string; ucscBrowserUrl: string | null; diff --git a/files/build-catalog.ts b/files/build-catalog.ts index ee6029e..e3f7b88 100644 --- a/files/build-catalog.ts +++ b/files/build-catalog.ts @@ -65,6 +65,7 @@ async function buildGenomes( scaffoldCount: parseNumber(row.scaffoldCount), scaffoldL50: parseNumber(row.scaffoldL50), scaffoldN50: parseNumber(row.scaffoldN50), + strain: parseStringOrNull(row.strain), tags: organismsByTaxon.get(row.taxon)?.tags ?? [], taxon: row.taxon, ucscBrowserUrl: parseStringOrNull(row.ucscBrowser), diff --git a/files/build-files-from-ncbi.py b/files/build-files-from-ncbi.py index 3cb9562..190f188 100644 --- a/files/build-files-from-ncbi.py +++ b/files/build-files-from-ncbi.py @@ -15,7 +15,7 @@ def build_taxonomy_request_body(taxa): return {"taxons": taxa, "children": False, "ranks": ["genus"]} -def get_organism_row(organism_info): +def get_organism_row(organism_info, accession): if len(organism_info.get("errors", [])) > 0: raise Exception(organism_info) @@ -25,11 +25,12 @@ def get_organism_row(organism_info): "taxon": organism_taxonomy["current_scientific_name"]["name"], "taxonomyId": str(organism_taxonomy["tax_id"]), "assemblyCount": next(count["count"] for count in organism_taxonomy["counts"] if count["type"] == "COUNT_TYPE_ASSEMBLY"), + "accession": accession, } -def get_organisms_df(taxa): - organisms_info = requests.post(TAXONOMY_URL, json=build_taxonomy_request_body(taxa)).json()["reports"] - return pd.DataFrame([get_organism_row(organism_info) for organism_info in organisms_info]) +def get_organisms_df(taxa_with_accessions): + organisms_info_with_accessions = [(organism_info, accession) for taxon, accession in taxa_with_accessions for organism_info in requests.post(TAXONOMY_URL, json=build_taxonomy_request_body([taxon])).json()["reports"]] + return pd.DataFrame([get_organism_row(organism_info, accession) for organism_info, accession in organisms_info_with_accessions]) def get_tax_ids(organisms_df): return list(organisms_df["taxonomyId"]) @@ -37,10 +38,11 @@ def get_tax_ids(organisms_df): def build_genomes_url(tax_ids): return f"https://api.ncbi.nlm.nih.gov/datasets/v2/genome/taxon/{urllib.parse.quote(",".join([str(id) for id in tax_ids]))}/dataset_report?filters.assembly_source=refseq&filters.has_annotation=true&filters.exclude_paired_reports=true&filters.exclude_atypical=true&filters.assembly_level=scaffold&filters.assembly_level=chromosome&filters.assembly_level=complete_genome" -def get_genome_row(genome_info): +def get_genome_row(genome_info, taxon): refseq_category = genome_info["assembly_info"].get("refseq_category") return { - "taxon": genome_info["organism"]["organism_name"], + "taxon": taxon, + "strain": genome_info["organism"].get("infraspecific_names", {}).get("strain", ""), "taxonomyId": genome_info["organism"]["tax_id"], "accession": genome_info["accession"], "isRef": refseq_category == "reference genome", @@ -56,8 +58,12 @@ def get_genome_row(genome_info): "pairedAccession": genome_info["paired_accession"], } -def get_genomes_df(tax_ids): - return pd.DataFrame(data=[get_genome_row(genome_info) for genome_info in requests.get(build_genomes_url(tax_ids)).json()["reports"]]) +def get_organism_genomes(tax_id, accession): + return [genome_info for genome_info in requests.get(build_genomes_url([tax_id])).json()["reports"] if genome_info["accession"] == accession] + +def get_genomes_df(organism_ids): + genomes_info_with_organisms = [(genome_info, taxon) for tax_id, taxon, accession in organism_ids for genome_info in get_organism_genomes(tax_id, accession)] + return pd.DataFrame(data=[get_genome_row(*info) for info in genomes_info_with_organisms]) def _id_to_gene_model_url(asm_id): hubs_url = "https://hgdownload.soe.ucsc.edu/hubs/" @@ -95,7 +101,7 @@ def build_files(): taxa_df = pd.read_csv(TAXA_URL, keep_default_na=False) - organisms_source_df = get_organisms_df([taxon.strip() for taxon in taxa_df["Name"] if taxon]) + organisms_source_df = get_organisms_df([(taxon.strip(), accession.strip()) for taxon, accession in zip(taxa_df["Name"], taxa_df["RefSeq Accession"]) if taxon]) organisms_df = organisms_source_df.merge(taxa_df[["TaxId", "CustomTags"]], how="left", left_on="taxonomyId", right_on="TaxId").drop(columns=["TaxId"]) @@ -103,7 +109,7 @@ def build_files(): print(f"Wrote to {ORGANISMS_OUTPUT_PATH}") - genomes_source_df = get_genomes_df(get_tax_ids(organisms_df)) + genomes_source_df = get_genomes_df(zip(organisms_df["taxonomyId"], organisms_df["taxon"], organisms_df["accession"])) assemblies_df = pd.DataFrame(requests.get(ASSEMBLIES_URL).json()["data"])[["ucscBrowser", "genBank", "refSeq"]] gen_bank_merge_df = genomes_source_df.merge(assemblies_df, how="left", left_on="accession", right_on="genBank") diff --git a/files/entities.ts b/files/entities.ts index 40c1774..a96f44f 100644 --- a/files/entities.ts +++ b/files/entities.ts @@ -11,6 +11,7 @@ export interface SourceGenome { scaffoldCount: string; scaffoldL50: string; scaffoldN50: string; + strain: string; taxon: string; taxonomyId: string; ucscBrowser: string; diff --git a/files/out/genomes.json b/files/out/genomes.json index e8ab3b0..7fe173d 100644 --- a/files/out/genomes.json +++ b/files/out/genomes.json @@ -13,6 +13,7 @@ "scaffoldCount": 2747, "scaffoldL50": 6, "scaffoldN50": 1678596, + "strain": "Salvador I", "tags": [ "VEuPathDB" ], @@ -33,8 +34,11 @@ "scaffoldCount": 12, "scaffoldL50": 4, "scaffoldN50": 2481190, - "tags": [], - "taxon": "Trypanosoma brucei brucei TREU927", + "strain": null, + "tags": [ + "VEuPathDB" + ], + "taxon": "Trypanosoma brucei", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002445.2" }, { @@ -51,8 +55,9 @@ "scaffoldCount": 8, "scaffoldL50": 4, "scaffoldN50": 3948441, + "strain": "Af293", "tags": [], - "taxon": "Aspergillus fumigatus Af293", + "taxon": "Aspergillus fumigatus", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002655.1" }, { @@ -69,8 +74,11 @@ "scaffoldCount": 36, "scaffoldL50": 11, "scaffoldN50": 1091540, - "tags": [], - "taxon": "Leishmania major strain Friedlin", + "strain": "Friedlin", + "tags": [ + "VEuPathDB" + ], + "taxon": "Leishmania major", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002725.2" }, { @@ -87,8 +95,11 @@ "scaffoldCount": 14, "scaffoldL50": 5, "scaffoldN50": 1687656, - "tags": [], - "taxon": "Plasmodium falciparum 3D7", + "strain": null, + "tags": [ + "VEuPathDB" + ], + "taxon": "Plasmodium falciparum", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002765.6" }, { @@ -105,8 +116,11 @@ "scaffoldCount": 138, "scaffoldL50": 11, "scaffoldN50": 992961, - "tags": [], - "taxon": "Leishmania braziliensis MHOM/BR/75/M2904", + "strain": "MHOM/BR/75/M2904", + "tags": [ + "VEuPathDB" + ], + "taxon": "Leishmania braziliensis", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002845.2" }, { @@ -123,8 +137,11 @@ "scaffoldCount": 2276, "scaffoldL50": 6, "scaffoldN50": 4973582, - "tags": [], - "taxon": "Toxoplasma gondii ME49", + "strain": "ME49", + "tags": [ + "VEuPathDB" + ], + "taxon": "Toxoplasma gondii", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000006565.2" }, { @@ -141,8 +158,9 @@ "scaffoldCount": 14, "scaffoldL50": 6, "scaffoldN50": 1438950, + "strain": "JEC21", "tags": [], - "taxon": "Cryptococcus neoformans var. neoformans JEC21", + "taxon": "Cryptococcus neoformans", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000091045.1" }, { @@ -159,8 +177,9 @@ "scaffoldCount": 6, "scaffoldL50": 3, "scaffoldN50": 4323945, + "strain": "RS", "tags": [], - "taxon": "Coccidioides immitis RS", + "taxon": "Coccidioides immitis", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000149335.2" }, { @@ -177,8 +196,9 @@ "scaffoldCount": 8, "scaffoldL50": 3, "scaffoldN50": 2231883, + "strain": "SC5314", "tags": [], - "taxon": "Candida albicans SC5314", + "taxon": "Candida albicans", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000182965.3" }, { @@ -195,8 +215,11 @@ "scaffoldCount": 1, "scaffoldL50": 1, "scaffoldN50": 4411532, - "tags": [], - "taxon": "Mycobacterium tuberculosis H37Rv", + "strain": "H37Rv", + "tags": [ + "Bact" + ], + "taxon": "Mycobacterium tuberculosis", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000195955.2" }, { @@ -213,6 +236,7 @@ "scaffoldCount": 29495, "scaffoldL50": 212, "scaffoldN50": 88624, + "strain": "CL Brener", "tags": [ "VEuPathDB" ], @@ -233,6 +257,7 @@ "scaffoldCount": 36, "scaffoldL50": 11, "scaffoldN50": 1024085, + "strain": "BPK282A1", "tags": [ "VEuPathDB" ], @@ -240,22 +265,46 @@ "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000227135.1" }, { - "accession": "GCF_000277735.2", + "accession": "GCF_000857045.1", "annotationStatus": null, "chromosomes": 1, "coverage": null, - "gcPercent": 65.5, + "gcPercent": 33, "geneModelUrl": null, "isRef": "No", - "length": 4411709, + "length": 196858, "level": "Complete Genome", - "ncbiTaxonomyId": "83332", + "ncbiTaxonomyId": "10244", "scaffoldCount": 1, "scaffoldL50": 1, - "scaffoldN50": 4411709, - "tags": [], - "taxon": "Mycobacterium tuberculosis H37Rv", - "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000277735.2" + "scaffoldN50": 196858, + "strain": "Zaire-96-I-16", + "tags": [ + "Virus" + ], + "taxon": "Monkeypox virus", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000857045.1" + }, + { + "accession": "GCF_009858895.2", + "annotationStatus": null, + "chromosomes": 1, + "coverage": null, + "gcPercent": 38, + "geneModelUrl": null, + "isRef": "No", + "length": 29903, + "level": "Complete Genome", + "ncbiTaxonomyId": "2697049", + "scaffoldCount": 1, + "scaffoldL50": 1, + "scaffoldN50": 29903, + "strain": null, + "tags": [ + "Virus" + ], + "taxon": "Severe acute respiratory syndrome coronavirus 2", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_009858895.2" }, { "accession": "GCF_015732765.1", @@ -271,6 +320,7 @@ "scaffoldCount": 56, "scaffoldL50": 2, "scaffoldN50": 201550677, + "strain": "JHB", "tags": [ "VEuPathDB" ], @@ -291,6 +341,7 @@ "scaffoldCount": 289, "scaffoldL50": 2, "scaffoldN50": 186194774, + "strain": null, "tags": [], "taxon": "Culex pipiens pallens", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_016801865.2" @@ -309,8 +360,11 @@ "scaffoldCount": 9, "scaffoldL50": 2, "scaffoldN50": 8079863, - "tags": [], - "taxon": "Coccidioides posadasii str. Silveira", + "strain": "Silveira", + "tags": [ + "VEuPathDB" + ], + "taxon": "Coccidioides posadasii", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_018416015.2" }, { @@ -327,6 +381,7 @@ "scaffoldCount": 14, "scaffoldL50": 5, "scaffoldN50": 2046250, + "strain": "17X", "tags": [ "VEuPathDB" ], @@ -347,8 +402,11 @@ "scaffoldCount": 14, "scaffoldL50": 5, "scaffoldN50": 1692345, - "tags": [], - "taxon": "Plasmodium vinckei vinckei", + "strain": null, + "tags": [ + "VEuPathDB" + ], + "taxon": "Plasmodium vinckei", "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_900681995.1" }, { @@ -365,6 +423,7 @@ "scaffoldCount": 190, "scaffoldL50": 2, "scaffoldN50": 99149756, + "strain": null, "tags": [ "VEuPathDB" ], diff --git a/files/source/genomes-from-ncbi.tsv b/files/source/genomes-from-ncbi.tsv index 468f878..5b137dc 100644 --- a/files/source/genomes-from-ncbi.tsv +++ b/files/source/genomes-from-ncbi.tsv @@ -1,21 +1,22 @@ -taxon taxonomyId accession isRef level chromosomeCount length scaffoldCount scaffoldN50 scaffoldL50 coverage gcPercent annotationStatus pairedAccession ucscBrowser genBank refSeq geneModelUrl -Mycobacterium tuberculosis H37Rv 83332 GCF_000195955.2 True Complete Genome 1.0 4411532 1 4411532 1 65.5 GCA_000195955.2 https://genome.ucsc.edu/h/GCF_000195955.2 GCA_000195955.2 GCF_000195955.2 -Plasmodium falciparum 3D7 36329 GCF_000002765.6 True Complete Genome 14.0 23292622 14 1687656 5 100.0x 19.5 Full annotation GCA_000002765.3 https://genome.ucsc.edu/h/GCF_000002765.6 GCA_000002765.3 GCF_000002765.6 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/765/GCF_000002765.6/genes/GCF_000002765.6_GCA_000002765.ncbiRefSeq.gtf.gz -Leishmania major strain Friedlin 347515 GCF_000002725.2 True Complete Genome 36.0 32855089 36 1091540 11 59.5 Full annotation GCA_000002725.2 https://genome.ucsc.edu/h/GCF_000002725.2 GCA_000002725.2 GCF_000002725.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/725/GCF_000002725.2/genes/GCF_000002725.2_ASM272v2.ncbiRefSeq.gtf.gz -Plasmodium yoelii 5861 GCF_900002385.2 True Complete Genome 14.0 23043114 14 2046250 5 100.0x 21.5 Full annotation GCA_900002385.2 https://genome.ucsc.edu/h/GCF_900002385.2 GCA_900002385.2 GCF_900002385.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/900/002/385/GCF_900002385.2/genes/GCF_900002385.2_GCA_900002385.ncbiRefSeq.gtf.gz -Coccidioides posadasii str. Silveira 443226 GCF_018416015.2 True Complete Genome 9.0 28193268 9 8079863 2 475.0x 46.5 Full annotation GCA_018416015.2 https://genome.ucsc.edu/h/GCF_018416015.2 GCA_018416015.2 GCF_018416015.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/018/416/015/GCF_018416015.2/genes/GCF_018416015.2_ASM1841601v2.ncbiRefSeq.gtf.gz -Plasmodium vinckei vinckei 54757 GCF_900681995.1 True Chromosome 14.0 18338688 14 1692345 5 155.0x 23.0 Full annotation GCA_900681995.1 https://genome.ucsc.edu/h/GCF_900681995.1 GCA_900681995.1 GCF_900681995.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/900/681/995/GCF_900681995.1/genes/GCF_900681995.1_PVVCY_v1.ncbiRefSeq.gtf.gz -Candida albicans SC5314 237561 GCF_000182965.3 True Chromosome 8.0 14282666 8 2231883 3 700.0x 33.5 Full annotation GCA_000182965.3 https://genome.ucsc.edu/h/GCF_000182965.3 GCA_000182965.3 GCF_000182965.3 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/182/965/GCF_000182965.3/genes/GCF_000182965.3_ASM18296v3.ncbiRefSeq.gtf.gz -Cryptococcus neoformans var. neoformans JEC21 214684 GCF_000091045.1 True Chromosome 14.0 19051922 14 1438950 6 48.5 Full annotation GCA_000091045.1 https://genome.ucsc.edu/h/GCF_000091045.1 GCA_000091045.1 GCF_000091045.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/091/045/GCF_000091045.1/genes/GCF_000091045.1_ASM9104v1.ncbiRefSeq.gtf.gz -Leishmania donovani 5661 GCF_000227135.1 True Chromosome 36.0 32444968 36 1024085 11 59.5 Full annotation GCA_000227135.2 https://genome.ucsc.edu/h/GCF_000227135.1 GCA_000227135.2 GCF_000227135.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/227/135/GCF_000227135.1/genes/GCF_000227135.1_ASM22713v2.ncbiRefSeq.gtf.gz -Aspergillus fumigatus Af293 330879 GCF_000002655.1 True Chromosome 8.0 29384958 8 3948441 4 50.0 Full annotation GCA_000002655.1 https://genome.ucsc.edu/h/GCF_000002655.1 GCA_000002655.1 GCF_000002655.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/655/GCF_000002655.1/genes/GCF_000002655.1_ASM265v1.ncbiRefSeq.gtf.gz -Toxoplasma gondii ME49 508771 GCF_000006565.2 True Chromosome 14.0 65633124 2276 4973582 6 26.5x 52.5 GCA_000006565.2 https://genome.ucsc.edu/h/GCF_000006565.2 GCA_000006565.2 GCF_000006565.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/006/565/GCF_000006565.2/genes/GCF_000006565.2_TGA4.ncbiRefSeq.gtf.gz -Trypanosoma brucei brucei TREU927 185431 GCF_000002445.2 True Chromosome 11.0 26075494 12 2481190 4 46.5 Full annotation GCA_000002445.1 https://genome.ucsc.edu/h/GCF_000002445.2 GCA_000002445.1 GCF_000002445.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/445/GCF_000002445.2/genes/GCF_000002445.2_ASM244v1.ncbiRefSeq.gtf.gz -Anopheles gambiae 7165 GCF_943734735.2 True Chromosome 3.0 264451381 190 99149756 2 54.0x 44.5 Full annotation GCA_943734735.2 https://genome.ucsc.edu/h/GCF_943734735.2 GCA_943734735.2 GCF_943734735.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/943/734/735/GCF_943734735.2/genes/GCF_943734735.2_idAnoGambNW_F1_1.ncbiRefSeq.gtf.gz -Plasmodium vivax 5855 GCF_000002415.2 True Chromosome 14.0 27007701 2747 1678596 6 42.5 Full annotation GCA_000002415.2 https://genome.ucsc.edu/h/GCF_000002415.2 GCA_000002415.2 GCF_000002415.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/415/GCF_000002415.2/genes/GCF_000002415.2_ASM241v2.ncbiRefSeq.gtf.gz -Culex quinquefasciatus 7176 GCF_015732765.1 True Chromosome 3.0 573214445 56 201550677 2 76.0x 37.0 Full annotation GCA_015732765.1 https://genome.ucsc.edu/h/GCF_015732765.1 GCA_015732765.1 GCF_015732765.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/015/732/765/GCF_015732765.1/genes/GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal.ncbiRefSeq.gtf.gz -Culex pipiens pallens 42434 GCF_016801865.2 True Chromosome 3.0 566339288 289 186194774 2 250.0x 37.0 Full annotation GCA_016801865.2 https://genome.ucsc.edu/h/GCF_016801865.2 GCA_016801865.2 GCF_016801865.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/016/801/865/GCF_016801865.2/genes/GCF_016801865.2_TS_CPP_V2.ncbiRefSeq.gtf.gz -Leishmania braziliensis MHOM/BR/75/M2904 420245 GCF_000002845.2 True Chromosome 35.0 32068771 138 992961 11 58.0 GCA_000002845.2 https://genome.ucsc.edu/h/GCF_000002845.2 GCA_000002845.2 GCF_000002845.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/845/GCF_000002845.2/genes/GCF_000002845.2_ASM284v2.ncbiRefSeq.gtf.gz -Trypanosoma cruzi 5693 GCF_000209065.1 True Scaffold 89937456 29495 88624 212 51.5 Full annotation GCA_000209065.1 https://genome.ucsc.edu/h/GCF_000209065.1 GCA_000209065.1 GCF_000209065.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/209/065/GCF_000209065.1/genes/GCF_000209065.1_ASM20906v1.ncbiRefSeq.gtf.gz -Coccidioides immitis RS 246410 GCF_000149335.2 True Scaffold 28947925 6 4323945 3 46.0 Full annotation GCA_000149335.2 https://genome.ucsc.edu/h/GCF_000149335.2 GCA_000149335.2 GCF_000149335.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/149/335/GCF_000149335.2/genes/GCF_000149335.2_ASM14933v2.ncbiRefSeq.gtf.gz -Mycobacterium tuberculosis H37Rv 83332 GCF_000277735.2 False Complete Genome 1.0 4411709 1 4411709 1 65.5 GCA_000277735.2 https://genome.ucsc.edu/h/GCF_000277735.2 GCA_000277735.2 GCF_000277735.2 +taxon strain taxonomyId accession isRef level chromosomeCount length scaffoldCount scaffoldN50 scaffoldL50 coverage gcPercent annotationStatus pairedAccession ucscBrowser genBank refSeq geneModelUrl +Plasmodium falciparum 36329 GCF_000002765.6 True Complete Genome 14.0 23292622 14 1687656 5 100.0x 19.5 Full annotation GCA_000002765.3 https://genome.ucsc.edu/h/GCF_000002765.6 GCA_000002765.3 GCF_000002765.6 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/765/GCF_000002765.6/genes/GCF_000002765.6_GCA_000002765.ncbiRefSeq.gtf.gz +Plasmodium vivax Salvador I 5855 GCF_000002415.2 True Chromosome 14.0 27007701 2747 1678596 6 42.5 Full annotation GCA_000002415.2 https://genome.ucsc.edu/h/GCF_000002415.2 GCA_000002415.2 GCF_000002415.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/415/GCF_000002415.2/genes/GCF_000002415.2_ASM241v2.ncbiRefSeq.gtf.gz +Plasmodium yoelii 17X 5861 GCF_900002385.2 True Complete Genome 14.0 23043114 14 2046250 5 100.0x 21.5 Full annotation GCA_900002385.2 https://genome.ucsc.edu/h/GCF_900002385.2 GCA_900002385.2 GCF_900002385.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/900/002/385/GCF_900002385.2/genes/GCF_900002385.2_GCA_900002385.ncbiRefSeq.gtf.gz +Plasmodium vinckei 54757 GCF_900681995.1 True Chromosome 14.0 18338688 14 1692345 5 155.0x 23.0 Full annotation GCA_900681995.1 https://genome.ucsc.edu/h/GCF_900681995.1 GCA_900681995.1 GCF_900681995.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/900/681/995/GCF_900681995.1/genes/GCF_900681995.1_PVVCY_v1.ncbiRefSeq.gtf.gz +Culex pipiens pallens 42434 GCF_016801865.2 True Chromosome 3.0 566339288 289 186194774 2 250.0x 37.0 Full annotation GCA_016801865.2 https://genome.ucsc.edu/h/GCF_016801865.2 GCA_016801865.2 GCF_016801865.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/016/801/865/GCF_016801865.2/genes/GCF_016801865.2_TS_CPP_V2.ncbiRefSeq.gtf.gz +Culex quinquefasciatus JHB 7176 GCF_015732765.1 True Chromosome 3.0 573214445 56 201550677 2 76.0x 37.0 Full annotation GCA_015732765.1 https://genome.ucsc.edu/h/GCF_015732765.1 GCA_015732765.1 GCF_015732765.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/015/732/765/GCF_015732765.1/genes/GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal.ncbiRefSeq.gtf.gz +Anopheles gambiae 7165 GCF_943734735.2 True Chromosome 3.0 264451381 190 99149756 2 54.0x 44.5 Full annotation GCA_943734735.2 https://genome.ucsc.edu/h/GCF_943734735.2 GCA_943734735.2 GCF_943734735.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/943/734/735/GCF_943734735.2/genes/GCF_943734735.2_idAnoGambNW_F1_1.ncbiRefSeq.gtf.gz +Toxoplasma gondii ME49 508771 GCF_000006565.2 True Chromosome 14.0 65633124 2276 4973582 6 26.5x 52.5 GCA_000006565.2 https://genome.ucsc.edu/h/GCF_000006565.2 GCA_000006565.2 GCF_000006565.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/006/565/GCF_000006565.2/genes/GCF_000006565.2_TGA4.ncbiRefSeq.gtf.gz +Mycobacterium tuberculosis H37Rv 83332 GCF_000195955.2 True Complete Genome 1.0 4411532 1 4411532 1 65.5 GCA_000195955.2 https://genome.ucsc.edu/h/GCF_000195955.2 GCA_000195955.2 GCF_000195955.2 +Coccidioides posadasii Silveira 443226 GCF_018416015.2 True Complete Genome 9.0 28193268 9 8079863 2 475.0x 46.5 Full annotation GCA_018416015.2 https://genome.ucsc.edu/h/GCF_018416015.2 GCA_018416015.2 GCF_018416015.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/018/416/015/GCF_018416015.2/genes/GCF_018416015.2_ASM1841601v2.ncbiRefSeq.gtf.gz +Coccidioides immitis RS 246410 GCF_000149335.2 True Scaffold 28947925 6 4323945 3 46.0 Full annotation GCA_000149335.2 https://genome.ucsc.edu/h/GCF_000149335.2 GCA_000149335.2 GCF_000149335.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/149/335/GCF_000149335.2/genes/GCF_000149335.2_ASM14933v2.ncbiRefSeq.gtf.gz +Trypanosoma cruzi CL Brener 5693 GCF_000209065.1 True Scaffold 89937456 29495 88624 212 51.5 Full annotation GCA_000209065.1 https://genome.ucsc.edu/h/GCF_000209065.1 GCA_000209065.1 GCF_000209065.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/209/065/GCF_000209065.1/genes/GCF_000209065.1_ASM20906v1.ncbiRefSeq.gtf.gz +Trypanosoma brucei 185431 GCF_000002445.2 True Chromosome 11.0 26075494 12 2481190 4 46.5 Full annotation GCA_000002445.1 https://genome.ucsc.edu/h/GCF_000002445.2 GCA_000002445.1 GCF_000002445.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/445/GCF_000002445.2/genes/GCF_000002445.2_ASM244v1.ncbiRefSeq.gtf.gz +Leishmania major Friedlin 347515 GCF_000002725.2 True Complete Genome 36.0 32855089 36 1091540 11 59.5 Full annotation GCA_000002725.2 https://genome.ucsc.edu/h/GCF_000002725.2 GCA_000002725.2 GCF_000002725.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/725/GCF_000002725.2/genes/GCF_000002725.2_ASM272v2.ncbiRefSeq.gtf.gz +Leishmania donovani BPK282A1 5661 GCF_000227135.1 True Chromosome 36.0 32444968 36 1024085 11 59.5 Full annotation GCA_000227135.2 https://genome.ucsc.edu/h/GCF_000227135.1 GCA_000227135.2 GCF_000227135.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/227/135/GCF_000227135.1/genes/GCF_000227135.1_ASM22713v2.ncbiRefSeq.gtf.gz +Leishmania braziliensis MHOM/BR/75/M2904 420245 GCF_000002845.2 True Chromosome 35.0 32068771 138 992961 11 58.0 GCA_000002845.2 https://genome.ucsc.edu/h/GCF_000002845.2 GCA_000002845.2 GCF_000002845.2 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/845/GCF_000002845.2/genes/GCF_000002845.2_ASM284v2.ncbiRefSeq.gtf.gz +Severe acute respiratory syndrome coronavirus 2 2697049 GCF_009858895.2 False Complete Genome 1.0 29903 1 29903 1 38.0 GCA_009858895.3 https://genome.ucsc.edu/h/GCF_009858895.2 GCA_009858895.3 GCF_009858895.2 +Monkeypox virus Zaire-96-I-16 10244 GCF_000857045.1 False Complete Genome 1.0 196858 1 196858 1 33.0 GCA_000857045.1 https://genome.ucsc.edu/h/GCF_000857045.1 GCA_000857045.1 GCF_000857045.1 +Aspergillus fumigatus Af293 330879 GCF_000002655.1 True Chromosome 8.0 29384958 8 3948441 4 50.0 Full annotation GCA_000002655.1 https://genome.ucsc.edu/h/GCF_000002655.1 GCA_000002655.1 GCF_000002655.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/655/GCF_000002655.1/genes/GCF_000002655.1_ASM265v1.ncbiRefSeq.gtf.gz +Candida albicans SC5314 237561 GCF_000182965.3 True Chromosome 8.0 14282666 8 2231883 3 700.0x 33.5 Full annotation GCA_000182965.3 https://genome.ucsc.edu/h/GCF_000182965.3 GCA_000182965.3 GCF_000182965.3 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/182/965/GCF_000182965.3/genes/GCF_000182965.3_ASM18296v3.ncbiRefSeq.gtf.gz +Cryptococcus neoformans JEC21 214684 GCF_000091045.1 True Chromosome 14.0 19051922 14 1438950 6 48.5 Full annotation GCA_000091045.1 https://genome.ucsc.edu/h/GCF_000091045.1 GCA_000091045.1 GCF_000091045.1 https://hgdownload.soe.ucsc.edu/hubs/GCF/000/091/045/GCF_000091045.1/genes/GCF_000091045.1_ASM9104v1.ncbiRefSeq.gtf.gz diff --git a/files/source/organisms-from-ncbi.tsv b/files/source/organisms-from-ncbi.tsv index eb42060..a7a0d3a 100644 --- a/files/source/organisms-from-ncbi.tsv +++ b/files/source/organisms-from-ncbi.tsv @@ -1,22 +1,22 @@ -taxon taxonomyId assemblyCount CustomTags -Anopheles gambiae 7165 7 VEuPathDB -Aspergillus fumigatus 746128 352 -Candida albicans 5476 117 -Coccidioides immitis 5501 5 -Coccidioides posadasii 199306 13 VEuPathDB -Cryptococcus neoformans 5207 183 -Culex pipiens pallens 42434 1 -Culex quinquefasciatus 7176 3 VEuPathDB -Leishmania braziliensis 5660 11 VEuPathDB -Leishmania donovani 5661 12 VEuPathDB -Leishmania major 5664 7 VEuPathDB -Monkeypox virus 10244 6911 Virus -Mycobacterium tuberculosis 1773 7829 Bact -Plasmodium falciparum 5833 67 VEuPathDB -Plasmodium vinckei 5860 10 VEuPathDB -Plasmodium vivax 5855 19 VEuPathDB -Plasmodium yoelii 5861 15 VEuPathDB -Severe acute respiratory syndrome coronavirus 2 2697049 12408 Virus -Toxoplasma gondii 5811 29 VEuPathDB -Trypanosoma brucei 5691 6 VEuPathDB -Trypanosoma cruzi 5693 44 VEuPathDB +taxon taxonomyId assemblyCount accession CustomTags +Plasmodium falciparum 5833 67 GCF_000002765.6 VEuPathDB +Plasmodium vivax 5855 19 GCF_000002415.2 VEuPathDB +Plasmodium yoelii 5861 15 GCF_900002385.2 VEuPathDB +Plasmodium vinckei 5860 10 GCF_900681995.1 VEuPathDB +Culex pipiens pallens 42434 1 GCF_016801865.2 +Culex quinquefasciatus 7176 3 GCF_015732765.1 VEuPathDB +Anopheles gambiae 7165 7 GCF_943734735.2 VEuPathDB +Toxoplasma gondii 5811 29 GCF_000006565.2 VEuPathDB +Mycobacterium tuberculosis 1773 7829 GCF_000195955.2 Bact +Coccidioides posadasii 199306 13 GCF_018416015.2 VEuPathDB +Coccidioides immitis 5501 5 GCF_000149335.2 +Trypanosoma cruzi 5693 44 GCF_000209065.1 VEuPathDB +Trypanosoma brucei 5691 6 GCF_000002445.2 VEuPathDB +Leishmania major 5664 7 GCF_000002725.2 VEuPathDB +Leishmania donovani 5661 12 GCF_000227135.1 VEuPathDB +Leishmania braziliensis 5660 11 GCF_000002845.2 VEuPathDB +Severe acute respiratory syndrome coronavirus 2 2697049 12408 GCF_009858895.2 Virus +Monkeypox virus 10244 6911 GCF_000857045.1 Virus +Aspergillus fumigatus 746128 352 GCF_000002655.1 +Candida albicans 5476 117 GCF_000182965.3 +Cryptococcus neoformans 5207 183 GCF_000091045.1 From 625a3650e817dd75d0ac443701fbbf4985986892 Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Wed, 11 Dec 2024 22:36:30 -0800 Subject: [PATCH 15/30] feat: link to filtered genomes from organism list (#177) --- .../common/viewModelBuilders.ts | 46 +++++++++++++++++-- .../local/index/genomeEntityConfig.ts | 2 +- .../local/index/organismEntityConfig.ts | 6 +-- 3 files changed, 45 insertions(+), 9 deletions(-) diff --git a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts index 6968b98..a17458f 100644 --- a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts +++ b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts @@ -3,6 +3,7 @@ import { Key, Value, } from "@databiosphere/findable-ui/lib/components/common/KeyValuePairs/keyValuePairs"; +import { LinkProps } from "@databiosphere/findable-ui/lib/components/Links/components/Link/link"; import { ViewContext } from "@databiosphere/findable-ui/lib/config/entities"; import { ComponentProps } from "react"; import { ROUTES } from "../../../../../routes/constants"; @@ -126,6 +127,19 @@ export const buildGcPercent = ( }; }; +/** + * Build props for the taxon cell. + * @param genome - Genome entity. + * @returns Props to be used for the cell. + */ +export const buildGenomeTaxon = ( + genome: BRCDataCatalogGenome +): ComponentProps => { + return { + value: genome.taxon, + }; +}; + /** * Build props for the "is ref" cell. * @param genome - Genome entity. @@ -167,14 +181,15 @@ export const buildLevel = ( /** * Build props for the taxon cell. - * @param genome - Genome entity. + * @param organism - Organism entity. * @returns Props to be used for the cell. */ -export const buildTaxon = ( - genome: BRCDataCatalogOrganism | BRCDataCatalogGenome -): ComponentProps => { +export const buildOrganismTaxon = ( + organism: BRCDataCatalogOrganism +): ComponentProps => { return { - value: genome.taxon, + label: organism.taxon, + url: getTaxonGenomesUrlObject(organism.taxon), }; }; @@ -355,3 +370,24 @@ function getGenomeEntityChooseAnalysisMethodBreadcrumbs( { path: "", text: "Choose Analysis Methods" }, ]; } + +/** + * Get URL object for genomes filtered by a given taxon. + * @param taxon - Taxon. + * @returns URL object. + */ +function getTaxonGenomesUrlObject(taxon: string): LinkProps["url"] { + return { + href: ROUTES.GENOMES, + query: encodeURIComponent( + JSON.stringify({ + filter: [ + { + categoryKey: "taxon", + value: [taxon], + }, + ], + }) + ), + }; +} diff --git a/site-config/brc-analytics/local/index/genomeEntityConfig.ts b/site-config/brc-analytics/local/index/genomeEntityConfig.ts index de0f495..e2ad667 100644 --- a/site-config/brc-analytics/local/index/genomeEntityConfig.ts +++ b/site-config/brc-analytics/local/index/genomeEntityConfig.ts @@ -99,7 +99,7 @@ export const genomeEntityConfig: BRCEntityConfig = { { componentConfig: { component: C.BasicCell, - viewBuilder: V.buildTaxon, + viewBuilder: V.buildGenomeTaxon, } as ComponentConfig, header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXON, id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON, diff --git a/site-config/brc-analytics/local/index/organismEntityConfig.ts b/site-config/brc-analytics/local/index/organismEntityConfig.ts index 1a39944..8c70ac2 100644 --- a/site-config/brc-analytics/local/index/organismEntityConfig.ts +++ b/site-config/brc-analytics/local/index/organismEntityConfig.ts @@ -52,9 +52,9 @@ export const organismEntityConfig: BRCEntityConfig = { columns: [ { componentConfig: { - component: C.BasicCell, - viewBuilder: V.buildTaxon, - } as ComponentConfig, + component: C.Link, + viewBuilder: V.buildOrganismTaxon, + } as ComponentConfig, header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXON, id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON, width: "auto", From d7935a9027ec5dad050fc51db82d80a2e20d3996 Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Wed, 11 Dec 2024 22:46:26 -0800 Subject: [PATCH 16/30] feat: add strain to genomes list (#177) --- .../common/viewModelBuilders.ts | 13 +++++++++++++ site-config/brc-analytics/category.ts | 2 ++ .../local/index/genomeEntityConfig.ts | 15 ++++++++++++++- 3 files changed, 29 insertions(+), 1 deletion(-) diff --git a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts index a17458f..9b61ff8 100644 --- a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts +++ b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts @@ -232,6 +232,19 @@ export const buildScaffoldN50 = ( }; }; +/** + * Build props for the strain cell. + * @param genome - Genome entity. + * @returns Props to be used for the cell. + */ +export const buildStrain = ( + genome: BRCDataCatalogGenome +): ComponentProps => { + return { + value: genome.strain, + }; +}; + /** * Build props for the tags cell. * @param genome - Genome entity. diff --git a/site-config/brc-analytics/category.ts b/site-config/brc-analytics/category.ts index 122bf19..6b11043 100644 --- a/site-config/brc-analytics/category.ts +++ b/site-config/brc-analytics/category.ts @@ -12,6 +12,7 @@ export const BRC_DATA_CATALOG_CATEGORY_KEY = { SCAFFOLD_COUNT: "scaffoldCount", SCAFFOLD_L50: "scaffoldL50", SCAFFOLD_N50: "scaffoldN50", + STRAIN: "strain", TAGS: "tags", TAXON: "taxon", TAXONOMY_ID: "ncbiTaxonomyId", @@ -32,6 +33,7 @@ export const BRC_DATA_CATALOG_CATEGORY_LABEL = { SCAFFOLD_COUNT: "Scaffolds", SCAFFOLD_L50: "Scaffold L50", SCAFFOLD_N50: "Scaffold N50", + STRAIN: "Strain", TAGS: "Tags", TAXON: "Taxon", TAXONOMY_ID: "Taxonomy ID", diff --git a/site-config/brc-analytics/local/index/genomeEntityConfig.ts b/site-config/brc-analytics/local/index/genomeEntityConfig.ts index e2ad667..41962bf 100644 --- a/site-config/brc-analytics/local/index/genomeEntityConfig.ts +++ b/site-config/brc-analytics/local/index/genomeEntityConfig.ts @@ -33,6 +33,10 @@ export const genomeEntityConfig: BRCEntityConfig = { key: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON, label: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXON, }, + { + key: BRC_DATA_CATALOG_CATEGORY_KEY.STRAIN, + label: BRC_DATA_CATALOG_CATEGORY_LABEL.STRAIN, + }, { key: BRC_DATA_CATALOG_CATEGORY_KEY.TAXONOMY_ID, label: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXONOMY_ID, @@ -103,7 +107,16 @@ export const genomeEntityConfig: BRCEntityConfig = { } as ComponentConfig, header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXON, id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON, - width: { max: "1fr", min: "284px" }, + width: { max: "1fr", min: "240px" }, + }, + { + componentConfig: { + component: C.BasicCell, + viewBuilder: V.buildStrain, + } as ComponentConfig, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.STRAIN, + id: BRC_DATA_CATALOG_CATEGORY_KEY.STRAIN, + width: { max: "0.5fr", min: "180px" }, }, { componentConfig: { From 9c7338af9dbcb146f043f9141fdead7da7af1ddc Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Wed, 11 Dec 2024 22:55:04 -0800 Subject: [PATCH 17/30] feat: hardcode organism assembly count as 1 (#177) --- files/build-files-from-ncbi.py | 2 +- files/out/organisms.json | 40 ++++++++++++++-------------- files/source/organisms-from-ncbi.tsv | 40 ++++++++++++++-------------- 3 files changed, 41 insertions(+), 41 deletions(-) diff --git a/files/build-files-from-ncbi.py b/files/build-files-from-ncbi.py index 190f188..41a32f0 100644 --- a/files/build-files-from-ncbi.py +++ b/files/build-files-from-ncbi.py @@ -24,7 +24,7 @@ def get_organism_row(organism_info, accession): return { "taxon": organism_taxonomy["current_scientific_name"]["name"], "taxonomyId": str(organism_taxonomy["tax_id"]), - "assemblyCount": next(count["count"] for count in organism_taxonomy["counts"] if count["type"] == "COUNT_TYPE_ASSEMBLY"), + "assemblyCount": 1, "accession": accession, } diff --git a/files/out/organisms.json b/files/out/organisms.json index 1bf4697..6d29b69 100644 --- a/files/out/organisms.json +++ b/files/out/organisms.json @@ -1,6 +1,6 @@ [ { - "assemblyCount": 6911, + "assemblyCount": 1, "ncbiTaxonomyId": "10244", "tags": [ "Virus" @@ -8,7 +8,7 @@ "taxon": "Monkeypox virus" }, { - "assemblyCount": 7829, + "assemblyCount": 1, "ncbiTaxonomyId": "1773", "tags": [ "Bact" @@ -16,7 +16,7 @@ "taxon": "Mycobacterium tuberculosis" }, { - "assemblyCount": 13, + "assemblyCount": 1, "ncbiTaxonomyId": "199306", "tags": [ "VEuPathDB" @@ -24,7 +24,7 @@ "taxon": "Coccidioides posadasii" }, { - "assemblyCount": 12408, + "assemblyCount": 1, "ncbiTaxonomyId": "2697049", "tags": [ "Virus" @@ -38,25 +38,25 @@ "taxon": "Culex pipiens pallens" }, { - "assemblyCount": 183, + "assemblyCount": 1, "ncbiTaxonomyId": "5207", "tags": [], "taxon": "Cryptococcus neoformans" }, { - "assemblyCount": 117, + "assemblyCount": 1, "ncbiTaxonomyId": "5476", "tags": [], "taxon": "Candida albicans" }, { - "assemblyCount": 5, + "assemblyCount": 1, "ncbiTaxonomyId": "5501", "tags": [], "taxon": "Coccidioides immitis" }, { - "assemblyCount": 11, + "assemblyCount": 1, "ncbiTaxonomyId": "5660", "tags": [ "VEuPathDB" @@ -64,7 +64,7 @@ "taxon": "Leishmania braziliensis" }, { - "assemblyCount": 12, + "assemblyCount": 1, "ncbiTaxonomyId": "5661", "tags": [ "VEuPathDB" @@ -72,7 +72,7 @@ "taxon": "Leishmania donovani" }, { - "assemblyCount": 7, + "assemblyCount": 1, "ncbiTaxonomyId": "5664", "tags": [ "VEuPathDB" @@ -80,7 +80,7 @@ "taxon": "Leishmania major" }, { - "assemblyCount": 6, + "assemblyCount": 1, "ncbiTaxonomyId": "5691", "tags": [ "VEuPathDB" @@ -88,7 +88,7 @@ "taxon": "Trypanosoma brucei" }, { - "assemblyCount": 44, + "assemblyCount": 1, "ncbiTaxonomyId": "5693", "tags": [ "VEuPathDB" @@ -96,7 +96,7 @@ "taxon": "Trypanosoma cruzi" }, { - "assemblyCount": 29, + "assemblyCount": 1, "ncbiTaxonomyId": "5811", "tags": [ "VEuPathDB" @@ -104,7 +104,7 @@ "taxon": "Toxoplasma gondii" }, { - "assemblyCount": 67, + "assemblyCount": 1, "ncbiTaxonomyId": "5833", "tags": [ "VEuPathDB" @@ -112,7 +112,7 @@ "taxon": "Plasmodium falciparum" }, { - "assemblyCount": 19, + "assemblyCount": 1, "ncbiTaxonomyId": "5855", "tags": [ "VEuPathDB" @@ -120,7 +120,7 @@ "taxon": "Plasmodium vivax" }, { - "assemblyCount": 10, + "assemblyCount": 1, "ncbiTaxonomyId": "5860", "tags": [ "VEuPathDB" @@ -128,7 +128,7 @@ "taxon": "Plasmodium vinckei" }, { - "assemblyCount": 15, + "assemblyCount": 1, "ncbiTaxonomyId": "5861", "tags": [ "VEuPathDB" @@ -136,7 +136,7 @@ "taxon": "Plasmodium yoelii" }, { - "assemblyCount": 7, + "assemblyCount": 1, "ncbiTaxonomyId": "7165", "tags": [ "VEuPathDB" @@ -144,7 +144,7 @@ "taxon": "Anopheles gambiae" }, { - "assemblyCount": 3, + "assemblyCount": 1, "ncbiTaxonomyId": "7176", "tags": [ "VEuPathDB" @@ -152,7 +152,7 @@ "taxon": "Culex quinquefasciatus" }, { - "assemblyCount": 352, + "assemblyCount": 1, "ncbiTaxonomyId": "746128", "tags": [], "taxon": "Aspergillus fumigatus" diff --git a/files/source/organisms-from-ncbi.tsv b/files/source/organisms-from-ncbi.tsv index a7a0d3a..0615f1a 100644 --- a/files/source/organisms-from-ncbi.tsv +++ b/files/source/organisms-from-ncbi.tsv @@ -1,22 +1,22 @@ taxon taxonomyId assemblyCount accession CustomTags -Plasmodium falciparum 5833 67 GCF_000002765.6 VEuPathDB -Plasmodium vivax 5855 19 GCF_000002415.2 VEuPathDB -Plasmodium yoelii 5861 15 GCF_900002385.2 VEuPathDB -Plasmodium vinckei 5860 10 GCF_900681995.1 VEuPathDB +Plasmodium falciparum 5833 1 GCF_000002765.6 VEuPathDB +Plasmodium vivax 5855 1 GCF_000002415.2 VEuPathDB +Plasmodium yoelii 5861 1 GCF_900002385.2 VEuPathDB +Plasmodium vinckei 5860 1 GCF_900681995.1 VEuPathDB Culex pipiens pallens 42434 1 GCF_016801865.2 -Culex quinquefasciatus 7176 3 GCF_015732765.1 VEuPathDB -Anopheles gambiae 7165 7 GCF_943734735.2 VEuPathDB -Toxoplasma gondii 5811 29 GCF_000006565.2 VEuPathDB -Mycobacterium tuberculosis 1773 7829 GCF_000195955.2 Bact -Coccidioides posadasii 199306 13 GCF_018416015.2 VEuPathDB -Coccidioides immitis 5501 5 GCF_000149335.2 -Trypanosoma cruzi 5693 44 GCF_000209065.1 VEuPathDB -Trypanosoma brucei 5691 6 GCF_000002445.2 VEuPathDB -Leishmania major 5664 7 GCF_000002725.2 VEuPathDB -Leishmania donovani 5661 12 GCF_000227135.1 VEuPathDB -Leishmania braziliensis 5660 11 GCF_000002845.2 VEuPathDB -Severe acute respiratory syndrome coronavirus 2 2697049 12408 GCF_009858895.2 Virus -Monkeypox virus 10244 6911 GCF_000857045.1 Virus -Aspergillus fumigatus 746128 352 GCF_000002655.1 -Candida albicans 5476 117 GCF_000182965.3 -Cryptococcus neoformans 5207 183 GCF_000091045.1 +Culex quinquefasciatus 7176 1 GCF_015732765.1 VEuPathDB +Anopheles gambiae 7165 1 GCF_943734735.2 VEuPathDB +Toxoplasma gondii 5811 1 GCF_000006565.2 VEuPathDB +Mycobacterium tuberculosis 1773 1 GCF_000195955.2 Bact +Coccidioides posadasii 199306 1 GCF_018416015.2 VEuPathDB +Coccidioides immitis 5501 1 GCF_000149335.2 +Trypanosoma cruzi 5693 1 GCF_000209065.1 VEuPathDB +Trypanosoma brucei 5691 1 GCF_000002445.2 VEuPathDB +Leishmania major 5664 1 GCF_000002725.2 VEuPathDB +Leishmania donovani 5661 1 GCF_000227135.1 VEuPathDB +Leishmania braziliensis 5660 1 GCF_000002845.2 VEuPathDB +Severe acute respiratory syndrome coronavirus 2 2697049 1 GCF_009858895.2 Virus +Monkeypox virus 10244 1 GCF_000857045.1 Virus +Aspergillus fumigatus 746128 1 GCF_000002655.1 +Candida albicans 5476 1 GCF_000182965.3 +Cryptococcus neoformans 5207 1 GCF_000091045.1 From d4a8841f6c0e76f042305cc9861e0ce910bf405f Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Wed, 11 Dec 2024 23:19:09 -0800 Subject: [PATCH 18/30] fix: account for pagination when getting genomes (#177) --- files/build-files-from-ncbi.py | 18 +++++++++++++++--- 1 file changed, 15 insertions(+), 3 deletions(-) diff --git a/files/build-files-from-ncbi.py b/files/build-files-from-ncbi.py index 41a32f0..a882381 100644 --- a/files/build-files-from-ncbi.py +++ b/files/build-files-from-ncbi.py @@ -35,8 +35,8 @@ def get_organisms_df(taxa_with_accessions): def get_tax_ids(organisms_df): return list(organisms_df["taxonomyId"]) -def build_genomes_url(tax_ids): - return f"https://api.ncbi.nlm.nih.gov/datasets/v2/genome/taxon/{urllib.parse.quote(",".join([str(id) for id in tax_ids]))}/dataset_report?filters.assembly_source=refseq&filters.has_annotation=true&filters.exclude_paired_reports=true&filters.exclude_atypical=true&filters.assembly_level=scaffold&filters.assembly_level=chromosome&filters.assembly_level=complete_genome" +def build_genomes_url(tax_ids, next_page_token): + return f"https://api.ncbi.nlm.nih.gov/datasets/v2/genome/taxon/{urllib.parse.quote(",".join([str(id) for id in tax_ids]))}/dataset_report?page_size=1000{"&page_token=" + next_page_token if next_page_token else ""}&filters.assembly_source=refseq&filters.has_annotation=true&filters.exclude_paired_reports=true&filters.exclude_atypical=true&filters.assembly_level=scaffold&filters.assembly_level=chromosome&filters.assembly_level=complete_genome" def get_genome_row(genome_info, taxon): refseq_category = genome_info["assembly_info"].get("refseq_category") @@ -58,8 +58,20 @@ def get_genome_row(genome_info, taxon): "pairedAccession": genome_info["paired_accession"], } +def get_organism_genomes_results(tax_id): + page = 1 + next_page_token = None + results = [] + while next_page_token or page == 1: + print(f"Requesting page {page} of taxon {tax_id}") + page_data = requests.get(build_genomes_url([tax_id], next_page_token)).json() + results += page_data["reports"] + next_page_token = page_data.get("next_page_token") + page += 1 + return results + def get_organism_genomes(tax_id, accession): - return [genome_info for genome_info in requests.get(build_genomes_url([tax_id])).json()["reports"] if genome_info["accession"] == accession] + return [genome_info for genome_info in get_organism_genomes_results(tax_id) if genome_info["accession"] == accession] def get_genomes_df(organism_ids): genomes_info_with_organisms = [(genome_info, taxon) for tax_id, taxon, accession in organism_ids for genome_info in get_organism_genomes(tax_id, accession)] From 62d7edb4b1a83a891bc131d1a8b1885ed0582e15 Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Thu, 12 Dec 2024 02:06:40 -0800 Subject: [PATCH 19/30] feat: add underline to genome links in organisms list (#177) --- app/components/common/StyledLink/styledLink.styles.tsx | 6 ++++++ app/components/index.ts | 1 + .../brc-analytics-catalog/common/viewModelBuilders.ts | 2 +- .../brc-analytics/local/index/organismEntityConfig.ts | 4 ++-- 4 files changed, 10 insertions(+), 3 deletions(-) create mode 100644 app/components/common/StyledLink/styledLink.styles.tsx diff --git a/app/components/common/StyledLink/styledLink.styles.tsx b/app/components/common/StyledLink/styledLink.styles.tsx new file mode 100644 index 0000000..c0e74c5 --- /dev/null +++ b/app/components/common/StyledLink/styledLink.styles.tsx @@ -0,0 +1,6 @@ +import { Link } from "@databiosphere/findable-ui/lib/components/Links/components/Link/link"; +import styled from "@emotion/styled"; + +export const StyledLink = styled(Link)` + text-decoration: underline; +`; diff --git a/app/components/index.ts b/app/components/index.ts index 4a868b3..88553d9 100644 --- a/app/components/index.ts +++ b/app/components/index.ts @@ -24,6 +24,7 @@ export { Link } from "@databiosphere/findable-ui/lib/components/Links/components export { BasicCell } from "@databiosphere/findable-ui/lib/components/Table/components/TableCell/components/BasicCell/basicCell"; export { NTagCell } from "@databiosphere/findable-ui/lib/components/Table/components/TableCell/components/NTagCell/nTagCell"; export { CopyText } from "./common/CopyText/copyText"; +export { StyledLink } from "./common/StyledLink/styledLink.styles"; export { AnalysisMethod } from "./Entity/components/AnalysisMethod/analysisMethod"; export { AnalysisMethods } from "./Entity/components/AnalysisMethods/analysisMethods"; export { AnalysisMethodsTitle } from "./Entity/components/AnalysisMethodsTitle/analysisMethodsTitle"; diff --git a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts index 9b61ff8..cd0edbf 100644 --- a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts +++ b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts @@ -186,7 +186,7 @@ export const buildLevel = ( */ export const buildOrganismTaxon = ( organism: BRCDataCatalogOrganism -): ComponentProps => { +): ComponentProps => { return { label: organism.taxon, url: getTaxonGenomesUrlObject(organism.taxon), diff --git a/site-config/brc-analytics/local/index/organismEntityConfig.ts b/site-config/brc-analytics/local/index/organismEntityConfig.ts index 8c70ac2..6c007c0 100644 --- a/site-config/brc-analytics/local/index/organismEntityConfig.ts +++ b/site-config/brc-analytics/local/index/organismEntityConfig.ts @@ -52,9 +52,9 @@ export const organismEntityConfig: BRCEntityConfig = { columns: [ { componentConfig: { - component: C.Link, + component: C.StyledLink, viewBuilder: V.buildOrganismTaxon, - } as ComponentConfig, + } as ComponentConfig, header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXON, id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON, width: "auto", From b1226dd69b7f3338048362dcbecfd55cbf5d89eb Mon Sep 17 00:00:00 2001 From: Danielle Callan <53306535+d-callan@users.noreply.github.com> Date: Mon, 6 Jan 2025 08:44:13 -0500 Subject: [PATCH 20/30] content: re-apply "correcting spelling of VEuPathDB (#202)" refactor: correcting spelling of VEuPathDB (#197) --- .../Organisms/content/organismsWarning.mdx | 2 +- .../Home/content/sectionSubHero.mdx | 2 +- app/components/content/sectionAbout.mdx | 2 +- app/components/content/sectionRoadmap.mdx | 20 +++++++++---------- app/views/RoadmapView/roadmapView.tsx | 2 +- 5 files changed, 14 insertions(+), 14 deletions(-) diff --git a/app/components/EntityList/components/Organisms/content/organismsWarning.mdx b/app/components/EntityList/components/Organisms/content/organismsWarning.mdx index 6645d3d..f2da0ca 100644 --- a/app/components/EntityList/components/Organisms/content/organismsWarning.mdx +++ b/app/components/EntityList/components/Organisms/content/organismsWarning.mdx @@ -1,7 +1,7 @@ If you do not see your organism in this list: it will be there! We are in the process of ingesting sequences and annotations for all 785 taxa from - VEuPathDb. The table below is generated by comparing the list maintained by + VEuPathDB. The table below is generated by comparing the list maintained by VEuPathDB against official NCBI genome builds. The three buttons adjacent to each taxon direct you to a page listing available analytical workflows as well as direct links to genomic data (NCBI Datasets) and a genome browser (UCSC). A diff --git a/app/components/Home/content/sectionSubHero.mdx b/app/components/Home/content/sectionSubHero.mdx index 0512771..44d748f 100644 --- a/app/components/Home/content/sectionSubHero.mdx +++ b/app/components/Home/content/sectionSubHero.mdx @@ -1,5 +1,5 @@ BRC Analytics is your new destination for analysis of biological -data related to pathogens. Building on the foundation of VEuPathDb +data related to pathogens. Building on the foundation of VEuPathDB the platform will provide access and analysis capabilities for [785 eukaryotic pathogens](/data/genomes), hosts, and vectors. The functionality will be developed and made available incrementally over the [following months](/roadmap). diff --git a/app/components/content/sectionAbout.mdx b/app/components/content/sectionAbout.mdx index d1b0f9d..7f03fea 100644 --- a/app/components/content/sectionAbout.mdx +++ b/app/components/content/sectionAbout.mdx @@ -170,7 +170,7 @@ Biotechnology Information (NCBI) supplemented with custom annotations stored and distributed by the UCSC Table Browser. This data will include annotations that were previously available from - the VEuPathDb resource. Users will be able to view, download and + the VEuPathDB resource. Users will be able to view, download and visualize the data.{" "} diff --git a/app/components/content/sectionRoadmap.mdx b/app/components/content/sectionRoadmap.mdx index 2a8f336..60c56b6 100644 --- a/app/components/content/sectionRoadmap.mdx +++ b/app/components/content/sectionRoadmap.mdx @@ -10,28 +10,28 @@ - VEuPathDb database migration + VEuPathDB database migration - This set of tasks deals with transferring data from VEuPathDb + This set of tasks deals with transferring data from VEuPathDB infrastructure and creating a list of genomes that will be initially maintained within BRC Analytics. The number of taxa included in our system will - 1. Transferring databases and associated data from VEuPathDb servers to TACC infrastructure. - 1. Understanding the structure of VEuPathDb database and deciding which data will be ingested as custom + 1. Transferring databases and associated data from VEuPathDB servers to TACC infrastructure. + 1. Understanding the structure of VEuPathDB database and deciding which data will be ingested as custom tracks for the BRC Analytics instance of the UCSC Genome Browser. - 1. Uncovering how JBrowse instances were created within VEuPathDb gene pages and replicating this data at + 1. Uncovering how JBrowse instances were created within VEuPathDB gene pages and replicating this data at the BRC Analytics instance of the UCSC Genome Browser. Harmonization of genomic data for all taxa - This set of tasks ensures that BRC Analytics provides access to the latest versions of all 785 VEuPathDb + This set of tasks ensures that BRC Analytics provides access to the latest versions of all 785 VEuPathDB taxa and associated annotations. - 1. Build UCSC Genome Browsers for all 785 taxa by matching genomes found in VEuPathDb against NCBI Datasets. - 1. Add annotations that can be extracted from the VEuPathDb databases and JBrowse instances (related to 2 + 1. Build UCSC Genome Browsers for all 785 taxa by matching genomes found in VEuPathDB against NCBI Datasets. + 1. Add annotations that can be extracted from the VEuPathDB databases and JBrowse instances (related to 2 and 3 above) 1. Create links from UCSC Gene Pages to NCBI Gene pages 1. Work with NCBI on evolution of gene pages to contain information valuable for understanding the structure @@ -52,7 +52,7 @@ 1. Develop "simplified workflow" interface (see [Simplified workflow run interface galaxy#18883](https://github.com/galaxyproject/galaxy/issues/18883)) 1. Develop and polish workflows for variant discovery, epigenetics, transcriptomics, assembly, and protein - folding that were previously available to the users on VEuPathDb Galaxy instance. + folding that were previously available to the users on VEuPathDB Galaxy instance. @@ -60,7 +60,7 @@ 1. Create dedicated linkedin, mastodon, and bluesky accounts 1. Create a dedicated support channel using Discourse infrastructure. - 1. Try to connect with as many users of VEuPathDb as possible to solicit their feedback across multiple + 1. Try to connect with as many users of VEuPathDB as possible to solicit their feedback across multiple areas including: which features are needed, what genomes should be integrated, which key datasets need to be re-analyzed in put in the context of available genomic data. 1. Beginning on Oct 1st begin posting regular updates via social media channels. diff --git a/app/views/RoadmapView/roadmapView.tsx b/app/views/RoadmapView/roadmapView.tsx index b17a17b..059bcd5 100644 --- a/app/views/RoadmapView/roadmapView.tsx +++ b/app/views/RoadmapView/roadmapView.tsx @@ -9,7 +9,7 @@ export const RoadmapView = (): JSX.Element => { From fcf35759efa35151d8669a0360ccb82d231b79fc Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Tue, 14 Jan 2025 22:28:00 -0800 Subject: [PATCH 21/30] feat: remove links to genomes list (#208) --- .../components/Section/components/SectionHero/sectionHero.tsx | 2 +- app/components/Home/content/sectionSubHero.mdx | 2 +- pages/_app.tsx | 2 +- site-config/brc-analytics/local/config.ts | 1 - 4 files changed, 3 insertions(+), 4 deletions(-) diff --git a/app/components/Home/components/Section/components/SectionHero/sectionHero.tsx b/app/components/Home/components/Section/components/SectionHero/sectionHero.tsx index 21faa17..0069043 100644 --- a/app/components/Home/components/Section/components/SectionHero/sectionHero.tsx +++ b/app/components/Home/components/Section/components/SectionHero/sectionHero.tsx @@ -32,7 +32,7 @@ export const SectionHero = (): JSX.Element => { annotations and functional insights into disease-causing organisms and their carriers - diff --git a/app/components/Home/content/sectionSubHero.mdx b/app/components/Home/content/sectionSubHero.mdx index 44d748f..de87de0 100644 --- a/app/components/Home/content/sectionSubHero.mdx +++ b/app/components/Home/content/sectionSubHero.mdx @@ -1,5 +1,5 @@ BRC Analytics is your new destination for analysis of biological data related to pathogens. Building on the foundation of VEuPathDB the platform will provide access and analysis capabilities for -[785 eukaryotic pathogens](/data/genomes), hosts, and vectors. The functionality will +[785 eukaryotic pathogens](/data/organisms), hosts, and vectors. The functionality will be developed and made available incrementally over the [following months](/roadmap). diff --git a/pages/_app.tsx b/pages/_app.tsx index 799c6e6..b22a50f 100644 --- a/pages/_app.tsx +++ b/pages/_app.tsx @@ -21,7 +21,7 @@ import { config } from "../app/config/config"; import { mergeAppTheme } from "../app/theme/theme"; import { GoogleSignInAuthenticationProvider } from "@databiosphere/findable-ui/lib/providers/googleSignInAuthentication/provider"; -const DEFAULT_ENTITY_LIST_TYPE = "genomes"; +const DEFAULT_ENTITY_LIST_TYPE = "organisms"; export interface PageProps extends AzulEntitiesStaticResponse { pageTitle?: string; diff --git a/site-config/brc-analytics/local/config.ts b/site-config/brc-analytics/local/config.ts index 627af71..f68453d 100644 --- a/site-config/brc-analytics/local/config.ts +++ b/site-config/brc-analytics/local/config.ts @@ -76,7 +76,6 @@ export function makeConfig(browserUrl: string, gitHubUrl: string): SiteConfig { [ { label: "About", url: ROUTES.ABOUT }, { label: "Organisms", url: ROUTES.ORGANISMS }, - { label: "Genomes", url: ROUTES.GENOMES }, { label: "Roadmap", url: ROUTES.ROADMAP }, ], undefined, From ff061a1c2c1dcbb83143d9562f0ccdc4a6a9be67 Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Wed, 15 Jan 2025 13:12:27 -0800 Subject: [PATCH 22/30] feat: add genomes to organism model (#208) --- .../brc-analytics-catalog/common/entities.ts | 1 + files/build-catalog.ts | 8 +- files/out/organisms.json | 473 ++++++++++++++++++ 3 files changed, 480 insertions(+), 2 deletions(-) diff --git a/app/apis/catalog/brc-analytics-catalog/common/entities.ts b/app/apis/catalog/brc-analytics-catalog/common/entities.ts index fb529c2..75f309c 100644 --- a/app/apis/catalog/brc-analytics-catalog/common/entities.ts +++ b/app/apis/catalog/brc-analytics-catalog/common/entities.ts @@ -31,6 +31,7 @@ export interface BRCDataCatalogGenome { export interface BRCDataCatalogOrganism { assemblyCount: number; + genomes: BRCDataCatalogGenome[]; ncbiTaxonomyId: string; tags: string[]; taxon: string; diff --git a/files/build-catalog.ts b/files/build-catalog.ts index e3f7b88..aa4e57a 100644 --- a/files/build-catalog.ts +++ b/files/build-catalog.ts @@ -36,6 +36,7 @@ async function buildOrganisms(): Promise { const mappedRows = sourceRows.map((row): BRCDataCatalogOrganism => { return { assemblyCount: parseNumber(row.assemblyCount), + genomes: [], ncbiTaxonomyId: row.taxonomyId, tags: row.CustomTags ? [row.CustomTags] : [], taxon: row.taxon, @@ -51,7 +52,8 @@ async function buildGenomes( ): Promise { const sourceRows = await readValuesFile(SOURCE_PATH_GENOMES); const mappedRows = sourceRows.map((row): BRCDataCatalogGenome => { - return { + const organism = organismsByTaxon.get(row.taxon); + const genome: BRCDataCatalogGenome = { accession: row.accession, annotationStatus: parseStringOrNull(row.annotationStatus), chromosomes: parseNumberOrNull(row.chromosomeCount), @@ -66,10 +68,12 @@ async function buildGenomes( scaffoldL50: parseNumber(row.scaffoldL50), scaffoldN50: parseNumber(row.scaffoldN50), strain: parseStringOrNull(row.strain), - tags: organismsByTaxon.get(row.taxon)?.tags ?? [], + tags: organism?.tags ?? [], taxon: row.taxon, ucscBrowserUrl: parseStringOrNull(row.ucscBrowser), }; + organism?.genomes.push(genome); + return genome; }); return mappedRows.sort((a, b) => a.accession.localeCompare(b.accession)); } diff --git a/files/out/organisms.json b/files/out/organisms.json index 6d29b69..3af027b 100644 --- a/files/out/organisms.json +++ b/files/out/organisms.json @@ -1,6 +1,29 @@ [ { "assemblyCount": 1, + "genomes": [ + { + "accession": "GCF_000857045.1", + "annotationStatus": null, + "chromosomes": 1, + "coverage": null, + "gcPercent": 33, + "geneModelUrl": null, + "isRef": "No", + "length": 196858, + "level": "Complete Genome", + "ncbiTaxonomyId": "10244", + "scaffoldCount": 1, + "scaffoldL50": 1, + "scaffoldN50": 196858, + "strain": "Zaire-96-I-16", + "tags": [ + "Virus" + ], + "taxon": "Monkeypox virus", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000857045.1" + } + ], "ncbiTaxonomyId": "10244", "tags": [ "Virus" @@ -9,6 +32,29 @@ }, { "assemblyCount": 1, + "genomes": [ + { + "accession": "GCF_000195955.2", + "annotationStatus": null, + "chromosomes": 1, + "coverage": null, + "gcPercent": 65.5, + "geneModelUrl": null, + "isRef": "Yes", + "length": 4411532, + "level": "Complete Genome", + "ncbiTaxonomyId": "83332", + "scaffoldCount": 1, + "scaffoldL50": 1, + "scaffoldN50": 4411532, + "strain": "H37Rv", + "tags": [ + "Bact" + ], + "taxon": "Mycobacterium tuberculosis", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000195955.2" + } + ], "ncbiTaxonomyId": "1773", "tags": [ "Bact" @@ -17,6 +63,29 @@ }, { "assemblyCount": 1, + "genomes": [ + { + "accession": "GCF_018416015.2", + "annotationStatus": "Full annotation", + "chromosomes": 9, + "coverage": "475.0x", + "gcPercent": 46.5, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/018/416/015/GCF_018416015.2/genes/GCF_018416015.2_ASM1841601v2.ncbiRefSeq.gtf.gz", + "isRef": "Yes", + "length": 28193268, + "level": "Complete Genome", + "ncbiTaxonomyId": "443226", + "scaffoldCount": 9, + "scaffoldL50": 2, + "scaffoldN50": 8079863, + "strain": "Silveira", + "tags": [ + "VEuPathDB" + ], + "taxon": "Coccidioides posadasii", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_018416015.2" + } + ], "ncbiTaxonomyId": "199306", "tags": [ "VEuPathDB" @@ -25,6 +94,29 @@ }, { "assemblyCount": 1, + "genomes": [ + { + "accession": "GCF_009858895.2", + "annotationStatus": null, + "chromosomes": 1, + "coverage": null, + "gcPercent": 38, + "geneModelUrl": null, + "isRef": "No", + "length": 29903, + "level": "Complete Genome", + "ncbiTaxonomyId": "2697049", + "scaffoldCount": 1, + "scaffoldL50": 1, + "scaffoldN50": 29903, + "strain": null, + "tags": [ + "Virus" + ], + "taxon": "Severe acute respiratory syndrome coronavirus 2", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_009858895.2" + } + ], "ncbiTaxonomyId": "2697049", "tags": [ "Virus" @@ -33,30 +125,137 @@ }, { "assemblyCount": 1, + "genomes": [ + { + "accession": "GCF_016801865.2", + "annotationStatus": "Full annotation", + "chromosomes": 3, + "coverage": "250.0x", + "gcPercent": 37, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/016/801/865/GCF_016801865.2/genes/GCF_016801865.2_TS_CPP_V2.ncbiRefSeq.gtf.gz", + "isRef": "Yes", + "length": 566339288, + "level": "Chromosome", + "ncbiTaxonomyId": "42434", + "scaffoldCount": 289, + "scaffoldL50": 2, + "scaffoldN50": 186194774, + "strain": null, + "tags": [], + "taxon": "Culex pipiens pallens", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_016801865.2" + } + ], "ncbiTaxonomyId": "42434", "tags": [], "taxon": "Culex pipiens pallens" }, { "assemblyCount": 1, + "genomes": [ + { + "accession": "GCF_000091045.1", + "annotationStatus": "Full annotation", + "chromosomes": 14, + "coverage": null, + "gcPercent": 48.5, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/091/045/GCF_000091045.1/genes/GCF_000091045.1_ASM9104v1.ncbiRefSeq.gtf.gz", + "isRef": "Yes", + "length": 19051922, + "level": "Chromosome", + "ncbiTaxonomyId": "214684", + "scaffoldCount": 14, + "scaffoldL50": 6, + "scaffoldN50": 1438950, + "strain": "JEC21", + "tags": [], + "taxon": "Cryptococcus neoformans", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000091045.1" + } + ], "ncbiTaxonomyId": "5207", "tags": [], "taxon": "Cryptococcus neoformans" }, { "assemblyCount": 1, + "genomes": [ + { + "accession": "GCF_000182965.3", + "annotationStatus": "Full annotation", + "chromosomes": 8, + "coverage": "700.0x", + "gcPercent": 33.5, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/182/965/GCF_000182965.3/genes/GCF_000182965.3_ASM18296v3.ncbiRefSeq.gtf.gz", + "isRef": "Yes", + "length": 14282666, + "level": "Chromosome", + "ncbiTaxonomyId": "237561", + "scaffoldCount": 8, + "scaffoldL50": 3, + "scaffoldN50": 2231883, + "strain": "SC5314", + "tags": [], + "taxon": "Candida albicans", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000182965.3" + } + ], "ncbiTaxonomyId": "5476", "tags": [], "taxon": "Candida albicans" }, { "assemblyCount": 1, + "genomes": [ + { + "accession": "GCF_000149335.2", + "annotationStatus": "Full annotation", + "chromosomes": null, + "coverage": null, + "gcPercent": 46, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/149/335/GCF_000149335.2/genes/GCF_000149335.2_ASM14933v2.ncbiRefSeq.gtf.gz", + "isRef": "Yes", + "length": 28947925, + "level": "Scaffold", + "ncbiTaxonomyId": "246410", + "scaffoldCount": 6, + "scaffoldL50": 3, + "scaffoldN50": 4323945, + "strain": "RS", + "tags": [], + "taxon": "Coccidioides immitis", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000149335.2" + } + ], "ncbiTaxonomyId": "5501", "tags": [], "taxon": "Coccidioides immitis" }, { "assemblyCount": 1, + "genomes": [ + { + "accession": "GCF_000002845.2", + "annotationStatus": null, + "chromosomes": 35, + "coverage": null, + "gcPercent": 58, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/845/GCF_000002845.2/genes/GCF_000002845.2_ASM284v2.ncbiRefSeq.gtf.gz", + "isRef": "Yes", + "length": 32068771, + "level": "Chromosome", + "ncbiTaxonomyId": "420245", + "scaffoldCount": 138, + "scaffoldL50": 11, + "scaffoldN50": 992961, + "strain": "MHOM/BR/75/M2904", + "tags": [ + "VEuPathDB" + ], + "taxon": "Leishmania braziliensis", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002845.2" + } + ], "ncbiTaxonomyId": "5660", "tags": [ "VEuPathDB" @@ -65,6 +264,29 @@ }, { "assemblyCount": 1, + "genomes": [ + { + "accession": "GCF_000227135.1", + "annotationStatus": "Full annotation", + "chromosomes": 36, + "coverage": null, + "gcPercent": 59.5, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/227/135/GCF_000227135.1/genes/GCF_000227135.1_ASM22713v2.ncbiRefSeq.gtf.gz", + "isRef": "Yes", + "length": 32444968, + "level": "Chromosome", + "ncbiTaxonomyId": "5661", + "scaffoldCount": 36, + "scaffoldL50": 11, + "scaffoldN50": 1024085, + "strain": "BPK282A1", + "tags": [ + "VEuPathDB" + ], + "taxon": "Leishmania donovani", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000227135.1" + } + ], "ncbiTaxonomyId": "5661", "tags": [ "VEuPathDB" @@ -73,6 +295,29 @@ }, { "assemblyCount": 1, + "genomes": [ + { + "accession": "GCF_000002725.2", + "annotationStatus": "Full annotation", + "chromosomes": 36, + "coverage": null, + "gcPercent": 59.5, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/725/GCF_000002725.2/genes/GCF_000002725.2_ASM272v2.ncbiRefSeq.gtf.gz", + "isRef": "Yes", + "length": 32855089, + "level": "Complete Genome", + "ncbiTaxonomyId": "347515", + "scaffoldCount": 36, + "scaffoldL50": 11, + "scaffoldN50": 1091540, + "strain": "Friedlin", + "tags": [ + "VEuPathDB" + ], + "taxon": "Leishmania major", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002725.2" + } + ], "ncbiTaxonomyId": "5664", "tags": [ "VEuPathDB" @@ -81,6 +326,29 @@ }, { "assemblyCount": 1, + "genomes": [ + { + "accession": "GCF_000002445.2", + "annotationStatus": "Full annotation", + "chromosomes": 11, + "coverage": null, + "gcPercent": 46.5, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/445/GCF_000002445.2/genes/GCF_000002445.2_ASM244v1.ncbiRefSeq.gtf.gz", + "isRef": "Yes", + "length": 26075494, + "level": "Chromosome", + "ncbiTaxonomyId": "185431", + "scaffoldCount": 12, + "scaffoldL50": 4, + "scaffoldN50": 2481190, + "strain": null, + "tags": [ + "VEuPathDB" + ], + "taxon": "Trypanosoma brucei", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002445.2" + } + ], "ncbiTaxonomyId": "5691", "tags": [ "VEuPathDB" @@ -89,6 +357,29 @@ }, { "assemblyCount": 1, + "genomes": [ + { + "accession": "GCF_000209065.1", + "annotationStatus": "Full annotation", + "chromosomes": null, + "coverage": null, + "gcPercent": 51.5, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/209/065/GCF_000209065.1/genes/GCF_000209065.1_ASM20906v1.ncbiRefSeq.gtf.gz", + "isRef": "Yes", + "length": 89937456, + "level": "Scaffold", + "ncbiTaxonomyId": "5693", + "scaffoldCount": 29495, + "scaffoldL50": 212, + "scaffoldN50": 88624, + "strain": "CL Brener", + "tags": [ + "VEuPathDB" + ], + "taxon": "Trypanosoma cruzi", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000209065.1" + } + ], "ncbiTaxonomyId": "5693", "tags": [ "VEuPathDB" @@ -97,6 +388,29 @@ }, { "assemblyCount": 1, + "genomes": [ + { + "accession": "GCF_000006565.2", + "annotationStatus": null, + "chromosomes": 14, + "coverage": "26.5x", + "gcPercent": 52.5, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/006/565/GCF_000006565.2/genes/GCF_000006565.2_TGA4.ncbiRefSeq.gtf.gz", + "isRef": "Yes", + "length": 65633124, + "level": "Chromosome", + "ncbiTaxonomyId": "508771", + "scaffoldCount": 2276, + "scaffoldL50": 6, + "scaffoldN50": 4973582, + "strain": "ME49", + "tags": [ + "VEuPathDB" + ], + "taxon": "Toxoplasma gondii", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000006565.2" + } + ], "ncbiTaxonomyId": "5811", "tags": [ "VEuPathDB" @@ -105,6 +419,29 @@ }, { "assemblyCount": 1, + "genomes": [ + { + "accession": "GCF_000002765.6", + "annotationStatus": "Full annotation", + "chromosomes": 14, + "coverage": "100.0x", + "gcPercent": 19.5, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/765/GCF_000002765.6/genes/GCF_000002765.6_GCA_000002765.ncbiRefSeq.gtf.gz", + "isRef": "Yes", + "length": 23292622, + "level": "Complete Genome", + "ncbiTaxonomyId": "36329", + "scaffoldCount": 14, + "scaffoldL50": 5, + "scaffoldN50": 1687656, + "strain": null, + "tags": [ + "VEuPathDB" + ], + "taxon": "Plasmodium falciparum", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002765.6" + } + ], "ncbiTaxonomyId": "5833", "tags": [ "VEuPathDB" @@ -113,6 +450,29 @@ }, { "assemblyCount": 1, + "genomes": [ + { + "accession": "GCF_000002415.2", + "annotationStatus": "Full annotation", + "chromosomes": 14, + "coverage": null, + "gcPercent": 42.5, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/415/GCF_000002415.2/genes/GCF_000002415.2_ASM241v2.ncbiRefSeq.gtf.gz", + "isRef": "Yes", + "length": 27007701, + "level": "Chromosome", + "ncbiTaxonomyId": "5855", + "scaffoldCount": 2747, + "scaffoldL50": 6, + "scaffoldN50": 1678596, + "strain": "Salvador I", + "tags": [ + "VEuPathDB" + ], + "taxon": "Plasmodium vivax", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002415.2" + } + ], "ncbiTaxonomyId": "5855", "tags": [ "VEuPathDB" @@ -121,6 +481,29 @@ }, { "assemblyCount": 1, + "genomes": [ + { + "accession": "GCF_900681995.1", + "annotationStatus": "Full annotation", + "chromosomes": 14, + "coverage": "155.0x", + "gcPercent": 23, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/900/681/995/GCF_900681995.1/genes/GCF_900681995.1_PVVCY_v1.ncbiRefSeq.gtf.gz", + "isRef": "Yes", + "length": 18338688, + "level": "Chromosome", + "ncbiTaxonomyId": "54757", + "scaffoldCount": 14, + "scaffoldL50": 5, + "scaffoldN50": 1692345, + "strain": null, + "tags": [ + "VEuPathDB" + ], + "taxon": "Plasmodium vinckei", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_900681995.1" + } + ], "ncbiTaxonomyId": "5860", "tags": [ "VEuPathDB" @@ -129,6 +512,29 @@ }, { "assemblyCount": 1, + "genomes": [ + { + "accession": "GCF_900002385.2", + "annotationStatus": "Full annotation", + "chromosomes": 14, + "coverage": "100.0x", + "gcPercent": 21.5, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/900/002/385/GCF_900002385.2/genes/GCF_900002385.2_GCA_900002385.ncbiRefSeq.gtf.gz", + "isRef": "Yes", + "length": 23043114, + "level": "Complete Genome", + "ncbiTaxonomyId": "5861", + "scaffoldCount": 14, + "scaffoldL50": 5, + "scaffoldN50": 2046250, + "strain": "17X", + "tags": [ + "VEuPathDB" + ], + "taxon": "Plasmodium yoelii", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_900002385.2" + } + ], "ncbiTaxonomyId": "5861", "tags": [ "VEuPathDB" @@ -137,6 +543,29 @@ }, { "assemblyCount": 1, + "genomes": [ + { + "accession": "GCF_943734735.2", + "annotationStatus": "Full annotation", + "chromosomes": 3, + "coverage": "54.0x", + "gcPercent": 44.5, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/943/734/735/GCF_943734735.2/genes/GCF_943734735.2_idAnoGambNW_F1_1.ncbiRefSeq.gtf.gz", + "isRef": "Yes", + "length": 264451381, + "level": "Chromosome", + "ncbiTaxonomyId": "7165", + "scaffoldCount": 190, + "scaffoldL50": 2, + "scaffoldN50": 99149756, + "strain": null, + "tags": [ + "VEuPathDB" + ], + "taxon": "Anopheles gambiae", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943734735.2" + } + ], "ncbiTaxonomyId": "7165", "tags": [ "VEuPathDB" @@ -145,6 +574,29 @@ }, { "assemblyCount": 1, + "genomes": [ + { + "accession": "GCF_015732765.1", + "annotationStatus": "Full annotation", + "chromosomes": 3, + "coverage": "76.0x", + "gcPercent": 37, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/015/732/765/GCF_015732765.1/genes/GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal.ncbiRefSeq.gtf.gz", + "isRef": "Yes", + "length": 573214445, + "level": "Chromosome", + "ncbiTaxonomyId": "7176", + "scaffoldCount": 56, + "scaffoldL50": 2, + "scaffoldN50": 201550677, + "strain": "JHB", + "tags": [ + "VEuPathDB" + ], + "taxon": "Culex quinquefasciatus", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_015732765.1" + } + ], "ncbiTaxonomyId": "7176", "tags": [ "VEuPathDB" @@ -153,6 +605,27 @@ }, { "assemblyCount": 1, + "genomes": [ + { + "accession": "GCF_000002655.1", + "annotationStatus": "Full annotation", + "chromosomes": 8, + "coverage": null, + "gcPercent": 50, + "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/655/GCF_000002655.1/genes/GCF_000002655.1_ASM265v1.ncbiRefSeq.gtf.gz", + "isRef": "Yes", + "length": 29384958, + "level": "Chromosome", + "ncbiTaxonomyId": "330879", + "scaffoldCount": 8, + "scaffoldL50": 4, + "scaffoldN50": 3948441, + "strain": "Af293", + "tags": [], + "taxon": "Aspergillus fumigatus", + "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002655.1" + } + ], "ncbiTaxonomyId": "746128", "tags": [], "taxon": "Aspergillus fumigatus" From dbbf8c12b40c2daf91e65c6e08d083a936ac3173 Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Wed, 15 Jan 2025 15:38:17 -0800 Subject: [PATCH 23/30] feat: add basic organism detail page with genome list (#208) --- app/components/index.ts | 1 + .../common/viewModelBuilders.ts | 165 +++++++++++++++--- .../entity/organism/assembliesMainColumn.ts | 15 ++ .../local/entity/organism/assembliesTop.ts | 14 ++ .../local/index/organismEntityConfig.ts | 11 +- 5 files changed, 180 insertions(+), 26 deletions(-) create mode 100644 site-config/brc-analytics/local/entity/organism/assembliesMainColumn.ts create mode 100644 site-config/brc-analytics/local/entity/organism/assembliesTop.ts diff --git a/app/components/index.ts b/app/components/index.ts index 88553d9..c7ff915 100644 --- a/app/components/index.ts +++ b/app/components/index.ts @@ -19,6 +19,7 @@ export { BackPageContentSideColumn, BackPageContentSingleColumn, } from "@databiosphere/findable-ui/lib/components/Layout/components/BackPage/backPageView.styles"; +export { DetailViewTable } from "@databiosphere/findable-ui/lib/components/Detail/components/DetailViewTable/detailViewTable"; export { Logo } from "@databiosphere/findable-ui/lib/components/Layout/components/Header/components/Content/components/Logo/logo"; export { Link } from "@databiosphere/findable-ui/lib/components/Links/components/Link/link"; export { BasicCell } from "@databiosphere/findable-ui/lib/components/Table/components/TableCell/components/BasicCell/basicCell"; diff --git a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts index cd0edbf..9cdb6ab 100644 --- a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts +++ b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts @@ -3,8 +3,6 @@ import { Key, Value, } from "@databiosphere/findable-ui/lib/components/common/KeyValuePairs/keyValuePairs"; -import { LinkProps } from "@databiosphere/findable-ui/lib/components/Links/components/Link/link"; -import { ViewContext } from "@databiosphere/findable-ui/lib/config/entities"; import { ComponentProps } from "react"; import { ROUTES } from "../../../../../routes/constants"; import { @@ -13,6 +11,15 @@ import { } from "../../../../apis/catalog/brc-analytics-catalog/common/entities"; import * as C from "../../../../components"; import { GENOME_BROWSER, NCBI_DATASETS_URL } from "./constants"; +import { ColumnDef } from "@tanstack/react-table"; +import { + BRC_DATA_CATALOG_CATEGORY_KEY, + BRC_DATA_CATALOG_CATEGORY_LABEL, +} from "site-config/brc-analytics/category"; +import { + getGenomeId, + getOrganismId, +} from "../../../../apis/catalog/brc-analytics-catalog/common/utils"; /** * Build props for the accession cell. @@ -30,19 +37,16 @@ export const buildAccession = ( /** * Build props for the genome analysis cell. * @param genome - Genome entity. - * @param viewContext - View context. * @returns Props to be used for the AnalyzeGenome component. */ export const buildAnalyzeGenome = ( - genome: BRCDataCatalogGenome, - viewContext: ViewContext + genome: BRCDataCatalogGenome ): ComponentProps => { const { accession, ncbiTaxonomyId, ucscBrowserUrl } = genome; - const rowId = viewContext.cellContext?.row?.id; return { analyze: { label: "Analyze", - url: rowId ? `${ROUTES.GENOMES}/${rowId}` : "", + url: `${ROUTES.GENOMES}/${encodeURIComponent(getGenomeId(genome))}`, }, views: [ ...(ucscBrowserUrl @@ -189,7 +193,7 @@ export const buildOrganismTaxon = ( ): ComponentProps => { return { label: organism.taxon, - url: getTaxonGenomesUrlObject(organism.taxon), + url: `${ROUTES.ORGANISMS}/${encodeURIComponent(getOrganismId(organism))}`, }; }; @@ -369,6 +373,123 @@ export const buildGenomeDetails = ( }; }; +/** + * Build props for the organism DetailViewHero component. + * @param organism - Organism entity. + * @returns Props to be used for the DetailViewHero component. + */ +export const buildOrganismAssembliesDetailViewHero = ( + organism: BRCDataCatalogOrganism +): ComponentProps => { + return { + breadcrumbs: C.Breadcrumbs({ + breadcrumbs: getOrganismEntityAssembliesBreadcrumbs(organism), + }), + title: "Assemblies", + }; +}; + +/** + * Build props for the genomes table for the given organism. + * @param organism - Organism entity. + * @returns props to be used for the table. + */ +export function buildOrganismGenomesTable( + organism: BRCDataCatalogOrganism +): ComponentProps> { + return { + columns: buildOrganismGenomesTableColumns(), + gridTemplateColumns: + "auto auto minmax(240px, 1fr) minmax(180px, 0.5fr) minmax(100px, 0.5fr) minmax(164px, 1fr) minmax(100px, 0.5fr) repeat(2, minmax(142px, 0.5fr)) minmax(120px, 0.5fr) minmax(80px, 0.5fr) minmax(142px, 0.5fr) repeat(3, minmax(80px, 0.5fr)) minmax(142px, 0.5fr)", + items: organism.genomes, + noResultsTitle: "No Assemblies", + }; +} + +/** + * Build the column definitions for the organism genomes table. + * @returns column definitions. + */ +function buildOrganismGenomesTableColumns(): ColumnDef[] { + return [ + { + accessorKey: BRC_DATA_CATALOG_CATEGORY_KEY.ANALYZE_GENOME, + cell: ({ row }) => C.AnalyzeGenome(buildAnalyzeGenome(row.original)), + header: BRC_DATA_CATALOG_CATEGORY_LABEL.ANALYZE_GENOME, + }, + { + accessorKey: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON, + cell: ({ row }) => C.BasicCell(buildGenomeTaxon(row.original)), + header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXON, + }, + { + accessorKey: BRC_DATA_CATALOG_CATEGORY_KEY.STRAIN, + cell: ({ row }) => C.BasicCell(buildStrain(row.original)), + header: BRC_DATA_CATALOG_CATEGORY_LABEL.STRAIN, + }, + { + accessorKey: BRC_DATA_CATALOG_CATEGORY_KEY.TAXONOMY_ID, + cell: ({ row }) => C.BasicCell(buildTaxonomyId(row.original)), + header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXONOMY_ID, + }, + { + accessorKey: BRC_DATA_CATALOG_CATEGORY_KEY.ACCESSION, + cell: ({ row }) => C.BasicCell(buildAccession(row.original)), + header: BRC_DATA_CATALOG_CATEGORY_LABEL.ACCESSION, + }, + { + accessorKey: BRC_DATA_CATALOG_CATEGORY_KEY.IS_REF, + cell: ({ row }) => C.BasicCell(buildIsRef(row.original)), + header: BRC_DATA_CATALOG_CATEGORY_LABEL.IS_REF, + }, + { + accessorKey: BRC_DATA_CATALOG_CATEGORY_KEY.LEVEL, + cell: ({ row }) => C.BasicCell(buildLevel(row.original)), + header: BRC_DATA_CATALOG_CATEGORY_LABEL.LEVEL, + }, + { + accessorKey: BRC_DATA_CATALOG_CATEGORY_KEY.CHROMOSOMES, + cell: ({ row }) => C.BasicCell(buildChromosomes(row.original)), + header: BRC_DATA_CATALOG_CATEGORY_LABEL.CHROMOSOMES, + }, + { + accessorKey: BRC_DATA_CATALOG_CATEGORY_KEY.LENGTH, + cell: ({ row }) => C.BasicCell(buildLength(row.original)), + header: BRC_DATA_CATALOG_CATEGORY_LABEL.LENGTH, + }, + { + accessorKey: BRC_DATA_CATALOG_CATEGORY_KEY.SCAFFOLD_COUNT, + cell: ({ row }) => C.BasicCell(buildScaffoldCount(row.original)), + header: BRC_DATA_CATALOG_CATEGORY_LABEL.SCAFFOLD_COUNT, + }, + { + accessorKey: BRC_DATA_CATALOG_CATEGORY_KEY.SCAFFOLD_N50, + cell: ({ row }) => C.BasicCell(buildScaffoldN50(row.original)), + header: BRC_DATA_CATALOG_CATEGORY_LABEL.SCAFFOLD_N50, + }, + { + accessorKey: BRC_DATA_CATALOG_CATEGORY_KEY.SCAFFOLD_L50, + cell: ({ row }) => C.BasicCell(buildScaffoldL50(row.original)), + header: BRC_DATA_CATALOG_CATEGORY_LABEL.SCAFFOLD_L50, + }, + { + accessorKey: BRC_DATA_CATALOG_CATEGORY_KEY.COVERAGE, + cell: ({ row }) => C.BasicCell(buildCoverage(row.original)), + header: BRC_DATA_CATALOG_CATEGORY_LABEL.COVERAGE, + }, + { + accessorKey: BRC_DATA_CATALOG_CATEGORY_KEY.GC_PERCENT, + cell: ({ row }) => C.BasicCell(buildGcPercent(row.original)), + header: BRC_DATA_CATALOG_CATEGORY_LABEL.GC_PERCENT, + }, + { + accessorKey: BRC_DATA_CATALOG_CATEGORY_KEY.ANNOTATION_STATUS, + cell: ({ row }) => C.BasicCell(buildAnnotationStatus(row.original)), + header: BRC_DATA_CATALOG_CATEGORY_LABEL.ANNOTATION_STATUS, + }, + ]; +} + /** * Get the genome entity breadcrumbs. * @param genome - Genome entity. @@ -385,22 +506,16 @@ function getGenomeEntityChooseAnalysisMethodBreadcrumbs( } /** - * Get URL object for genomes filtered by a given taxon. - * @param taxon - Taxon. - * @returns URL object. + * Get the organism entity breadcrumbs. + * @param organism - Organism entity. + * @returns Breadcrumbs. */ -function getTaxonGenomesUrlObject(taxon: string): LinkProps["url"] { - return { - href: ROUTES.GENOMES, - query: encodeURIComponent( - JSON.stringify({ - filter: [ - { - categoryKey: "taxon", - value: [taxon], - }, - ], - }) - ), - }; +function getOrganismEntityAssembliesBreadcrumbs( + organism: BRCDataCatalogOrganism +): Breadcrumb[] { + return [ + { path: ROUTES.ORGANISMS, text: "Organisms" }, + { path: "", text: `${organism.taxon}` }, + { path: "", text: "Assemblies" }, + ]; } diff --git a/site-config/brc-analytics/local/entity/organism/assembliesMainColumn.ts b/site-config/brc-analytics/local/entity/organism/assembliesMainColumn.ts new file mode 100644 index 0000000..fc12500 --- /dev/null +++ b/site-config/brc-analytics/local/entity/organism/assembliesMainColumn.ts @@ -0,0 +1,15 @@ +import { ComponentsConfig } from "@databiosphere/findable-ui/lib/config/entities"; +import * as C from "../../../../../app/components"; +import * as V from "../../../../../app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders"; + +export const assembliesMainColumn: ComponentsConfig = [ + { + children: [ + { + component: C.DetailViewTable, + viewBuilder: V.buildOrganismGenomesTable, + }, + ], + component: C.BackPageContentMainColumn, + }, +]; diff --git a/site-config/brc-analytics/local/entity/organism/assembliesTop.ts b/site-config/brc-analytics/local/entity/organism/assembliesTop.ts new file mode 100644 index 0000000..eaff453 --- /dev/null +++ b/site-config/brc-analytics/local/entity/organism/assembliesTop.ts @@ -0,0 +1,14 @@ +import { + ComponentConfig, + ComponentsConfig, +} from "@databiosphere/findable-ui/lib/config/entities"; +import { BRCDataCatalogOrganism } from "../../../../../app/apis/catalog/brc-analytics-catalog/common/entities"; +import * as C from "../../../../../app/components"; +import * as V from "../../../../../app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders"; + +export const assembliesTop: ComponentsConfig = [ + { + component: C.DetailViewHero, + viewBuilder: V.buildOrganismAssembliesDetailViewHero, + } as ComponentConfig, +]; diff --git a/site-config/brc-analytics/local/index/organismEntityConfig.ts b/site-config/brc-analytics/local/index/organismEntityConfig.ts index 6c007c0..7704d19 100644 --- a/site-config/brc-analytics/local/index/organismEntityConfig.ts +++ b/site-config/brc-analytics/local/index/organismEntityConfig.ts @@ -13,6 +13,8 @@ import { BRC_DATA_CATALOG_CATEGORY_KEY, BRC_DATA_CATALOG_CATEGORY_LABEL, } from "../../category"; +import { assembliesMainColumn } from "../entity/organism/assembliesMainColumn"; +import { assembliesTop } from "../entity/organism/assembliesTop"; /** * Entity config object responsible to config anything related to the /genomes route. @@ -42,7 +44,14 @@ export const organismEntityConfig: BRCEntityConfig = { detail: { detailOverviews: [], staticLoad: true, - tabs: [], + tabs: [ + { + label: "Assemblies", + mainColumn: assembliesMainColumn, + route: "", + top: assembliesTop, + }, + ], }, exploreMode: EXPLORE_MODE.CS_FETCH_CS_FILTERING, explorerTitle: "Organisms", From 68d70f74bb10748940682573529f5f88d04884b9 Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Wed, 15 Jan 2025 16:00:02 -0800 Subject: [PATCH 24/30] feat: make organism genome list full-width and without row number (#208) --- .../brc-analytics-catalog/common/viewModelBuilders.ts | 9 ++++++++- .../local/entity/organism/assembliesMainColumn.ts | 2 +- 2 files changed, 9 insertions(+), 2 deletions(-) diff --git a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts index 9cdb6ab..e0b341d 100644 --- a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts +++ b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts @@ -20,6 +20,7 @@ import { getGenomeId, getOrganismId, } from "../../../../apis/catalog/brc-analytics-catalog/common/utils"; +import { COLUMN_IDENTIFIER } from "@databiosphere/findable-ui/lib/components/Table/common/columnIdentifier"; /** * Build props for the accession cell. @@ -400,9 +401,15 @@ export function buildOrganismGenomesTable( return { columns: buildOrganismGenomesTableColumns(), gridTemplateColumns: - "auto auto minmax(240px, 1fr) minmax(180px, 0.5fr) minmax(100px, 0.5fr) minmax(164px, 1fr) minmax(100px, 0.5fr) repeat(2, minmax(142px, 0.5fr)) minmax(120px, 0.5fr) minmax(80px, 0.5fr) minmax(142px, 0.5fr) repeat(3, minmax(80px, 0.5fr)) minmax(142px, 0.5fr)", + "auto minmax(240px, 1fr) minmax(180px, 0.5fr) minmax(100px, 0.5fr) minmax(164px, 1fr) minmax(100px, 0.5fr) repeat(2, minmax(142px, 0.5fr)) minmax(120px, 0.5fr) minmax(80px, 0.5fr) minmax(142px, 0.5fr) repeat(3, minmax(80px, 0.5fr)) minmax(142px, 0.5fr)", items: organism.genomes, noResultsTitle: "No Assemblies", + tableOptions: { + enableRowPosition: false, + initialState: { + columnVisibility: { [COLUMN_IDENTIFIER.ROW_POSITION]: false }, + }, + }, }; } diff --git a/site-config/brc-analytics/local/entity/organism/assembliesMainColumn.ts b/site-config/brc-analytics/local/entity/organism/assembliesMainColumn.ts index fc12500..2b14bbf 100644 --- a/site-config/brc-analytics/local/entity/organism/assembliesMainColumn.ts +++ b/site-config/brc-analytics/local/entity/organism/assembliesMainColumn.ts @@ -10,6 +10,6 @@ export const assembliesMainColumn: ComponentsConfig = [ viewBuilder: V.buildOrganismGenomesTable, }, ], - component: C.BackPageContentMainColumn, + component: C.BackPageContentSingleColumn, }, ]; From dc24f63e71aacb126e2c15e77f9f0e04e26dce87 Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Wed, 15 Jan 2025 16:04:34 -0800 Subject: [PATCH 25/30] feat: remove detail page back button (#208) --- .../BackButton/backButton.styles.ts | 10 ------ .../components/BackButton/backButton.tsx | 32 ------------------- .../DetailViewHero/detailViewHero.tsx | 2 -- 3 files changed, 44 deletions(-) delete mode 100644 app/components/Layout/components/Detail/components/DetailViewHero/components/BackButton/backButton.styles.ts delete mode 100644 app/components/Layout/components/Detail/components/DetailViewHero/components/BackButton/backButton.tsx diff --git a/app/components/Layout/components/Detail/components/DetailViewHero/components/BackButton/backButton.styles.ts b/app/components/Layout/components/Detail/components/DetailViewHero/components/BackButton/backButton.styles.ts deleted file mode 100644 index 8d60439..0000000 --- a/app/components/Layout/components/Detail/components/DetailViewHero/components/BackButton/backButton.styles.ts +++ /dev/null @@ -1,10 +0,0 @@ -import { mediaDesktopSmallUp } from "@databiosphere/findable-ui/lib/styles/common/mixins/breakpoints"; -import styled from "@emotion/styled"; -import { HeroActions as DetailViewActions } from "../../detailViewHero.styles"; - -export const HeroActions = styled(DetailViewActions)` - ${mediaDesktopSmallUp} { - align-self: flex-start; - margin: 8px 0; - } -`; diff --git a/app/components/Layout/components/Detail/components/DetailViewHero/components/BackButton/backButton.tsx b/app/components/Layout/components/Detail/components/DetailViewHero/components/BackButton/backButton.tsx deleted file mode 100644 index 4adab81..0000000 --- a/app/components/Layout/components/Detail/components/DetailViewHero/components/BackButton/backButton.tsx +++ /dev/null @@ -1,32 +0,0 @@ -import { SouthIcon } from "@databiosphere/findable-ui/lib/components/common/CustomIcon/components/SouthIcon/southIcon"; -import { IconButton } from "@mui/material"; -import { useRouter } from "next/router"; -import { useCallback } from "react"; -import { HeroActions } from "./backButton.styles"; - -export const BackButton = (): JSX.Element => { - const { asPath, push } = useRouter(); - const onNavigate = useCallback( - () => push(getNextPath(asPath)), - [asPath, push] - ); - return ( - - - - - - ); -}; - -/** - * Returns the next path to navigate to when the back button is clicked. - * The back button will navigate to the parent path of the current path. - * @param asPath - Current path. - * @returns next path. - */ -function getNextPath(asPath: string): string { - const path = asPath.split("/"); - path.pop(); - return path.join("/"); -} diff --git a/app/components/Layout/components/Detail/components/DetailViewHero/detailViewHero.tsx b/app/components/Layout/components/Detail/components/DetailViewHero/detailViewHero.tsx index 00019d2..71b3389 100644 --- a/app/components/Layout/components/Detail/components/DetailViewHero/detailViewHero.tsx +++ b/app/components/Layout/components/Detail/components/DetailViewHero/detailViewHero.tsx @@ -3,7 +3,6 @@ import { SubTitle } from "@databiosphere/findable-ui/lib/components/Layout/compo import { TEXT_HEADING } from "@databiosphere/findable-ui/lib/theme/common/typography"; import { HeroTitle as Typography } from "@databiosphere/findable-ui/src/components/common/Title/title.styles"; import { ReactNode } from "react"; -import { BackButton } from "./components/BackButton/backButton"; import { DetailViewHeroHeadline, DetailViewHero as DetailViewHeroLayout, @@ -29,7 +28,6 @@ export const DetailViewHero = ({ {(breadcrumbs || title) && ( - {breadcrumbs} From ee9547d007c20b3bc7fdae6f140b0dbbd911bc13 Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Wed, 15 Jan 2025 16:10:22 -0800 Subject: [PATCH 26/30] feat: remove genomes to assemblies in interface (#208) --- .../brc-analytics-catalog/common/viewModelBuilders.ts | 2 +- routes/constants.ts | 2 +- .../brc-analytics/local/index/genomeEntityConfig.ts | 10 +++++----- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts index e0b341d..fbf2746 100644 --- a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts +++ b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts @@ -506,7 +506,7 @@ function getGenomeEntityChooseAnalysisMethodBreadcrumbs( genome: BRCDataCatalogGenome ): Breadcrumb[] { return [ - { path: ROUTES.GENOMES, text: "Genomes" }, + { path: ROUTES.GENOMES, text: "Assemblies" }, { path: "", text: `${genome.taxon}` }, { path: "", text: "Choose Analysis Methods" }, ]; diff --git a/routes/constants.ts b/routes/constants.ts index b1f6088..2992aad 100644 --- a/routes/constants.ts +++ b/routes/constants.ts @@ -1,6 +1,6 @@ export const ROUTES = { ABOUT: "/about", - GENOMES: "/data/genomes", + GENOMES: "/data/assemblies", ORGANISMS: "/data/organisms", ROADMAP: "/roadmap", }; diff --git a/site-config/brc-analytics/local/index/genomeEntityConfig.ts b/site-config/brc-analytics/local/index/genomeEntityConfig.ts index 41962bf..a46c3ac 100644 --- a/site-config/brc-analytics/local/index/genomeEntityConfig.ts +++ b/site-config/brc-analytics/local/index/genomeEntityConfig.ts @@ -22,7 +22,7 @@ import { top as analysisMethodsTop } from "../entity/genome/analysisMethodsTop"; import { listHero } from "../listView/listHero"; /** - * Entity config object responsible to config anything related to the /genomes route. + * Entity config object responsible to config anything related to the /assemblies route. */ export const genomeEntityConfig: BRCEntityConfig = { categoryGroupConfig: { @@ -68,7 +68,7 @@ export const genomeEntityConfig: BRCEntityConfig = { ], }, ], - key: "genomes", + key: "assemblies", }, detail: { detailOverviews: [], @@ -84,10 +84,10 @@ export const genomeEntityConfig: BRCEntityConfig = { ], }, exploreMode: EXPLORE_MODE.CS_FETCH_CS_FILTERING, - explorerTitle: "Genomes", + explorerTitle: "Assemblies", getId: getGenomeId, getTitle: getGenomeTitle, - label: "Genomes", + label: "Assemblies", list: { columns: [ { @@ -255,6 +255,6 @@ export const genomeEntityConfig: BRCEntityConfig = { enableTab: false, listHero, }, - route: "genomes", + route: "assemblies", staticLoadFile: "files/out/genomes.json", }; From 977522cc8ee6b33b686444d0c7161c3e835a73a0 Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Wed, 15 Jan 2025 16:11:37 -0800 Subject: [PATCH 27/30] feat: restore assemblies navigation link (#208) --- site-config/brc-analytics/local/config.ts | 1 + 1 file changed, 1 insertion(+) diff --git a/site-config/brc-analytics/local/config.ts b/site-config/brc-analytics/local/config.ts index f68453d..dd7b366 100644 --- a/site-config/brc-analytics/local/config.ts +++ b/site-config/brc-analytics/local/config.ts @@ -76,6 +76,7 @@ export function makeConfig(browserUrl: string, gitHubUrl: string): SiteConfig { [ { label: "About", url: ROUTES.ABOUT }, { label: "Organisms", url: ROUTES.ORGANISMS }, + { label: "Assemblies", url: ROUTES.GENOMES }, { label: "Roadmap", url: ROUTES.ROADMAP }, ], undefined, From 0b3b8d626d0409b0961f864cc844ac33d8b6c5db Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Wed, 15 Jan 2025 16:52:19 -0800 Subject: [PATCH 28/30] feat: adjust columns for organisms and assemblies (#208) --- .../common/viewModelBuilders.ts | 26 ++++----------- site-config/brc-analytics/category.ts | 4 +-- .../local/index/genomeEntityConfig.ts | 33 ++++++------------- .../local/index/organismEntityConfig.ts | 13 -------- 4 files changed, 17 insertions(+), 59 deletions(-) diff --git a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts index fbf2746..125e78e 100644 --- a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts +++ b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts @@ -250,20 +250,6 @@ export const buildStrain = ( }; }; -/** - * Build props for the tags cell. - * @param genome - Genome entity. - * @returns Props to be used for the cell. - */ -export const buildTags = ( - genome: BRCDataCatalogOrganism | BRCDataCatalogGenome -): ComponentProps => { - return { - label: "Tags", - values: genome.tags, - }; -}; - /** * Build props for the taxonomy ID cell. * @param genome - Genome entity. @@ -401,7 +387,7 @@ export function buildOrganismGenomesTable( return { columns: buildOrganismGenomesTableColumns(), gridTemplateColumns: - "auto minmax(240px, 1fr) minmax(180px, 0.5fr) minmax(100px, 0.5fr) minmax(164px, 1fr) minmax(100px, 0.5fr) repeat(2, minmax(142px, 0.5fr)) minmax(120px, 0.5fr) minmax(80px, 0.5fr) minmax(142px, 0.5fr) repeat(3, minmax(80px, 0.5fr)) minmax(142px, 0.5fr)", + "auto minmax(164px, 1fr) minmax(240px, 1fr) minmax(180px, 0.5fr) minmax(100px, 0.5fr) minmax(100px, 0.5fr) repeat(2, minmax(142px, 0.5fr)) minmax(120px, 0.5fr) minmax(80px, 0.5fr) minmax(142px, 0.5fr) repeat(3, minmax(80px, 0.5fr)) minmax(142px, 0.5fr)", items: organism.genomes, noResultsTitle: "No Assemblies", tableOptions: { @@ -424,6 +410,11 @@ function buildOrganismGenomesTableColumns(): ColumnDef[] { cell: ({ row }) => C.AnalyzeGenome(buildAnalyzeGenome(row.original)), header: BRC_DATA_CATALOG_CATEGORY_LABEL.ANALYZE_GENOME, }, + { + accessorKey: BRC_DATA_CATALOG_CATEGORY_KEY.ACCESSION, + cell: ({ row }) => C.BasicCell(buildAccession(row.original)), + header: BRC_DATA_CATALOG_CATEGORY_LABEL.ACCESSION, + }, { accessorKey: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON, cell: ({ row }) => C.BasicCell(buildGenomeTaxon(row.original)), @@ -439,11 +430,6 @@ function buildOrganismGenomesTableColumns(): ColumnDef[] { cell: ({ row }) => C.BasicCell(buildTaxonomyId(row.original)), header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXONOMY_ID, }, - { - accessorKey: BRC_DATA_CATALOG_CATEGORY_KEY.ACCESSION, - cell: ({ row }) => C.BasicCell(buildAccession(row.original)), - header: BRC_DATA_CATALOG_CATEGORY_LABEL.ACCESSION, - }, { accessorKey: BRC_DATA_CATALOG_CATEGORY_KEY.IS_REF, cell: ({ row }) => C.BasicCell(buildIsRef(row.original)), diff --git a/site-config/brc-analytics/category.ts b/site-config/brc-analytics/category.ts index 6b11043..d6dbbf7 100644 --- a/site-config/brc-analytics/category.ts +++ b/site-config/brc-analytics/category.ts @@ -13,7 +13,6 @@ export const BRC_DATA_CATALOG_CATEGORY_KEY = { SCAFFOLD_L50: "scaffoldL50", SCAFFOLD_N50: "scaffoldN50", STRAIN: "strain", - TAGS: "tags", TAXON: "taxon", TAXONOMY_ID: "ncbiTaxonomyId", UCSC_BROWSER_URL: "ucscBrowserUrl", @@ -34,8 +33,7 @@ export const BRC_DATA_CATALOG_CATEGORY_LABEL = { SCAFFOLD_L50: "Scaffold L50", SCAFFOLD_N50: "Scaffold N50", STRAIN: "Strain", - TAGS: "Tags", - TAXON: "Taxon", + TAXON: "Species", TAXONOMY_ID: "Taxonomy ID", UCSC_BROWSER_URL: "UCSC Browser", }; diff --git a/site-config/brc-analytics/local/index/genomeEntityConfig.ts b/site-config/brc-analytics/local/index/genomeEntityConfig.ts index a46c3ac..4fc878f 100644 --- a/site-config/brc-analytics/local/index/genomeEntityConfig.ts +++ b/site-config/brc-analytics/local/index/genomeEntityConfig.ts @@ -61,10 +61,6 @@ export const genomeEntityConfig: BRCEntityConfig = { key: BRC_DATA_CATALOG_CATEGORY_KEY.ANNOTATION_STATUS, label: BRC_DATA_CATALOG_CATEGORY_LABEL.ANNOTATION_STATUS, }, - { - key: BRC_DATA_CATALOG_CATEGORY_KEY.TAGS, - label: BRC_DATA_CATALOG_CATEGORY_LABEL.TAGS, - }, ], }, ], @@ -100,6 +96,16 @@ export const genomeEntityConfig: BRCEntityConfig = { id: BRC_DATA_CATALOG_CATEGORY_KEY.ANALYZE_GENOME, width: "auto", }, + { + columnPinned: true, + componentConfig: { + component: C.BasicCell, + viewBuilder: V.buildAccession, + } as ComponentConfig, + header: BRC_DATA_CATALOG_CATEGORY_LABEL.ACCESSION, + id: BRC_DATA_CATALOG_CATEGORY_KEY.ACCESSION, + width: { max: "1fr", min: "164px" }, + }, { componentConfig: { component: C.BasicCell, @@ -127,16 +133,6 @@ export const genomeEntityConfig: BRCEntityConfig = { id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXONOMY_ID, width: { max: "0.5fr", min: "100px" }, }, - { - columnPinned: true, - componentConfig: { - component: C.BasicCell, - viewBuilder: V.buildAccession, - } as ComponentConfig, - header: BRC_DATA_CATALOG_CATEGORY_LABEL.ACCESSION, - id: BRC_DATA_CATALOG_CATEGORY_KEY.ACCESSION, - width: { max: "1fr", min: "164px" }, - }, { componentConfig: { component: C.BasicCell, @@ -227,15 +223,6 @@ export const genomeEntityConfig: BRCEntityConfig = { id: BRC_DATA_CATALOG_CATEGORY_KEY.ANNOTATION_STATUS, width: { max: "0.5fr", min: "142px" }, }, - { - componentConfig: { - component: C.NTagCell, - viewBuilder: V.buildTags, - } as ComponentConfig, - header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAGS, - id: BRC_DATA_CATALOG_CATEGORY_KEY.TAGS, - width: { max: "0.5fr", min: "142px" }, - }, ], tableOptions: { initialState: { diff --git a/site-config/brc-analytics/local/index/organismEntityConfig.ts b/site-config/brc-analytics/local/index/organismEntityConfig.ts index 7704d19..b9f6285 100644 --- a/site-config/brc-analytics/local/index/organismEntityConfig.ts +++ b/site-config/brc-analytics/local/index/organismEntityConfig.ts @@ -32,10 +32,6 @@ export const organismEntityConfig: BRCEntityConfig = { key: BRC_DATA_CATALOG_CATEGORY_KEY.TAXONOMY_ID, label: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXONOMY_ID, }, - { - key: BRC_DATA_CATALOG_CATEGORY_KEY.TAGS, - label: BRC_DATA_CATALOG_CATEGORY_LABEL.TAGS, - }, ], }, ], @@ -86,15 +82,6 @@ export const organismEntityConfig: BRCEntityConfig = { id: BRC_DATA_CATALOG_CATEGORY_KEY.ASSEMBLY_COUNT, width: { max: "0.5fr", min: "164px" }, }, - { - componentConfig: { - component: C.NTagCell, - viewBuilder: V.buildTags, - } as ComponentConfig, - header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAGS, - id: BRC_DATA_CATALOG_CATEGORY_KEY.TAGS, - width: { max: "0.5fr", min: "142px" }, - }, ], defaultSort: { desc: SORT_DIRECTION.ASCENDING, From e52fc0c2d6118a45406896e50ba7436ca775260b Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Wed, 15 Jan 2025 16:55:58 -0800 Subject: [PATCH 29/30] feat: remove organisms warning (#208) --- .../components/Organisms/content/index.tsx | 1 - .../Organisms/content/organismsWarning.mdx | 9 --------- .../local/index/genomeEntityConfig.ts | 2 -- .../brc-analytics/local/listView/listHero.ts | 19 ------------------- 4 files changed, 31 deletions(-) delete mode 100644 app/components/EntityList/components/Organisms/content/index.tsx delete mode 100644 app/components/EntityList/components/Organisms/content/organismsWarning.mdx delete mode 100644 site-config/brc-analytics/local/listView/listHero.ts diff --git a/app/components/EntityList/components/Organisms/content/index.tsx b/app/components/EntityList/components/Organisms/content/index.tsx deleted file mode 100644 index 17c83f6..0000000 --- a/app/components/EntityList/components/Organisms/content/index.tsx +++ /dev/null @@ -1 +0,0 @@ -export { default as OrganismsWarning } from "./organismsWarning.mdx"; diff --git a/app/components/EntityList/components/Organisms/content/organismsWarning.mdx b/app/components/EntityList/components/Organisms/content/organismsWarning.mdx deleted file mode 100644 index f2da0ca..0000000 --- a/app/components/EntityList/components/Organisms/content/organismsWarning.mdx +++ /dev/null @@ -1,9 +0,0 @@ - - If you do not see your organism in this list: it will be there! We are in the - process of ingesting sequences and annotations for all 785 taxa from - VEuPathDB. The table below is generated by comparing the list maintained by - VEuPathDB against official NCBI genome builds. The three buttons adjacent to - each taxon direct you to a page listing available analytical workflows as well - as direct links to genomic data (NCBI Datasets) and a genome browser (UCSC). A - comprehensive search functionality will be developed to allow complex queries. - diff --git a/site-config/brc-analytics/local/index/genomeEntityConfig.ts b/site-config/brc-analytics/local/index/genomeEntityConfig.ts index 4fc878f..3f477a7 100644 --- a/site-config/brc-analytics/local/index/genomeEntityConfig.ts +++ b/site-config/brc-analytics/local/index/genomeEntityConfig.ts @@ -19,7 +19,6 @@ import { import { mainColumn as analysisMethodsMainColumn } from "../entity/genome/analysisMethodMainColumn"; import { sideColumn as analysisMethodsSideColumn } from "../entity/genome/analysisMethodsSideColumn"; import { top as analysisMethodsTop } from "../entity/genome/analysisMethodsTop"; -import { listHero } from "../listView/listHero"; /** * Entity config object responsible to config anything related to the /assemblies route. @@ -240,7 +239,6 @@ export const genomeEntityConfig: BRCEntityConfig = { disablePagination: true, enableDownload: true, enableTab: false, - listHero, }, route: "assemblies", staticLoadFile: "files/out/genomes.json", diff --git a/site-config/brc-analytics/local/listView/listHero.ts b/site-config/brc-analytics/local/listView/listHero.ts deleted file mode 100644 index 2be3b33..0000000 --- a/site-config/brc-analytics/local/listView/listHero.ts +++ /dev/null @@ -1,19 +0,0 @@ -import { ALERT_PROPS } from "@databiosphere/findable-ui/lib/components/common/Alert/constants"; -import { - ComponentConfig, - ComponentsConfig, -} from "@databiosphere/findable-ui/lib/config/entities"; -import { SIZE } from "@databiosphere/findable-ui/lib/styles/common/constants/size"; -import * as C from "../../../../app/components"; -import * as MDX from "../../../../app/components/EntityList/components/Organisms/content/index"; - -export const listHero: ComponentsConfig = [ - { - component: MDX.OrganismsWarning, - props: { - ...ALERT_PROPS.STANDARD_WARNING, - component: C.FluidPaper, - size: SIZE.LARGE, - }, - } as ComponentConfig, -]; From f1321d5572a0435bb0a02ca38f2ac4eaf24b2817 Mon Sep 17 00:00:00 2001 From: hunterckx <118154470+hunterckx@users.noreply.github.com> Date: Wed, 15 Jan 2025 16:59:17 -0800 Subject: [PATCH 30/30] feat: remove styled link component as it appears to now be unnecessary (#208) --- app/components/common/StyledLink/styledLink.styles.tsx | 6 ------ app/components/index.ts | 1 - .../brc-analytics-catalog/common/viewModelBuilders.ts | 2 +- .../brc-analytics/local/index/organismEntityConfig.ts | 4 ++-- 4 files changed, 3 insertions(+), 10 deletions(-) delete mode 100644 app/components/common/StyledLink/styledLink.styles.tsx diff --git a/app/components/common/StyledLink/styledLink.styles.tsx b/app/components/common/StyledLink/styledLink.styles.tsx deleted file mode 100644 index c0e74c5..0000000 --- a/app/components/common/StyledLink/styledLink.styles.tsx +++ /dev/null @@ -1,6 +0,0 @@ -import { Link } from "@databiosphere/findable-ui/lib/components/Links/components/Link/link"; -import styled from "@emotion/styled"; - -export const StyledLink = styled(Link)` - text-decoration: underline; -`; diff --git a/app/components/index.ts b/app/components/index.ts index c7ff915..7932423 100644 --- a/app/components/index.ts +++ b/app/components/index.ts @@ -25,7 +25,6 @@ export { Link } from "@databiosphere/findable-ui/lib/components/Links/components export { BasicCell } from "@databiosphere/findable-ui/lib/components/Table/components/TableCell/components/BasicCell/basicCell"; export { NTagCell } from "@databiosphere/findable-ui/lib/components/Table/components/TableCell/components/NTagCell/nTagCell"; export { CopyText } from "./common/CopyText/copyText"; -export { StyledLink } from "./common/StyledLink/styledLink.styles"; export { AnalysisMethod } from "./Entity/components/AnalysisMethod/analysisMethod"; export { AnalysisMethods } from "./Entity/components/AnalysisMethods/analysisMethods"; export { AnalysisMethodsTitle } from "./Entity/components/AnalysisMethodsTitle/analysisMethodsTitle"; diff --git a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts index 125e78e..7ea2445 100644 --- a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts +++ b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts @@ -191,7 +191,7 @@ export const buildLevel = ( */ export const buildOrganismTaxon = ( organism: BRCDataCatalogOrganism -): ComponentProps => { +): ComponentProps => { return { label: organism.taxon, url: `${ROUTES.ORGANISMS}/${encodeURIComponent(getOrganismId(organism))}`, diff --git a/site-config/brc-analytics/local/index/organismEntityConfig.ts b/site-config/brc-analytics/local/index/organismEntityConfig.ts index b9f6285..03fc65d 100644 --- a/site-config/brc-analytics/local/index/organismEntityConfig.ts +++ b/site-config/brc-analytics/local/index/organismEntityConfig.ts @@ -57,9 +57,9 @@ export const organismEntityConfig: BRCEntityConfig = { columns: [ { componentConfig: { - component: C.StyledLink, + component: C.Link, viewBuilder: V.buildOrganismTaxon, - } as ComponentConfig, + } as ComponentConfig, header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXON, id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON, width: "auto",