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Annotate all existing WFs with edam topics and operations #639

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Annotate all existing WFs with edam topics and operations #639

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wm75
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@wm75 wm75 commented Dec 17, 2024

work in progress, but seems to play out nicely overall.

Will remove comments breaking json format when done, but until then they help to understand what's behind the edam IDs.

@wm75 wm75 added the WIP label Dec 17, 2024
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wm75 commented Dec 17, 2024 •
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Strcitly speaking, iuc has one more level of nesting under an edam_ontology tag. Not sure if it's worthwhile replicating this here. (misremembered this)

Part of the ongoing work is to include a guide for contributors on which topics and operations to pick.

Longer term it would be great to support workflow edams in Galaxy (don't lose them, make them searchable, add them to best practices).

bebatut
bebatut reviewed Dec 18, 2024
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workflows/amplicon/dada2/dada2_paired.ga
@@ -15,6 +15,8 @@
"format-version": "0.1",
"license": "MIT",
"name": "dada2 amplicon analysis pipeline - for paired end data",
"edam_topics": ["topic_3837"], # Metagenomic sequencing
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Suggested change
"edam_topics": ["topic_3837"], # Metagenomic sequencing
"edam_topics": ["topic_3837", "topic_4038"], # Metagenomic sequencing, Metabarcoding

workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ia-multiplexed-data-single-end.ga
@@ -17,6 +17,8 @@
"license": "MIT",
"release": "0.3",
"name": "QIIME2 Ia: multiplexed data (single-end)",
"edam_topics": ["topic_3168", "topic_3301"], # Sequencing, Microbiology
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Suggested change
"edam_topics": ["topic_3168", "topic_3301"], # Sequencing, Microbiology
"edam_topics": ["topic_3168", "topic_3301", "topic_4038"], # Sequencing, Microbiology, Metabarcoding

workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ib-multiplexed-data-paired-end.ga
@@ -17,6 +17,8 @@
"license": "MIT",
"release": "0.3",
"name": "QIIME2 Ib: multiplexed data (paired-end)",
"edam_topics": ["topic_3168", "topic_3301"], # Sequencing, Microbiology
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Suggested change
"edam_topics": ["topic_3168", "topic_3301"], # Sequencing, Microbiology
"edam_topics": ["topic_3168", "topic_3301", "topic_4038"], # Sequencing, Microbiology, Metabarcoding

workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ic-demultiplexed-data-single-end.ga
@@ -17,6 +17,8 @@
"license": "MIT",
"release": "0.3",
"name": "QIIME2 Ic: Demultiplexed data (single-end)",
"edam_topics": ["topic_3168", "topic_3301"], # Sequencing, Microbiology
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Suggested change
"edam_topics": ["topic_3168", "topic_3301"], # Sequencing, Microbiology
"edam_topics": ["topic_3168", "topic_3301", "topic_4038"], # Sequencing, Microbiology, Metabarcoding

workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Id-demultiplexed-data-paired-end.ga
@@ -17,6 +17,8 @@
"release": "0.3",
"license": "MIT",
"name": "QIIME2 Id: Demultiplexed data (paired-end)",
"edam_topics": ["topic_3168", "topic_3301"], # Sequencing, Microbiology
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Suggested change
"edam_topics": ["topic_3168", "topic_3301"], # Sequencing, Microbiology
"edam_topics": ["topic_3168", "topic_3301", "topic_4038"], # Sequencing, Microbiology, Metabarcoding

...con/qiime2/qiime2-II-denoising/QIIME2-IIa-denoising-and-feature-table-creation-single-end.ga
@@ -18,6 +18,8 @@
"release": "0.3",
"license": "MIT",
"name": "QIIME2 IIa: Denoising (sequence quality control) and feature table creation (single-end)",
"edam_topics": ["topic_3168", "topic_3301"], # Sequencing, Microbiology
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Suggested change
"edam_topics": ["topic_3168", "topic_3301"], # Sequencing, Microbiology
"edam_topics": ["topic_3168", "topic_3301", "topic_4038"], # Sequencing, Microbiology, Metabarcoding

...con/qiime2/qiime2-II-denoising/QIIME2-IIb-denoising-and-feature-table-creation-paired-end.ga
@@ -18,6 +18,8 @@
"release": "0.3",
"license": "MIT",
"name": "QIIME2 IIb: Denoising (sequence quality control) and feature table creation (paired-end)",
"edam_topics": ["topic_3168", "topic_3301"], # Sequencing, Microbiology
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Suggested change
"edam_topics": ["topic_3168", "topic_3301"], # Sequencing, Microbiology
"edam_topics": ["topic_3168", "topic_3301", "topic_4038"], # Sequencing, Microbiology, Metabarcoding

...icon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga
@@ -17,6 +17,8 @@
"format-version": "0.1",
"license": "MIT",
"name": "QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis",
"edam_topics": ["topic_3168", "topic_3837"], # Microbiology, Metagenomic sequencing
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Suggested change
"edam_topics": ["topic_3168", "topic_3837"], # Microbiology, Metagenomic sequencing
"edam_topics": ["topic_3168", "topic_3837", "topic_4038"], # Microbiology, Metagenomic sequencing, Metabarcoding

...flows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-VI-diversity-metrics-and-estimations.ga
@@ -121,6 +121,8 @@
"format-version": "0.1",
"license": "MIT",
"name": "QIIME2 VI: Diversity metrics and estimations",
"edam_topics": ["topic_3168", "topic_3837"], # Microbiology, Metagenomic sequencing
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Suggested change
"edam_topics": ["topic_3168", "topic_3837"], # Microbiology, Metagenomic sequencing
"edam_topics": ["topic_3168", "topic_3837", "topic_4038"], # Microbiology, Metagenomic sequencing, Metabarcoding

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wm75 commented Dec 18, 2024

@bebatut thanks! I was very much hoping that somebody'd review my dada2/qiime2 annotations :-)
The problem with metabarcoding specifically is that it's not currently part of a stable EDAM release, but seems to be available in "latest (unstable)" only.

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bebatut commented Dec 18, 2024

@bebatut thanks! I was very much hoping that somebody'd review my dada2/qiime2 annotations :-) The problem with metabarcoding specifically is that it's not currently part of a stable EDAM release, but seems to be available in "latest (unstable)" only.

I thought it was released. I found it there: https://www.ebi.ac.uk/ols4/ontologies/edam/classes/http%253A%252F%252Fedamontology.org%252Ftopic_4038?lang=en

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wm75 commented Dec 18, 2024

@bebatut thanks! I was very much hoping that somebody'd review my dada2/qiime2 annotations :-) The problem with metabarcoding specifically is that it's not currently part of a stable EDAM release, but seems to be available in "latest (unstable)" only.

I thought it was released. I found it there: https://www.ebi.ac.uk/ols4/ontologies/edam/classes/http%253A%252F%252Fedamontology.org%252Ftopic_4038?lang=en

bit weird, I'm using https://edamontology.github.io/edam-browser/ and it says that 1.25 is the latest release.
The page linked in edamontology/edamontology#856 (comment) says that metabarcoding is added with 1.26

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wm75 commented Dec 18, 2024

Aha, https://github.com/orgs/edamontology/projects/6

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