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ENCM-239-ljungman-enums #4440

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ENCM-239-ljungman-enums #4440

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2a93cd1
Update annotation and file enums for Ljungman submission
jenjou Jan 16, 2025
5499956
Fix inserts and test
jenjou Jan 16, 2025
6fa289b
Fix tests
jenjou Jan 17, 2025
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4 changes: 4 additions & 0 deletions src/encoded/schemas/analysis_step.json
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Expand Up @@ -189,6 +189,7 @@
"gene quantifications",
"gene stabilities",
"genic features quantifications",
"genic regions quantifications",
"genome compartments",
"genome index",
"genome reference",
Expand Down Expand Up @@ -237,6 +238,7 @@
"models",
"motif clusters reference",
"motif model",
"mRNA stabilities",
"nanopore signal",
"negative control regions",
"nested contact domains",
Expand Down Expand Up @@ -473,6 +475,7 @@
"genome subcompartments",
"gene stabilities",
"genic features quantifications",
"genic regions quantifications",
"gRNAs",
"guide locations",
"guide quantifications",
Expand Down Expand Up @@ -516,6 +519,7 @@
"models",
"motif clusters reference",
"motif model",
"mRNA stabilities",
"negative control regions",
"nested contact domains",
"non-targeting gRNAs",
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1 change: 1 addition & 0 deletions src/encoded/schemas/annotation.json
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Expand Up @@ -138,6 +138,7 @@
"in vivo enhancer evaluations",
"loops",
"methylation summary",
"mRNA stabilities",
"other",
"overlap",
"physical modeling",
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1 change: 1 addition & 0 deletions src/encoded/schemas/changelogs/analysis_step.md
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@@ -1,6 +1,7 @@
## Changelog for analysis_step.json

### Minor changes since schema version 17
* Added *mRNA stabilities* and *genic regions quantifications* to enum list for *input_file_types* and *output_file_types*.
* Added *variant functional prediction* to enum list for *input_file_types* and *output_file_types*.
* Added *topic gene weights* and *cell topic participation* to enum list for *input_file_types* and *output_file_types*.
* Added *topic modeling*, *TF binding site identification*, and *element annotation* to enum list for *analysis_step_types*.
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1 change: 1 addition & 0 deletions src/encoded/schemas/changelogs/annotation.md
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@@ -1,6 +1,7 @@
## Changelog for annotation.json

### Minor changes since schema version 40
* Added *mRNA stabilities* to enum for *annotation_type*.
* Added *single-nucleus RNA sequencing assay* to enum for *assay_term_name*.
* Added *variant functional prediction* to enum for *annotation_type*.
* Added *transcription factor ancestral origin estimate* to enum for *annotation_type*.
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1 change: 1 addition & 0 deletions src/encoded/schemas/changelogs/file.md
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@@ -1,6 +1,7 @@
## Changelog for file.json

### Minor changes since schema version 31
* Added *mRNA stabilities* and *genic regions quantifications* to enum list for *output_type*.
* Added *variant functional prediction* to enum list for *output_type*.
* Added *topic gene weights* and *cell topic participation* to enum list for *output_type*.
* Added *yaml* to enum list for *file_format*.
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4 changes: 4 additions & 0 deletions src/encoded/schemas/file.json
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Expand Up @@ -2196,6 +2196,7 @@
"gene quantifications",
"gene stabilities",
"genic features quantifications",
"genic regions quantifications",
"genome compartments",
"genome index",
"genome reference",
Expand Down Expand Up @@ -2242,6 +2243,7 @@
"models",
"motif clusters reference",
"motif model",
"mRNA stabilities",
"nanopore signal",
"negative control regions",
"nested contact domains",
Expand Down Expand Up @@ -2960,6 +2962,7 @@
"UV enriched segment quantifications": "quantification",
"sparse gene count matrix": "quantification",
"gene stabilities": "quantification",
"mRNA stabilities": "quantification",
"guide quantifications": "quantification",
"sparse transcript count matrix": "quantification",
"sparse gRNA count matrix": "quantification",
Expand All @@ -2977,6 +2980,7 @@
"cell type data": "quantification",
"variant effect quantifications": "quantification",
"genic features quantifications": "quantification",
"genic regions quantifications": "quantification",

"3D structure": "annotation",
"depth normalized signals matrix": "annotation",
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6 changes: 4 additions & 2 deletions src/encoded/tests/data/inserts/analysis_step.json
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Expand Up @@ -712,12 +712,14 @@
"input_file_types": [
"alignments",
"promoter prediction model",
"topic gene weights"
"topic gene weights",
"genic regions quantifications"
],
"output_file_types": [
"regulatory elements prediction model",
"enhancer prediction model",
"cell topic participation"
"cell topic participation",
"mRNA stabilities"
],
"status": "released",
"uuid": "1351fd89-27f0-40ed-b6bb-2a0dca45793e"
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12 changes: 12 additions & 0 deletions src/encoded/tests/data/inserts/annotation.json
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Expand Up @@ -323,5 +323,17 @@
"submitted_by": "[email protected]",
"uuid": "45ddd3ad-4b36-4fe9-9f88-4eeaf753f1fe",
"date_released": "2023-03-15"
},
{
"_test": "annotation_type mRNA stabilities",
"accession": "ENCSR702MSB",
"award": "U54HG007004",
"annotation_type": "mRNA stabilities",
"description": "Test for annotation_type mRNA stabilities",
"lab": "j-michael-cherry",
"status": "released",
"submitted_by": "[email protected]",
"uuid": "40b8a3ad-d498-4fe9-50ec-894bf41151fe",
"date_released": "2024-03-15"
}
]
12 changes: 7 additions & 5 deletions src/encoded/tests/data/inserts/expected_annotation_batch_download.tsv
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"http://localhost/metadata/?type=Annotation"
http://localhost/files/ENCFF762DWI/@@download/ENCFF762DWI.bigBed
http://localhost/files/ENCFF015OKV/@@download/ENCFF015OKV.bed.gz
http://localhost/files/ENCFF129CVS/@@download/ENCFF129CVS.bigWig
http://localhost/files/ENCFF129CRE/@@download/ENCFF129CRE.bed.gz
http://localhost/files/ENCFF880RDH/@@download/ENCFF880RDH.bed.gz
http://localhost/files/ENCFF629EGL/@@download/ENCFF629EGL.bed.gz
http://localhost/files/ENCFF629TGL/@@download/ENCFF629TGL.bed.gz
http://localhost/files/ENCFF292KWT/@@download/ENCFF292KWT.tsv
http://localhost/files/ENCFF575TRS/@@download/ENCFF575TRS.bed.gz
http://localhost/files/ENCFF880RDZ/@@download/ENCFF880RDZ.bed.gz
http://localhost/files/ENCFF762DWI/@@download/ENCFF762DWI.bigBed
http://localhost/files/ENCFF015OKV/@@download/ENCFF015OKV.bed.gz
http://localhost/files/ENCFF129CRE/@@download/ENCFF129CRE.bed.gz
http://localhost/files/ENCFF880RDH/@@download/ENCFF880RDH.bed.gz
http://localhost/files/ENCFF129CVS/@@download/ENCFF129CVS.bigWig
http://localhost/files/ENCFF001KEK/@@download/ENCFF001KEK.tsv
http://localhost/files/ENCFF002KEK/@@download/ENCFF002KEK.tsv
http://localhost/files/ENCFF301TWB/@@download/ENCFF301TWB.tsv
http://localhost/files/ENCFF291MSB/@@download/ENCFF291MSB.tsv
http://localhost/files/ENCFF599GRQ/@@download/ENCFF599GRQ.tsv
12 changes: 7 additions & 5 deletions src/encoded/tests/data/inserts/expected_annotation_metadata.tsv
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@@ -1,14 +1,16 @@
File accession File format Output type Assay term name Dataset accession Annotation type Software used Encyclopedia Version Biosample term id Biosample term name Biosample type Life stage Age Age units Organism Targets Dataset date released Project Lab md5sum dbxrefs File download URL Assembly Controlled by File Status Derived from S3 URL Azure URL Size Audit WARNING Audit NOT_COMPLIANT Audit ERROR
ENCFF292KWT tsv kmer weights ENCSR831GKM gkm-SVM-model Homo sapiens 2020-06-13 ENCODE J. Michael Cherry, Stanford b809e3f5625bf66456b316d5bd946d9b http://localhost/files/ENCFF292KWT/@@download/ENCFF292KWT.tsv released 300000 missing analysis_step_run inconsistent replicate
ENCFF575TRS bed narrowPeak training set ENCSR831GKM gkm-SVM-model Homo sapiens 2020-06-13 ENCODE J. Michael Cherry, Stanford 2809e3d056d90d5ad6e416f5663f6bd4 http://localhost/files/ENCFF575TRS/@@download/ENCFF575TRS.bed.gz GRCh38 released 300000 missing analysis_step_run inconsistent replicate
ENCFF880RDZ bed bed3+ representative IDR thresholded peaks ENCSR831GKM gkm-SVM-model Homo sapiens 2020-06-13 ENCODE J. Michael Cherry, Stanford 475fb823acff51433b068f5af45a37a5 http://localhost/files/ENCFF880RDZ/@@download/ENCFF880RDZ.bed.gz GRCh38 released 13224 missing analysis_step_run
ENCFF129CVS bigWig candidate Cis-Regulatory Elements ENCSR129CCR candidate Cis-Regulatory Elements ENCODE v2, current Homo sapiens 2020-05-20 ENCODE John Stamatoyannopoulos, UW 5c78ceaa13a380990ca16d8dcaeffd0b http://localhost/files/ENCFF129CVS/@@download/ENCFF129CVS.bigWig hg19 released /files/ENCFF002COS/, /files/ENCFF129CRE/, /files/ENCFF129DNA/ 200 inconsistent assembly, missing analysis_step_run
ENCFF129CVS bigWig candidate Cis-Regulatory Elements ENCSR129CCR candidate Cis-Regulatory Elements current, ENCODE v2 Homo sapiens 2020-05-20 ENCODE John Stamatoyannopoulos, UW 5c78ceaa13a380990ca16d8dcaeffd0b http://localhost/files/ENCFF129CVS/@@download/ENCFF129CVS.bigWig hg19 released /files/ENCFF002COS/, /files/ENCFF129CRE/, /files/ENCFF129DNA/ 200 inconsistent assembly, missing analysis_step_run
ENCFF629EGL bed bed9 element gene links ENCSR000CFC cross-species functional conservation Homo sapiens 2019-05-20 ENCODE Richard Myers, HAIB 3904fa99de87d37fc36bfdccec349cdb http://localhost/files/ENCFF629EGL/@@download/ENCFF629EGL.bed.gz GRCh38 released 2000000 missing analysis_step_run
ENCFF629TGL bed bed9 thresholded element gene links ENCSR000CFC cross-species functional conservation Homo sapiens 2019-05-20 ENCODE Richard Myers, HAIB 80ceca99de87d37fc36bfa282c34fab4 http://localhost/files/ENCFF629TGL/@@download/ENCFF629TGL.bed.gz GRCh38 released 2000000 missing analysis_step_run
ENCFF762DWI bigBed narrowPeak semi-automated genome annotation ENCSR575ZXX chromatin state Bowtie, Bismark ENCODE v0.2 EFO:0001196 IMR-90 cell line Homo sapiens 2014-07-15 ENCODE J. Michael Cherry, Stanford 0747b8235146194602a201ac967c3abf http://localhost/files/ENCFF762DWI/@@download/ENCFF762DWI.bigBed hg19 released 26444 missing analysis_step_run
ENCFF762DWI bigBed narrowPeak semi-automated genome annotation ENCSR575ZXX chromatin state Bismark, Bowtie ENCODE v0.2 EFO:0001196 IMR-90 cell line Homo sapiens 2014-07-15 ENCODE J. Michael Cherry, Stanford 0747b8235146194602a201ac967c3abf http://localhost/files/ENCFF762DWI/@@download/ENCFF762DWI.bigBed hg19 released 26444 missing analysis_step_run
ENCFF015OKV bed enhancer predictions predicted heart enhancers ENCSR356VQT loops Samtools, Picard ENCODE v0.2 UBERON:0000948 heart tissue embryonic 11.5 day Mus musculus 2015-02-27 ENCODE J. Michael Cherry, Stanford a5f849c78025c80dca58771492c97318 http://localhost/files/ENCFF015OKV/@@download/ENCFF015OKV.bed.gz mm10 released 1544154147 missing analysis_step_run
ENCFF129CRE bed bed3+ candidate Cis-Regulatory Elements ENCSR129RHS candidate Cis-Regulatory Elements ENCODE v2 Homo sapiens 2020-05-20 ENCODE J. Michael Cherry, Stanford b5f849c78025c80dca58771492c97318 http://localhost/files/ENCFF129CRE/@@download/ENCFF129CRE.bed.gz GRCh38 released /files/ENCFF880RDH/ 1544154 missing analysis_step_run
ENCFF880RDH bed bed3+ representative DNase hypersensitivity sites ENCSR129RHS candidate Cis-Regulatory Elements ENCODE v2 Homo sapiens 2020-05-20 ENCODE J. Michael Cherry, Stanford d650631e31df3993044cb78128d65de6 http://localhost/files/ENCFF880RDH/@@download/ENCFF880RDH.bed.gz GRCh38 released 13224 missing analysis_step_run
ENCFF292KWT tsv kmer weights ENCSR831GKM gkm-SVM-model Homo sapiens 2020-06-13 ENCODE J. Michael Cherry, Stanford b809e3f5625bf66456b316d5bd946d9b http://localhost/files/ENCFF292KWT/@@download/ENCFF292KWT.tsv released 300000 missing analysis_step_run inconsistent replicate
ENCFF575TRS bed narrowPeak training set ENCSR831GKM gkm-SVM-model Homo sapiens 2020-06-13 ENCODE J. Michael Cherry, Stanford 2809e3d056d90d5ad6e416f5663f6bd4 http://localhost/files/ENCFF575TRS/@@download/ENCFF575TRS.bed.gz GRCh38 released 300000 missing analysis_step_run inconsistent replicate
ENCFF880RDZ bed bed3+ representative IDR thresholded peaks ENCSR831GKM gkm-SVM-model Homo sapiens 2020-06-13 ENCODE J. Michael Cherry, Stanford 475fb823acff51433b068f5af45a37a5 http://localhost/files/ENCFF880RDZ/@@download/ENCFF880RDZ.bed.gz GRCh38 released 13224 missing analysis_step_run
ENCFF001KEK tsv transposable element TF ancestral origin percent by subfamily ENCSR767PSZ transcription factor ancestral origin estimate Homo sapiens 2023-03-15 ENCODE Michael Snyder, Stanford a94628feb64c6c2050181e45e3d29fe4 http://localhost/files/ENCFF001KEK/@@download/ENCFF001KEK.tsv hg19 released 289435 missing analysis_step_run
ENCFF002KEK tsv transposable element TF ancestral origin percent by motif ENCSR767PSZ transcription factor ancestral origin estimate Homo sapiens 2023-03-15 ENCODE Michael Snyder, Stanford 4f637c4a2dd0fccd6eed3d6ede385d35 http://localhost/files/ENCFF002KEK/@@download/ENCFF002KEK.tsv hg19 released 289435 missing analysis_step_run
ENCFF301TWB tsv variant functional prediction ENCSR222QSB variant functional prediction 2023-03-15 ENCODE J. Michael Cherry, Stanford 6397caa0e43ea5aa249a16ac20e02cab http://localhost/files/ENCFF301TWB/@@download/ENCFF301TWB.tsv released 502729395 missing analysis_step_run
ENCFF291MSB tsv mRNA stabilities ENCSR222QSB variant functional prediction 2023-03-15 ENCODE J. Michael Cherry, Stanford 4a5e28c6fb4363adc466258a39411422 http://localhost/files/ENCFF291MSB/@@download/ENCFF291MSB.tsv released 9829103 missing analysis_step_run
ENCFF599GRQ tsv genic regions quantifications ENCSR222QSB variant functional prediction 2023-03-15 ENCODE J. Michael Cherry, Stanford 654d3e7ca09a16aa5aa2439c20e0750e http://localhost/files/ENCFF599GRQ/@@download/ENCFF599GRQ.tsv released 2301943 missing analysis_step_run
30 changes: 30 additions & 0 deletions src/encoded/tests/data/inserts/file.json
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Expand Up @@ -6351,5 +6351,35 @@
"file_size": 502729395,
"lab":"j-michael-cherry",
"output_type": "variant functional prediction"
},
{
"_test": "output_type mRNA stabilities",
"status": "released",
"submitted_file_name": "test_mrna_stabilities.tsv",
"uuid": "f85dab00-9bb0-4531-4f03-82eb4908f8b9",
"submitted_by": "/users/4c23ec32-c7c8-4ac0-affb-04befcc881d4/",
"md5sum": "4a5e28c6fb4363adc466258a39411422",
"accession": "ENCFF291MSB",
"file_format": "tsv",
"award": "/awards/U54HG006998/",
"dataset": "ENCSR222QSB",
"file_size": 9829103,
"lab":"j-michael-cherry",
"output_type": "mRNA stabilities"
},
{
"_test": "output_type genic regions quantifications",
"status": "released",
"submitted_file_name": "test_genic_regions_quantifications.tsv",
"uuid": "157e20a6-aef8-4531-dc34-6b719280eb49",
"submitted_by": "/users/4c23ec32-c7c8-4ac0-affb-04befcc881d4/",
"md5sum": "654d3e7ca09a16aa5aa2439c20e0750e",
"accession": "ENCFF599GRQ",
"file_format": "tsv",
"award": "/awards/U54HG006998/",
"dataset": "ENCSR222QSB",
"file_size": 2301943,
"lab":"j-michael-cherry",
"output_type": "genic regions quantifications"
}
]