From 3b4c2086bb0f00a83a10a77de4836cf30832be18 Mon Sep 17 00:00:00 2001 From: Jennifer Jou Date: Wed, 22 Jul 2026 14:02:29 -0700 Subject: [PATCH 1/3] Add new content types for Luo data --- src/igvfd/schemas/changelogs/analysis_step.md | 10 ++ src/igvfd/schemas/changelogs/tabular_file.md | 5 + src/igvfd/schemas/tabular_file.json | 21 ++++- .../tests/data/inserts/tabular_file.json | 94 +++++++++++++++++++ 4 files changed, 127 insertions(+), 3 deletions(-) diff --git a/src/igvfd/schemas/changelogs/analysis_step.md b/src/igvfd/schemas/changelogs/analysis_step.md index 9fb2299460..45cce51c54 100644 --- a/src/igvfd/schemas/changelogs/analysis_step.md +++ b/src/igvfd/schemas/changelogs/analysis_step.md @@ -2,6 +2,16 @@ ### Minor changes since schema version 15 +* Extend `input_content_types` enum list to include `chromatin conformation compartments`. +* Extend `output_content_types` enum list to include `chromatin conformation compartments`. +* Extend `input_content_types` enum list to include `differentially methylated regions`. +* Extend `output_content_types` enum list to include `differentially methylated regions`. +* Extend `input_content_types` enum list to include `methylation regions`. +* Extend `output_content_types` enum list to include `methylation regions`. +* Extend `input_content_types` enum list to include `topologically associating domains`. +* Extend `output_content_types` enum list to include `topologically associating domains`. +* Extend `input_content_types` enum list to include `spatial transcriptomics slide-level cell boundaries`. +* Extend `output_content_types` enum list to include `spatial transcriptomics slide-level cell boundaries`. * Extend `input_content_types` enum list to include `cell by gene program matrix`. * Extend `output_content_types` enum list to include `cell by gene program matrix`. * Extend `input_content_types` enum list to include `program-program correlation`. diff --git a/src/igvfd/schemas/changelogs/tabular_file.md b/src/igvfd/schemas/changelogs/tabular_file.md index bcb58716b3..e59e566589 100644 --- a/src/igvfd/schemas/changelogs/tabular_file.md +++ b/src/igvfd/schemas/changelogs/tabular_file.md @@ -2,6 +2,11 @@ ### Minor changes since schema version 25 +* Extend `content_type` enum list to include `chromatin conformation compartments`. +* Extend `content_type` enum list to include `differentially methylated regions`. +* Extend `content_type` enum list to include `methylation regions`. +* Extend `content_type` enum list to include `topologically associating domains`. +* Extend `content_type` enum list to include `spatial transcriptomics slide-level cell boundaries`. * Extend `catalog_collections` enum list to include `genomic_elements_phenotypes`. * Extend `content_type` enum list to include `program-program correlation`. * Extend `content_type` enum list to include `regulator-regulator correlation`. diff --git a/src/igvfd/schemas/tabular_file.json b/src/igvfd/schemas/tabular_file.json index 229f290946..f784d2a1f3 100644 --- a/src/igvfd/schemas/tabular_file.json +++ b/src/igvfd/schemas/tabular_file.json @@ -154,6 +154,7 @@ "bin paired count", "calibrated coding variant effects", "caQTL", + "chromatin conformation compartments", "chromatin contact quantifications", "cis-trans regulatory differences", "co-localization scores", @@ -168,6 +169,7 @@ "motif-overlapping differential guide quantifications", "differential peak quantifications", "differential transcript expression quantifications", + "differentially methylated regions", "domain constraint", "DNA footprint scores", "DUAL-IPA score", @@ -191,6 +193,7 @@ "local differential expression", "loci", "methylation counts", + "methylation regions", "minus strand modification state", "modification state", "MPRA sequence designs", @@ -219,6 +222,7 @@ "reporter variants", "spliceQTL", "target transcripts", + "topologically associating domains", "trans differential expression quantifications per element", "trans differential expression quantifications per guide", "transcript quantifications", @@ -296,6 +300,7 @@ "sample sort parameters", "selected normalized variants profile", "spatial transcriptomics cell metadata", + "spatial transcriptomics slide-level cell boundaries", "spatial transcriptomics slide-level cell coordinates", "spatial transcriptomics slide-level transcripts", "studies_variants_phenotypes", @@ -361,6 +366,7 @@ "caQTL", "cell annotations", "cell hashing barcodes", + "chromatin conformation compartments", "chromatin contact quantifications", "cis differential expression quantifications per element", "cis differential expression quantifications per guide", @@ -376,6 +382,7 @@ "motif-overlapping differential guide quantifications", "differential peak quantifications", "differential transcript expression quantifications", + "differentially methylated regions", "domain constraint", "DNA footprint scores", "DUAL-IPA score", @@ -408,6 +415,7 @@ "motifs", "marker gene activity", "methylation counts", + "methylation regions", "minus strand modification state", "modification state", "MPRA sequence designs", @@ -448,10 +456,12 @@ "sample sort parameters", "selected normalized variants profile", "spatial transcriptomics cell metadata", + "spatial transcriptomics slide-level cell boundaries", "spatial transcriptomics slide-level cell coordinates", "spatial transcriptomics slide-level transcripts", "spliceQTL", "target transcripts", + "topologically associating domains", "trans differential expression quantifications per element", "trans differential expression quantifications per guide", "tissue positions", @@ -485,6 +495,7 @@ "calibrated coding variant effect thresholds": "A file contains calibration thresholds for coding variant effects defining score ranges for ACMG/AMP evidence levels (PS3/BS3 Supporting through Very Strong) for all functional assays.", "cell annotations": "A file containing cell classifications and/or labels based on their unique transcriptome and genomic signatures, usually generated from single cell sequencing experiments.", "cell hashing barcodes": "The barcodes used for cell hashing.", + "chromatin conformation compartments": "A BED file containing genomic intervals and their compartment annotation.", "chromatin contact quantifications": "A file containing chromatin conformation contacts.", "cis differential expression quantifications per element": "Element-level differential expression results aggregated across guides targeting each element for nearby genes within a configured interval.", "cis differential expression quantifications per guide": "Guide-level differential expression results for nearby genes within a configured interval around the guide target.", @@ -499,6 +510,7 @@ "motif-overlapping differential guide quantifications": "The quantified differences in guide RNA (gRNA) abundance between experimental conditions, for gRNAs overlapping specific motifs.", "differential peak quantifications": "The quantified changes in peaks detected between experimental conditions.", "differential transcript expression quantifications": "The quantified changes in expression levels of transcripts between conditions or groups.", + "differentially methylated regions": "A BED file containing regions that are called as differentially methylated between samples.", "domain constraint": "A file containing model estimates for the probability that a variant observed in the population is missense within a protein domain or interdomain region.", "DNA footprint scores": "A file containing DNA footprint scores, which represents the binding sites between DNA and proteins called from assays like ATAC-seq data.", "DUAL-IPA score": "A z-score that quantifies the relative abundance of a protein variant by comparing its GFP expression in HEK293T cells to that of the reference allele, with both signals normalized to mCherry expression as a control.", @@ -530,6 +542,7 @@ "motifs": "A table listing sequence motifs.", "marker gene activity": "A set of cell-type-specific genes identified in pseudobulked data sets with gene activity scores (GAS). These scores infer potential expression levels from single-cell ATAC-seq data by quantifying chromatin accessibility within and around specific gene loci.", "methylation counts": "A CpG-level summary of methylation counts and coverage.", + "methylation regions": "A BED file containing methylation summaries at genomic intervals.", "minus strand modification state": "A file with the bases on the minus strand where a DNA or RNA modification was detected.", "modification state": "An unstranded file with the bases where a DNA or RNA modification was detected.", "MPRA sequence designs": "Sequences designed for an MPRA experiment. Formatting should follow https://github.com/IGVF-DACC/checkfiles/blob/dev/src/schemas/table_schemas/mpra_sequence_designs.json.", @@ -572,11 +585,13 @@ "reporter genomic element effects": "Defines the activity of an element/region within a genome associated with a reporter assay. Formatting should follow https://github.com/IGVF-DACC/checkfiles/blob/dev/src/schemas/as/reporter_genomic_element_effects.as.", "reporter genomic variant effects": "Defines the activity of a variant within a genome associated with a reporter assay. Formatting should follow https://github.com/IGVF-DACC/checkfiles/blob/dev/src/schemas/as/reporter_genomic_variant_effects.as.", "sample sort parameters": "The parameters/quantifications used for sorting biological samples, such as those in flow cytometry.", - "spatial transcriptomics cell metadata": "A csv file containing cell morphology descriptions and transcript summaries.", - "spatial transcriptomics slide-level cell coordinates": "A csv file containing field of view, cell, and spatial coordinates based on cell segmentation.", - "spatial transcriptomics slide-level transcripts": "A csv file containing spatial information of transcriptomics data.", + "spatial transcriptomics cell metadata": "A CSV file containing cell morphology descriptions and transcript summaries.", + "spatial transcriptomics slide-level cell boundaries": "A CSV file containing per-cell polygon boundary coordinates.", + "spatial transcriptomics slide-level cell coordinates": "A CSV file containing field of view, cell, and spatial coordinates based on cell segmentation.", + "spatial transcriptomics slide-level transcripts": "A CSV file containing spatial information of transcriptomics data.", "target transcripts": "A GTF file containing annotations of targeted transcripts by the TAP-seq primer panel.", "tissue positions": "The spatial coordinates or positions of tissue samples or sections in experiments.", + "topologically associating domains": "A BED file containing genomic intervals and their TAD/boundary annotation.", "transcript quantifications": "The quantified levels of transcripts.", "trans differential expression quantifications per guide": "Guide-level differential expression results across the full gene annotation.", "trans differential expression quantifications per element": "Element-level differential expression results aggregated across guides targeting each element across the full gene annotation.", diff --git a/src/igvfd/tests/data/inserts/tabular_file.json b/src/igvfd/tests/data/inserts/tabular_file.json index 8ae6a513e9..d81235ef8a 100644 --- a/src/igvfd/tests/data/inserts/tabular_file.json +++ b/src/igvfd/tests/data/inserts/tabular_file.json @@ -2096,5 +2096,99 @@ "filtered": false, "file_set": "igvf:curated_set_pathway_gene_mapping", "controlled_access": false + }, + { + "uuid": "29f29094-2802-415b-a7bf-c7a510faae2c", + "accession": "IGVFFI0021MTHR", + "lab": "danwei-huangfu", + "award": "1U01HG012051-01", + "aliases": [ + "igvf:tabular_file_methylation_regions" + ], + "md5sum": "effd99bdcb39037446aecdd991adcd96", + "file_format": "bed", + "file_format_type": "bed3+", + "content_type": "methylation regions", + "submitted_file_name": "/Users/igvf/igvf_files/methylation_regions.bed.gz", + "file_size": 388200, + "upload_status": "validated", + "filtered": false, + "file_set": "igvf:curated_set_pathway_gene_mapping", + "controlled_access": false + }, + { + "uuid": "fc64cb1d-2802-415b-a7bf-c7a510faae2c", + "accession": "IGVFFI0022TADS", + "lab": "danwei-huangfu", + "award": "1U01HG012051-01", + "aliases": [ + "igvf:tabular_file_topologically_associating_domains" + ], + "md5sum": "919d969454cf6acdda446ae99bdcb390", + "file_format": "bed", + "file_format_type": "bed3+", + "content_type": "topologically associating domains", + "submitted_file_name": "/Users/igvf/igvf_files/topologically_associating_domains.bed.gz", + "file_size": 4200, + "upload_status": "validated", + "filtered": false, + "file_set": "igvf:curated_set_pathway_gene_mapping", + "controlled_access": false + }, + { + "uuid": "0db6840d-2802-415b-a7bf-c7a510faae2c", + "accession": "IGVFFI0023CHCC", + "lab": "danwei-huangfu", + "award": "1U01HG012051-01", + "aliases": [ + "igvf:tabular_file_chromatin_conformation_compartments" + ], + "md5sum": "ebefa6cd1acdd0446aeb39d9673c6959", + "file_format": "bed", + "file_format_type": "bed3+", + "content_type": "chromatin conformation compartments", + "submitted_file_name": "/Users/igvf/igvf_files/chromatin_conformation_compartments.bed.gz", + "file_size": 4200, + "upload_status": "validated", + "filtered": false, + "file_set": "igvf:curated_set_pathway_gene_mapping", + "controlled_access": false + }, + { + "uuid": "0873c695-2802-415b-40e7-c7a510faae2c", + "accession": "IGVFFI0024DMRS", + "lab": "danwei-huangfu", + "award": "1U01HG012051-01", + "aliases": [ + "igvf:tabular_file_differentially_methylated_regions" + ], + "md5sum": "c9edb26ae99fee0d969f439091acdd94", + "file_format": "bed", + "file_format_type": "bed3+", + "content_type": "differentially methylated regions", + "submitted_file_name": "/Users/igvf/igvf_files/differentially_methylated_regions.bed.gz", + "file_size": 4200, + "upload_status": "validated", + "filtered": false, + "file_set": "igvf:curated_set_pathway_gene_mapping", + "controlled_access": false + }, + { + "uuid": "b7e4a128-6d48-415b-8e4c-c7a510faae2c", + "accession": "IGVFFI0025CEBO", + "lab": "danwei-huangfu", + "award": "1U01HG012051-01", + "aliases": [ + "igvf:tabular_file_spatial_transcriptomics_slide-level_cell_boundaries" + ], + "md5sum": "7cdfd4466b00b39091f6d6ae99bdc9ca", + "file_format": "csv", + "content_type": "spatial transcriptomics slide-level cell boundaries", + "submitted_file_name": "/Users/igvf/igvf_files/spatial_transcriptomics_slide-level_cell boundaries.csv.gz", + "file_size": 4200, + "upload_status": "validated", + "filtered": false, + "file_set": "igvf:curated_set_pathway_gene_mapping", + "controlled_access": false } ] From 090c71f350d8f989e8346d23839b0206f1a8d821 Mon Sep 17 00:00:00 2001 From: Jennifer Jou Date: Wed, 22 Jul 2026 14:05:41 -0700 Subject: [PATCH 2/3] Update audit --- src/igvfd/audit/file_set.py | 1 + 1 file changed, 1 insertion(+) diff --git a/src/igvfd/audit/file_set.py b/src/igvfd/audit/file_set.py index 3098cf6cf2..67227288fb 100644 --- a/src/igvfd/audit/file_set.py +++ b/src/igvfd/audit/file_set.py @@ -1322,6 +1322,7 @@ def audit_missing_genome_transcriptome_references(value, system): 'pseudobulk annotations', 'sample sort parameters', 'spatial transcriptomics cell metadata', + 'spatial transcriptomics slide-level cell boundaries', 'spatial transcriptomics slide-level cell coordinates', 'spatial transcriptomics slide-level transcripts', 'studies_variants_phenotypes', From 6f050dbad98e0feb41486d5bd1a25d49b1349858 Mon Sep 17 00:00:00 2001 From: Jennifer Jou Date: Wed, 22 Jul 2026 15:31:41 -0700 Subject: [PATCH 3/3] Update inserts --- src/igvfd/tests/data/inserts/tabular_file.json | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/src/igvfd/tests/data/inserts/tabular_file.json b/src/igvfd/tests/data/inserts/tabular_file.json index d81235ef8a..c4ebbdd24f 100644 --- a/src/igvfd/tests/data/inserts/tabular_file.json +++ b/src/igvfd/tests/data/inserts/tabular_file.json @@ -2114,6 +2114,9 @@ "upload_status": "validated", "filtered": false, "file_set": "igvf:curated_set_pathway_gene_mapping", + "reference_files": [ + "IGVFFI0001GNRF" + ], "controlled_access": false }, { @@ -2133,6 +2136,9 @@ "upload_status": "validated", "filtered": false, "file_set": "igvf:curated_set_pathway_gene_mapping", + "reference_files": [ + "IGVFFI0001GNRF" + ], "controlled_access": false }, { @@ -2152,6 +2158,9 @@ "upload_status": "validated", "filtered": false, "file_set": "igvf:curated_set_pathway_gene_mapping", + "reference_files": [ + "IGVFFI0001GNRF" + ], "controlled_access": false }, { @@ -2171,6 +2180,9 @@ "upload_status": "validated", "filtered": false, "file_set": "igvf:curated_set_pathway_gene_mapping", + "reference_files": [ + "IGVFFI0001GNRF" + ], "controlled_access": false }, {