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jmvera255 merged 3 commits into from
Dec 8, 2025
Merged

create spatial context for spatial transcriptomics and imaging-based data #82

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5aa3967
create spatial context for spatial transcriptomics and imaging-based …
jmvera255 Dec 8, 2025
006cbb4
Merge 5aa39675bad6c747c7999202e021bf4c679b6707 into 5772fbe3d9ab0ad3a…
jmvera255 Dec 8, 2025
dad4804
GitHub Action: commit results of ci-schema-convert workflow
jmvera255 Dec 8, 2025
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6 changes: 3 additions & 3 deletions ark.all_attributes.csv
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
"Attribute","Description","Valid Values","DependsOn","Properties","Required","Parent","DependsOn Component","Source","Validation Rules","columnType"
"Component","A high-level attribute for grouping attributes into templates.","","","","True","","","","","string"
"fileFormat","Standard file format name or file extension","bai, bam, bed, bim, csv, docx, dose, erate, fam, fastq, fcs, geojson, h5, h5ad, info, mtx, parquet, pdf, rds, rec, tbi, tgz, tsv, txt, vcf, xls, xlsx, zip","","","True","","","","","string"
"fileFormat","Standard file format name or file extension","bai, bam, bed, bim, csv, czi, docx, dose, erate, fam, fastq, fcs, geojson, h5, h5ad, info, mcd, mtx, parquet, pdf, rds, rec, svs, tbi, tgz, tsv, txt, vcf, xls, xlsx, zip","","","True","","","","","string"
"publicationSynID","The synID of the corresponding Synapse entity that stores metadata about the publication. This is used to differentiate publication-specific files, often consisting of level 4 processed data and expanded subject metadata, in a publication dataset that also includes raw or minimally processed files from experimental datasets. This provides an easy way to distinguish and select for the publication-specific data from which the research findings were derived. When this attribute is used to annotate a Dataset it serves as a way to directly link the Dataset entity with the publication metadata stored in Synapse.","","","","False","","","","regex search ^syn[0-9]{8} error","string"
"associatedDataset","The synID of a Dataset entity. This serves to link other Synapse entities to Dataset entities. When used to annotate a publication Dataset this attribute should include the synID for an experimental Datasets from which the publication data was derived. Multiple synID can be specified using a comma-delimited list.","","","","False","","","","list like::regex search ^syn[0-9]{8} error","string"
"program","Name of the funding program that supported the generation of data and associated files","AMP AIM, AMP RA/SLE, Community Contribution","","","True","","","","","string"
Expand All @@ -10,7 +10,7 @@
"dataType","High-level classification of the type of data contained in the file, loosely related to the experimental method or biological entity that is being profiled. Select all that apply using a comma-delimited list, though in most cases only a single label is expected. For multimodal datasets with concomitant profiling of biospecimen include 'multimodal'.","cytometry, epigenomics, genomics, histology, immune repertoire profiling, immunostaining, lipidomics, metabolomics, microbiome, multimodal, proteomics, transcriptomics","","","True","","","","list like error","string"
"dataSubtype","General classification to differentiate between omics profiling modalities. If N/A please select 'none'. Multiple selections can be provided in a comma-delimited list, however this is largely only expected in the context of Datasets and files that contain integrated experimental data spanning multiple types.","bulk, none, pseudobulk, single-cell, single-nucleus, spatial","","","True","","","","list like error","string"
"dataLevel","Level of data processing applied to file. Levels refer to pre-defined standards of processing for the given assay.","1, 2, 3, 4, 5","","","True","","","","","string"
"assay","The technology used to generate the data in this file. For multimodal datasets with concomitant profiling of biospecimen select all assays that apply. e.g., the GEX files from a CITE-seq experiment should be labeled with both 'scRNASeq' and 'CITESeq'.","ASAPSeq, CE-MS, CITESeq, CosMX, CyTOF, H&E, LC-MS/MS, NULISA, Olink Explore HT, Olink Flex, Olink Focus, Olink Reveal, Olink Target 48, Olink Target 96, RNASeq, SNP array, SomaScan, VDJSeq, WES, WGS, Xenium, feature barcode sequencing, flow cytometry, imaging mass cytometry, imaging mass spectrometry, kiloplex, multiplexed ELISA, scRNASeq, scVDJSeq, serial IHC, snATACSeq, snRNASeq","","","True","","","","list like error","string"
"assay","The technology used to generate the data in this file. For multimodal datasets with concomitant profiling of biospecimen select all assays that apply. e.g., the GEX files from a CITE-seq experiment should be labeled with both 'scRNASeq' and 'CITESeq'.","ASAPSeq, CE-MS, CITESeq, CosMX, CyTOF, GenePS SeqFISH, H&E, LC-MS/MS, NULISA, Olink Explore HT, Olink Flex, Olink Focus, Olink Reveal, Olink Target 48, Olink Target 96, RNASeq, SNP array, SomaScan, VDJSeq, Visium, WES, WGS, Xenium, feature barcode sequencing, flow cytometry, imaging mass cytometry, imaging mass spectrometry, kiloplex, multiplexed ELISA, scRNASeq, scVDJSeq, serial IHC, snATACSeq, snRNASeq","","","True","","","","list like error","string"
"10xProbeSetReference","Name of probe set used in 10x Chromium Flex, Xenium, or Visium data. If custom modified probe set was used the probe reference should be included as metadata accompanying the experimental data files.","Flex Human Transcriptome Probe Set v1.0.1, Flex Human Transcriptome Probe Set v1.1.0, Visium Human Transcriptome v1, Visium Human Transcriptome v2, custom probe set","","","True","","","","","string"
"custom10xProbeSetSynID","If custom modified probe sets were used for collecting 10x Chromium Flex scRNA-seq data, then the probe reference files should be grouped as a zip or tar archive and uploaded as metadata. This attribute links the experimental data back to the probe set archive file via a synapse ID.","","","","True","","","","regex search ^syn[0-9]{8} error","string"
"platform","The specific version (manufacturer, model, etc.) of a technology that is used to carry out a laboratory or computational experiment. Specify where applicable for experimental data files, else enter 'none'. In most cases only a single label is expected, however multiple selections can be provided in comma-delimited list where applicable e.g., for 10x Genomics fastq files please specify both the 10x instrument and the sequencing platform.","BD FACSAria Fusion cell sorter, BD FACSAria III, BD FACSCanto, BD FACSCanto II, BD FACSDiscover A8, BD FACSDiscover S8, BD FACSLyric Clinical, BD FACSMelody, BD FACSymphony S6, BD LSRFortessa, Chromium Controller, Chromium GEM-X Single Cell 3' Chip v4, Chromium Next GEM Chip G, Chromium Next GEM Chip H, Chromium Next GEM Chip K, Chromium Next GEM Chip M, Chromium Next GEM Chip Q, Chromium X, Chromium Xo, Chromium iX, CyTOF XT, Cytek Aurora, Cytek Aurora Evo, Fluidigm BioMark, GEM-X Flex Gene Expression Chip, GEM-X OCM 5' Chip, Helios Mass Cytometer, Hyperion, Illumina HiSeq 2500, Illumina HiSeq X Ten, Illumina NextSeq 500, Illumina NovaSeq 6000, Illumina NovaSeq X, Not Applicable, Olink Signature Q100, Sony MA900, Thermo Fisher Attune CytPix, Thermo Fisher Attune NxT, Thermo Fisher Attune Xenith, Visium CytAssist, Xenium, none, unknown","","","True","","","","list like error","string"
Expand All @@ -20,7 +20,7 @@
"parentBiospecimenID","The biospecimenID associated with the originating biospecimen for derived or child biospecimens.","","","","False","","","","","string"
"biospecimenType","A label indicating the biological material collected for experimentation and data collection. Where applicable, provide all types in a comma-separated list.","PBMCs, cell line, fibroblast-like synoviocyte, kidney biopsy, none, plasma, primary cell culture, saliva, salivary gland, serum, skin biopsy, skin swab, stool, suction blister cells, suction blister fluid, synovial fluid, synovial tissue, total leukocytes, urine, uvea, whole blood","","","True","","","","#BiospecimenMetadataTemplate str^^#InVitroBiospecimenMetadataTemplate^^list like error","string"
"primaryCellSource","A label indicating the biological source material from which a primary cell culture was derived.","PBMCs, kidney, pannus-derived dermis, pannus-derived epidermis, salivary gland, synovial tissue, total leukocytes, urine, uvea, whole blood","","","True","","","","","string"
"metadataType","A label further classifying the content of metadata resource.","assay, biospecimen, data dictionary, file manifest, medication, phenotype, protocol, single-cell metadata, target panel, template, user manual","","","True","","","","","string"
"metadataType","A label further classifying the content of metadata resource.","assay, biospecimen, cell coordinates, data dictionary, file manifest, medication, other, phenotype, protocol, single-cell metadata, target panel, template, tissue multiarray map, user manual","","","True","","","","","string"
"codingLanguage","The coding, aka programming, language(s) contained in the file marked with `resourceType = code`. Select all that apply.","C, C#, C++, Fortan, Java, Julia, Matlab, Python, R, Ruby, SAS","","","True","","","","","string"
"visitID","Ordinal ID distinguishing different patient visits.","","","","True","","","","","string"
"softwareAndVersion","Relevant software and version used to generate the data file.","BD FACSDiva 8.0.1, Cell Ranger 9.0.1, Cell Ranger ATAC v1.1.0, Cell Ranger v3.0.0, Cell Ranger v3.0.1, Cell Ranger v3.0.2, Cell Ranger v3.1.0, Cell Ranger v4.0.0, Cell Ranger v5.0.0, Cell Ranger v5.0.1, Cell Ranger v6.0.0, Cell Ranger v6.0.1, Cell Ranger v6.0.2, Cell Ranger v6.1.0, Cell Ranger v6.1.1, Cell Ranger v6.1.2, Cell Ranger v7.0.0, Cell Ranger v7.0.1, Cell Ranger v7.1.0, Cell Ranger v7.2.0, Cell Ranger v8.0.0, Cell Ranger v8.0.1, Cell Ranger v9.0.0, Space Ranger 3.0.0, Space Ranger 3.0.1, Space Ranger 3.1.0, Space Ranger 3.1.1, Space Ranger 3.1.2, Space Ranger 3.1.3, demuxlet","","","False","","","","","string"
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6 changes: 3 additions & 3 deletions model_contexts/biospecimen/ark.biospecimen_model.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@
"cell line","Is a valid value of 'biospecimenType' that triggers conditional dependencies for additional attributes.","","cellType, cellOntologyID","","","","","","",""
"individualID","Unique identifier assigned to each study participant. For multi-specimen data files provide all IDs in a comma-separated list.","","","","FALSE","","","","#BiospecimenMetadataTemplate required^^","string"
"Component","A high-level attribute for grouping attributes into templates.","","","","True","","","","","string"
"fileFormat","Standard file format name or file extension","bai, bam, bed, bim, csv, docx, dose, erate, fam, fastq, fcs, geojson, h5, h5ad, info, mtx, parquet, pdf, rds, rec, tbi, tgz, tsv, txt, vcf, xls, xlsx, zip","","","True","","","","","string"
"fileFormat","Standard file format name or file extension","bai, bam, bed, bim, csv, czi, docx, dose, erate, fam, fastq, fcs, geojson, h5, h5ad, info, mcd, mtx, parquet, pdf, rds, rec, svs, tbi, tgz, tsv, txt, vcf, xls, xlsx, zip","","","True","","","","","string"
"publicationSynID","The synID of the corresponding Synapse entity that stores metadata about the publication. This is used to differentiate publication-specific files, often consisting of level 4 processed data and expanded subject metadata, in a publication dataset that also includes raw or minimally processed files from experimental datasets. This provides an easy way to distinguish and select for the publication-specific data from which the research findings were derived. When this attribute is used to annotate a Dataset it serves as a way to directly link the Dataset entity with the publication metadata stored in Synapse.","","","","False","","","","regex search ^syn[0-9]{8} error","string"
"associatedDataset","The synID of a Dataset entity. This serves to link other Synapse entities to Dataset entities. When used to annotate a publication Dataset this attribute should include the synID for an experimental Datasets from which the publication data was derived. Multiple synID can be specified using a comma-delimited list.","","","","False","","","","list like::regex search ^syn[0-9]{8} error","string"
"program","Name of the funding program that supported the generation of data and associated files","AMP AIM, AMP RA/SLE, Community Contribution","","","True","","","","","string"
Expand All @@ -27,7 +27,7 @@
"dataType","High-level classification of the type of data contained in the file, loosely related to the experimental method or biological entity that is being profiled. Select all that apply using a comma-delimited list, though in most cases only a single label is expected. For multimodal datasets with concomitant profiling of biospecimen include 'multimodal'.","cytometry, epigenomics, genomics, histology, immune repertoire profiling, immunostaining, lipidomics, metabolomics, microbiome, multimodal, proteomics, transcriptomics","","","True","","","","list like error","string"
"dataSubtype","General classification to differentiate between omics profiling modalities. If N/A please select 'none'. Multiple selections can be provided in a comma-delimited list, however this is largely only expected in the context of Datasets and files that contain integrated experimental data spanning multiple types.","bulk, none, pseudobulk, single-cell, single-nucleus, spatial","","","True","","","","list like error","string"
"dataLevel","Level of data processing applied to file. Levels refer to pre-defined standards of processing for the given assay.","1, 2, 3, 4, 5","","","True","","","","","string"
"assay","The technology used to generate the data in this file. For multimodal datasets with concomitant profiling of biospecimen select all assays that apply. e.g., the GEX files from a CITE-seq experiment should be labeled with both 'scRNASeq' and 'CITESeq'.","ASAPSeq, CE-MS, CITESeq, CosMX, CyTOF, H&E, LC-MS/MS, NULISA, Olink Explore HT, Olink Flex, Olink Focus, Olink Reveal, Olink Target 48, Olink Target 96, RNASeq, SNP array, SomaScan, VDJSeq, WES, WGS, Xenium, feature barcode sequencing, flow cytometry, imaging mass cytometry, imaging mass spectrometry, kiloplex, multiplexed ELISA, scRNASeq, scVDJSeq, serial IHC, snATACSeq, snRNASeq","","","True","","","","list like error","string"
"assay","The technology used to generate the data in this file. For multimodal datasets with concomitant profiling of biospecimen select all assays that apply. e.g., the GEX files from a CITE-seq experiment should be labeled with both 'scRNASeq' and 'CITESeq'.","ASAPSeq, CE-MS, CITESeq, CosMX, CyTOF, GenePS SeqFISH, H&E, LC-MS/MS, NULISA, Olink Explore HT, Olink Flex, Olink Focus, Olink Reveal, Olink Target 48, Olink Target 96, RNASeq, SNP array, SomaScan, VDJSeq, Visium, WES, WGS, Xenium, feature barcode sequencing, flow cytometry, imaging mass cytometry, imaging mass spectrometry, kiloplex, multiplexed ELISA, scRNASeq, scVDJSeq, serial IHC, snATACSeq, snRNASeq","","","True","","","","list like error","string"
"10xProbeSetReference","Name of probe set used in 10x Chromium Flex, Xenium, or Visium data. If custom modified probe set was used the probe reference should be included as metadata accompanying the experimental data files.","Flex Human Transcriptome Probe Set v1.0.1, Flex Human Transcriptome Probe Set v1.1.0, Visium Human Transcriptome v1, Visium Human Transcriptome v2, custom probe set","","","True","","","","","string"
"custom10xProbeSetSynID","If custom modified probe sets were used for collecting 10x Chromium Flex scRNA-seq data, then the probe reference files should be grouped as a zip or tar archive and uploaded as metadata. This attribute links the experimental data back to the probe set archive file via a synapse ID.","","","","True","","","","regex search ^syn[0-9]{8} error","string"
"platform","The specific version (manufacturer, model, etc.) of a technology that is used to carry out a laboratory or computational experiment. Specify where applicable for experimental data files, else enter 'none'. In most cases only a single label is expected, however multiple selections can be provided in comma-delimited list where applicable e.g., for 10x Genomics fastq files please specify both the 10x instrument and the sequencing platform.","BD FACSAria Fusion cell sorter, BD FACSAria III, BD FACSCanto, BD FACSCanto II, BD FACSDiscover A8, BD FACSDiscover S8, BD FACSLyric Clinical, BD FACSMelody, BD FACSymphony S6, BD LSRFortessa, Chromium Controller, Chromium GEM-X Single Cell 3' Chip v4, Chromium Next GEM Chip G, Chromium Next GEM Chip H, Chromium Next GEM Chip K, Chromium Next GEM Chip M, Chromium Next GEM Chip Q, Chromium X, Chromium Xo, Chromium iX, CyTOF XT, Cytek Aurora, Cytek Aurora Evo, Fluidigm BioMark, GEM-X Flex Gene Expression Chip, GEM-X OCM 5' Chip, Helios Mass Cytometer, Hyperion, Illumina HiSeq 2500, Illumina HiSeq X Ten, Illumina NextSeq 500, Illumina NovaSeq 6000, Illumina NovaSeq X, Not Applicable, Olink Signature Q100, Sony MA900, Thermo Fisher Attune CytPix, Thermo Fisher Attune NxT, Thermo Fisher Attune Xenith, Visium CytAssist, Xenium, none, unknown","","","True","","","","list like error","string"
Expand All @@ -36,7 +36,7 @@
"parentBiospecimenID","The biospecimenID associated with the originating biospecimen for derived or child biospecimens.","","","","False","","","","","string"
"biospecimenType","A label indicating the biological material collected for experimentation and data collection. Where applicable, provide all types in a comma-separated list.","PBMCs, cell line, fibroblast-like synoviocyte, kidney biopsy, none, plasma, primary cell culture, saliva, salivary gland, serum, skin biopsy, skin swab, stool, suction blister cells, suction blister fluid, synovial fluid, synovial tissue, total leukocytes, urine, uvea, whole blood","","","True","","","","#BiospecimenMetadataTemplate str^^#InVitroBiospecimenMetadataTemplate^^list like error","string"
"primaryCellSource","A label indicating the biological source material from which a primary cell culture was derived.","PBMCs, kidney, pannus-derived dermis, pannus-derived epidermis, salivary gland, synovial tissue, total leukocytes, urine, uvea, whole blood","","","True","","","","","string"
"metadataType","A label further classifying the content of metadata resource.","assay, biospecimen, data dictionary, file manifest, medication, phenotype, protocol, single-cell metadata, target panel, template, user manual","","","True","","","","","string"
"metadataType","A label further classifying the content of metadata resource.","assay, biospecimen, cell coordinates, data dictionary, file manifest, medication, other, phenotype, protocol, single-cell metadata, target panel, template, tissue multiarray map, user manual","","","True","","","","","string"
"codingLanguage","The coding, aka programming, language(s) contained in the file marked with `resourceType = code`. Select all that apply.","C, C#, C++, Fortan, Java, Julia, Matlab, Python, R, Ruby, SAS","","","True","","","","","string"
"visitID","Ordinal ID distinguishing different patient visits.","","","","True","","","","","string"
"softwareAndVersion","Relevant software and version used to generate the data file.","BD FACSDiva 8.0.1, Cell Ranger 9.0.1, Cell Ranger ATAC v1.1.0, Cell Ranger v3.0.0, Cell Ranger v3.0.1, Cell Ranger v3.0.2, Cell Ranger v3.1.0, Cell Ranger v4.0.0, Cell Ranger v5.0.0, Cell Ranger v5.0.1, Cell Ranger v6.0.0, Cell Ranger v6.0.1, Cell Ranger v6.0.2, Cell Ranger v6.1.0, Cell Ranger v6.1.1, Cell Ranger v6.1.2, Cell Ranger v7.0.0, Cell Ranger v7.0.1, Cell Ranger v7.1.0, Cell Ranger v7.2.0, Cell Ranger v8.0.0, Cell Ranger v8.0.1, Cell Ranger v9.0.0, Space Ranger 3.0.0, Space Ranger 3.0.1, Space Ranger 3.1.0, Space Ranger 3.1.1, Space Ranger 3.1.2, Space Ranger 3.1.3, demuxlet","","","False","","","","","string"
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