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Merged
merged 4 commits into from
Apr 15, 2025
Merged

Release 1.93.1 #2238

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a0d61c5
Updating to latest ingest, convention versions
bistline Apr 9, 2025
b574294
Merge pull request #2236 from broadinstitute/jb-alexandria-3.0.0
bistline Apr 10, 2025
6e4f133
Updating to scp-ingest-pipeline:1.41.3
bistline Apr 15, 2025
0ed96c8
Merge pull request #2237 from broadinstitute/jb-ingest-1.41.3
eweitz Apr 15, 2025
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2 changes: 1 addition & 1 deletion config/application.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ class Application < Rails::Application
config.middleware.use Rack::Brotli

# Docker image for file parsing via scp-ingest-pipeline
config.ingest_docker_image = 'gcr.io/broad-singlecellportal-staging/scp-ingest-pipeline:1.41.1'
config.ingest_docker_image = 'gcr.io/broad-singlecellportal-staging/scp-ingest-pipeline:1.41.3'

# Docker image for image pipeline jobs
config.image_pipeline_docker_image = 'gcr.io/broad-singlecellportal-staging/image-pipeline:0.1.0_c2b090043'
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37 changes: 1 addition & 36 deletions lib/assets/metadata_schemas/alexandria_convention/alexandria_convention_schema.json
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@@ -1,5 +1,5 @@
{
"$id": "https://singlecell.broadinstitute.org/single_cell/api/v1/metadata_schemas/alexandria_convention/2.3.0/json",
"$id": "https://singlecell.broadinstitute.org/single_cell/api/v1/metadata_schemas/alexandria_convention/3.0.0/json",
"$schema": "https://json-schema.org/draft-07/schema#",
"dependencies": {
"cell_type__ontology_label": [
Expand All @@ -14,9 +14,6 @@
"culture_duration__unit_label": [
"culture_duration__unit"
],
"development_stage__ontology_label": [
"development_stage"
],
"disease__intracellular_pathogen": [
"disease"
],
Expand Down Expand Up @@ -119,16 +116,9 @@
"organism_age__unit_label": [
"organism_age__unit"
],
"race__ontology_label": [
"race"
],
"sequencing_instrument_manufacturer_model__ontology_label": [
"sequencing_instrument_manufacturer_model"
],
"small_molecule_perturbation__concentration": [
"small_molecule_perturbation",
"small_molecule_perturbation__concentration__unit"
],
"small_molecule_perturbation__concentration__unit": [
"small_molecule_perturbation__concentration"
],
Expand Down Expand Up @@ -225,9 +215,6 @@
},
"development_stage": {
"description": "A classification of the developmental stage of the organism",
"ontology": "https://www.ebi.ac.uk/ols/api/ontologies/hsapdv,https://www.ebi.ac.uk/ols/api/ontologies/mmusdv",
"ontology_browser_url": "https://www.ebi.ac.uk/ols/ontologies/hsapdv,https://www.ebi.ac.uk/ols/ontologies/mmusdv",
"pattern": "^[-A-Za-z0-9]+[_:][-A-Za-z0-9]+",
"type": "string"
},
"development_stage__ontology_label": {
Expand Down Expand Up @@ -374,11 +361,8 @@
"gene_perturbation": {
"description": "A perturbation to a gene done to a cell culture",
"items": {
"ontology_browser_url": "https://www.ebi.ac.uk/ols/ontologies/ogg",
"pattern": "^[-A-Za-z0-9]+[_:][-A-Za-z0-9]+",
"type": "string"
},
"ontology": "https://www.ebi.ac.uk/ols/api/ontologies/ogg",
"type": "array"
},
"gene_perturbation__direction": {
Expand Down Expand Up @@ -406,9 +390,6 @@
},
"geographical_region": {
"description": "Location where the sample was collected/donated",
"ontology": "https://www.ebi.ac.uk/ols/api/ontologies/gaz",
"ontology_browser_url": "https://www.ebi.ac.uk/ols/ontologies/gaz",
"pattern": "^[-A-Za-z0-9]+[_:][-A-Za-z0-9]+",
"type": "string"
},
"geographical_region__ontology_label": {
Expand All @@ -419,11 +400,8 @@
"dependency_condition": "sample_type in cell line, organoid, cultured primary cells",
"description": "a growth factor added to a cell culture media",
"items": {
"ontology_browser_url": "https://www.ebi.ac.uk/ols/ontologies/pr",
"pattern": "^[-A-Za-z0-9]+[_:][-A-Za-z0-9]+",
"type": "string"
},
"ontology": "https://www.ebi.ac.uk/ols/api/ontologies/pr",
"type": "array"
},
"growth_factor_perturbation__concentration": {
Expand Down Expand Up @@ -494,9 +472,6 @@
"mouse_strain": {
"dependency_condition": "species == NCBITaxon_10090",
"description": "Mouse strain of the donor organism (ex. C57BL/6, BALB/c, 129, undetermined)",
"ontology": "https://www.ebi.ac.uk/ols/api/ontologies/ncit",
"ontology_browser_url": "https://www.ebi.ac.uk/ols/ontologies/ncit",
"pattern": "^[-A-Za-z0-9]+[_:][-A-Za-z0-9]+",
"type": "string"
},
"mouse_strain__ontology_label": {
Expand Down Expand Up @@ -564,14 +539,10 @@
"type": "string"
},
"race": {
"dependency_condition": "species == NCBITaxon_9606",
"description": "An arbitrary classification of a taxonomic group that is a division of a species",
"items": {
"ontology_browser_url": "https://www.ebi.ac.uk/ols/ontologies/ncit",
"pattern": "^[-A-Za-z0-9]+[_:][-A-Za-z0-9]+",
"type": "string"
},
"ontology": "https://www.ebi.ac.uk/ols/api/ontologies/ncit",
"type": "array"
},
"race__ontology_label": {
Expand Down Expand Up @@ -604,11 +575,8 @@
"small_molecule_perturbation": {
"description": "a small molecule added to a cell culture (ex. A drug) growth factor (and if it is recombinant, concentration), gene)",
"items": {
"ontology_browser_url": "https://www.ebi.ac.uk/ols/ontologies/chebi",
"pattern": "^[-A-Za-z0-9]+[_:][-A-Za-z0-9]+",
"type": "string"
},
"ontology": "https://www.ebi.ac.uk/ols/api/ontologies/chebi",
"type": "array"
},
"small_molecule_perturbation__concentration": {
Expand Down Expand Up @@ -677,11 +645,8 @@
"vaccination": {
"description": "Any known vaccines administered to the donor organism. NOT a full vaccine history",
"items": {
"ontology_browser_url": "https://www.ebi.ac.uk/ols/ontologies/vo",
"pattern": "^[-A-Za-z0-9]+[_:][-A-Za-z0-9]+",
"type": "string"
},
"ontology": "https://www.ebi.ac.uk/ols/api/ontologies/vo",
"type": "array"
},
"vaccination__adjuvants": {
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34 changes: 17 additions & 17 deletions lib/assets/metadata_schemas/alexandria_convention/alexandria_convention_schema.tsv
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Expand Up @@ -19,8 +19,8 @@ cell_type__custom string cell_type__custom
culture_duration number sample_type in cell line, organoid, cultured primary cells culture_duration__unit length of time cells have been in culture
culture_duration__unit string ontology https://www.ebi.ac.uk/ols/api/ontologies/uo https://www.ebi.ac.uk/ols/ontologies/uo UO_0000003 culture_duration culture_duration__unit
culture_duration__unit_label string unit_label culture_duration__unit culture_duration__unit_label
development_stage string ontology https://www.ebi.ac.uk/ols/api/ontologies/hsapdv,https://www.ebi.ac.uk/ols/api/ontologies/mmusdv https://www.ebi.ac.uk/ols/ontologies/hsapdv,https://www.ebi.ac.uk/ols/ontologies/mmusdv A classification of the developmental stage of the organism
development_stage__ontology_label string ontology_label development_stage development_stage__ontology_label
development_stage string A classification of the developmental stage of the organism
development_stage__ontology_label string development_stage__ontology_label
disease__intracellular_pathogen string TRUE ontology https://www.ebi.ac.uk/ols/api/ontologies/mondo https://www.ebi.ac.uk/ols/ontologies/mondo MONDO_0005550 disease If evidence of a pathogen is detected in this cell
disease__intracellular_pathogen__ontology_label string TRUE ontology_label disease__intracellular_pathogen disease__intracellular_pathogen__ontology_label
disease__time_since_onset number TRUE disease disease__time_since_onset__unit Amount of time since disease onset
Expand All @@ -38,26 +38,26 @@ enrichment__facs_markers string TRUE enrichment_method The surface marke
enrichment_method string TRUE enum "[""cell size selection"", ""fluorescence-activated cell sorting"", ""magnetic affinity cell sorting"", ""laser capture microdissection"", ""density gradient centrifugation"", ""Ficoll-Hypaque method"", ""enrichment of methylated DNA""]" Method used to enrich cells before running library preparation. This could be flow cytometry, column enrichments, etc.
ethnicity string TRUE ontology https://www.ebi.ac.uk/ols/api/ontologies/hancestro https://www.ebi.ac.uk/ols/ontologies/hancestro HANCESTRO:0004 species == NCBITaxon_9606 The ethnicity or ethnicities of the human donor if known
ethnicity__ontology_label string TRUE ontology_label ethnicity ethnicity__ontology_label
gene_perturbation string TRUE ontology https://www.ebi.ac.uk/ols/api/ontologies/ogg https://www.ebi.ac.uk/ols/ontologies/ogg OGG_0000000002 A perturbation to a gene done to a cell culture
gene_perturbation string TRUE A perturbation to a gene done to a cell culture
gene_perturbation__direction string enum "[""knock in"", ""knock out"",""activation"",""repression""]" gene_perturbation The type of perturbation of the gene defined in gene_perturbation. Knock in and knock out are complete additions/depletions of the gene, activation and repression refer to changes in magnitude of expression.
gene_perturbation__dynamics string gene_perturbation Description of the timing with respect to sequencing and other logistical considerations of the gene perturbation
gene_perturbation__method string TRUE gene_perturbation Process by which the gene was perturbed. Ex. CRISPR knock-out
gene_perturbation__ontology_label string TRUE ontology_label gene_perturbation gene_perturbation__ontology_label
geographical_region string ontology https://www.ebi.ac.uk/ols/api/ontologies/gaz https://www.ebi.ac.uk/ols/ontologies/gaz GAZ_00000013 Location where the sample was collected/donated
geographical_region__ontology_label string ontology_label geographical_region geographical_region__ontology_label
growth_factor_perturbation string TRUE ontology https://www.ebi.ac.uk/ols/api/ontologies/pr https://www.ebi.ac.uk/ols/ontologies/pr PR_000000001 sample_type in cell line, organoid, cultured primary cells a growth factor added to a cell culture media
gene_perturbation__ontology_label string TRUE gene_perturbation gene_perturbation__ontology_label
geographical_region string Location where the sample was collected/donated
geographical_region__ontology_label string geographical_region geographical_region__ontology_label
growth_factor_perturbation string TRUE sample_type in cell line, organoid, cultured primary cells a growth factor added to a cell culture media
growth_factor_perturbation__concentration number TRUE growth_factor_perturbation growth_factor_perturbation__concentration__unit Concentration of of each growth factor in the final tissue culture media. Order should be consistent with growth_factor_perturbation
growth_factor_perturbation__concentration__unit string ontology https://www.ebi.ac.uk/ols/api/ontologies/uo https://www.ebi.ac.uk/ols/ontologies/uo UO_0000003 growth_factor_perturbation__concentration growth_factor_perturbation__concentration__unit
growth_factor_perturbation__concentration__unit_label string unit_label growth_factor_perturbation__concentration__unit growth_factor_perturbation__concentration__unit_label
growth_factor_perturbation__ontology_label string TRUE ontology_label growth_factor_perturbation growth_factor_perturbation__ontology_label
growth_factor_perturbation__solvent string TRUE growth_factor_perturbation Solvent in which the growth factor was added to the cells. Ex. the base media.
growth_factor_perturbation__source string TRUE growth_factor_perturbation Source from which the growth factor was purchased
has_electrophysiology boolean boolean
has_morphology boolean boolean
has_electrophysiology boolean boolean
has_morphology boolean boolean
is_living string enum "[""yes"", ""no"", ""unknown""]" Whether organism was alive at time of biomaterial collection
mhc_genotype string MHC genotype for humans and other species
mouse_strain string ontology https://www.ebi.ac.uk/ols/api/ontologies/ncit https://www.ebi.ac.uk/ols/ontologies/ncit "NCIT_C14420 " species == NCBITaxon_10090 Mouse strain of the donor organism (ex. C57BL/6, BALB/c, 129, undetermined)
mouse_strain__ontology_label string ontology_label mouse_strain mouse_strain__ontology_label
mouse_strain string " " species == NCBITaxon_10090 Mouse strain of the donor organism (ex. C57BL/6, BALB/c, 129, undetermined)
mouse_strain__ontology_label string mouse_strain mouse_strain__ontology_label
number_of_reads number Number of reads mapped to that cell
organ_region string TRUE ontology https://api.brain-map.org/api/v2/structure_graph_download/1.json https://atlas.brain-map.org/atlas?atlas=602630314 organ_region
organ_region__ontology_label string TRUE ontology_label organ_region organ_region__ontology_label
Expand All @@ -67,13 +67,13 @@ organism_age__unit_label string unit_label organism_age__unit organism_a
paired_ends boolean true if the sequence library has paired end data (false for 10x)
preservation_method string enum "[""Cryopreservation"",""FFPE"",""Fresh"",""Frozen"",""OCT-embedded"",""Snap Frozen""]" Method used for sample preservation
primer string enum "[""poly-dT"",""random""]" Primer used for cDNA synthesis from RNA
race string TRUE ontology https://www.ebi.ac.uk/ols/api/ontologies/ncit https://www.ebi.ac.uk/ols/ontologies/ncit NCIT:C17049 species == NCBITaxon_9606 An arbitrary classification of a taxonomic group that is a division of a species
race__ontology_label string TRUE ontology_label race race__ontology_label
race string TRUE An arbitrary classification of a taxonomic group that is a division of a species
race__ontology_label string TRUE race__ontology_label
read_length string the read structure of the sequencing run
sequencing_instrument_manufacturer_model string ontology https://www.ebi.ac.uk/ols/api/ontologies/efo https://www.ebi.ac.uk/ols/ontologies/efo EFO_0003739 name of sequencing instrument manufacturer
sequencing_instrument_manufacturer_model__ontology_label string ontology_label sequencing_instrument_manufacturer_model sequencing_instrument_manufacturer_model__ontology_label
small_molecule_perturbation string TRUE ontology https://www.ebi.ac.uk/ols/api/ontologies/chebi https://www.ebi.ac.uk/ols/ontologies/chebi CHEBI_24431 a small molecule added to a cell culture (ex. A drug) growth factor (and if it is recombinant, concentration), gene)
small_molecule_perturbation__concentration number TRUE small_molecule_perturbation small_molecule_perturbation__concentration__unit Concentration of each small molecule in the final tissue culture media. Order should be consistent with small_molecule_perturbation
small_molecule_perturbation string TRUE a small molecule added to a cell culture (ex. A drug) growth factor (and if it is recombinant, concentration), gene)
small_molecule_perturbation__concentration number TRUE Concentration of each small molecule in the final tissue culture media. Order should be consistent with small_molecule_perturbation
small_molecule_perturbation__concentration__unit string ontology https://www.ebi.ac.uk/ols/api/ontologies/uo https://www.ebi.ac.uk/ols/ontologies/uo UO_0000003 small_molecule_perturbation__concentration small_molecule_perturbation__concentration__unit
small_molecule_perturbation__concentration__unit_label string unit_label small_molecule_perturbation__concentration__unit small_molecule_perturbation__concentration__unit_label
small_molecule_perturbation__ontology_label string TRUE ontology_label small_molecule_perturbation small_molecule_perturbation__ontology_label
Expand All @@ -82,10 +82,10 @@ small_molecule_perturbation__source string TRUE small_molecule_perturbatio
spike_in_concentration string spike_in_kit spike in concentration
spike_in_kit string name of spike in kit
strand string enum "[""first"",""second"",""unstranded""]" library strandedness
vaccination string TRUE ontology https://www.ebi.ac.uk/ols/api/ontologies/vo https://www.ebi.ac.uk/ols/ontologies/vo VO_0000001 Any known vaccines administered to the donor organism. NOT a full vaccine history
vaccination string TRUE Any known vaccines administered to the donor organism. NOT a full vaccine history
vaccination__adjuvants string TRUE vaccination Any adjuvants administered in the vaccine
vaccination__dosage string TRUE vaccination The dosage and units for the vaccine
vaccination__ontology_label string TRUE ontology_label vaccination vaccination__ontology_label
vaccination__ontology_label string TRUE vaccination vaccination__ontology_label
vaccination__route string TRUE enum "[""intradermal"", ""intranasal"", ""intravenous"", ""aerosol"", ""intramuscular"", ""mucosal"", ""oral""]" vaccination Intradermal, Intranasal, Intravenous, Aerosol
vaccination__time_since number TRUE vaccination vaccination__time_since__unit Amount of time since vaccine was administered
vaccination__time_since__unit string ontology https://www.ebi.ac.uk/ols/api/ontologies/uo https://www.ebi.ac.uk/ols/ontologies/uo UO_0000003 vaccination__time_since Time since each vaccine in the vaccination field was administered
Expand Down
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