Update model to produce instances from ASCT+B cells

hubmapconsortium · Aug 23, 2024 · 079af45 · 079af45
1 parent 967426e
commit 079af45
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Showing 2 changed files with 159 additions and 58 deletions.
diff --git a/schemas/src/digital-objects/asct-b.yaml b/schemas/src/digital-objects/asct-b.yaml
@@ -125,6 +125,37 @@ classes:
         annotations:
           owl: AnnotationAssertion, AnnotationProperty
 
+  AnatomicalStructureInstance:
+    mixins:
+      - Named
+      - Instance
+    slots:
+      - ccf_pref_label
+      - source_concept
+      - record_number
+      - order_number
+
+  CellTypeInstance:
+    mixins:
+      - Named
+      - Instance
+    slots:
+      - ccf_pref_label
+      - source_concept
+      - record_number
+      - order_number
+
+  BiomarkerInstance:
+    mixins:
+      - Named
+      - Instance
+    slots:
+      - ccf_pref_label
+      - ccf_biomarker_type
+      - source_concept
+      - record_number
+      - order_number
+
   CellMarkerDescriptor:
     mixins:
       - Named
@@ -260,59 +291,78 @@ slots:
     slot_uri: ccf:ccf_biomarker_type
     annotations:
       owl: AnnotationAssertion, AnnotationProperty
+  source_concept:
+    required: true
+    slot_uri: ccf:source_concept
+    range: AsctbConcept
+    annotations:
+      owl: AnnotationAssertion, AnnotationProperty
   record_number:
     required: true
     slot_uri: ccf:record_number
     range: integer
     annotations:
       owl: AnnotationAssertion, AnnotationProperty
+  order_number:
+    required: true
+    slot_uri: ccf:order_number
+    range: integer
+    annotations:
+      owl: AnnotationAssertion, AnnotationProperty
   anatomical_structure_list:
     required: true
     multivalued: true
-    range: AnatomicalStructure
-    slot_uri: ccf:anatomical_structure_item
+    inlined_as_list: true
+    range: AnatomicalStructureInstance
+    slot_uri: ccf:anatomical_structure
     annotations:
       owl: AnnotationAssertion, AnnotationProperty
   cell_type_list:
     required: true
     multivalued: true
-    range: CellType
-    slot_uri: ccf:cell_type_item
+    inlined_as_list: true
+    range: CellTypeInstance
+    slot_uri: ccf:cell_type
     annotations:
       owl: AnnotationAssertion, AnnotationProperty
   gene_marker_list:
     required: true
     multivalued: true
-    range: Biomarker
-    slot_uri: ccf:gene_marker_item
+    inlined_as_list: true
+    range: BiomarkerInstance
+    slot_uri: ccf:gene_marker
     annotations:
       owl: AnnotationAssertion, AnnotationProperty
   protein_marker_list:
     required: false
     multivalued: true
-    range: Biomarker
-    slot_uri: ccf:protein_marker_item
+    inlined_as_list: true
+    range: BiomarkerInstance
+    slot_uri: ccf:protein_marker
     annotations:
       owl: AnnotationAssertion, AnnotationProperty
   lipid_marker_list:
     required: false
     multivalued: true
-    range: Biomarker
-    slot_uri: ccf:lipid_marker_item
+    inlined_as_list: true
+    range: BiomarkerInstance
+    slot_uri: ccf:lipid_marker
     annotations:
       owl: AnnotationAssertion, AnnotationProperty
   metabolites_marker_list:
     required: false
     multivalued: true
-    range: Biomarker
-    slot_uri: ccf:metabolites_marker_item
+    inlined_as_list: true
+    range: BiomarkerInstance
+    slot_uri: ccf:metabolites_marker
     annotations:
       owl: AnnotationAssertion, AnnotationProperty
   proteoforms_marker_list:
     required: false
     multivalued: true
-    range: Biomarker
-    slot_uri: ccf:proteoforms_marker_item
+    inlined_as_list: true
+    range: BiomarkerInstance
+    slot_uri: ccf:proteoforms_marker
     annotations:
       owl: AnnotationAssertion, AnnotationProperty
   primary_cell_type:

diff --git a/src/normalization/normalize-asct-b.js b/src/normalization/normalize-asct-b.js
@@ -265,29 +265,23 @@ function normalizeAsctbRecord(context, data) {
     // Determine record number
     const recordNumber = index + 1;
 
-    // Populate all valid anatomical structure concepts
-    const validAs = row.anatomical_structures
-      .filter(({ id, name }) => checkNotEmpty(id) || checkNotEmpty(name))
-      .map(({ id, name }) => generateIdWhenEmpty(id, name))
-      .filter((id) => passAsIdFilterCriteria(context, id));
+    // Generate anatomical structure instances
+    const asInstances = row.anatomical_structures
+      .map((item, order) => generateAsInstance(context, recordNumber, item, order))
+      .filter(({ source_concept }) => passAsIdFilterCriteria(context, source_concept));
 
-    // Populate all valid cell type concepts
-    const validCt = row.cell_types
-      .filter(({ id, name }) => checkNotEmpty(id) || checkNotEmpty(name))
-      .map(({ id, name }) => generateIdWhenEmpty(id, name))
-      .filter((id) => passCtIdFilterCriteria(context, id));
+    // Generate cell type instances
+    const ctInstances = row.cell_types
+      .map((item, order) => generateCtInstance(context, recordNumber, item, order))
+      .filter(({ source_concept }) => passCtIdFilterCriteria(context, source_concept));
 
-    // Populate all valid biomarker concepts
-    const validBm = row.biomarkers
-      .filter(({ id, name }) => checkNotEmpty(id) || checkNotEmpty(name))
-      .map(({ id, name, b_type }) => ({
-        id: generateIdWhenEmpty(id, name),
-        b_type
-      }))
-      .filter(({ id }) => passIdFilterCriteria(context, id));
+    // Generate biomarker instances
+    const bmInstances = row.biomarkers
+      .map((item, order) => generateBmInstance(context, recordNumber, item, order))
+      .filter(({ source_concept }) => passIdFilterCriteria(context, source_concept));
 
     // Populate all valid references
-    const validReferences = row.references
+    const references = row.references
       .map((ref) => {
         const refId = checkNotEmpty(ref.id) ? ref.id : "N/A";
         return checkIsDoi(refId) ? normalizeDoi(refId) : refId;
@@ -299,14 +293,14 @@ function normalizeAsctbRecord(context, data) {
       label: `Record ${recordNumber}`,
       type_of: [`AsctbRecord`],
       record_number: recordNumber,
-      anatomical_structure_list: validAs,
-      cell_type_list: validCt,
-      gene_marker_list: validBm.filter(({ b_type }) => b_type === BM_TYPE.G).map(getConceptId),
-      protein_marker_list: validBm.filter(({ b_type }) => b_type === BM_TYPE.P).map(getConceptId),
-      lipid_marker_list: validBm.filter(({ b_type }) => b_type === BM_TYPE.BL).map(getConceptId),
-      metabolites_marker_list: validBm.filter(({ b_type }) => b_type === BM_TYPE.BM).map(getConceptId),
-      proteoforms_marker_list: validBm.filter(({ b_type }) => b_type === BM_TYPE.BF).map(getConceptId),
-      references: validReferences
+      anatomical_structure_list: asInstances,
+      cell_type_list: ctInstances,
+      gene_marker_list: bmInstances.filter(({ ccf_biomarker_type }) => ccf_biomarker_type === BM_TYPE.G),
+      protein_marker_list: bmInstances.filter(({ ccf_biomarker_type }) => ccf_biomarker_type === BM_TYPE.P),
+      lipid_marker_list: bmInstances.filter(({ ccf_biomarker_type }) => ccf_biomarker_type === BM_TYPE.BL),
+      metabolites_marker_list: bmInstances.filter(({ ccf_biomarker_type }) => ccf_biomarker_type === BM_TYPE.BM),
+      proteoforms_marker_list: bmInstances.filter(({ ccf_biomarker_type }) => ccf_biomarker_type === BM_TYPE.BF),
+      references: references
     });
     return collector;
   }, []);
@@ -317,31 +311,31 @@ function normalizeCellMarkerDescriptor(context, data) {
     // Determine record number
     const recordNumber = index + 1;
 
-    // Populate all valid anatomical structure concepts
-    const validAs = row.anatomical_structures
+    // Get the last anatomical structure from the list as the primary
+    const primaryAs = row.anatomical_structures
       .filter(({ id, name }) => checkNotEmpty(id) || checkNotEmpty(name))
       .map(({ id, name }) => generateIdWhenEmpty(id, name))
-      .filter((id) => passAsIdFilterCriteria(context, id));
-    const lastAs = validAs.pop();
+      .filter((id) => passAsIdFilterCriteria(context, id))
+      .pop();
 
-    // Populate all valid cell type concepts
-    const validCt = row.cell_types
+    // Get the last cell type from the list as the primary
+    const primaryCt = row.cell_types
       .filter(({ id, name }) => checkNotEmpty(id) || checkNotEmpty(name))
       .map(({ id, name }) => ({
         id: generateIdWhenEmpty(id, name),
         name
       }))
-      .filter(({ id }) => passCtIdFilterCriteria(context, id));
-    const lastCt = validCt.pop();
+      .filter(({ id }) => passCtIdFilterCriteria(context, id))
+      .pop();
 
     // Populate all valid biomarker concepts
-    const validBm = row.biomarkers
+    const biomarkers = row.biomarkers
       .filter(({ id, name }) => checkNotEmpty(id) || checkNotEmpty(name))
       .map(({ id, name }) => generateIdWhenEmpty(id, name))
       .filter((id) => passIdFilterCriteria(context, id));
 
     // Populate all valid references
-    const validReferences = row.references
+    const references = row.references
       .map((ref) => {
         const refId = checkNotEmpty(ref.id) ? ref.id : "N/A";
         return checkIsDoi(refId) ? normalizeDoi(refId) : refId;
@@ -350,27 +344,84 @@ function normalizeCellMarkerDescriptor(context, data) {
     // Collect all the items
     collector.push({
       id: generateCellMarkerDescriptorId(context, recordNumber),
-      label: `Cell marker descriptor for ${lastCt.name}`,
+      label: `Cell marker descriptor for ${primaryCt.name}`,
       type_of: [`CellMarkerDescriptor`],
-      primary_cell_type: lastCt.id,
-      primary_anatomical_structure: lastAs,
-      biomarker_set: validBm,
-      references: validReferences,
+      primary_cell_type: primaryCt.id,
+      primary_anatomical_structure: primaryAs,
+      biomarker_set: biomarkers,
+      references: references,
       derived_from: generateAsctbRecordId(context, recordNumber)
     });
     return collector;
   }, []);
 }
 
-function getConceptId({ id }) {
-  return id;
+function generateAsInstance(context, recordNumber, data, index) {
+  const { name: doName } = context.selectedDigitalObject
+  const { id, name: asName } = data;
+  const orderNumber = index + 1
+  return {
+    id: generateAsInstanceId(context, recordNumber, orderNumber),
+    label: `${asName} (${doName}-R${recordNumber}-AS${orderNumber})`,
+    type_of: [generateIdWhenEmpty(id, asName)],
+    ccf_pref_label: asName,
+    source_concept: generateIdWhenEmpty(id, asName),
+    record_number: recordNumber,
+    order_number: orderNumber
+  }
+}
+
+function generateCtInstance(context, recordNumber, data, index) {
+  const { name: doName } = context.selectedDigitalObject
+  const { id, name: ctName } = data;
+  const orderNumber = index + 1
+  return {
+    id: generateCtInstanceId(context, recordNumber, orderNumber),
+    label: `${ctName} (${doName}-R${recordNumber}-CT${orderNumber})`,
+    type_of: [generateIdWhenEmpty(id, ctName)],
+    ccf_pref_label: ctName,
+    source_concept: generateIdWhenEmpty(id, ctName),
+    record_number: recordNumber,
+    order_number: orderNumber
+  }
+}
+
+function generateBmInstance(context, recordNumber, data, index) {
+  const { name: doName } = context.selectedDigitalObject
+  const { id, name: bmName, b_type } = data;
+  const orderNumber = index + 1
+  return {
+    id: generateBmInstanceId(context, recordNumber, orderNumber),
+    label: `${bmName} (${doName}-R${recordNumber}-BM${orderNumber})`,
+    type_of: [generateIdWhenEmpty(id, bmName)],
+    ccf_pref_label: bmName,
+    ccf_biomarker_type: b_type,
+    source_concept: generateIdWhenEmpty(id, bmName),
+    record_number: recordNumber,
+    order_number: orderNumber
+  }
 }
 
 function generateAsctbRecordId(context, recordNumber) {
   const { type: doType, name: doName, version: doVersion } = context.selectedDigitalObject;
   return `${context.purlIri}${doType}/${doName}/${doVersion}#R${recordNumber}`;
 }
 
+function generateAsInstanceId(context, recordNumber, orderNumber) {
+  const { type: doType, name: doName, version: doVersion } = context.selectedDigitalObject;
+  return `${context.purlIri}${doType}/${doName}/${doVersion}#R${recordNumber}-AS${orderNumber}`;
+}
+
+function generateCtInstanceId(context, recordNumber, orderNumber) {
+  const { type: doType, name: doName, version: doVersion } = context.selectedDigitalObject;
+  return `${context.purlIri}${doType}/${doName}/${doVersion}#R${recordNumber}-CT${orderNumber}`;
+}
+
+function generateBmInstanceId(context, recordNumber, orderNumber) {
+  const { type: doType, name: doName, version: doVersion } = context.selectedDigitalObject;
+  return `${context.purlIri}${doType}/${doName}/${doVersion}#R${recordNumber}-BM${orderNumber}`;
+}
+
 function generateCellMarkerDescriptorId(context, recordNumber) {
   const { type: doType, name: doName, version: doVersion } = context.selectedDigitalObject;
   return `${context.purlIri}${doType}/${doName}/${doVersion}#R${recordNumber}-cell-marker-descriptor`;