multiple service provider kps: comment out, remove, adjust response-m…

…appings for trapi compliance, part 2
NCATS-Tangerine · Jul 14, 2023 · a370256 · a370256
1 parent 3703119
commit a370256
Show file tree

Hide file tree

Showing 5 changed files with 238 additions and 186 deletions.
diff --git a/litvar/smartapi.yaml b/litvar/smartapi.yaml
@@ -69,4 +69,5 @@ components:
   x-bte-response-mapping:
     variant_located_in_gene:
       NCBIGene: gene.id  ## no prefix
-      "biolink:source_web_page": links.url
+      ## commenting out because data-processing / biolink-modeling issues
+      # "biolink:source_web_page": links.url
diff --git a/pfocr/smartapi.yaml b/pfocr/smartapi.yaml
@@ -594,9 +594,11 @@ components:
           - id: MESH
             semantic: SmallMolecule
         parameters:
-          fields: >-
-            associatedWith.mentions.chemicals.mesh,
-            associatedWith.figureUrl,associatedWith.pmc,associatedWith.title
+        ## commenting out because data-processing / biolink-modeling issues
+          # fields: >-
+          #   associatedWith.mentions.chemicals.mesh,
+          #   associatedWith.figureUrl,associatedWith.pmc,associatedWith.title
+          fields: associatedWith.mentions.chemicals.mesh
           size: 1000
         predicate: occurs_together_in_literature_with
         source: "infores:pfocr"
@@ -622,9 +624,11 @@ components:
           - id: NCBIGene
             semantic: Gene
         parameters:
-          fields: >-
-            associatedWith.mentions.genes.ncbigene,
-            associatedWith.figureUrl,associatedWith.pmc,associatedWith.title
+        ## commenting out because data-processing / biolink-modeling issues
+          # fields: >-
+          #   associatedWith.mentions.genes.ncbigene,
+          #   associatedWith.figureUrl,associatedWith.pmc,associatedWith.title
+          fields: associatedWith.mentions.genes.ncbigene
           size: 1000
         predicate: occurs_together_in_literature_with
         source: "infores:pfocr"
@@ -652,9 +656,11 @@ components:
           - id: MESH
             semantic: SmallMolecule
         parameters:
-          fields: >-
-            associatedWith.mentions.chemicals.mesh,
-            associatedWith.figureUrl,associatedWith.pmc,associatedWith.title
+        ## commenting out because data-processing / biolink-modeling issues
+          # fields: >-
+          #   associatedWith.mentions.chemicals.mesh,
+          #   associatedWith.figureUrl,associatedWith.pmc,associatedWith.title
+          fields: associatedWith.mentions.chemicals.mesh
           size: 1000
         predicate: occurs_together_in_literature_with
         source: "infores:pfocr"
@@ -680,9 +686,11 @@ components:
           - id: MESH
             semantic: Disease
         parameters:
-          fields: >-
-            associatedWith.mentions.diseases.mesh,
-            associatedWith.figureUrl,associatedWith.pmc,associatedWith.title
+        ## commenting out because data-processing / biolink-modeling issues
+          # fields: >-
+          #   associatedWith.mentions.diseases.mesh,
+          #   associatedWith.figureUrl,associatedWith.pmc,associatedWith.title
+          fields: associatedWith.mentions.diseases.mesh
           size: 1000
         predicate: occurs_together_in_literature_with
         source: "infores:pfocr"
@@ -710,9 +718,11 @@ components:
           - id: NCBIGene
             semantic: Gene
         parameters:
-          fields: >-
-            associatedWith.mentions.genes.ncbigene,
-            associatedWith.figureUrl,associatedWith.pmc,associatedWith.title
+        ## commenting out because data-processing / biolink-modeling issues
+          # fields: >-
+          #   associatedWith.mentions.diseases.mesh,
+          #   associatedWith.figureUrl,associatedWith.pmc,associatedWith.title
+          fields: associatedWith.mentions.genes.ncbigene
           size: 1000
         predicate: occurs_together_in_literature_with
         source: "infores:pfocr"
@@ -738,9 +748,11 @@ components:
           - id: MESH
             semantic: Disease
         parameters:
-          fields: >-
-            associatedWith.mentions.diseases.mesh,
-            associatedWith.figureUrl,associatedWith.pmc,associatedWith.title
+        ## commenting out because data-processing / biolink-modeling issues
+          # fields: >-
+          #   associatedWith.mentions.diseases.mesh,
+          #   associatedWith.figureUrl,associatedWith.pmc,associatedWith.title
+          fields: associatedWith.mentions.diseases.mesh
           size: 1000
         predicate: occurs_together_in_literature_with
         source: "infores:pfocr"
@@ -755,16 +767,19 @@ components:
     ## not easy to make it clear with biolink-model terms: the publication (PMC ID) vs the figure (title and url)
     chem:
       MESH: associatedWith.mentions.chemicals.mesh   ## no prefix
-      figure_download_url: associatedWith.figureUrl
-      figure_title: associatedWith.title
-      pmc_reference: associatedWith.pmc
+      ## commenting out because data-processing / biolink-modeling issues
+      # figure_download_url: associatedWith.figureUrl
+      # figure_title: associatedWith.title
+      # pmc_reference: associatedWith.pmc
     gene:
       NCBIGene: associatedWith.mentions.genes.ncbigene   ## no prefix
-      figure_download_url: associatedWith.figureUrl
-      figure_title: associatedWith.title
-      pmc_reference: associatedWith.pmc
+      ## commenting out because data-processing / biolink-modeling issues
+      # figure_download_url: associatedWith.figureUrl
+      # figure_title: associatedWith.title
+      # pmc_reference: associatedWith.pmc
     disease:
       MESH: associatedWith.mentions.diseases.mesh   ## no prefix
-      figure_download_url: associatedWith.figureUrl
-      figure_title: associatedWith.title
-      pmc_reference: associatedWith.pmc
+      ## commenting out because data-processing / biolink-modeling issues
+      # figure_download_url: associatedWith.figureUrl
+      # figure_title: associatedWith.title
+      # pmc_reference: associatedWith.pmc
diff --git a/pharmgkb/smartapi.yaml b/pharmgkb/smartapi.yaml
@@ -1937,30 +1937,35 @@ components:
       output_name: data.obj2Name
       input_name: data.obj1Name
       pubmed: data.pmid
-      pharmgkb_source_of_connection: data.relType
+      ## commenting out because data-processing / biolink-modeling issues
+      # pharmgkb_source_of_connection: data.relType
     connection-obj-pathway:
       "PHARMGKB.PATHWAYS": data.obj2Id
       output_name: data.obj2Name
       input_name: data.obj1Name
       pubmed: data.pmid
-      pharmgkb_source_of_connection: data.relType
+      ## commenting out because data-processing / biolink-modeling issues
+      # pharmgkb_source_of_connection: data.relType
     connection-obj-disease:
       "PHARMGKB.DISEASE": data.obj2Id
       output_name: data.obj2Name
       input_name: data.obj1Name
       pubmed: data.pmid
-      pharmgkb_source_of_connection: data.relType
+      ## commenting out because data-processing / biolink-modeling issues
+      # pharmgkb_source_of_connection: data.relType
     connection-obj-gene:
       "PHARMGKB.GENE": data.obj2Id
       output_name: data.obj2Name
       input_name: data.obj1Name
       pubmed: data.pmid
-      pharmgkb_source_of_connection: data.relType
+      ## commenting out because data-processing / biolink-modeling issues
+      # pharmgkb_source_of_connection: data.relType
     connection-obj-dbsnp:
       DBSNP: data.obj2Name    ## DBSNP rs ID is put there
       input_name: data.obj1Name
       pubmed: data.pmid
-      pharmgkb_source_of_connection: data.relType
+      ## commenting out because data-processing / biolink-modeling issues
+      # pharmgkb_source_of_connection: data.relType
     pathEnd-chem:
       "PHARMGKB.CHEMICAL": data.relatedChemicals.id
       ## doesn't work: takes name from all records -> single node's names has this whole list
@@ -1983,121 +1988,136 @@ components:
       input_name: data.name
     guidelineEnd-gene:
       "PHARMGKB.GENE": data.relatedGenes.id
-      ## related gene alleles
-      related_gene_alleles: data.relatedAlleles.symbol
-      ## provenance
-      guideline_literature_urls: data.literature._sameAs
-      clinical_guideline_source: data.source      ## probably an enum of {cpic, dpwg, pro}
       ## guideline annotation info
-      clinical_guideline_name: data.name
-      clinical_guideline_summary: data.summaryMarkdown.html
-      flag_has_recommendation: data.recommendation
-      flag_has_alternative_drug_info: data.alternateDrugAvailable
-      flag_gene_or_variant_in_cancer_cell: data.cancerGenome
-      flag_has_dosing_information: data.dosingInformation
-      flag_has_testing_information: data.hasTestingInfo
-      flag_has_pediatric_information: data.pediatric
+      "biolink:supporting_text": data.summaryMarkdown.html
+      ## commenting out because data-processing / biolink-modeling issues
+      # ## related gene alleles
+      # related_gene_alleles: data.relatedAlleles.symbol
+      # ## provenance
+      # guideline_literature_urls: data.literature._sameAs
+      # clinical_guideline_source: data.source      ## probably an enum of {cpic, dpwg, pro}
+      # ## guideline annotation info
+      # clinical_guideline_name: data.name
+      # flag_has_recommendation: data.recommendation
+      # flag_has_alternative_drug_info: data.alternateDrugAvailable
+      # flag_gene_or_variant_in_cancer_cell: data.cancerGenome
+      # flag_has_dosing_information: data.dosingInformation
+      # flag_has_testing_information: data.hasTestingInfo
+      # flag_has_pediatric_information: data.pediatric
     guidelineEnd-chem:
       "PHARMGKB.CHEMICAL": data.relatedChemicals.id
-      ## related gene alleles
-      related_gene_alleles: data.relatedAlleles.symbol
-      ## provenance
-      guideline_literature_urls: data.literature._sameAs
-      clinical_guideline_source: data.source      ## probably an enum of {cpic, dpwg, pro}
       ## guideline annotation info
-      clinical_guideline_name: data.name
-      clinical_guideline_summary: data.summaryMarkdown.html
-      flag_has_recommendation: data.recommendation
-      flag_has_alternative_drug_info: data.alternateDrugAvailable
-      flag_gene_or_variant_in_cancer_cell: data.cancerGenome
-      flag_has_dosing_information: data.dosingInformation
-      flag_has_testing_information: data.hasTestingInfo
-      flag_has_pediatric_information: data.pediatric
+      "biolink:supporting_text": data.summaryMarkdown.html
+      ## commenting out because data-processing / biolink-modeling issues
+      # ## related gene alleles
+      # related_gene_alleles: data.relatedAlleles.symbol
+      # ## provenance
+      # guideline_literature_urls: data.literature._sameAs
+      # clinical_guideline_source: data.source      ## probably an enum of {cpic, dpwg, pro}
+      # ## guideline annotation info
+      # clinical_guideline_name: data.name
+      # flag_has_recommendation: data.recommendation
+      # flag_has_alternative_drug_info: data.alternateDrugAvailable
+      # flag_gene_or_variant_in_cancer_cell: data.cancerGenome
+      # flag_has_dosing_information: data.dosingInformation
+      # flag_has_testing_information: data.hasTestingInfo
+      # flag_has_pediatric_information: data.pediatric
     labelEnd-gene:
       ## not sure if prescribingGenes provides different info or not. using relatedGenes section instead
       "PHARMGKB.GENE": data.relatedGenes.id
-      ## related gene alleles
-      related_gene_alleles: data.relatedAlleles.symbol
-      ## provenance
-      label_literature_urls: data.literature._sameAs
-      label_source: data.source      ## probably an enum of {fda, ema, pmda, hcsc}
       ## label annotation info
-      label_title: data.name
-      label_summary: data.summaryMarkdown.html
-      pgx_level: data.testing.term
-      flag_has_alternative_drug_info: data.alternateDrugAvailable
-      flag_gene_or_variant_in_cancer_cell: data.cancerGenome
-      flag_has_dosing_information: data.dosingInformation
-      flag_has_pediatric_information: data.pediatric
+      "biolink:supporting_text": data.summaryMarkdown.html
+      ## commenting out because data-processing / biolink-modeling issues
+      # ## related gene alleles
+      # related_gene_alleles: data.relatedAlleles.symbol
+      # ## provenance
+      # label_literature_urls: data.literature._sameAs
+      # label_source: data.source      ## probably an enum of {fda, ema, pmda, hcsc}
+      # ## label annotation info
+      # label_title: data.name
+      # pgx_level: data.testing.term
+      # flag_has_alternative_drug_info: data.alternateDrugAvailable
+      # flag_gene_or_variant_in_cancer_cell: data.cancerGenome
+      # flag_has_dosing_information: data.dosingInformation
+      # flag_has_pediatric_information: data.pediatric
     labelEnd-chem:
       "PHARMGKB.CHEMICAL": data.relatedChemicals.id
-      ## related gene alleles
-      related_gene_alleles: data.relatedAlleles.symbol
-      ## provenance
-      label_literature_urls: data.literature._sameAs
-      label_source: data.source      ## probably an enum of {fda, ema, pmda, hcsc}
       ## label annotation info
-      label_title: data.name
-      label_summary: data.summaryMarkdown.html
-      pgx_level: data.testing.term
-      flag_has_alternative_drug_info: data.alternateDrugAvailable
-      flag_gene_or_variant_in_cancer_cell: data.cancerGenome
-      flag_has_dosing_information: data.dosingInformation
-      flag_has_pediatric_information: data.pediatric
+      "biolink:supporting_text": data.summaryMarkdown.html
+      ## commenting out because data-processing / biolink-modeling issues
+      # ## related gene alleles
+      # related_gene_alleles: data.relatedAlleles.symbol
+      # ## provenance
+      # label_literature_urls: data.literature._sameAs
+      # label_source: data.source      ## probably an enum of {fda, ema, pmda, hcsc}
+      # ## label annotation info
+      # label_title: data.name
+      # pgx_level: data.testing.term
+      # flag_has_alternative_drug_info: data.alternateDrugAvailable
+      # flag_gene_or_variant_in_cancer_cell: data.cancerGenome
+      # flag_has_dosing_information: data.dosingInformation
+      # flag_has_pediatric_information: data.pediatric
     clinicalAnnotEnd-variant:
       DBSNP: data.location.rsid
-      annotation_title: data.name
-      pharmgkb_annotation_phenotype_category: data.types
-      pharmgkb_annotation_level_of_evidence: data.levelOfEvidence.term  
-      allele_phenotype_information: data.allelePhenotypes.phenotype
-      related_genes: data.location.genes.symbol
-      related_diseases: data.relatedDiseases.name
+      ## commenting out because data-processing / biolink-modeling issues
+      # annotation_title: data.name
+      # pharmgkb_annotation_phenotype_category: data.types
+      # pharmgkb_annotation_level_of_evidence: data.levelOfEvidence.term  
+      # allele_phenotype_information: data.allelePhenotypes.phenotype
+      # related_genes: data.location.genes.symbol
+      # related_diseases: data.relatedDiseases.name
     clinicalAnnotEnd-chem:
       "PHARMGKB.CHEMICAL": data.relatedChemicals.id
-      annotation_title: data.name
-      pharmgkb_annotation_phenotype_category: data.types
-      pharmgkb_annotation_level_of_evidence: data.levelOfEvidence.term  
-      allele_phenotype_information: data.allelePhenotypes.phenotype
-      related_genes: data.location.genes.symbol
-      related_diseases: data.relatedDiseases.name
+      ## commenting out because data-processing / biolink-modeling issues
+      # annotation_title: data.name
+      # pharmgkb_annotation_phenotype_category: data.types
+      # pharmgkb_annotation_level_of_evidence: data.levelOfEvidence.term  
+      # allele_phenotype_information: data.allelePhenotypes.phenotype
+      # related_genes: data.location.genes.symbol
+      # related_diseases: data.relatedDiseases.name
     clinicalAnnotEnd-gene:
       "PHARMGKB.GENE": data.location.genes.id
-      annotation_title: data.name
-      pharmgkb_annotation_phenotype_category: data.types
-      pharmgkb_annotation_level_of_evidence: data.levelOfEvidence.term  
-      allele_phenotype_information: data.allelePhenotypes.phenotype
-      related_variants: data.location.rsid
-      related_diseases: data.relatedDiseases.name
+      ## commenting out because data-processing / biolink-modeling issues
+      # annotation_title: data.name
+      # pharmgkb_annotation_phenotype_category: data.types
+      # pharmgkb_annotation_level_of_evidence: data.levelOfEvidence.term  
+      # allele_phenotype_information: data.allelePhenotypes.phenotype
+      # related_variants: data.location.rsid
+      # related_diseases: data.relatedDiseases.name
     variantAnnotEnd-chem:
       "PHARMGKB.CHEMICAL": data.relatedChemicals.id
-      related_genes: data.location.genes.symbol
-      flag_significant_association: data.significance.term  ## yes/no values?
       ## provenance
-      annotation_literature_urls: data.literature._sameAs
-      sentence: data.sentence
-      description: data.description
-      ## phenotypic effect
-      phenotype_name: data.phenotypes.phenotype
-      phenotype_context: data.phenotypes.phenotypeContext
-      pharmgkb_annotation_phenotype_category: data.phenotypeCategories.term
-      direction_of_phenotypic_effect: data.polarity.term
-      ## context: what did the population start out with (there's more under data.studyParameters)
-      population_phenotype_name: data.populationPhenotypes.phenotype
+      "biolink:supporting_text": data.sentence
+      ## commenting out because data-processing / biolink-modeling issues
+      # related_genes: data.location.genes.symbol
+      # flag_significant_association: data.significance.term  ## yes/no values?
+      # ## provenance
+      # annotation_literature_urls: data.literature._sameAs
+      # description: data.description
+      # ## phenotypic effect
+      # phenotype_name: data.phenotypes.phenotype
+      # phenotype_context: data.phenotypes.phenotypeContext
+      # pharmgkb_annotation_phenotype_category: data.phenotypeCategories.term
+      # direction_of_phenotypic_effect: data.polarity.term
+      # ## context: what did the population start out with (there's more under data.studyParameters)
+      # population_phenotype_name: data.populationPhenotypes.phenotype
     variantAnnotEnd-variant:
       DBSNP: data.location.rsid
-      related_genes: data.location.genes.symbol
-      flag_significant_association: data.significance.term  ## yes/no values?
       ## provenance
-      annotation_literature_urls: data.literature._sameAs
-      sentence: data.sentence
-      description: data.description
-      ## phenotypic effect
-      phenotype_name: data.phenotypes.phenotype
-      phenotype_context: data.phenotypes.phenotypeContext
-      pharmgkb_annotation_phenotype_category: data.phenotypeCategories.term
-      direction_of_phenotypic_effect: data.polarity.term
-      ## context: what did the population start out with (there's more under data.studyParameters)
-      population_phenotype_name: data.populationPhenotypes.phenotype
+      "biolink:supporting_text": data.sentence
+      ## commenting out because data-processing / biolink-modeling issues
+      # related_genes: data.location.genes.symbol
+      # flag_significant_association: data.significance.term  ## yes/no values?
+      # ## provenance
+      # annotation_literature_urls: data.literature._sameAs
+      # description: data.description
+      # ## phenotypic effect
+      # phenotype_name: data.phenotypes.phenotype
+      # phenotype_context: data.phenotypes.phenotypeContext
+      # pharmgkb_annotation_phenotype_category: data.phenotypeCategories.term
+      # direction_of_phenotypic_effect: data.polarity.term
+      # ## context: what did the population start out with (there's more under data.studyParameters)
+      # population_phenotype_name: data.populationPhenotypes.phenotype
   schemas:
     JSendSuccess:
       required: