diff --git a/mydisease.info/smartapi.yaml b/mydisease.info/smartapi.yaml index 80c3aeaf..8e0aa088 100644 --- a/mydisease.info/smartapi.yaml +++ b/mydisease.info/smartapi.yaml @@ -10,7 +10,7 @@ info: component: KP team: - Service Provider - biolink-version: "2.1.0" + biolink-version: "2.2.3" description: Documentation of the MyDisease.info disease query web services. Learn more about [mydisease.info](http://mydisease.info/) termsOfService: http://mydisease.info/terms @@ -544,9 +544,9 @@ components: requestBody: body: q: "{inputs[0]}" ## no prefix - scopes: hpo.omim ## example: put 246900 here (Dihydrolipoamide Dehydrogenase Deficiency) ## should get HP:0001254 (Lethargy) in response + scopes: hpo.omim header: application/x-www-form-urlencoded inputs: - id: OMIM @@ -626,7 +626,7 @@ components: fields: ctd.chemical_related_to_disease requestBody: body: - q: "{inputs[0]}" + q: "{inputs[0]}" ## no prefix ## example: put 146850 here (IMMUNE SUPPRESSION) ## should get D014810 (Vitamin E) in response scopes: ctd.omim diff --git a/mygene.info/openapi_full.yml b/mygene.info/openapi_full.yml index aacc1abe..4d55084b 100644 --- a/mygene.info/openapi_full.yml +++ b/mygene.info/openapi_full.yml @@ -218,7 +218,9 @@ components: x-bte-kgs-operations: ## notes: ## - for ConsensusPathDB, look at "content information" tab at http://cpdb.molgen.mpg.de/CPDB to see versions of the pathway databases they used - PathwayHasGene: ## using Reactome, KEGG, Wikipathways + ## - pathway info includes Reactome, KEGG, Wikipathways, Biocarta + ## However, SRI ID resolver only accepts SMPDB, REACT, GO, PANTHER.PATHWAY right now + PathwayHasGene: ## future: use relation RO:0000057 (has_participant). this currently maps to biolink has_participant - inputSeparator: "," @@ -238,9 +240,11 @@ components: predicate: has_participant requestBody: body: - q: "{inputs[0]}" - scopes: pathway.reactome.id ## example: R-HSA-70895 - size: 1000 + q: "{inputs[0]}" ## no prefix + ## example: put R-HSA-70895 (Branched-chain amino acid catabolism) here + ## should get 10295 in response (BCKDK) + scopes: pathway.reactome.id + size: 1000 ## note the size limit header: application/x-www-form-urlencoded response_mapping: $ref: "#/components/x-bte-response-mapping/entrezgene" @@ -264,9 +268,11 @@ components: predicate: has_participant requestBody: body: - q: "{inputs[0]}" - scopes: pathway.kegg.id ## example: hsa00120 - size: 1000 + q: "{inputs[0]}" ## no prefix + ## example: put hsa00120 (Primary bile acid biosynthesis - Homo sapiens (human)) here + ## should get 8309 in response (ACOX2) + scopes: pathway.kegg.id + size: 1000 ## note the size limit header: application/x-www-form-urlencoded response_mapping: $ref: "#/components/x-bte-response-mapping/entrezgene" @@ -290,9 +296,11 @@ components: predicate: has_participant requestBody: body: - q: "{inputs[0]}" - scopes: pathway.wikipathways.id ## example: WP3942 - size: 1000 + q: "{inputs[0]}" ## no prefix + ## example: put WP2034 (Leptin signaling pathway) here + ## should get 3953 in response (LEPR) + scopes: pathway.wikipathways.id + size: 1000 ## note the size limit header: application/x-www-form-urlencoded response_mapping: $ref: "#/components/x-bte-response-mapping/entrezgene" @@ -316,9 +324,11 @@ components: predicate: has_participant requestBody: body: - q: "{inputs[0]}" - scopes: pathway.biocarta.id ## example: WP3942 - size: 1000 + q: "{inputs[0]}" ## no prefix + ## example: put raspathway here + ## should get 3265 in response (HRAS) + scopes: pathway.biocarta.id + size: 1000 ## note the size limit header: application/x-www-form-urlencoded response_mapping: $ref: "#/components/x-bte-response-mapping/entrezgene" @@ -343,7 +353,9 @@ components: predicate: enables requestBody: body: - q: "{inputs[0]}" + q: "{inputs[0]}" ## no prefix + ## example: put 1629 here (DBT) + ## should get GO:0031405 (lipoic acid binding) in response ## all records with go.MF field also have entrezgene field scopes: entrezgene header: application/x-www-form-urlencoded @@ -371,70 +383,77 @@ components: predicate: enabled_by requestBody: body: - q: "{inputs[0]}" + q: "{inputs[0]}" ## HAS PREFIX (GO) + ## example: put GO:0008147 here (structural constituent of bone) + ## should get 632 (BGLAP) in response scopes: go.MF.id - size: 1000 + size: 1000 ## note size limit header: application/x-www-form-urlencoded response_mapping: $ref: "#/components/x-bte-response-mapping/entrezgene" source: "infores:ncbi-gene" ## which got from GO Annotations... supportBatch: true - GeneToProtein: - ## future: relation could be RO:0002205 (has_gene_product), currently mapped to biolink:has_gene_product - - - inputSeparator: "," - inputs: - - - id: ENSEMBL - semantic: Gene - outputs: - - - id: UniProtKB - semantic: Protein - parameters: - fields: uniprot.Swiss-Prot - ## there are >107,000 records with both uniprot and ensembl.gene fields - ## (vs >244,000 records with only uniprot fields) - species: human - predicate: has_gene_product - requestBody: - body: - q: "{inputs[0]}" - scopes: ensembl.gene - header: application/x-www-form-urlencoded - response_mapping: - $ref: "#/components/x-bte-response-mapping/uniprotProtein" - ## specifically from the ID mapping file https://www.uniprot.org/downloads#uniprotkblink - source: "infores:uniprot" - supportBatch: true - ProteinToGene: - ## relation: use RO:0002204 (gene_product_of) - - - inputSeparator: "," - inputs: - - - id: UniProtKB - semantic: Protein - outputs: - - - id: ENSEMBL - semantic: Gene - parameters: - fields: ensembl.gene - ## there are >107,000 records with both uniprot and ensembl.gene fields - ## (vs >244,000 records with only uniprot fields) - species: human - predicate: gene_product_of - requestBody: - body: - q: "{inputs[0]}" - scopes: uniprot.Swiss-Prot - header: application/x-www-form-urlencoded - response_mapping: - $ref: "#/components/x-bte-response-mapping/ensemblGene" - ## specifically from the ID mapping file https://www.uniprot.org/downloads#uniprotkblink - source: "infores:uniprot" - supportBatch: true + ## removing because of gene-protein conflation + # GeneToProtein: + # ## future: relation could be RO:0002205 (has_gene_product), currently mapped to biolink:has_gene_product + # - + # inputSeparator: "," + # inputs: + # - + # id: ENSEMBL + # semantic: Gene + # outputs: + # - + # id: UniProtKB + # semantic: Protein + # parameters: + # fields: uniprot.Swiss-Prot + # ## there are >107,000 records with both uniprot and ensembl.gene fields + # ## (vs >244,000 records with only uniprot fields) + # species: human + # predicate: has_gene_product + # requestBody: + # body: + # q: "{inputs[0]}" ## no prefix + # ## example: put ENSG00000107771 here (CCSER2) + # ## should get Q9H7U1 in response + # scopes: ensembl.gene + # header: application/x-www-form-urlencoded + # response_mapping: + # $ref: "#/components/x-bte-response-mapping/uniprotProtein" + # ## specifically from the ID mapping file https://www.uniprot.org/downloads#uniprotkblink + # source: "infores:uniprot" + # supportBatch: true + # ProteinToGene: + # ## relation: use RO:0002204 (gene_product_of) + # - + # inputSeparator: "," + # inputs: + # - + # id: UniProtKB + # semantic: Protein + # outputs: + # - + # id: ENSEMBL + # semantic: Gene + # parameters: + # fields: ensembl.gene + # ## there are >107,000 records with both uniprot and ensembl.gene fields + # ## (vs >244,000 records with only uniprot fields) + # species: human + # predicate: gene_product_of + # requestBody: + # body: + # q: "{inputs[0]}" ## no prefix + # ## example: put O75688 here (PPM1B) + # ## should get ENSG00000138032 in response + # scopes: uniprot.Swiss-Prot + # header: application/x-www-form-urlencoded + # response_mapping: + # $ref: "#/components/x-bte-response-mapping/ensemblGene" + # ## specifically from the ID mapping file https://www.uniprot.org/downloads#uniprotkblink + # source: "infores:uniprot" + # supportBatch: true ## pantherdb gives orthologs and paralogs, which are both homologs. Hence we use homolog ## currently written: MGI, RGD, ZFIN, WormBase, SGD, dictyBase, POMBASE ## Biolink questions: using FB (rather than FlyBase)?? Also no TAIR. @@ -457,7 +476,9 @@ components: predicate: homologous_to requestBody: body: - q: "{inputs[0]}" + q: "{inputs[0]}" ## no prefix + ## example: put 56888 here (KCMF1) + ## should get 1921537 (Kcmf1) in response scopes: entrezgene header: application/x-www-form-urlencoded response_mapping: @@ -596,31 +617,89 @@ components: # $ref: "#/components/x-bte-response-mapping/pantherPom" # source: "infores:panther" # supportBatch: true - hasTranscript: - ## future: relation could be RO:0002511 (transcribed_to) + hasHomolog-rev: - inputSeparator: "," inputs: - - id: ENSEMBL + id: MGI semantic: Gene - outputs: + outputs: - - id: ENSEMBL - semantic: Transcript + id: NCBIGene + semantic: Gene parameters: - fields: ensembl.transcript - species: human - predicate: transcribed_to ## in biolink 2.0 + fields: entrezgene + ## almost all records with pantherdb.ortholog fields also have the entrezgene field + ## > 145,000 records have both fields, vs ~ 3600 records don't have the entrezgene field + predicate: homologous_to requestBody: body: - q: "{inputs[0]}" - scopes: ensembl.gene + q: "{inputs[0]}" ## no prefix + ## example: put in 1916384 + ## should get 643161 back (FAM25A) + scopes: pantherdb.ortholog.MGI header: application/x-www-form-urlencoded response_mapping: - $ref: "#/components/x-bte-response-mapping/ensemblTranscript" - source: "infores:ensembl-gene" ## ensembl or specifically ensembl-gene? + $ref: "#/components/x-bte-response-mapping/entrezgene" + source: "infores:panther" supportBatch: true + ## removing because Transcript isn't supported by SRI-ID-resolver + ## and it doesn't seem useful + # hasTranscript: + # ## future: relation could be RO:0002511 (transcribed_to) + # - + # inputSeparator: "," + # inputs: + # - + # id: ENSEMBL + # semantic: Gene + # outputs: + # - + # id: ENSEMBL + # semantic: Transcript + # parameters: + # fields: ensembl.transcript + # species: human + # predicate: transcribed_to ## in biolink 2.0 + # requestBody: + # body: + # q: "{inputs[0]}" ## no prefix + # ## example: put ENSG00000196911 here (KPNA5) + # ## should get ENST00000356348 in response + # scopes: ensembl.gene + # header: application/x-www-form-urlencoded + # response_mapping: + # $ref: "#/components/x-bte-response-mapping/ensemblTranscript" + # source: "infores:ensembl-gene" ## ensembl or specifically ensembl-gene? + # supportBatch: true + # hasTranscript-rev: + # ## future: relation could be RO's transcribed from + # - + # inputSeparator: "," + # inputs: + # - + # id: ENSEMBL + # semantic: Transcript + # outputs: + # - + # id: ENSEMBL + # semantic: Gene + # parameters: + # fields: ensembl.gene + # species: human + # predicate: transcribed_from ## in biolink 2.0 + # requestBody: + # body: + # q: "{inputs[0]}" + # ## example: put in ENST00000264676 + # ## should get ENSG00000114248 aka LRRC31 back + # scopes: ensembl.transcript + # header: application/x-www-form-urlencoded + # response_mapping: + # $ref: "#/components/x-bte-response-mapping/ensemblGene" + # source: "infores:ensembl-gene" ## ensembl or specifically ensembl-gene? + # supportBatch: true involvedInBP: ## biolink: confusing. biolink currently doesn't have involved_in; this could also be contributes_to? ## future: relation could be NCIT:gene_plays_role_in_process or RO:0000056 (participates in); both currently map to biolink:participates_in @@ -641,7 +720,9 @@ components: predicate: participates_in requestBody: body: - q: "{inputs[0]}" + q: "{inputs[0]}" ## no prefix + ## example: put 632 here (BGLAP) + ## should get GO:0001501 (skeletal system development) in response scopes: entrezgene header: application/x-www-form-urlencoded response_mapping: @@ -668,9 +749,11 @@ components: predicate: has_participant requestBody: body: - q: "{inputs[0]}" + q: "{inputs[0]}" ## HAS PREFIX (GO) + ## example: put GO:0001501 here (skeletal system development) + ## should get 5741 (PTH) in response scopes: go.BP.id - size: 1000 + size: 1000 ## note size limit header: application/x-www-form-urlencoded response_mapping: $ref: "#/components/x-bte-response-mapping/entrezgene" @@ -697,7 +780,9 @@ components: predicate: expressed_in requestBody: body: - q: "{inputs[0]}" + q: "{inputs[0]}" ## no prefix + ## example: put 5741 here (PTH) + ## should get GO:0005576 (extracellular region) in response scopes: entrezgene header: application/x-www-form-urlencoded response_mapping: @@ -725,9 +810,11 @@ components: predicate: expresses requestBody: body: - q: "{inputs[0]}" + q: "{inputs[0]}" ## HAS PREFIX (GO) + ## example: put GO:0033268 here (node of Ranvier) + ## should get 6326 (SCN2A) in response scopes: go.CC.id - size: 1000 + size: 1000 ## note size limit header: application/x-www-form-urlencoded response_mapping: $ref: "#/components/x-bte-response-mapping/entrezgene" @@ -752,7 +839,9 @@ components: predicate: participates_in requestBody: body: - q: "{inputs[0]}" + q: "{inputs[0]}" ## no prefix + ## example: put 1629 here (DBT) + ## should get R-HSA-70895 (Branched-chain amino acid catabolism) in response ## all records with pathway.reactome.id field also have entrezgene field scopes: entrezgene header: application/x-www-form-urlencoded @@ -777,7 +866,9 @@ components: predicate: participates_in requestBody: body: - q: "{inputs[0]}" + q: "{inputs[0]}" ## no prefix + ## example: put 1629 here (DBT) + ## should get hsa00280 (Valine, leucine and isoleucine degradation - Homo sapiens (human)) in response ## all records with pathway.kegg field also have entrezgene field scopes: entrezgene header: application/x-www-form-urlencoded @@ -802,7 +893,9 @@ components: predicate: participates_in requestBody: body: - q: "{inputs[0]}" + q: "{inputs[0]}" ## no prefix + ## example: put 8309 here (ACOX2) + ## should get WP3942 (PPAR signaling pathway) in response ## all records with pathway.wikipathways field also have entrezgene field scopes: entrezgene header: application/x-www-form-urlencoded @@ -827,7 +920,9 @@ components: predicate: participates_in requestBody: body: - q: "{inputs[0]}" + q: "{inputs[0]}" ## no prefix + ## example: put 5608 here (MAP2K6) + ## should get p38mapkpathway (p38 mapk signaling pathway) in response ## all records with pathway.biocarta field also have entrezgene field scopes: entrezgene header: application/x-www-form-urlencoded @@ -846,48 +941,51 @@ components: # UMLS: umls.cui # description: summary biologicalProcess: - GO: go.BP.id - evidence: go.BP.evidence + GO: go.BP.id ## HAS PREFIX (GO) + evidence: go.BP.evidence ## categorical variable? pubmed: go.BP.pubmed name: go.BP.term - qualifiers: go.BP.qualifier + ## seems to be like a relation + relation: go.BP.qualifier cellularComponent: - GO: go.CC.id - evidence: go.CC.evidence + GO: go.CC.id ## HAS PREFIX (GO) + evidence: go.CC.evidence ## categorical variable? pubmed: go.CC.pubmed name: go.CC.term - qualifiers: go.CC.qualifier + ## seems to be like a relation + relation: go.CC.qualifier molecularFunction: - GO: go.MF.id - evidence: go.MF.evidence + GO: go.MF.id ## HAS PREFIX (GO) + evidence: go.MF.evidence ## categorical variable? pubmed: go.MF.pubmed name: go.MF.term - qualifiers: go.MF.qualifier + ## seems to be like a relation + relation: go.MF.qualifier reactomePathway: - REACT: pathway.reactome.id + REACT: pathway.reactome.id ## no prefix name: pathway.reactome.name entrezgene: - NCBIGene: entrezgene + NCBIGene: entrezgene ## no prefix wikipathway: - WIKIPATHWAYS: pathway.wikipathways.id + WIKIPATHWAYS: pathway.wikipathways.id ## no prefix name: pathway.wikipathways.name biocarta: - BIOCARTA: pathway.biocarta.id + BIOCARTA: pathway.biocarta.id ## no prefix name: pathway.biocarta.name keggPathway: - KEGG: pathway.kegg.id + KEGG: pathway.kegg.id ## no prefix name: pathway.kegg.name - ensemblTranscript: - ENSEMBL: ensembl.transcript - ensemblProtein: - ENSEMBL: ensembl.protein - uniprotProtein: - UniProtKB: uniprot.Swiss-Prot - ensemblGene: - ENSEMBL: ensembl.gene + # ensemblTranscript: + # ENSEMBL: ensembl.transcript ## no prefix + # ensemblProtein: + # ENSEMBL: ensembl.protein ## no prefix + # uniprotProtein: + # UniProtKB: uniprot.Swiss-Prot ## no prefix + # ensemblGene: + # ENSEMBL: ensembl.gene ## no prefix ## include ortholog_type for panther? pantherMGI: - MGI: pantherdb.ortholog.MGI + MGI: pantherdb.ortholog.MGI ## no prefix inTaxon: pantherdb.ortholog.taxid # pantherRGD: # RGD: pantherdb.ortholog.RGD @@ -926,7 +1024,7 @@ info: component: KP team: - "Service Provider" - biolink-version: "2.1.0" + biolink-version: "2.2.3" openapi: "3.0.0" paths: /gene: @@ -1154,12 +1252,16 @@ paths: $ref: "#/components/x-bte-kgs-operations/involvedInPathway" - $ref: "#/components/x-bte-kgs-operations/hasTranscript" + - + $ref: "#/components/x-bte-kgs-operations/hasTranscript-rev" - $ref: "#/components/x-bte-kgs-operations/GeneToProtein" - $ref: "#/components/x-bte-kgs-operations/ProteinToGene" - $ref: "#/components/x-bte-kgs-operations/hasHomolog" + - + $ref: "#/components/x-bte-kgs-operations/hasHomolog-rev" - $ref: "#/components/x-bte-kgs-operations/PathwayHasGene" servers: