├── .github └── ISSUE_TEMPLATE │ └── a_data_source_wanted.md ├── .gitignore ├── .travis.yml ├── AGR └── agr.yaml ├── API_LIST.yml ├── CTD └── smartapi.yaml ├── CTD_api └── CTD_openapi.yml ├── DATASET_LIST.yml ├── DISEASES └── smartapi.yaml ├── EBIgene2phenotype └── smartapi.yaml ├── FooDB_api ├── FooDB_openapi-pt1.yaml └── FooDB_openapi-pt2.yaml ├── GTEx_api └── GTEx_openapi.yaml ├── GT_cmaq_exposures_api ├── cmaq_exposures_openapi.yml └── jsonld_context │ └── cmaq_exposures_api_context.json ├── GT_endotypes_api └── endotypes_openapi.yml ├── GT_exposures_api └── exposures_openapi.yml ├── ID_MAPPING.csv ├── LINCS └── smartapi.yml ├── MGIgene2phenotype └── smartapi.yaml ├── README.md ├── RGD └── smartapi.yaml ├── _example_api ├── EXAMPLEAPI_openapi.yml └── jsonld_context │ └── EXAMPLEAPI_ENDPOINT1_context.json ├── annotator └── smartapi.yaml ├── api_catalog ├── API_Catalog_Types.txt ├── README.md ├── example_metadata.yml ├── records │ ├── biolink_metadata.yml │ └── garbanzo_metadata.yaml ├── schema.yml └── template.yml ├── automat-covid-phenotypes └── smartapi.yaml ├── bicluster_api └── bicluster_api_spec.yaml ├── bindingdb └── smartapi.yaml ├── biolink ├── jsonld_context │ ├── .DS_Store │ ├── biolinks_disease_context.json │ ├── biolinks_gene_context.json │ ├── biolinks_homolog_context.json │ ├── biolinks_interact_context.json │ ├── biolinks_interaction_context.json │ └── biolinks_phenotype_context.json └── openapi.yml ├── biomuta └── smartapi.yml ├── bioplanet ├── bioplanet-pathway-disease.yaml └── bioplanet-pathway-gene.yaml ├── biothings_explorer ├── qualifier-sri-test-service.json ├── service-provider-trapi.yaml ├── smartapi.yaml ├── sri-test-bte-ara.json ├── sri-test-multiomics.json ├── sri-test-service-provider.json └── sri-test-text-mining.json ├── biothings_foodb └── smartapi.yaml ├── broad-pgm └── openapi.yml ├── ccle └── smartapi.yml ├── cell_ontology └── smartapi.yml ├── chebi └── smartapi.yaml ├── chembio └── smartapi.yaml ├── chembl └── smartapi.yaml ├── civic └── jsonld_context │ ├── civic_evidence_context.json │ ├── civic_gene_context.json │ ├── civic_general_context.json │ └── civic_variant_context.json ├── clinical_risk_factor └── smartapi.yml ├── cohd └── smartapi.yaml ├── complexportal └── smartapi.yaml ├── cord ├── cord_anatomy.yml ├── cord_bp.yml ├── cord_cc.yml ├── cord_cell.yml ├── cord_chemical.yml ├── cord_disease.yml ├── cord_gene.yml ├── cord_genomic_entity.yml ├── cord_ma.yml └── cord_protein.yml ├── ddinter └── ddinter.yaml ├── denovodb └── smartapi.yaml ├── depmap └── openapi.yml ├── depmap_bicluster_api └── depmap_bicluster_api_spec.yaml ├── dgidb ├── jsonld_context │ └── dgidb_context.json ├── openapi.yml └── smartapi.yml ├── disbiome └── smartapi.yml ├── disease ontology api ├── jsonld_context │ └── do_context.json └── openapi.yml ├── doid └── smartapi.yaml ├── drug_response_kp └── smartapi.yaml ├── ebi_ontology_lookup_service_api ├── jsonld_context │ └── ols_query_1.1.json └── openapi.yml ├── ebi_ontology_mapping_service_api └── openapi.yml ├── ebi_proteins └── openapi.yml ├── ebi_proteins_taxonomy └── openapi.yml ├── ensembl └── openapi.yml ├── fda_drugs └── smartapi.yml ├── fooddata_central └── smartapi.yaml ├── gene_knockout_correlation └── openapi.yml ├── genetics_provider └── smartapi.yaml ├── gmmad2 └── smartapi.yaml ├── go └── smartapi.yml ├── go_bp └── smartapi.yaml ├── go_cc └── smartapi.yaml ├── go_mf └── smartapi.yaml ├── greent ├── greent.yml └── jsonld_context │ └── exposureConditions.jsonld ├── gtrx └── gtrx.yaml ├── harmonize └── smartapi.yaml ├── hetio └── smartapi.yaml ├── hmdb └── smartapi.yaml ├── hpo └── smartapi.yaml ├── hpotomondo_bicluster_api └── hpotomondo_bicluster_api_spec.yaml ├── iPTMnet └── smartapi.yaml ├── idisk └── smartapi.yaml ├── indigo └── openapi.yml ├── innatedb └── smartapi.yaml ├── kaviar └── smartapi.yaml ├── litvar └── smartapi.yaml ├── molecular_data_provider ├── GeLiNEA-TRAPI-1.4.yaml ├── GeLiNEA-TRAPI-1.5.yaml ├── MolePro-TRAPI-1.0.yaml ├── MolePro-TRAPI-1.1.yaml ├── MolePro-TRAPI-1.2.yaml ├── MolePro-TRAPI-1.3.yaml ├── MolePro-TRAPI-1.4.yaml └── MolePro-TRAPI-1.5.yaml ├── mondo └── smartapi.yml ├── mrcoc └── smartapi.yaml ├── multiomics_clinical_trials └── smartapi.yaml ├── mychem.info ├── jsonld_context │ ├── mychem_context.json │ ├── mychem_drug_1.1.json │ └── mychem_query_1.1.json ├── mychem_auto.yaml ├── openapi_full.yml └── openapi_minimum.yml ├── mydisease.info └── smartapi.yaml ├── mygene.info ├── jsonld_context │ ├── mygene_context.json │ ├── mygene_gene_1.1.json │ └── mygene_query_1.1.json ├── openapi_full.yml ├── openapi_full_temp.yml └── openapi_minimum.yml ├── mygeneset.info └── smartapi.yml ├── mytaxon.info └── mytaxon_auto.yaml ├── myvariant.info ├── jsonld_context │ ├── myvariant_context.json │ ├── myvariant_query_1.1.json │ └── myvariant_variant_1.1.json ├── openapi_full.yml ├── openapi_full_temp.yml └── openapi_minimum.yml ├── ncats_rare_source └── smartapi.yaml ├── ncit └── smartapi.yml ├── ols └── smartapi.yaml ├── openfda └── jsonld_context │ └── openfda_context.json ├── opentarget └── smartapi.yaml ├── pfocr └── smartapi.yaml ├── pharmgkb └── smartapi.yaml ├── pharos └── smartapi.yaml ├── phewas └── smartapi.yml ├── pseudocap_go └── smartapi.yml ├── pubtator3 └── smartapi.yaml ├── quickgo └── smartapi.yaml ├── reactome └── jsonld_context │ ├── .DS_Store │ ├── protein_interaction_context.json │ ├── reactome_context.json │ └── reactome_lower_context.json ├── repodb └── smartapi.yaml ├── rhea └── smartapi.yaml ├── rnaseqdb_bicluster_api └── rnaseqdb_bicluster_api_spec.yaml ├── robokop └── openapi.yml ├── robokop_extend └── smartapi.yaml ├── robokop_messenger └── openapi.yml ├── rtx └── TranslatorReasonerRTX.yaml ├── scibite └── smartapi.yml ├── scigraph └── smartapi.yaml ├── semmed ├── semmed_anatomy.yaml ├── semmed_biological_process.yaml ├── semmed_chemical.yaml ├── semmed_disease.yaml ├── semmed_gene.yaml └── semmed_phenotype.yaml ├── semmeddb ├── AutoGen_SEMMEDDB.ipynb ├── AutoGen_SEMMEDDB_Old.ipynb ├── generated_list.yaml ├── generated_operations.yaml ├── meta_triple_document_stat_20250410_165534.tsv ├── smartapi.yaml └── version_without_operations.yaml ├── sepid_mab └── smartapi.yaml ├── stanford_kp └── smartapi.yaml ├── suppkg └── suppkg.yaml ├── tcga_mut_freq └── smartapi.yaml ├── tests.py ├── text_mining ├── autogenerate_co-occurrence_smartapi.py ├── cooccurrence.yaml ├── smartapi.yaml ├── x_bte_operations.yml ├── x_bte_operations_ref.yml └── x_response_mapping.yml ├── tissues └── smartapi.yaml ├── ttd └── smartapi.yaml ├── uberon └── smartapi.yaml └── upheno_ontology └── smartapi.yaml /.github/ISSUE_TEMPLATE/a_data_source_wanted.md: -------------------------------------------------------------------------------- 1 | --- 2 | name: Data source wanted 3 | about: "Request for a particular data/knowledge source or type of connecting data" 4 | assignees: cmungall, tomconlin 5 | labels: 'data wanted' 6 | --- 7 | 8 | Please enter information where you see elipses `...` below. The template is a guide, follow it where you can. 9 | 10 | **Data Source** 11 | 12 | _Optional. Name of the preferred source for this data. E.g. OMIM, DrugBank_ 13 | 14 | * DATABASE: ... 15 | 16 | **Main Entity Type** 17 | 18 | _What kind of entity are you interested in? Biolink type preferred, e.g. variant, disease, gene_ 19 | 20 | * SUBJECT: ... 21 | 22 | **Connected Entity Type** 23 | 24 | _What kind of thing should the subject be connected to? E.g. for drug-disease links this would be 'disease'. Biolink type preferred_ 25 | 26 | * OBJECT: ... 27 | 28 | * RELATION: ... 29 | 30 | **Example statement** 31 | 32 | _Enter one or more examples of statements/edges you would expect to retrieve using this source. For example, "aldehydes exacerbates Fanconi anemia". In future this could be used to drive integration tests_ 33 | 34 | * EXAMPLE 1: ... 35 | * EXAMPLE 2: ... 36 | 37 | **Preferred format or ingest method** 38 | 39 | _How would you prefer to get the data? Via API or Data dump that can be ingested into your KG? Would you prefer a smart API registry entry, a neo4j dump, biolink-compliant CSV/RDF/JSON that can be loaded with KGX?_ 40 | 41 | * METHOD: ... 42 | 43 | **Usage** 44 | 45 | _How will this be used? Give a URL of a workflow if possible_ 46 | 47 | * USAGE: ... 48 | 49 | **Any other information:** 50 | 51 | _Enter any information you like here_ 52 | 53 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # Ignore file with github OAuth IDs 2 | .ghenv 3 | 4 | # Python directories 5 | __pycache__ 6 | 7 | *.pyc 8 | 9 | ENV* -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 1 | language: python 2 | python: 3 | - "3.6" 4 | # command to install dependencies 5 | install: "pip install requests PyYAML" 6 | # command to run tests 7 | script: "pytest tests.py" 8 | -------------------------------------------------------------------------------- /API_LIST.yml: -------------------------------------------------------------------------------- 1 | # The master list for the translator APIs 2 | # Each API provider should add one entry under APIs 3 | # 4 | # "metadata" points to the API's openapi metadata 5 | # a relative path in this repo, or a full URL 6 | # "translator" is a placeholder for translator specific attributes 7 | 8 | APIs: 9 | - metadata: mygene.info/openapi_full.yml 10 | translator: 11 | - returnjson: true 12 | notes: "" 13 | 14 | - metadata: myvariant.info/openapi_full.yml 15 | translator: 16 | - returnjson: true 17 | notes: "" 18 | 19 | - metadata: mychem.info/openapi_full.yml 20 | translator: 21 | - returnjson: true 22 | notes: "" 23 | - metadata: dgidb/openapi.yml 24 | translator: 25 | - returnjson: true 26 | notes: "" 27 | - metadata: biolink/openapi.yml 28 | translator: 29 | - returnjson: true 30 | notes: "" 31 | - metadata: disease ontology api/openapi.yml 32 | translator: 33 | - returnjson: true 34 | notes: "" 35 | - metadata: ebi_ontology_lookup_service_api/openapi.yml 36 | translator: 37 | - returnjson: true 38 | notes: "" 39 | - metadata: ensembl/openapi.yml 40 | translator: 41 | - returnjson: true 42 | notes: "" 43 | - metadata: ebi_proteins/openapi.yml 44 | translator: 45 | - returnjson: true 46 | notes: "" 47 | - metadata: ebi_proteins_taxonomy/openapi.yml 48 | translator: 49 | - returnjson: true 50 | notes: "" 51 | - metadata: broad-pgm/openapi.yml 52 | translator: 53 | - returnjson: true 54 | notes: "" 55 | - metadata: GT_endotypes_api/endotypes_openapi.yml 56 | translator: 57 | - returnjson: true 58 | notes: "" 59 | - metadata: GT_exposures_api/exposures_openapi.yml 60 | translator: 61 | - returnjson: true 62 | notes: "" 63 | - metadata: GT_cmaq_exposures_api/cmaq_exposures_openapi.yml 64 | translator: 65 | - returnjson: true 66 | notes: "" 67 | - metadata: CTD_api/CTD_openapi.yml 68 | translator: 69 | - returnjson: true 70 | notes: "" 71 | - metadata: robokop/openapi.yml 72 | translator: 73 | - returnjson: true 74 | notes: "" 75 | - metadata: robokop_messenger/openapi.yml 76 | translator: 77 | - returnjson: true 78 | notes: "" 79 | 80 | - metadata: GTEx_api/GTEx_openapi.yaml 81 | translator: 82 | - returnjson: true 83 | notes: "" 84 | 85 | - metadata: FooDB_api/FooDB_openapi-pt1.yaml 86 | translator: 87 | - returnjson: true 88 | notes: "" 89 | 90 | - metadata: FooDB_api/FooDB_openapi-pt2.yaml 91 | translator: 92 | - returnjson: true 93 | notes: "" 94 | -------------------------------------------------------------------------------- /DATASET_LIST.yml: -------------------------------------------------------------------------------- 1 | # The master list for the translator Datasets, 2 | # which are subject to convert to an API. 3 | # 4 | # Some basic metadata fields are defined as: 5 | # "name": a short name for the dataset 6 | # "description": a longer description about the dataset 7 | # "url": a url that points to the dataset 8 | # "translator" translator-specific attributes: 9 | # "enpoint" dataset access information 10 | # "url" endpoint url 11 | # "biolink_model" yes/no - whether the dataset conforms to the biolink data model 12 | # "source_format" a format of the source file/API 13 | # "api_type" a type of the API (OpenAPI/smartAPI/REST/knowledge-beacon/...) 14 | # "api_registry" a link to a registry contaninig additional information about the endpoint 15 | # "parse_code" a link to code used to parse/generate the dataset 16 | # "categories" categories of data contained in the dataset 17 | 18 | 19 | datasets: 20 | - name: BioLink 21 | description: Monarch BioLink API 22 | url: https://monarchinitiative.org/page/services 23 | translator: 24 | endpoint: 25 | - url: https://biolink-kb.ncats.io/beacon/biolink/ 26 | biolink_model: yes 27 | source_format: API/JSON 28 | api_type: knowledge-beacon 29 | api_registry: 30 | parse_code: 31 | - url: https://api.monarchinitiative.org/api/ 32 | biolink_model: yes 33 | source_format: API/JSON 34 | api_type: knowledge-beacon 35 | api_registry: https://github.com/NCATS-Tangerine/translator-api-registry/blob/master/biolink/openapi.yml 36 | parse_code: 37 | categories: 38 | - sequence feature 39 | - gene 40 | - anatomical entity 41 | - phenotype 42 | - cellular component 43 | - cell 44 | - disease 45 | - quality 46 | - variant locus 47 | - sequence alteration 48 | - molecular entity 49 | - clinical_course 50 | - snv 51 | - organism 52 | - genotype 53 | - inheritance 54 | 55 | - name: HMDB 56 | description: Human Metabolome Database 57 | url: http://www.hmdb.ca/ 58 | translator: 59 | endpoint: 60 | - url: http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip 61 | biolink_model: no 62 | source_format: XML 63 | - url: https://translator.ncats.io/hmdb-knowledge-beacon 64 | biolink_model: yes 65 | source_format: API/JSON 66 | api_type: knowledge-beacon 67 | api_registry: 68 | parse-code: https://github.com/NCATS-Tangerine/HMDB-knowledge-beacon 69 | categories: 70 | - metabolite 71 | - disease 72 | - pathway 73 | - cellular location 74 | - biospecimen 75 | - tissue 76 | - protein 77 | 78 | - name: PubChem 79 | description: PubChem is an open chemistry database at the National Institutes of Health (NIH). 80 | url: https://pubchem.ncbi.nlm.nih.gov/ 81 | translator: 82 | endpoint: 83 | - url: https://pubchemdocs.ncbi.nlm.nih.gov/power-user-gateway 84 | biolink_model: no 85 | source_format: API/XML 86 | api_type: custom 87 | categories: 88 | - chemical substance 89 | - assay 90 | 91 | -------------------------------------------------------------------------------- /GT_cmaq_exposures_api/jsonld_context/cmaq_exposures_api_context.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context": { 3 | "obo": "http://purl.obolibrary.org/obo/", 4 | "CHEBI": "http://purl.obolibrary.org/obo/CHEBI_", 5 | "ENVO": "http://purl.obolibrary.org/obo/ENVO_", 6 | "NCIT": "http://purl.obolibrary.org/obo/NCIT_", 7 | "EOL": "http://opendata.inra.fr/EOL/EOL_", 8 | "ald2": "CHEBI:15343", 9 | "benzene": "CHEBI:16716", 10 | "co": "CHEBI:17245", 11 | "eth": "CHEBI:62801", 12 | "etha": "CHEBI:42266", 13 | "form": "CHEBI:16842", 14 | "h2o2": "CHEBI:16240", 15 | "hn03": "CHEBI:48107", 16 | "hono": "CHEBI:25567", 17 | "oh": "CHEBI:16234", 18 | "isop": "CHEBI:35194", 19 | "n2o5": "CHEBI:29802", 20 | "nh3": "CHEBI:16134", 21 | "no": "CHEBI:35196", 22 | "no2": "CHEBI:33101", 23 | "o3": "CHEBI:25812", 24 | "pan": "CHEBI:53571", 25 | "so2": "CHEBI:18422", 26 | "sulf": "CHEBI:16189", 27 | "terp": "CHEBI:35187", 28 | "tol": "CHEBI:17578", 29 | "voc": "CHEBI:134179", 30 | "xyl": "CHEBI:17151", 31 | "pm10": "ENVO:01000060", 32 | "sfc_tmp": "ENVO:09200001", 33 | "sol_rad": "NCIT:C44445", 34 | "air_dens":"EOL:0001778", 35 | "variables": "http://example.org/variables", 36 | "variable": { 37 | "@id": "http://example.org/variable", 38 | "@type": "@vocab" 39 | }, 40 | "description": "http://purl.org/dc/terms/description", 41 | "has_quality_metric": "http://purl.org/dc/terms/has_quality_metric", 42 | "quality_metric": "http://example.org/quality_metric", 43 | "common_name": "http://purl.org/dc/terms/common_name", 44 | "variable": { 45 | "@id": "http://example.org/variable", 46 | "@type": "@vocab" 47 | }, 48 | "units": "http://purl.org/dc/terms/units", 49 | "common_name": "http://purl.org/dc/terms/common_name", 50 | "utc_min_date_time": "http://purl.org/dc/terms/utc_min_date_time", 51 | "utc_max_date_time": "http://purl.org/dc/terms/utc_max_date_time", 52 | "resolution": "http://purl.org/dc/terms/resolution", 53 | "aggregation": "http://purl.org/dc/terms/aggregation" 54 | }, 55 | } 56 | -------------------------------------------------------------------------------- /GT_endotypes_api/endotypes_openapi.yml: -------------------------------------------------------------------------------- 1 | openapi: 3.0.0 2 | servers: 3 | - url: 'https://endotypes.renci.org/v1' 4 | info: 5 | description: >- 6 | NIH Endotypes API - Refer to User Manual on how to use the API. 7 | version: 1.0.0 8 | title: NIH Endotypes API 9 | termsOfService: None 10 | contact: 11 | name: Hong Yi 12 | url: 'https://github.com/renci/nih-endotypes-api' 13 | email: hongyi@renci.org 14 | license: 15 | name: MIT 16 | url: 'http://opensource.org/licenses/MIT' 17 | tags: 18 | - name: patient 19 | - name: endotype 20 | - name: query 21 | ## deprecate this registry entry? 22 | # - name: translator 23 | paths: 24 | /endotypes: 25 | post: 26 | summary: Get list of endotypes based on input as a POST request 27 | description: | 28 | list of endotypes based on input 29 | @input 30 | - JSON object with required input 31 | 32 | @return 33 | - JSON object that returns array of predicted endotypes 34 | operationId: endotypes_post 35 | responses: 36 | '200': 37 | description: OK 38 | content: 39 | application/json: 40 | schema: 41 | $ref: '#/components/schemas/response_200' 42 | '400': 43 | description: Invalid parameter 44 | '404': 45 | description: No endotypes found 46 | '500': 47 | description: Server error 48 | x-swagger-router-controller: controllers.default_controller 49 | requestBody: 50 | content: 51 | application/json: 52 | schema: 53 | $ref: '#/components/schemas/input' 54 | required: true 55 | components: 56 | schemas: 57 | exposure: 58 | type: object 59 | properties: 60 | value: 61 | type: number 62 | format: float 63 | example: 2 64 | units: 65 | type: string 66 | example: '' 67 | exposure_type: 68 | type: string 69 | example: pm25 70 | visit: 71 | type: object 72 | properties: 73 | time: 74 | type: string 75 | example: '2017-10-12 21:12:29' 76 | lat: 77 | type: string 78 | example: '20' 79 | lon: 80 | type: string 81 | example: '20' 82 | visit_type: 83 | type: string 84 | example: INPATIENT 85 | pattern: ^(INPATIENT|OUTPATIENT|EMERGENCY|inpatient|outpatient|emergency)$ 86 | x-regex: ^(INPATIENT|OUTPATIENT|EMERGENCY|inpatient|outpatient|emergency)$ 87 | x-modifiers: [] 88 | icd_codes: 89 | type: string 90 | example: 'ICD9:V12,ICD9:E002' 91 | description: >- 92 | comma-separated standard ICD-9 or ICD-10 codes associated with the 93 | visit 94 | exposures: 95 | type: array 96 | items: 97 | $ref: '#/components/schemas/exposure' 98 | input: 99 | type: object 100 | properties: 101 | date_of_birth: 102 | type: string 103 | example: '2017-10-04' 104 | race: 105 | type: string 106 | example: '1' 107 | description: | 108 | race code ranged from 1 to 6 with the following mapping: 109 | 1: WHITE OR CAUCASIAN 110 | 2: BLACK OR AFRICAN AMERICAN 111 | 3: AMERICAN INDIAN OR ALASKA NATIVE 112 | 4: ASIAN 113 | 5: NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER 114 | 6: OTHER/HISPANIC 115 | sex: 116 | type: string 117 | example: M 118 | pattern: ^(F|M|f|m)$ 119 | x-regex: ^(F|M|f|m)$ 120 | x-modifiers: [] 121 | model_type: 122 | type: string 123 | example: M0 124 | pattern: '^[M|m][0-9]$' 125 | x-regex: '^[M|m][0-9]$' 126 | x-modifiers: [] 127 | visits: 128 | type: array 129 | items: 130 | $ref: '#/components/schemas/visit' 131 | endotypes_period: 132 | type: object 133 | properties: 134 | start_time: 135 | type: string 136 | end_time: 137 | type: string 138 | response_200: 139 | type: object 140 | properties: 141 | output: 142 | type: array 143 | items: 144 | $ref: '#/components/schemas/response_200_output' 145 | response_200_output: 146 | properties: 147 | endotype_id: 148 | type: string 149 | endotype_description: 150 | type: string 151 | endotype_evidence: 152 | type: string 153 | periods: 154 | type: array 155 | items: 156 | $ref: '#/components/schemas/endotypes_period' 157 | type: object -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | [![Build Status](https://travis-ci.org/NCATS-Tangerine/translator-api-registry.svg?branch=master)](https://travis-ci.org/NCATS-Tangerine/translator-api-registry) 2 | 3 | # translator-api-registry 4 | This repo hosts the API metadata for the Translator project 5 | 6 | ## How to add your API 7 | 8 | 1. First, each API should create a separate folder to host its metadata. The folder "_example_api" provides basic template for adding API metadata, so you can start with copying "_example_api" folder and renaming it to your API name. 9 | 2. Second, fill in the metadata about your API according to the instruction. Also please refer to the existing examples like "[mygene.info](mygene.info)" and "[myvariant.info](myvariant.info)" APIs. See more details in the next section. 10 | 3. Add an entry to [API_LIST.yml](API_LIST.yml) file following the existing example. This is the master list of the APIs available in this repo. Our SmartAPI application will import all the API metadata based on this file. 11 | 12 | If you have the permission, commit your changes to this repo. Otherwise, feel free to submit a pull-request. Please check the "build status" badge above, and make sure it's green after your changes. We run some validation tests in this "[tests.py](tests.py)" for each commit. (Tip: you can run `python tests.py` locally from the root of this repo to make sure all tests pass before you commit your code.) 13 | 14 | ### Specific notes for adding a [Reasoner API](https://github.com/NCATS-Tangerine/NCATS-ReasonerStdAPI) 15 | In addition to follow the above steps, we recommend to add these extra info into your Reasoner API metadata: 16 | 17 | info: 18 | x-reasoner_standard_version: 0.9 19 | 20 | tags: 21 | name: translator 22 | name: reasoner 23 | 24 | ## How to create your OpenAPI v3 metadata 25 | 26 | ### Starting from the scratch 27 | You can use [this editor](http://smart-api.info/editor/) to write/edit your API metadata. You can start with an existing metadata example from "[mygene.info](mygene.info/openapi_minimum.yml)" or "[myvariant.info](myvariant.info/openapi_minimum.yml)" APIs. The editor automatically validates your API metadata and gives a live preview of auto-generated API documentation. 28 | 29 | This [OpenAPI GUI](http://smart-api.info/openapi-gui/) interface can also be useful for creating your API metadata from the scratch. But be aware of that this interface does not support any [SmartAPI extensions](https://github.com/SmartAPI/smartAPI-Specification/blob/OpenAPI.next/versions/smartapi-list.md) (those fields with "x-" prefix) we added to the standard OpenAPI v3 specifications. You can of course add extra SmartAPI fields after you export your metadata from the GUI interface to the editor. 30 | 31 | ### Converting from a Swagger/OpenAPI v2 metadata 32 | If you already have an API metadata document in older Swagger/OpenAPI v2 specification. You can try this conversion tool to convert it to the latest OpenAPI v3 format, and then edit it in the [editor](http://smart-api.info/editor/): 33 | 34 | https://mermade.org.uk/openapi-converter 35 | 36 | http://openapiconverter.azurewebsites.net/ 37 | 38 | 39 | This converter is not perfect, but still a good starting point. 40 | 41 | Tip: Feel free to play with your API metadata file with the tools we mentioned above, and commit your changes even when they are not fully complete or valid. As along as the metadata entry has not been added to the API_LIST.yml file (see below), you will be fine :-). When you are happy with your metadata, you can now move to the next step to add it to the API_LIST.yml file. 42 | 43 | A [code snippet](https://github.com/PriceLab/translator-bigquery-api/blob/6d652ec28d0ae7b893395b3e3c360c9d5b144fe3/app/api/bigquery/endpoints/metadata.py#L115) to convert [flask-restful](http://flask-restful.readthedocs.io) auto-generated swagger v2 specification to SmartAPI metedata, kindly provided by @JohnCEarls. 44 | 45 | 46 | ## API_LIST.yml file 47 | This is a YAML file at the root of this repo to keep track of all APIs available in this repo. Our SmartAPI application will import all the API metadata based on this file and render an API registry web frontend. 48 | 49 | For each API, you just need to add a text block like this: 50 | 51 | - metadata: mygene.info/openapi_minimum.yml 52 | translator: 53 | - returnjson: true 54 | notes: "" 55 | 56 | * ***metadata*** field 57 | 58 | The value of this field should be either the URL or the relative path pointing to the API metadata. The API metadata should follow [OpenAPI specifications](https://www.openapis.org/), in either JSON or YAML format. Specifically, we support OpenAPI v3 specification documented [here](https://github.com/OAI/OpenAPI-Specification/blob/OpenAPI.next/versions/3.0.0.md), plus the SmartAPI extensions documented [here](https://github.com/SmartAPI/OpenAPI-Specification/blob/OpenAPI.next/versions/3.0.0.md). 59 | 60 | * ***translator*** field 61 | 62 | This serves as the placeholder for any translator project specific API properties, e.g. adding some API-specific notes. 63 | 64 | * How to propose a new translator.* field? 65 | 66 | As we expand our list of APIs, we will need to expand our metadata fields as we needed. To do so, you can: 67 | * discuss it with us at our slack channel (#arch-working-group) 68 | * open an issue in this repo 69 | * submit a pull-request for your modified [API_LIST.yml](API_LIST.yml) file 70 | 71 | ## CORS support 72 | If you want users are able to request your API from the browser, e.g. in a web application, your API should support [CORS](https://en.wikipedia.org/wiki/Cross-origin_resource_sharing). We recommend every translator API to support CORS. Depending on your web server (e.g. Apache or Nginx) and/or the web framework (e.g. Django, Flask, Tornado) you use, you can find the relevant instruction to enable CORS for your API [here](https://enable-cors.org/), or via Google. 73 | 74 | ## How to pick URIs for annotating input parameters or the response data object? 75 | Typically for a JSON-based REST API, we use URIs to annotate both the acceptable parameter value types and the fields from the response data object, both in [OpenAPI](https://www.openapis.org/) metdata files and JSON-LD context files. You can find some examples for "[mygene.info](mygene.info)" and "[myvariant.info](myvariant.info)" APIs. 76 | 77 | To help you decide which URIs to use, we maintain a "[ID_MAPPING.csv](ID_MAPPING.csv)" file to keep records of all URIs we will use. Feel free to add URIs for additional field types. Please make sure not to break the csv format, as that will break github's nice csv rendering and search features. 78 | 79 | In general, we like to use the URIs from these repositories (also in that priority order)： 80 | 1. Identifiers.org 81 | 2. purl.uniprot.org (?) 82 | 3. [please add] 83 | 84 | 85 | ## Know a knowledge source useful for Translator, but no API available? 86 | You can add a knowledge source (or datasets) to this [DATASET_LIST.yml](DATASET_LIST.yml) file. Follow the instruction and existing entries there. 87 | 88 | Translator team members monitor this list and can potentially build an API to serve that particulara knowledge source, so that it can be better integrated in the rest of Translator API ecosystem. 89 | -------------------------------------------------------------------------------- /RGD/smartapi.yaml: -------------------------------------------------------------------------------- 1 | openapi: '3.0.0' 2 | info: 3 | version: '1.0' 4 | title: RGD API 5 | description: >- 6 | The RGD API 7 | termsOfService: http://www.rgd.org 8 | contact: 9 | name: rgd help desk 10 | x-role: responsible developer 11 | email: help@rgd.org 12 | servers: 13 | - url: 'https://rest.rgd.mcw.edu/rgdws' 14 | description: 'Production server' 15 | tags: 16 | - name: translator 17 | - name: gene 18 | 19 | paths: 20 | '/genes/{geneid}': 21 | get: 22 | summary: 'retrieve rgd data' 23 | parameters: 24 | - name: geneid 25 | in: path 26 | description: >- 27 | RGD id 28 | required: true 29 | example: "620465" 30 | schema: 31 | type: string 32 | responses: 33 | '200': 34 | description: 'A RGD object' 35 | x-bte-response-mapping: 36 | $ref: '#/components/x-bte-response-mapping/gene-homolog' 37 | x-bte-kgs-operations: 38 | associatedWith: 39 | $ref: '#/components/x-bte-kgs-operations/hasHomolog' 40 | components: 41 | x-bte-kgs-operations: 42 | hasHomolog: 43 | inputs: 44 | - id: rgd 45 | semantic: Gene 46 | outputs: 47 | - id: symbol 48 | semantic: Gene 49 | parameters: 50 | geneid: "{input1}" 51 | supportBatch: false 52 | response-mapping: 53 | $ref: '#/components/x-bte-response-mapping/gene-homolog' 54 | x-bte-response-mapping: 55 | gene-homolog: 56 | "@context": http://schema.org 57 | "@type": Gene 58 | bts:rgd: rgd 59 | bts:hasHomolog: 60 | "@type": Gene 61 | bts:symbol: ensemblGeneSymbol 62 | "$input": bts:rgd 63 | "$source": RGD -------------------------------------------------------------------------------- /_example_api/EXAMPLEAPI_openapi.yml: -------------------------------------------------------------------------------- 1 | # This file should store OpenAPI v3 metadata (https://www.openapis.org/) in either JSON or YAML format. 2 | # Ref 1: OpenAPI v3 specifications: 3 | # https://github.com/OAI/OpenAPI-Specification/blob/OpenAPI.next/versions/3.0.0.md 4 | # Ref 2: SmartAPI extensions (extra fields starting with "x-") 5 | # https://github.com/SmartAPI/OpenAPI-Specification/blob/OpenAPI.next/versions/3.0.0.md 6 | # You can also refer to this list of SmartAPI extensions (excluding all OpenAPI fields): 7 | # https://github.com/SmartAPI/smartAPI-Specification/blob/OpenAPI.next/versions/smartapi-list.md 8 | # 9 | # Or the simple way to get started is to follow our examples in this repo: 10 | # 1. This is a minimal example for MyGene.info API: 11 | # https://github.com/NCATS-Tangerine/translator-api-registry/blob/master/mygene.info/openapi_minimum.yml 12 | # 2. This is a full metadata example for MyGene.info API 13 | # https://github.com/NCATS-Tangerine/translator-api-registry/blob/master/mygene.info/openapi_full.yml 14 | -------------------------------------------------------------------------------- /_example_api/jsonld_context/EXAMPLEAPI_ENDPOINT1_context.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context": { 3 | "fieldname1": "http://identifiers.org/###", 4 | "fieldname2": "http://identifiers.org/###" 5 | } 6 | } -------------------------------------------------------------------------------- /annotator/smartapi.yaml: -------------------------------------------------------------------------------- 1 | openapi: 3.0.3 2 | info: 3 | contact: 4 | email: help@biothings.io 5 | name: BioThings Team 6 | x-id: https://github.com/biothings 7 | x-role: responsible developers 8 | description: Translator Annotation Service. 9 | termsOfService: https://biothings.io/about 10 | title: Translator Annotation Service 11 | version: '1.0' 12 | x-translator: 13 | component: Utility 14 | team: 15 | - Service Provider 16 | servers: 17 | - description: Production server 18 | url: https://biothings.ncats.io/annotator 19 | x-maturity: production 20 | - description: Staging server 21 | url: http://biothings.test.transltr.io/annotator 22 | - description: CI server 23 | url: http://biothings.ci.transltr.io/annotator 24 | tags: 25 | - name: gene 26 | - name: chemical 27 | - name: drug 28 | - name: disease 29 | - name: phenotype 30 | - name: annotation 31 | - name: translator 32 | paths: 33 | /: 34 | post: 35 | parameters: 36 | - $ref: '#/components/parameters/append' 37 | name: append 38 | requestBody: 39 | content: 40 | application/json: 41 | schema: 42 | properties: 43 | ids: 44 | description: 'multiple association IDs separated by comma. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. Type: string (list). Max: 1000.' 45 | type: string 46 | required: 47 | - ids 48 | responses: 49 | '200': 50 | content: 51 | application/json: 52 | schema: 53 | items: 54 | $ref: '#/components/schemas/Annotation' 55 | type: array 56 | description: A list of matching annotation objects 57 | '400': 58 | content: 59 | application/json: 60 | schema: 61 | $ref: '#/components/schemas/ErrorResult' 62 | description: A response indicating an improperly formatted query 63 | summary: For a list of curie IDs, return the expanded annotation objects 64 | /{curieid}: 65 | get: 66 | parameters: 67 | - description: Retrieve expanded annotation object based on a given curie ID. 68 | example: "NCBIGene:695" 69 | in: path 70 | name: curieid 71 | required: true 72 | schema: 73 | type: string 74 | - $ref: '#/components/parameters/raw' 75 | name: raw 76 | - $ref: '#/components/parameters/fields' 77 | name: fields 78 | responses: 79 | '200': 80 | content: 81 | application/json: 82 | schema: 83 | $ref: '#/components/schemas/Annotation' 84 | description: A matching annotation object 85 | '404': 86 | description: A response indicating an unknown or unsupported curie ID 87 | summary: Retrieve annotation objects based on a curie ID 88 | components: 89 | parameters: 90 | append: 91 | description: 'When true, append annotations to the existing "attributes" field, otherwise, overwrite the existing "attributes" field. Default: false.' 92 | in: query 93 | name: append 94 | schema: 95 | type: boolean 96 | raw: 97 | description: 'Whem true, return annotation fields in their original data structure before transformation, useful when doing some debugging. Default: false.' 98 | in: query 99 | name: raw 100 | schema: 101 | type: boolean 102 | fields: 103 | description: Can provide a comma-separated fields to override the default set of annotation fields, or passing "fields=all" to return all available fields from the original annotation source. 104 | in: query 105 | name: fields 106 | schema: 107 | type: string 108 | schemas: 109 | Annotation: 110 | properties: 111 | _id: 112 | type: string 113 | required: 114 | - _id 115 | type: object 116 | ErrorResult: 117 | properties: 118 | message: 119 | type: string 120 | success: 121 | type: boolean 122 | type: object 123 | -------------------------------------------------------------------------------- /api_catalog/API_Catalog_Types.txt: -------------------------------------------------------------------------------- 1 | # Semantic Types from the Translator API Catalog Specification 2 | # Note there is some multiple inheritance (e.g. CellComponent, Treatment/Therapy, LabTest) 3 | # * = term that has no equivalent in the Biolink core types (https://biolink.github.io/biolink-model/) 4 | 5 | - SequenceEntity 6 | - Genome 7 | - Genotype 8 | - Gene 9 | - Allele/Variant 10 | - Protein 11 | - Transcript 12 | - microRNA 13 | - ProteinDomain* 14 | - ProteinModification* 15 | - EpigeneticModification* 16 | - Operon* 17 | - GeneFamily 18 | - ChemicalEntity 19 | - Substance 20 | - SmallMolecule* 21 | - Metabolite* 22 | - Drug* 23 | - MacromolecularComplex 24 | - BiologicalProcess 25 | - MolecularInteraction* 26 | - Reaction* 27 | - Pathway 28 | - LifeStage 29 | - GOTerm 30 | - MolecularFunction 31 | - CellComponent 32 | - BiologicalProcess 33 | - AnatomicalEntity 34 | - Tissue/Organ (gross anatomical entity) 35 | - Cell 36 | - CellComponent 37 | - PhysicalCondition 38 | - Trait* 39 | - Phenotype 40 | - Disease 41 | - Organism 42 | - Person* 43 | - Patient/Case 44 | - Population 45 | - Taxon* 46 | - Strain* 47 | - Cohort 48 | - SocioEnvironmentalExposure 49 | - ChemicalExposure* 50 | - DrugExposure 51 | - Treatment/Therapy 52 | - Behavior* 53 | - SocioEconomicFactor* 54 | - GeographicalLocation* 55 | - ModelSystem 56 | - Taxon* 57 | - Strain* 58 | - CellLine 59 | - Xenograft* 60 | - Study 61 | - ExperimentalStudy* 62 | - Bioassay* 63 | - ClinicalStudy* 64 | - LabTest* 65 | - ResearchResource 66 | - Antibody* 67 | - GeneKnockdownReagent* 68 | - Construct* 69 | - Sample/Specimen* 70 | - ModelSystem* 71 | - ChemicalEntity 72 | - Device/Instrument* 73 | - InformationResource* 74 | - Identifier 75 | - DataModel 76 | - Ontology 77 | - Database 78 | - Protocol 79 | - Publication 80 | - ClinicalReport 81 | - ClinicalEntity 82 | - Patient/Case 83 | - Cohort 84 | - PharmaceuticalProduct* 85 | - ClinicalReport* 86 | - Diagnosis* 87 | - Outcome* 88 | - Stratification/Endotype* 89 | - ClinicalEvent 90 | - ClinicalEncounter* 91 | - LabTest* 92 | - Treatment/Therapy 93 | - DrugResponse* 94 | - AdverseEvent* 95 | - Geographical Location/Area 96 | 97 | 98 | 99 | ------------------------------- 100 | 101 | 102 | # Bioliink Core Types (https://biolink.github.io/biolink-model/) 103 | # All map to one of the terms above 104 | 105 | biological entity 106 | organismal entity 107 | organism taxon 108 | individual organism 109 | case 110 | population of individual organisms 111 | cohort 112 | biosample 113 | anatomical entity 114 | cellular component 115 | cell 116 | gross anatomical structure 117 | life stage 118 | disease or phenotypic feature 119 | disease 120 | phenotypic feature 121 | environment 122 | drug exposure 123 | treatment 124 | molecular entity 125 | chemical substance 126 | genomic entity 127 | genome 128 | transcript 129 | exon 130 | coding sequence 131 | gene or gene product 132 | gene 133 | gene product 134 | protein 135 | RNA product 136 | microRNA 137 | genotype 138 | sequence variant 139 | macromolecular complex 140 | gene family 141 | bioentity with go terms 142 | biological process 143 | pathway 144 | 145 | ------------------------- 146 | 147 | # Minimal Basic Types (Dumontier - https://docs.google.com/spreadsheets/d/14IKvsik_Hc6t0l0h01TGYpJFnHNcrnGRC_3rkR-yaBQ/edit#gid=2129974251) 148 | # Terms with * are not represented in API Catalog ENUM above. 149 | 150 | Object 151 | Biochemical Object 152 | Chemical 153 | Carbohydrate* 154 | Lipid* 155 | Nucleic Acid* 156 | Transcript 157 | Gene 158 | Variant 159 | Protein 160 | Molecular Complex 161 | Cell 162 | Tissue 163 | Organ 164 | Organism 165 | Food* 166 | Drug 167 | 168 | Device 169 | Publication 170 | Terminology 171 | Geographic Area* 172 | City* 173 | Country* 174 | Group* 175 | Organization* 176 | Characteristic 177 | Function 178 | Behavior 179 | Pathway 180 | Phenotype 181 | Disease 182 | 183 | Process 184 | Event 185 | Activity 186 | Procedure 187 | Clinical Study 188 | Bioassay 189 | Laboratory Test 190 | -------------------------------------------------------------------------------- /api_catalog/README.md: -------------------------------------------------------------------------------- 1 | ## Translator API Catalog 2 | 3 | As the Translator incorporrates more knowledge sources, there is a need for a human-friendly catalog of APIs in the system to support various users and use cases: 4 | 5 | 1. Enable **leadership** (team leaders, NCATS) to follow at a high level the evolution of data available in the Translator over time, and identify strengths and gaps in coverage. 6 | 2. Allow **domain experts** to know what types of data are available for defining CQs (and in particular to promote use of more diverse data types and sources across teams). 7 | 3. Help **notebook developers** to know where/how to find data to implement CQ notebooks, and extend them into new areas. 8 | 4. Help **external users/stakeholders** to understand scope of data/knowledge cataloged in the Translator system. 9 | 5. Inform the work of **smartAPI developers** who are wrapping and more formally defining API metadata 10 | 11 | At present, the [APIList.yaml](https://github.com/NCATS-Tangerine/translator-api-registry/blob/master/API_LIST.yml) file in the translator-api-registry repo is set up to collect structured, Translator-specific metadata about each registered API. We will make extensions to this yaml format by creating additional fields and value sets in support of the use cases above. 12 | 13 | API metadata for the Translator Catalog will be contributed by API developers using this yaml-based format, and live in the [APIList.yaml](https://github.com/NCATS-Tangerine/translator-api-registry/blob/master/API_LIST.yml) file. Once populated, these API metadata yaml files will be consumed by scripts to automatically generate more human-friendly Translator Catalog view of this metadata (e.g. a spreadsheet view, as mocked up [here](https://docs.google.com/spreadsheets/d/160Vzcgk5eGjtqbrKZzCyyJuPRKQV_zpk4BpZRMC70PA/edit#gid=0)). 14 | 15 | Initially we will target high-level metadata **about each API** in the Translator system. It should pose a minimal barrier for API developers/stewards to enter metadata (i.e. require 15 minutes or less) - so we can deliver a catalog quickly. This metadata will complement the more granular metadata captured in the smartAPI yaml config files for each API (e.g. for the [mygene.info API](https://github.com/NCATS-Tangerine/translator-api-registry/blob/master/mygene.info/openapi_full.yml)). Subsequent extensions to the metadata extension fields may be implemented at a later date to enable description of **each primary source** that aggregating APIs serve data from (e.g. Monarch-Biolink, Wikidata, Biothings, NSIDES). 16 | 17 | ### INSTRUCTIONS FOR CREATING AN API METADATA RECORD CAN BE FOUND IN ISSUE [#8](https://github.com/NCATS-Tangerine/translator-api-registry/issues/8). 18 | -------------------------------------------------------------------------------- /api_catalog/example_metadata.yml: -------------------------------------------------------------------------------- 1 | # The is an example metadata record for the Monarch-Biolink API 2 | 3 | APIs: 4 | - metadata: biolink/openapi.yaml 5 | translator: 6 | apiName: "Monarch-Biolink API" 7 | accessURL: "https://api.monarchinitiative.org/api/" 8 | serviceType: 9 | - data 10 | description: "The Biolink API serves data from the Monarch Initiative SciGraph database - a neo4j database holding semantically integrated data from a variety of biological/biomedical community databases, with a focus on genotype-phenotype related resources. Most data represents manually-curated knowledge derived from the published literature or research studies. For more see https://monarchinitiative.org/page/about." 11 | dataLevel: 12 | - curated data 13 | primarySources: "see https://monarchinitiative.org/about/sources" 14 | entityTypes: 15 | - Gene 16 | - Allele/Variant 17 | - Genotype 18 | - Protein 19 | - Phenotype 20 | - Disease 21 | - Organism/Strain 22 | - Environment 23 | - AnatomicalEntity 24 | - Cell Line 25 | - Cell Component 26 | - Molecular Function 27 | - Biological Process 28 | - Molecular Interaction 29 | - Pathway 30 | - GeneExpression 31 | - Publication 32 | - Patient/Case 33 | entityAssociations: 34 | - Allele/Variant - Gene 35 | - Allele/Variant - Genotype 36 | - Allele/Variant - Phenotype 37 | - AnatomicalEntity - Gene 38 | - AnatomicalEntity - Phenotype 39 | - Disease - AnatomicalEntity 40 | - Disease - MolecularFunction 41 | - Disease - Gene 42 | - Disease - Model 43 | - Disease - Phenotype 44 | - Environment - Phenotype 45 | - Gene - Gene (homology) 46 | - Gene - Gene (interaction) 47 | - Gene - Phenotype 48 | - Gene - Publication 49 | - Genotype - Disease 50 | - Genotype - Phenotype 51 | - GOTerm - Gene 52 | - GOTerm - Phenotype 53 | - Pathway - Gene 54 | - Pathway - Chemical Entity 55 | - Publication - Gene 56 | - Publication - Disease 57 | entityAttributes: 58 | - Variant/Allele - frequency 59 | - SequenceFeature - genomic position 60 | translatorTeam: 61 | - Orange 62 | license: "CC-BY-3.0 (where allowed by primary source)" 63 | termsOfService: "https://monarchinitiative.org/page/disclaimer" 64 | accessRestriction: 65 | - none 66 | returnsjson: true 67 | notes: "Biolink does not yet serve all data captured in the Monarch-SciGraph database. New API calls are being written to add additional data types, which will be updated here." 68 | -------------------------------------------------------------------------------- /api_catalog/records/biolink_metadata.yml: -------------------------------------------------------------------------------- 1 | # The metadata record for the Monarch-Biolink API 2 | 3 | APIs: 4 | - metadata: biolink/openapi.yaml 5 | translator: 6 | apiName: "Monarch-Biolink API" 7 | accessURL: "https://api.monarchinitiative.org/api/" 8 | serviceType: 9 | - data 10 | description: "The Biolink API serves data from the Monarch Initiative SciGraph database - a neo4j database holding semantically integrated data from a variety of biological/biomedical community databases, with a focus on genotype-phenotype related resources. Most data represents manually-curated knowledge derived from the published literature or research studies. For more see https://monarchinitiative.org/page/about." 11 | dataLevel: 12 | - curated data 13 | primarySources: "https://monarchinitiative.org/about/sources" 14 | entityTypes: 15 | - Gene 16 | - Allele/Variant 17 | - Genotype 18 | - Protein 19 | - Phenotype 20 | - Disease 21 | - Organism/Strain 22 | - Environment 23 | - AnatomicalEntity 24 | - Cell Line 25 | - Cell Component 26 | - Molecular Function 27 | - Biological Process 28 | - Molecular Interaction 29 | - Pathway 30 | - GeneExpression 31 | - Publication 32 | - Patient/Case 33 | entityAssociations: 34 | - Allele/Variant - Gene 35 | - Allele/Variant - Genotype 36 | - Allele/Variant - Phenotype 37 | - AnatomicalEntity - Gene 38 | - AnatomicalEntity - Phenotype 39 | - Disease - AnatomicalEntity 40 | - Disease - MolecularFunction 41 | - Disease - Gene 42 | - Disease - Model 43 | - Disease - Phenotype 44 | - Environment - Phenotype 45 | - Gene - Gene (homology) 46 | - Gene - Gene (interaction) 47 | - Gene - Phenotype 48 | - Gene - Publication 49 | - Genotype - Disease 50 | - Genotype - Phenotype 51 | - GOTerm - Gene 52 | - GOTerm - Phenotype 53 | - Pathway - Gene 54 | - Pathway - Chemical Entity 55 | - Publication - Gene 56 | - Publication - Disease 57 | entityAttributes: null 58 | translatorTeam: 59 | - Orange 60 | license: "CC-BY-3.0 (where allowed by primary source)" 61 | termsOfService: "https://monarchinitiative.org/page/disclaimer" 62 | accessRestriction: 63 | - none 64 | returnsjson: true 65 | notes: "Biolink does not yet serve all data captured in the Monarch-SciGraph database. New API calls are being written to add additional data types, which will be updated here." 66 | -------------------------------------------------------------------------------- /api_catalog/records/garbanzo_metadata.yaml: -------------------------------------------------------------------------------- 1 | # The metadata record for the Garbanzo API 2 | 3 | - metadata: null 4 | translator: 5 | apiName: "Garbanzo Wikidata API" 6 | accessURL: "http://garbanzo.sulab.org/ui" 7 | serviceType: 8 | - data 9 | description: "The Garbanzo API serves data from the Wikidata SPARQL endoint holding semantically integrated data from a variety of biological databases as well as 10 | crowd-sourced, unverified data. For for a class-level diagram see https://www.wikidata.org/wiki/Wikidata:WikiProject_Gene_Wiki#/media/File:Gene_wiki_world_network.png. For 11 | a description of data maintained by the Gene Wiki team see: https://www.wikidata.org/wiki/User:ProteinBoxBot/Bot_Status" 12 | dataLevel: 13 | - curated data 14 | - ontologies 15 | primarySources: "https://www.wikidata.org/wiki/User:ProteinBoxBot/Bot_Status" 16 | entityTypes: 17 | - Gene 18 | - Allele/Variant 19 | - Protein 20 | - ProteinDomain 21 | - Homolog 22 | - Operon 23 | - ChemicalEntity 24 | - Disease 25 | - Organism/Strain 26 | - AnatomicalEntity 27 | - Cell Component 28 | - Molecular Function 29 | - Biological Process 30 | - Molecular Interaction 31 | - Pathway 32 | - Publication 33 | - Identifier 34 | entityAssociationTypes: 35 | - Gene - Disease 36 | - Gene - Allele/Variant 37 | - Gene - Operon 38 | - Gene - Organism/Strain 39 | - Gene - Protein 40 | - Gene - Gene (Homolog) 41 | - Gene - Pathway 42 | - Gene - Operon 43 | - Gene - Identifier 44 | - Allele/Variant - ChemicalEntity 45 | - Allele/Variant - Disease 46 | - Allele/Variant - Gene 47 | - Allele/Variant - Identifier 48 | - Protein - Gene 49 | - Protein - Organism/Strain 50 | - Protein - Cell Component 51 | - Protein - Molecular Function 52 | - Protein - Biological Process 53 | - Protein - ProteinDomain 54 | - Protein - Protein (Protein Protein Interaction) 55 | - Protein - Identifier 56 | - ChemicalEntity - Disease 57 | - ChemicalEntity - Pathway 58 | - ChemicalEntity - Protein 59 | - ChemicalEntity - Identifier 60 | - Disease - Organism/Strain 61 | - Disease - Identifier 62 | - Identifier - Identifier 63 | - Pathway - Identifier 64 | - Organism/Strain - Identifier 65 | entityAttributeTypes: 66 | - SequenceEntity - genomic position 67 | - SequenceEntity - cytogenetic location 68 | translatorTeam: 69 | - Orange 70 | license: "CC0" 71 | termsOfService: "https://www.wikidata.org/wiki/Help:About_data" 72 | accessRestriction: 73 | - none 74 | returnsjson: true 75 | -------------------------------------------------------------------------------- /api_catalog/template.yml: -------------------------------------------------------------------------------- 1 | # A template for Translator API metadata records. Simply delete the provided data type description and add metadata for your API. 2 | # A more detailed schema including Value Set Enumerations (ENUMs) can be found here: https://github.com/NCATS-Tangerine/translator-api-registry/blob/master/api_catalog/schema.yml 3 | # A completed example record can be found here: https://github.com/NCATS-Tangerine/translator-api-registry/blob/master/api_catalog/records/biolink_metadata.yml 4 | 5 | APIs: 6 | - metadata: "string" 7 | translator: 8 | apiName: "string" 9 | 10 | accessURL: "url" 11 | 12 | serviceType: array of values from ENUM1 13 | - 14 | 15 | description: "string" 16 | 17 | dataLevel: array of values from ENUM2 18 | - 19 | primarySources: "string" 20 | 21 | entityTypes: array of values from ENUM3 22 | - 23 | 24 | entityAssociations: array of hyphen-separated pairs of entities from ENUM3 (and optionally a relationship type or entity role in parentheses) 25 | - 26 | 27 | entityAttributes: array or hyphen-separated pairs comprised of an entity from ENUM3 and a user defined data type. 28 | - 29 | 30 | translatorTeam: array of one or more values from ENUM4 31 | - 32 | 33 | license: "string" 34 | 35 | termsOfService: "url" 36 | 37 | accessRestriction: array of one or more values from ENUM5 38 | - 39 | 40 | returnsjson: boolean 41 | 42 | notes: "string" 43 | 44 | -------------------------------------------------------------------------------- /automat-covid-phenotypes/smartapi.yaml: -------------------------------------------------------------------------------- 1 | openapi: 3.0.0 2 | info: 3 | contact: 4 | email: help@renci.org 5 | name: Chris B. 6 | description: Scibite 7 | termsOfService: https://automat.renci.org 8 | title: Automat covid-phenotypes API 9 | version: '2.0' 10 | servers: 11 | - description: Production server 12 | url: curl -X GET "https://automat.renci.org/covid-phenotypes 13 | tags: 14 | - name: phenotype 15 | - name: disease 16 | - name: automat 17 | - name: translator 18 | paths: 19 | /disease/phenotype/{mondo}: 20 | get: 21 | parameters: 22 | - description: Put MONDO ID here, e.g. "MONDO:0100096" 23 | example: "MONDO:0100096" 24 | in: path 25 | name: mondo 26 | required: true 27 | schema: 28 | type: string 29 | responses: 30 | '200': 31 | description: An association object 32 | summary: disease2phenotype 33 | x-bte-kgs-operations: 34 | - $ref: '#/components/x-bte-kgs-operations/disease2phenotype' 35 | tags: 36 | - disease 37 | /phenotypic_feature/disease/{hp}: 38 | get: 39 | parameters: 40 | - description: Put HPO ID here, e.g. "HP:0002027" 41 | example: "HP:0002027" 42 | in: path 43 | name: hp 44 | required: true 45 | schema: 46 | type: string 47 | responses: 48 | '200': 49 | description: An association object 50 | summary: phenotype2disease 51 | x-bte-kgs-operations: 52 | - $ref: '#/components/x-bte-kgs-operations/phenotype2disease' 53 | tags: 54 | - phenotype 55 | components: 56 | x-bte-kgs-operations: 57 | disease2phenotype: 58 | - inputs: 59 | - id: MONDO 60 | semantic: Disease 61 | outputs: 62 | - id: HP 63 | semantic: PhenotypicFeature 64 | parameters: 65 | chebi: '{inputs[0]}' 66 | predicate: has_phenotype 67 | response_mapping: 68 | $ref: '#/components/x-bte-response-mapping/disease2phenotype' 69 | source: covid_phenotypes_csv 70 | supportBatch: false 71 | phenotype2disease: 72 | - inputs: 73 | - id: HP 74 | semantic: PhenotypicFeature 75 | outputs: 76 | - id: MONDO 77 | semantic: Disease 78 | parameters: 79 | chebi: '{inputs[0]}' 80 | predicate: related_to 81 | response_mapping: 82 | $ref: '#/components/x-bte-response-mapping/phenotype2disease' 83 | source: covid_phenotypes_csv 84 | supportBatch: false 85 | x-bte-response-mapping: 86 | disease2phenotype: 87 | HP: associated_with.hp 88 | phenotype2disease: 89 | MONDO: associated_with.mondo 90 | -------------------------------------------------------------------------------- /biolink/jsonld_context/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/4c76bc60d3a8dbdb7d8a761d2f988be9088cab67/biolink/jsonld_context/.DS_Store -------------------------------------------------------------------------------- /biolink/jsonld_context/biolinks_disease_context.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context": { 3 | "@version": 1.1, 4 | "_id": "@id", 5 | "HP": "http://identifiers.org/hp/", 6 | "ont": "http://biothings.io/ontology/", 7 | "objects": { 8 | "@type": "@id", 9 | "@id": "ont:associatedWittDisease" 10 | } 11 | } 12 | } -------------------------------------------------------------------------------- /biolink/jsonld_context/biolinks_gene_context.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context": { 3 | "@version": 1.1, 4 | "_id": "@id", 5 | "NCBIGENE": "http://identifiers.org/ncbigene/", 6 | "ont": "http://biothings.io/ontology/", 7 | "objects": { 8 | "@type": "@id", 9 | "@id": "ont:associatedWithGene" 10 | } 11 | } 12 | } -------------------------------------------------------------------------------- /biolink/jsonld_context/biolinks_homolog_context.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context": { 3 | "@version": 1.1, 4 | "_id": "@id", 5 | "NCBIGENE": "http://identifiers.org/ncbigene/", 6 | "MGI": "http://identifiers.org/mgi/", 7 | "ZFIN": "http://identifiers.org/zfin/", 8 | "ont": "http://biothings.io/ontology/", 9 | "objects": { 10 | "@type": "@id", 11 | "@id": "ont:hasHomolog" 12 | } 13 | } 14 | } -------------------------------------------------------------------------------- /biolink/jsonld_context/biolinks_interact_context.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context": { 3 | "mouse_gene_id": { 4 | "@id": "oban:interacts_with", 5 | "@type": "http://identifiers.org/mgi/" 6 | }, 7 | "entrez_gene_id": { 8 | "@id": "oban:interacts_with", 9 | "@type": "http://identifiers.org/hgnc/" 10 | } 11 | } 12 | } -------------------------------------------------------------------------------- /biolink/jsonld_context/biolinks_interaction_context.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context": { 3 | "@version": 1.1, 4 | "_id": "@id", 5 | "NCBIGENE": "http://identifiers.org/ncbigene/", 6 | "ont": "http://biothings.io/ontology/", 7 | "objects": { 8 | "@type": "@id", 9 | "@id": "ont:interactsWith" 10 | } 11 | } 12 | } -------------------------------------------------------------------------------- /biolink/jsonld_context/biolinks_phenotype_context.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context": { 3 | "@version": 1.1, 4 | "_id": "@id", 5 | "HP": "http://identifiers.org/hp/", 6 | "ont": "http://biothings.io/ontology/", 7 | "objects": { 8 | "@type": "@id", 9 | "@id": "ont:hasPhenotype" 10 | } 11 | } 12 | } -------------------------------------------------------------------------------- /biothings_explorer/qualifier-sri-test-service.json: -------------------------------------------------------------------------------- 1 | { 2 | "infores": "service-provider-trapi", 3 | "edges": [ 4 | { 5 | "underlying_api_infores": "biothings-dgidb", 6 | "underlying_source_infores": "dgidb", 7 | "subject_category": "biolink:SmallMolecule", 8 | "subject_id": "CHEMBL.COMPOUND:CHEMBL266510", 9 | "subject_name": "FLINDOKALNER", 10 | "predicate": "biolink:affects", 11 | "object_category": "biolink:Gene", 12 | "object_id": "NCBIGene:9132", 13 | "object_name": "KCNQ4", 14 | "qualifiers": [ 15 | { 16 | "qualifier_type_id": "biolink:qualified_predicate", 17 | "qualifier_value": "biolink:causes" 18 | }, 19 | { 20 | "qualifier_type_id": "biolink:object_aspect_qualifier", 21 | "qualifier_value": "activity" 22 | }, 23 | { 24 | "qualifier_type_id": "biolink:object_direction_qualifier", 25 | "qualifier_value": "increased" 26 | }, 27 | { 28 | "qualifier_type_id": "biolink:causal_mechanism_qualifier", 29 | "qualifier_value": "activation" 30 | } 31 | ] 32 | }, 33 | { 34 | "underlying_api_infores": "biothings-go-bp", 35 | "underlying_source_infores": "go", 36 | "subject_category": "biolink:BiologicalProcess", 37 | "subject_id": "GO:0090272", 38 | "subject_name": "negative regulation of fibroblast growth factor production", 39 | "predicate": "biolink:regulates", 40 | "object_category": "biolink:BiologicalProcess", 41 | "object_id": "GO:0090269", 42 | "object_name": "fibroblast growth factor production", 43 | "qualifiers": [ 44 | { 45 | "qualifier_type_id": "biolink:object_direction_qualifier", 46 | "qualifier_value": "downregulated" 47 | } 48 | ] 49 | }, 50 | { 51 | "underlying_api_infores": "text-mining-provider-targeted", 52 | "subject_category": "biolink:SmallMolecule", 53 | "subject_id": "CHEBI:3215", 54 | "subject_name": "bupivacaine", 55 | "predicate": "biolink:affects", 56 | "object_category": "biolink:Gene", 57 | "object_id": "UniProtKB:Q9P2L0", 58 | "object_name": "WDR35", 59 | "qualifiers": [ 60 | { 61 | "qualifier_type_id": "biolink:qualified_predicate", 62 | "qualifier_value": "biolink:causes" 63 | }, 64 | { 65 | "qualifier_type_id": "biolink:object_aspect_qualifier", 66 | "qualifier_value": "activity_or_abundance" 67 | }, 68 | { 69 | "qualifier_type_id": "biolink:object_direction_qualifier", 70 | "qualifier_value": "increased" 71 | } 72 | ] 73 | } 74 | ] 75 | } 76 | -------------------------------------------------------------------------------- /biothings_explorer/sri-test-bte-ara.json: -------------------------------------------------------------------------------- 1 | { 2 | "infores": "biothings-explorer", 3 | "KPs": [ 4 | "infores:service-provider-trapi", 5 | "infores:automat-biolink", 6 | "infores:automat-ctd", 7 | "infores:automat-drug-central", 8 | "infores:automat-gtex", 9 | "infores:automat-gtopdb", 10 | "infores:automat-gwas-catalog", 11 | "infores:automat-hetio", 12 | "infores:automat-hgnc", 13 | "infores:automat-hmdb", 14 | "infores:automat-human-goa", 15 | "infores:automat-icees-kg", 16 | "infores:automat-intact", 17 | "infores:automat-panther", 18 | "infores:automat-pharos", 19 | "infores:automat-viral-proteome", 20 | "infores:cohd", 21 | "infores:connections-hypothesis" 22 | ] 23 | } -------------------------------------------------------------------------------- /biothings_explorer/sri-test-multiomics.json: -------------------------------------------------------------------------------- 1 | { 2 | "infores": "service-provider-trapi", 3 | "edges": [ 4 | { 5 | "underlying_api_infores": "biothings-multiomics-wellness", 6 | "subject_category": "biolink:ClinicalFinding", 7 | "subject": "LOINC:47828-9", 8 | "subject_name": "ADIPONECTIN, SERUM", 9 | "predicate": "biolink:related_to", 10 | "object_category": "biolink:SmallMolecule", 11 | "object": "KEGG.COMPOUND:C05208", 12 | "object_name": "1-arachidonoyl-GPC (20:4n6)*" 13 | }, 14 | { 15 | "underlying_api_infores": "biothings-multiomics-wellness", 16 | "subject_category": "biolink:SmallMolecule", 17 | "subject": "KEGG.COMPOUND:C05328", 18 | "subject_name": "(S)-a-amino-omega-caprolactam", 19 | "predicate": "biolink:correlated_with", 20 | "object_category": "biolink:Protein", 21 | "object": "UniProtKB:P35318", 22 | "object_name": "CVD2_P35318" 23 | }, 24 | { 25 | "underlying_api_infores": "biothings-multiomics-ehr-risk", 26 | "subject_category": "biolink:Disease", 27 | "subject_id": "MONDO:0015925", 28 | "subject_name": "demyelinating disease of central nervous system", 29 | "object_category": "biolink:Disease", 30 | "object_id": "MONDO:0007179", 31 | "object_name": "autoimmune disease" , 32 | "predicate": "biolink:associated_with" 33 | }, 34 | { 35 | "underlying_api_infores": "biothings-multiomics-ehr-risk", 36 | "subject_category": "biolink:Disease", 37 | "subject_id": "MONDO:0010030", 38 | "subject_name": "Sjogren syndrome", 39 | "object_category": "biolink:Disease", 40 | "object_id": "MONDO:0007179", 41 | "object_name": "autoimmune disease" , 42 | "predicate": "biolink:associated_with" 43 | }, 44 | { 45 | "underlying_api_infores": "biothings-multiomics-ehr-risk", 46 | "subject_category": "biolink:ChemicalSubstance", 47 | "subject_id": "CHEBI:42797", 48 | "subject_name": "gabapentin", 49 | "object_category": "biolink:Disease", 50 | "object_id": "MONDO:0020108", 51 | "object_name": "autoimmune hemolytic anemia" , 52 | "predicate": "biolink:associated_with" 53 | }, 54 | { 55 | "underlying_api_infores": "biothings-multiomics-ehr-risk", 56 | "subject_category": "biolink:PhenotypicFeature", 57 | "subject_id": "HP:0040088", 58 | "subject_name": "Abnormal lymphocyte count", 59 | "object_category": "biolink:Disease", 60 | "object_id": "SNOMEDCT:237519003", 61 | "object_name": "Autoimmune hypothyroidism (disorder)", 62 | "predicate": "biolink:associated_with" 63 | }, 64 | { 65 | "underlying_api_infores": "biothings-multiomics-biggim-drugresponse", 66 | "subject_category": "biolink:Gene", 67 | "subject": "NCBIGene:3845", 68 | "subject_name": "KRAS", 69 | "predicate": "biolink:associated_with_sensitivity_to", 70 | "object_category": "biolink:SmallMolecule", 71 | "object": "PUBCHEM.COMPOUND:11707110", 72 | "object_name": "Trametinib" 73 | }, 74 | { 75 | "underlying_api_infores": "biothings-multiomics-biggim-drugresponse", 76 | "subject_category": "biolink:Disease", 77 | "subject": "MONDO:0007256", 78 | "subject_name": "LIHC", 79 | "predicate": "biolink:has_biomarker", 80 | "object_category": "biolink:Gene", 81 | "object": "NCBIGene:174", 82 | "object_name": "AFP" 83 | }, 84 | { 85 | "underlying_api_infores": "biothings-multiomics-biggim-drugresponse", 86 | "subject_category": "biolink:Protein", 87 | "subject": "NCBIGene:5910", 88 | "subject_name": "RAP1GDS1", 89 | "predicate": "biolink:physically_interacts_with", 90 | "object_category": "biolink:Protein", 91 | "object": "NCBIGene:3845", 92 | "object_name": "KRAS" 93 | }, 94 | { 95 | "underlying_api_infores": "biothings-multiomics-biggim-drugresponse", 96 | "subject_category": "biolink:Gene", 97 | "subject": "NCBIGene:472", 98 | "subject_name": "ATM", 99 | "predicate": "biolink:genetically_interacts_with", 100 | "object_category": "biolink:Gene", 101 | "object": "NCBIGene:7157", 102 | "object_name": "TP53" 103 | }, 104 | { 105 | "underlying_api_infores": "biothings-multiomics-biggim-drugresponse", 106 | "subject_category": "biolink:Gene", 107 | "subject": "NCBIGene:861", 108 | "subject_name": "RUNX1", 109 | "predicate": "biolink:gene_associated_with_condition", 110 | "object_category": "biolink:Disease", 111 | "object": "MONDO:0018874", 112 | "object_name": "TCGA_LAML" 113 | }, 114 | { 115 | "underlying_api_infores": "biothings-multiomics-biggim-drugresponse", 116 | "subject_category": "biolink:SmallMolecule", 117 | "subject": "PUBCHEM.COMPOUND:49846579", 118 | "subject_name": "Venetoclax", 119 | "predicate": "biolink:has_target", 120 | "object_category": "biolink:Gene", 121 | "object": "NCBIGene:596", 122 | "object_name": "BCL2" 123 | } 124 | ] 125 | } -------------------------------------------------------------------------------- /biothings_explorer/sri-test-service-provider.json: -------------------------------------------------------------------------------- 1 | { 2 | "infores": "service-provider-trapi", 3 | "edges": [ 4 | { 5 | "underlying_api_infores": "mygene-info", 6 | "underlying_source_infores": "clingen", 7 | "subject_category": "biolink:Gene", 8 | "subject": "NCBIGene:675", 9 | "subject_name": "BRCA2", 10 | "predicate": "biolink:related_to", 11 | "object_category": "biolink:Disease", 12 | "object": "MONDO:0012933", 13 | "object_name": "breast-ovarian cancer, familial, susceptibility to, 2" 14 | }, 15 | { 16 | "underlying_api_infores": "mychem-info", 17 | "underlying_source_infores": "chembl", 18 | "subject_category": "biolink:SmallMolecule", 19 | "subject": "CHEMBL.COMPOUND:CHEMBL941", 20 | "subject_name": "Imatinib", 21 | "predicate": "biolink:treats", 22 | "object_category": "biolink:Disease", 23 | "object": "MESH:D015464", 24 | "object_name": "chronic myelogenous leukemia, BCR-ABL1 positive" 25 | }, 26 | { 27 | "underlying_api_infores": "biothings-bioplanet-pathway-gene", 28 | "underlying_source_infores": "bioplanet", 29 | "subject_category": "biolink:Pathway", 30 | "subject": "ncats.bioplanet:bioplanet_68", 31 | "subject_name": "Cell cycle progression regulation by PLK3", 32 | "predicate": "biolink:has_participant", 33 | "object_category": "biolink:Gene", 34 | "object": "NCBIGene:7157", 35 | "object_name": "TP53" 36 | } 37 | ] 38 | } 39 | -------------------------------------------------------------------------------- /chembio/smartapi.yaml: -------------------------------------------------------------------------------- 1 | --- 2 | openapi: 3.0.0 3 | info: 4 | contact: 5 | email: help@renci.org 6 | name: Chris B. 7 | description: Scibite 8 | termsOfService: https://automat.renci.org 9 | title: Automat CHEMBIO API 10 | version: '2.0' 11 | x-translator: 12 | component: KP 13 | team: 14 | - Ranking Agent 15 | servers: 16 | - description: Production server 17 | url: https://automat.renci.org/chembio 18 | tags: 19 | - name: drug 20 | - name: gene 21 | - name: disease 22 | - name: automat 23 | - name: translator 24 | paths: 25 | "/gene/chemical_substance/{geneid}": 26 | get: 27 | summary: gene2chemical 28 | parameters: 29 | - description: Put NCBIGENE ID here, e.g. 1017 30 | example: NCBIGENE:1017 31 | in: path 32 | name: geneid 33 | required: true 34 | schema: 35 | type: string 36 | responses: 37 | '200': 38 | description: An association object 39 | x-bte-kgs-operations: 40 | - "$ref": "#/components/x-bte-kgs-operations/gene2chemical" 41 | "/chemical_substance/gene/{chebi}": 42 | get: 43 | summary: chemical2gene 44 | parameters: 45 | - description: Put CHEBI ID here, e.g. "CHEBI:661" 46 | example: CHEBI:661 47 | in: path 48 | name: chebi 49 | required: true 50 | schema: 51 | type: string 52 | responses: 53 | '200': 54 | description: An association object 55 | x-bte-kgs-operations: 56 | - "$ref": "#/components/x-bte-kgs-operations/chemical2gene" 57 | components: 58 | x-bte-kgs-operations: 59 | gene2chemical: 60 | - inputs: 61 | - id: NCBIGENE 62 | semantic: Gene 63 | outputs: 64 | - id: CHEMBL.COMPOUND 65 | semantic: ChemicalSubstance 66 | predicate: related_to 67 | source: chembio 68 | parameters: 69 | geneid: NCBIGENE:{inputs[0]} 70 | supportBatch: false 71 | response_mapping: 72 | "$ref": "#/components/x-bte-response-mapping/gene2chemical-chembl" 73 | - inputs: 74 | - id: NCBIGENE 75 | semantic: Gene 76 | outputs: 77 | - id: CHEBI 78 | semantic: ChemicalSubstance 79 | predicate: related_to 80 | source: chembio 81 | parameters: 82 | geneid: NCBIGENE:{inputs[0]} 83 | supportBatch: false 84 | response_mapping: 85 | "$ref": "#/components/x-bte-response-mapping/gene2chemical-chebi" 86 | gene2disease: 87 | - inputs: 88 | - id: NCBIGENE 89 | semantic: Gene 90 | outputs: 91 | - id: DOID 92 | semantic: Disease 93 | predicate: related_to 94 | source: chembio 95 | parameters: 96 | geneid: NCBIGENE:{inputs[0]} 97 | supportBatch: false 98 | response_mapping: 99 | "$ref": "#/components/x-bte-response-mapping/gene2disease-doid" 100 | - inputs: 101 | - id: NCBIGENE 102 | semantic: Gene 103 | outputs: 104 | - id: MONDO 105 | semantic: Disease 106 | predicate: related_to 107 | source: chembio 108 | parameters: 109 | geneid: NCBIGENE:{inputs[0]} 110 | supportBatch: false 111 | response_mapping: 112 | "$ref": "#/components/x-bte-response-mapping/gene2disease-mondo" 113 | chemical2gene: 114 | - inputs: 115 | - id: CHEBI 116 | semantic: ChemicalSubstance 117 | outputs: 118 | - id: NCBIGENE 119 | semantic: Gene 120 | predicate: related_to 121 | source: chembio 122 | parameters: 123 | chebi: "{inputs[0]}" 124 | supportBatch: false 125 | response_mapping: 126 | "$ref": "#/components/x-bte-response-mapping/chemical2gene" 127 | chemical2disease: 128 | - inputs: 129 | - id: CHEBI 130 | semantic: ChemicalSubstance 131 | outputs: 132 | - id: DOID 133 | semantic: Disease 134 | predicate: related_to 135 | source: chembio 136 | parameters: 137 | chebi: "{inputs[0]}" 138 | supportBatch: false 139 | response_mapping: 140 | "$ref": "#/components/x-bte-response-mapping/chemical2disease-doid" 141 | - inputs: 142 | - id: CHEBI 143 | semantic: ChemicalSubstance 144 | outputs: 145 | - id: MONDO 146 | semantic: Disease 147 | predicate: related_to 148 | source: chembio 149 | parameters: 150 | chebi: "{inputs[0]}" 151 | supportBatch: false 152 | response_mapping: 153 | "$ref": "#/components/x-bte-response-mapping/chemical2disease-mondo" 154 | disease2gene: 155 | - inputs: 156 | - id: MONDO 157 | semantic: Disease 158 | outputs: 159 | - id: NCBIGENE 160 | semantic: Gene 161 | predicate: related_to 162 | source: chembio 163 | parameters: 164 | mondo: "{inputs[0]}" 165 | supportBatch: false 166 | response_mapping: 167 | "$ref": "#/components/x-bte-response-mapping/disease2gene" 168 | disease2chemical: 169 | - inputs: 170 | - id: MONDO 171 | semantic: Disease 172 | outputs: 173 | - id: CHEMBL.COMPOUND 174 | semantic: ChemicalSubstance 175 | predicate: related_to 176 | source: chembio 177 | parameters: 178 | mondo: "{inputs[0]}" 179 | supportBatch: false 180 | response_mapping: 181 | "$ref": "#/components/x-bte-response-mapping/disease2chemical-chembl" 182 | - inputs: 183 | - id: MONDO 184 | semantic: Disease 185 | outputs: 186 | - id: CHEBI 187 | semantic: ChemicalSubstance 188 | predicate: related_to 189 | source: chembio 190 | parameters: 191 | mondo: "{inputs[0]}" 192 | supportBatch: false 193 | response_mapping: 194 | "$ref": "#/components/x-bte-response-mapping/disease2chemical-chebi" 195 | x-bte-response-mapping: 196 | gene2chemical-chebi: 197 | CHEBI: associated_with.chebi 198 | gene2chemical-chembl: 199 | CHEMBL.COMPOUND: associated_with.chembl 200 | gene2disease-mondo: 201 | MONDO: associated_with.mondo 202 | gene2disease-doid: 203 | DOID: associated_with.doid 204 | chemical2disease-mondo: 205 | MONDO: associated_with.mondo 206 | chemical2disease-doid: 207 | DOID: associated_with.doid 208 | chemical2gene: 209 | NCBIGENE: associated_with.ncbigene 210 | disease2gene: 211 | NCBIGENE: associated_with.ncbigene 212 | disease2chemical-chembl: 213 | CHEMBL.COMPOUND: associated_with.chembl 214 | disease2chemical-chebi: 215 | CHEBI: associated_with.chebi 216 | -------------------------------------------------------------------------------- /chembl/smartapi.yaml: -------------------------------------------------------------------------------- 1 | openapi: '3.0.0' 2 | info: 3 | version: '1.0' 4 | title: ChEMBL API 5 | description: >- 6 | The ChEMBL API 7 | termsOfService: http://www.ebi.ac.uk/chembl 8 | contact: 9 | name: chembl help desk 10 | x-role: responsible developer 11 | email: help@chembl.org 12 | servers: 13 | - url: 'http://www.ebi.ac.uk/chembl/api' 14 | description: 'Production server' 15 | tags: 16 | - name: publication 17 | - name: translator 18 | paths: 19 | '/data/mechanism.json': 20 | get: 21 | summary: 'retrieve drug mechanism' 22 | parameters: 23 | - name: molecule_chembl_id 24 | in: query 25 | description: >- 26 | chembl id 27 | required: true 28 | example: "CHEMBL744" 29 | schema: 30 | type: string 31 | responses: 32 | '200': 33 | description: 'A drug mechanism object' 34 | x-bte-response-mapping: 35 | $ref: '#/components/x-bte-response-mapping/drug-mechanism' 36 | x-bte-kgs-operations: 37 | treats: 38 | $ref: '#/components/x-bte-kgs-operations/target' 39 | components: 40 | x-bte-kgs-operations: 41 | target: 42 | inputs: 43 | - id: chembl 44 | semantic: ChemicalSubstance 45 | outputs: 46 | - id: chembl 47 | semantic: Gene 48 | parameters: 49 | molecule_chembl_id: "{input1}" 50 | supportBatch: false 51 | response-mapping: 52 | $ref: '#/components/x-bte-response-mapping/drug-mechanism' 53 | x-bte-response-mapping: 54 | drug-mechanism: 55 | "@context": http://schema.org 56 | "@type": ChemicalSubstance 57 | bts:chembl: chembl 58 | bts:target: 59 | "@type": Gene 60 | bts:chembl: mechanisms.target_chembl_id 61 | bts:action: mechanisms.action_type 62 | bts:mechanism: mechanisms.mechanism_of_action 63 | "$input": bts:chembl 64 | "$source": chembl 65 | -------------------------------------------------------------------------------- /civic/jsonld_context/civic_evidence_context.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context": { 3 | "gene_id": { 4 | "@id": "oban:is_related_to", 5 | "@type": "http://identifiers.org/civic_gene/" 6 | }, 7 | "variant_id": { 8 | "@id": "oban:is_related_to", 9 | "@type": "http://identifiers.org/civic_variant/" 10 | }, 11 | "evidence_items.id": { 12 | "@id": "oban:is_related_to", 13 | "@type": "http://identifiers.org/civic_evidence/" 14 | }, 15 | "source.pubmed_id": { 16 | "@id": "oban:is_related_to", 17 | "@type": "http://identifiers.org/pubmed/" 18 | }, 19 | "disease.display_name": { 20 | "@id": "oban:is_related_to", 21 | "@type": "http://identifiers.org/disease_name/" 22 | }, 23 | "name": { 24 | "@id": "oban:is_related_to", 25 | "@type": "http://identifiers.org/hgnc_symbol/" 26 | }, 27 | "disease.doid": { 28 | "@id": "oban:is_related_to", 29 | "@type": "http://identifiers.org/disease_ontology/" 30 | } 31 | } 32 | } -------------------------------------------------------------------------------- /civic/jsonld_context/civic_gene_context.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context": { 3 | "variants.id": { 4 | "@id": "oban:is_related_to", 5 | "@type": "http://identifiers.org/civic_variant/" 6 | }, 7 | "variant_groups.id": { 8 | "@id": "oban:is_related_to", 9 | "@type": "http://identifiers.org/civic_variant_group/" 10 | }, 11 | "sources.id": { 12 | "@id": "oban:is_related_to", 13 | "@type": "http://identifiers.org/civic_evidence/" 14 | }, 15 | "name": { 16 | "@id": "oban:is_related_to", 17 | "@type": "http://identifiers.org/hgnc_symbol/" 18 | }, 19 | "entrez_id": { 20 | "@id": "oban:is_related_to", 21 | "@type": "http://identifiers.org/hgnc/" 22 | } 23 | } 24 | } -------------------------------------------------------------------------------- /civic/jsonld_context/civic_general_context.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context": { 3 | "result.gene_id": { 4 | "@id": "oban:is_related_to", 5 | "@type": "http://identifiers.org/civic_gene/" 6 | }, 7 | "result.entrez_id": { 8 | "@id": "oban:is_related_to", 9 | "@type": "http://identifiers.org/hgnc/" 10 | }, 11 | "result.variant_id": { 12 | "@id": "oban:is_related_to", 13 | "@type": "http://identifiers.org/civic_variant/" 14 | }, 15 | "result.drug_names": { 16 | "@id": "oban:is_related_to", 17 | "@type": "http://identifiers.org/drug_symbol/" 18 | }, 19 | "result.disease_names": { 20 | "@id": "oban:is_related_to", 21 | "@type": "http://identifiers.org/disease_name/" 22 | } 23 | } 24 | } -------------------------------------------------------------------------------- /civic/jsonld_context/civic_variant_context.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context": { 3 | "gene_id": { 4 | "@id": "oban:is_related_to", 5 | "@type": "http://identifiers.org/civic_gene/" 6 | }, 7 | "variant_groups.id": { 8 | "@id": "oban:is_related_to", 9 | "@type": "http://identifiers.org/civic_variant_group/" 10 | }, 11 | "varaint_types.so_id": { 12 | "@id": "oban:is_related_to", 13 | "@type": "http://identifiers.org/so/" 14 | }, 15 | "evidence_items.id": { 16 | "@id": "oban:is_related_to", 17 | "@type": "http://identifiers.org/civic_evidence/" 18 | }, 19 | "evidence_items.disease.display_name": { 20 | "@id": "oban:is_related_to", 21 | "@type": "http://identifiers.org/disease_name/" 22 | }, 23 | "evidence_items.drugs.name": { 24 | "@id": "oban:is_related_to", 25 | "@type": "http://identifiers.org/drug.symbol/" 26 | }, 27 | "name": { 28 | "@id": "oban:is_related_to", 29 | "@type": "http://identifiers.org/hgnc_symbol/" 30 | }, 31 | "entrez_id": { 32 | "@id": "oban:is_related_to", 33 | "@type": "http://identifiers.org/hgnc/" 34 | }, 35 | "evidence_items.disease.doid": { 36 | "@id": "oban:is_related_to", 37 | "@type": "http://identifiers.org/disease_ontology/" 38 | } 39 | } 40 | } -------------------------------------------------------------------------------- /cohd/smartapi.yaml: -------------------------------------------------------------------------------- 1 | openapi: '3.0.0' 2 | info: 3 | version: '1.0' 4 | title: COHD API 5 | description: >- 6 | The COHD API 7 | termsOfService: http://www.cohd.org 8 | contact: 9 | name: cohd help desk 10 | x-role: responsible developer 11 | email: help@cohd.org 12 | servers: 13 | - url: 'http://tr-kp-clinical.ncats.io/api' 14 | description: 'Production server' 15 | tags: 16 | - name: translator1 17 | - name: disease 18 | - name: chemical 19 | 20 | paths: 21 | '/association/chiSquare': 22 | get: 23 | summary: 'retrieve associated concept data' 24 | parameters: 25 | - name: dataset_id 26 | in: query 27 | description: >- 28 | the dataset id 29 | required: true 30 | example: 1 31 | schema: 32 | type: integer 33 | - name: concept_id_1 34 | in: query 35 | description: >- 36 | the COHD concept id 37 | required: true 38 | example: "441554" 39 | schema: 40 | type: string 41 | - name: domain 42 | in: query 43 | description: >- 44 | the input type 45 | required: true 46 | example: "Drug" 47 | schema: 48 | type: string 49 | responses: 50 | '200': 51 | description: 'A COHD concept object' 52 | x-bte-kgs-operations: 53 | - $ref: '#/components/x-bte-kgs-operations/disease-disease' 54 | - $ref: '#/components/x-bte-kgs-operations/disease-chemical' 55 | - $ref: '#/components/x-bte-kgs-operations/chemical-disease' 56 | components: 57 | x-bte-kgs-operations: 58 | disease-disease: 59 | - inputs: 60 | - id: OMOP 61 | semantic: Disease 62 | outputs: 63 | - id: OMOP 64 | semantic: Disease 65 | predicate: correlated_with 66 | parameters: 67 | dataset_id: 3 68 | concept_id_1: "{inputs[0]}" 69 | domain: Condition 70 | supportBatch: false 71 | response_mapping: 72 | $ref: '#/components/x-bte-response-mapping/omop' 73 | disease-chemical: 74 | - inputs: 75 | - id: OMOP 76 | semantic: Disease 77 | outputs: 78 | - id: OMOP 79 | semantic: ChemicalSubstance 80 | predicate: correlated_with 81 | parameters: 82 | dataset_id: 3 83 | concept_id_1: "{inputs[0]}" 84 | domain: Drug 85 | supportBatch: false 86 | response_mapping: 87 | $ref: '#/components/x-bte-response-mapping/omop' 88 | chemical-disease: 89 | - outputs: 90 | - id: OMOP 91 | semantic: Disease 92 | inputs: 93 | - id: OMOP 94 | semantic: ChemicalSubstance 95 | predicate: correlated_with 96 | parameters: 97 | dataset_id: 3 98 | concept_id_1: "{inputs[0]}" 99 | domain: Condition 100 | supportBatch: false 101 | response_mapping: 102 | $ref: '#/components/x-bte-response-mapping/omop' 103 | x-bte-response-mapping: 104 | omop: 105 | OMOP: results.concept_id_2 106 | adj_pvalue: results.adj_p-value 107 | -------------------------------------------------------------------------------- /dgidb/jsonld_context/dgidb_context.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context": { 3 | "@version": 1.1, 4 | "@base": "http://identifiers.org/ncbigene/", 5 | "term": "http://biothings.io/terms/dgidb/", 6 | "ont": "http://biothings.io/ontology/", 7 | "_id": "@id", 8 | "matchedTerms": { 9 | "@type": "@id", 10 | "@id": "term:has_annotation", 11 | "@context": { 12 | "interactions": { 13 | "@type": "@id", 14 | "@id": "term:has_annotation", 15 | "@context": { 16 | "drugName": { 17 | "@type": "@id", 18 | "@id": "ont:interactsWith", 19 | "@context": { 20 | "@base": "http://biothings.io/terms/drugname/" 21 | } 22 | }, 23 | "geneName": { 24 | "@type": "@id", 25 | "@id": "ont:targets", 26 | "@context": { 27 | "@base": "http://identifiers.org/hgnc.symbol/" 28 | } 29 | }, 30 | "geneEntrezId": { 31 | "@type": "@id", 32 | "@id": "ont:targets", 33 | "@context": { 34 | "@base": "http://identifiers.org/ncbigene/" 35 | } 36 | } 37 | } 38 | } 39 | } 40 | } 41 | } 42 | } -------------------------------------------------------------------------------- /disease ontology api/jsonld_context/do_context.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context": { 3 | "@version": 1.1, 4 | "_id": "@id", 5 | "MESH": "http://identifiers.org/mesh/", 6 | "OMIM": "http://identifiers.org/omim/", 7 | "SNOMEDCT_US_2016_03_01": "http://identifiers.org/snomedct/", 8 | "NCI": "http://identifiers.org/ncit/", 9 | "UMLS_CUI": "http://identifiers.org/umls/", 10 | "DOID": "http://identifiers.org/doid/", 11 | "ont": "http://biothings.io/ontology/", 12 | "xrefs": { 13 | "@type": "@id", 14 | "@id": "ont:hasXref" 15 | }, 16 | "parents": { 17 | "@type": "@id", 18 | "@id": "ont:hasParent" 19 | } 20 | } 21 | } -------------------------------------------------------------------------------- /disease ontology api/openapi.yml: -------------------------------------------------------------------------------- 1 | openapi: '3.0.0' 2 | info: 3 | version: '0.1.1' 4 | title: Disease Ontology API 5 | description: >- 6 | A RESTful API service is also offered to users of the Disease Ontology browser website to allow for programmatic access to the metadata found in the database. 7 | termsOfService: http://disease-ontology.org/faq/ 8 | contact: 9 | name: Lynn Schriml 10 | x-role: responsible developer 11 | email: lschriml@som.umaryland.edu 12 | servers: 13 | - url: 'http://www.disease-ontology.org/api' 14 | description: 'Production server' 15 | tags: 16 | - name: disease 17 | - name: ontology 18 | - name: annotation 19 | ## deprecate this registry entry? 20 | # - name: translator 21 | paths: 22 | '/metadata/{doid}': 23 | get: 24 | summary: 'Returns xref related to a doid' 25 | parameters: 26 | - name: doid 27 | in: path 28 | description: >- 29 | DOID, e.g. DOID:678. 30 | required: true 31 | schema: 32 | type: string 33 | x-valueType: 34 | - 'http://identifiers.org/doid/' 35 | x-requestTemplate: 36 | - valueType: 'http://identifiers.org/doid/' 37 | template: /metadata/{{input}} 38 | responses: 39 | '200': 40 | description: 'A distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload' 41 | x-responseValueType: 42 | - path: xref 43 | valueType: 'http://identifiers.org/mesh/' 44 | - path: xref 45 | valueType: 'http://identifiers.org/ncit/' 46 | - path: xref 47 | valueType: 'http://identifiers.org/snomedct/' 48 | - path: xref 49 | valueType: 'http://identifiers.org/umls/' 50 | - path: xref 51 | valueType: 'http://identifiers.org/omim/' 52 | x-JSONLDContext: 53 | 'https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/disease ontology api/jsonld_context/do_context.json' 54 | -------------------------------------------------------------------------------- /ebi_ontology_lookup_service_api/jsonld_context/ols_query_1.1.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context": { 3 | "@version": 1.1, 4 | "term": "http://biothings.io/terms/ols/", 5 | "DOID": "http://identifiers.org/doid/", 6 | "ont": "http://identifiers.org/ontology/", 7 | "_id": "@id", 8 | "response": { 9 | "@type": "@id", 10 | "@id": "term:has_annotation", 11 | "@context": { 12 | "docs": { 13 | "@type": "@id", 14 | "@id": "term:has_annotation", 15 | "@context": { 16 | "obo_id": { 17 | "@type": "@id", 18 | "@id": "ont:isRelatedTo" 19 | } 20 | } 21 | } 22 | } 23 | } 24 | } 25 | } -------------------------------------------------------------------------------- /ebi_ontology_lookup_service_api/openapi.yml: -------------------------------------------------------------------------------- 1 | openapi: '3.0.0' 2 | info: 3 | version: '1.0' 4 | title: EBI Ontology Service API 5 | description: >- 6 | The Ontology Lookup Service (OLS) is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions. You can browse the ontologies through the website as well as programmatically via the OLS API. OLS is developed and maintained by the Samples, Phenotypes and Ontologies Team at EMBL-EBI. 7 | termsOfService: https://www.ebi.ac.uk/ols/docs/about 8 | contact: 9 | name: Jupp S. 10 | x-role: responsible developer 11 | email: ols-support@ebi.ac.uk 12 | x-id: 'https://github.com/EBISPOT/OLS' 13 | servers: 14 | - url: 'https://www.ebi.ac.uk/ols/api' 15 | description: 'Production server' 16 | tags: 17 | - name: ontology 18 | - name: query 19 | ## deprecate this registry entry? 20 | # - name: translator 21 | paths: 22 | /query: 23 | get: 24 | summary: 'The search API is independent of the REST API and supports free text search over the ontologies. The default search is across all textual fields in the ontology, but results are ranked towards hits in labels, then synonyms, then definitions, then annotations.' 25 | parameters: 26 | - name: q 27 | in: query 28 | description: >- 29 | The terms to search. By default the search is performed over term labels, synonyms, descriptions, identifiers and annotation properties. 30 | required: true 31 | x-valueType: 32 | - 'http://biothings.io/concepts/disease_name/' 33 | x-requestTemplate: 34 | - valueType: 'http://biothings.io/concepts/disease_name/' 35 | template: '{{input}}&ontology=doid' 36 | schema: 37 | type: string 38 | responses: 39 | '200': 40 | description: 'A query response object with "hits" property' 41 | x-responseValueType: 42 | - path: response.docs.obo_id 43 | valueType: 'http://identifiers.org/doid/' 44 | x-JSONLDContext: 45 | 'https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/ebi_ontology_lookup_service_api/jsonld_context/ols_query_1.1.json' 46 | -------------------------------------------------------------------------------- /ebi_ontology_mapping_service_api/openapi.yml: -------------------------------------------------------------------------------- 1 | openapi: '3.0.0' 2 | info: 3 | version: '1.0' 4 | title: EBI OxO Service API 5 | description: >- 6 | OxO is a service for finding mappings (or cross-references) between terms from ontologies, vocabularies and coding standards. OxO imports mappings from a variety of sources including the Ontology Lookup Service and a subset of mappings provided by the UMLS. 7 | termsOfService: https://www.ebi.ac.uk/spot/oxo/docs/about 8 | contact: 9 | name: Simon Jupp 10 | x-role: responsible developer 11 | email: jupp@ebi.ac.uk 12 | x-id: 'https://github.com/simonjupp' 13 | servers: 14 | - url: 'https://www.ebi.ac.uk/spot/oxo/api' 15 | description: 'Production server' 16 | paths: 17 | /mappings: 18 | get: 19 | tags: 20 | - mapping 21 | summary: 'Get direct xrefs between ontology terms. Xrefs are extracted from ontologies in the EBI Ontology Lookup Service.' 22 | parameters: 23 | - name: fromId 24 | in: query 25 | description: >- 26 | 'The input terms for mappings. The format of the id can be either the full IRI or compact URI (e.g. DOID:162) for the term.' 27 | required: true 28 | x-valueType: 29 | - 'http://biothings.io/concepts/ontology_term/curie' 30 | schema: 31 | type: string 32 | responses: 33 | '200': 34 | description: 'A query response object with "hits" property' 35 | x-responseValueType: 36 | - path: _embedded.mappings.toTerm.curie 37 | valueType: 'http://biothings.io/concepts/ontology_term/curie' 38 | description: 'The compact URI for the mapped term' 39 | - path: _embedded.mappings.sourcePrefix 40 | valueType: 'http://biothings.io/concepts/ontology_term/curie' 41 | description: 'The source that asserted the mapping' 42 | /search: 43 | post: 44 | summary: 'Search xrefs between terms extracted from ontologies in the EBI Ontology Lookup Service. The search endpoint provides support for filtering results and getting multi-hop mappings' 45 | tags: 46 | - search 47 | requestBody: 48 | content: 49 | 'application/json': 50 | schema: 51 | properties: 52 | ids: 53 | description: 'List of identifiers in compact URI format.' 54 | type: array 55 | mappingTarget: 56 | description: 'The target ontology or vocabulary e.g. MESH' 57 | type: array 58 | distance: 59 | description: 'The number of mappings to hop through to find a mapping' 60 | type: integer 61 | default: 1 62 | required: 63 | - ids 64 | responses: 65 | '200': 66 | description: 'A collection of ontology mappings search results with provenance' 67 | x-responseValueType: 68 | - path: _embedded.searchResults.mappingResponseList.curie 69 | valueType: 'http://biothings.io/concepts/ontology_term/curie' 70 | description: 'The compact URI for the mapped term' 71 | -------------------------------------------------------------------------------- /ensembl/openapi.yml: -------------------------------------------------------------------------------- 1 | openapi: '3.0.0' 2 | info: 3 | version: '1.0' 4 | title: Ensembl API 5 | description: >- 6 | Ensembl REST API provides language agnostic bindings to Ensembl data. 7 | termsOfService: http://dgidb.genome.wustl.edu/contact 8 | contact: 9 | name: Paul Flicek 10 | x-role: responsible developer 11 | email: help@ensembl.org 12 | x-id: 'https://github.com/paul' 13 | servers: 14 | - url: 'http://rest.ensembl.org' 15 | description: 'Production server' 16 | tags: 17 | - name: phenotype 18 | - name: variant 19 | - name: genotype 20 | ## deprecate this registry entry? 21 | # - name: translator 22 | paths: 23 | '/variation/human/{dbsnp}?phenotypes=1': 24 | get: 25 | summary: 'Uses a variant identifier (e.g. rsID) to return the variation phenotype' 26 | parameters: 27 | - name: dbsnp 28 | in: path 29 | description: >- 30 | Put dbsnp ids here, e.g. rs56116432 31 | required: true 32 | x-valueType: 33 | - 'http://identifiers.org/dbsnp/' 34 | x-requestTemplate: 35 | - valueType: 'http://identifiers.org/dbsnp/' 36 | template: '/variation/human/{{input}}?phenotypes=1' 37 | schema: 38 | type: string 39 | responses: 40 | '200': 41 | description: 'list of phenotypes related to the variant' 42 | x-responseValueType: 43 | - path: phenotypes 44 | valueType: 'http://biothings.io/concepts/phenotypes/' 45 | '/variation/human/{dbsnp}?genotypes=1': 46 | get: 47 | summary: 'Uses a variant identifier (e.g. rsID) to return the variation genotypes' 48 | parameters: 49 | - name: dbsnp 50 | in: path 51 | description: >- 52 | Put dbsnp ids here, e.g. rs56116432 53 | required: true 54 | x-valueType: 55 | - 'http://identifiers.org/dbsnp/' 56 | x-requestTemplate: 57 | - valueType: 'http://identifiers.org/dbsnp/' 58 | template: '/variation/human/{{input}}?genotypes=1' 59 | schema: 60 | type: string 61 | responses: 62 | '200': 63 | description: 'list of phenotypes related to the variant' 64 | x-responseValueType: 65 | - path: genotypes 66 | valueType: 'http://biothings.io/concepts/genotypes/' 67 | -------------------------------------------------------------------------------- /gene_knockout_correlation/openapi.yml: -------------------------------------------------------------------------------- 1 | openapi: 3.0.0 2 | info: 3 | version: 2019Q2 4 | title: Gene-knockout correlation 5 | description: This site provides an API access to gene-knockout correlations based 6 | on [Cancer Dependency Map (DepMap)](https://depmap.org/portal/download/) 7 | data. By using this site, you agree to DepMap's [Terms and 8 | Conditions](https://depmap.org/portal/terms/). 9 | termsOfService: https://depmap.org/portal/terms/ 10 | contact: 11 | name: Broad NCATS translator 12 | email: translator@broadinstitute.org 13 | paths: 14 | /genes: 15 | get: 16 | tags: 17 | - types 18 | summary: Retrieve list of genes 19 | responses: 20 | "200": 21 | description: successful operation 22 | content: 23 | application/json: 24 | schema: 25 | type: array 26 | items: 27 | $ref: "#/components/schemas/gene" 28 | "/correlations/{entrez_gene_id}": 29 | get: 30 | tags: 31 | - types 32 | summary: Retrieve correlations for a gene 33 | parameters: 34 | - name: entrez_gene_id 35 | in: path 36 | required: true 37 | schema: 38 | type: integer 39 | responses: 40 | "200": 41 | description: successful operation 42 | content: 43 | application/json: 44 | schema: 45 | type: array 46 | items: 47 | $ref: "#/components/schemas/correlation" 48 | servers: 49 | - url: http://indigo.ncats.io/gene_knockout_correlation 50 | components: 51 | schemas: 52 | gene: 53 | type: object 54 | properties: 55 | gene_symbol: 56 | type: string 57 | ensembl_gene: 58 | type: array 59 | items: 60 | type: string 61 | entrez_gene_id: 62 | type: integer 63 | synonym: 64 | type: array 65 | items: 66 | type: string 67 | correlation: 68 | type: object 69 | properties: 70 | entrez_gene_id_1: 71 | type: integer 72 | entrez_gene_id_2: 73 | type: integer 74 | correlation: 75 | type: number 76 | -------------------------------------------------------------------------------- /greent/greent.yml: -------------------------------------------------------------------------------- 1 | graphql: '0.0.0' 2 | info: 3 | version: '0.0.1' 4 | title: GreenT API 5 | description: >- 6 | Experimental description of a GraphQL endpoint using and extending the smartAPI format where feasible. 7 | API integration layer for environmental exposure and chemical biological data. 8 | contact: 9 | name: Steve Cox 10 | x-role: responsible developer 11 | email: scox@renci.org 12 | x-id: 'https://github.com/stevencox' 13 | servers: 14 | - url: 'http://stars-app.renci.org/greent/graphql' 15 | description: 'Production server' 16 | tags: 17 | - name: chemical 18 | paths: 19 | exposureConditions: 20 | parameters: 21 | chemicals: 22 | type: 23 | list: String 24 | x-requestTemplate: 25 | template: |+ 26 | query getExposureConditions($chemicals : [String] ) { 27 | exposureConditions(chemicals: $chemicals) { 28 | chemical 29 | gene 30 | pathway 31 | pathName 32 | pathID 33 | human 34 | } 35 | } 36 | valueType: http://identifiers.org/mesh/ 37 | variables: 38 | chemicals: [] 39 | x-valueType: http://identifiers.org/mesh/ 40 | responses: 41 | '200': 42 | x-JSONLDContext: https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/greent/jsonld_context/exposureConditions.jsonld 43 | x-responseValueType: 44 | path: '...' 45 | valueType: '...' 46 | 47 | 48 | 49 | -------------------------------------------------------------------------------- /greent/jsonld_context/exposureConditions.jsonld: -------------------------------------------------------------------------------- 1 | "@context": 2 | "@version": 1.1, 3 | "@base": http://identifiers.org/inchikey/, 4 | term: http://biothings.io/terms/mychem/ 5 | data: 6 | "@type": "@id" 7 | "@id": http://identifiers.org/_______________ 8 | "@context": 9 | exposureConditions: 10 | chemical: 11 | "@type": "@id" 12 | "@id": ont:some_relation_a 13 | "@context": 14 | "@base": "http://bio2rdf.org/mesh:" 15 | gene: 16 | "@type": "@id" 17 | "@id": ont:some_relation_b 18 | "@context": 19 | "@base": http://chem2bio2rdf.org/uniprot/resource/gene/ 20 | pathway: 21 | "@type": "@id" 22 | "@id": ont:some_relation_c 23 | "@content": 24 | "@base": http://chem2bio2rdf.org/kegg/resource/kegg_pathway/ 25 | -------------------------------------------------------------------------------- /hetio/smartapi.yaml: -------------------------------------------------------------------------------- 1 | --- 2 | openapi: 3.0.0 3 | info: 4 | contact: 5 | email: help@renci.org 6 | name: Chris B. 7 | description: Scibite 8 | termsOfService: https://automat.renci.org 9 | title: Automat Hetio API 10 | version: '2.0' 11 | x-translator: 12 | component: KP 13 | team: 14 | - Ranking Agent 15 | servers: 16 | - description: Production server 17 | url: https://automat.renci.org/hetio 18 | tags: 19 | - name: drug 20 | - name: gene 21 | - name: disease 22 | - name: automat 23 | - name: translator 24 | paths: 25 | "/gene/disease/{geneid}": 26 | get: 27 | summary: gene2disease 28 | parameters: 29 | - description: Put NCBIGENE ID here, e.g. 1017 30 | example: NCBIGENE:1017 31 | in: path 32 | name: geneid 33 | required: true 34 | schema: 35 | type: string 36 | responses: 37 | '200': 38 | description: An association object 39 | x-bte-kgs-operations: 40 | - "$ref": "#/components/x-bte-kgs-operations/gene2disease" 41 | "/disease/gene/{mondo}": 42 | get: 43 | summary: disease2gene 44 | parameters: 45 | - description: Put DOID ID here, e.g. "DOID:123" 46 | example: DOID:123 47 | in: path 48 | name: mondo 49 | required: true 50 | schema: 51 | type: string 52 | responses: 53 | '200': 54 | description: An association object 55 | x-bte-kgs-operations: 56 | - "$ref": "#/components/x-bte-kgs-operations/disease2gene" 57 | components: 58 | x-bte-kgs-operations: 59 | gene2chemical: 60 | - inputs: 61 | - id: NCBIGENE 62 | semantic: Gene 63 | outputs: 64 | - id: CHEMBL.COMPOUND 65 | semantic: ChemicalSubstance 66 | predicate: related_to 67 | source: hetio 68 | parameters: 69 | geneid: NCBIGENE:{inputs[0]} 70 | supportBatch: false 71 | response_mapping: 72 | "$ref": "#/components/x-bte-response-mapping/gene2chemical-chembl" 73 | - inputs: 74 | - id: NCBIGENE 75 | semantic: Gene 76 | outputs: 77 | - id: CHEBI 78 | semantic: ChemicalSubstance 79 | predicate: related_to 80 | source: hetio 81 | parameters: 82 | geneid: NCBIGENE:{inputs[0]} 83 | supportBatch: false 84 | response_mapping: 85 | "$ref": "#/components/x-bte-response-mapping/gene2chemical-chebi" 86 | gene2disease: 87 | - inputs: 88 | - id: NCBIGENE 89 | semantic: Gene 90 | outputs: 91 | - id: DOID 92 | semantic: Disease 93 | predicate: related_to 94 | source: hetio 95 | parameters: 96 | geneid: NCBIGENE:{inputs[0]} 97 | supportBatch: false 98 | response_mapping: 99 | "$ref": "#/components/x-bte-response-mapping/gene2disease-doid" 100 | - inputs: 101 | - id: NCBIGENE 102 | semantic: Gene 103 | outputs: 104 | - id: MONDO 105 | semantic: Disease 106 | predicate: related_to 107 | source: hetio 108 | parameters: 109 | geneid: NCBIGENE:{inputs[0]} 110 | supportBatch: false 111 | response_mapping: 112 | "$ref": "#/components/x-bte-response-mapping/gene2disease-mondo" 113 | chemical2gene: 114 | - inputs: 115 | - id: CHEBI 116 | semantic: ChemicalSubstance 117 | outputs: 118 | - id: NCBIGENE 119 | semantic: Gene 120 | predicate: related_to 121 | source: hetio 122 | parameters: 123 | chebi: "{inputs[0]}" 124 | supportBatch: false 125 | response_mapping: 126 | "$ref": "#/components/x-bte-response-mapping/chemical2gene" 127 | chemical2disease: 128 | - inputs: 129 | - id: CHEBI 130 | semantic: ChemicalSubstance 131 | outputs: 132 | - id: DOID 133 | semantic: Disease 134 | predicate: related_to 135 | source: hetio 136 | parameters: 137 | chebi: "{inputs[0]}" 138 | supportBatch: false 139 | response_mapping: 140 | "$ref": "#/components/x-bte-response-mapping/chemical2disease-doid" 141 | - inputs: 142 | - id: CHEBI 143 | semantic: ChemicalSubstance 144 | outputs: 145 | - id: MONDO 146 | semantic: Disease 147 | predicate: related_to 148 | source: hetio 149 | parameters: 150 | chebi: "{inputs[0]}" 151 | supportBatch: false 152 | response_mapping: 153 | "$ref": "#/components/x-bte-response-mapping/chemical2disease-mondo" 154 | disease2gene: 155 | - inputs: 156 | - id: MONDO 157 | semantic: Disease 158 | outputs: 159 | - id: NCBIGENE 160 | semantic: Gene 161 | predicate: related_to 162 | source: hetio 163 | parameters: 164 | mondo: "{inputs[0]}" 165 | supportBatch: false 166 | response_mapping: 167 | "$ref": "#/components/x-bte-response-mapping/disease2gene" 168 | disease2chemical: 169 | - inputs: 170 | - id: MONDO 171 | semantic: Disease 172 | outputs: 173 | - id: CHEMBL.COMPOUND 174 | semantic: ChemicalSubstance 175 | predicate: related_to 176 | source: hetio 177 | parameters: 178 | mondo: "{inputs[0]}" 179 | supportBatch: false 180 | response_mapping: 181 | "$ref": "#/components/x-bte-response-mapping/disease2chemical-chembl" 182 | - inputs: 183 | - id: MONDO 184 | semantic: Disease 185 | outputs: 186 | - id: CHEBI 187 | semantic: ChemicalSubstance 188 | predicate: related_to 189 | source: hetio 190 | parameters: 191 | mondo: "{inputs[0]}" 192 | supportBatch: false 193 | response_mapping: 194 | "$ref": "#/components/x-bte-response-mapping/disease2chemical-chebi" 195 | x-bte-response-mapping: 196 | gene2chemical-chebi: 197 | CHEBI: associated_with.chebi 198 | gene2chemical-chembl: 199 | CHEMBL.COMPOUND: associated_with.chembl 200 | gene2disease-mondo: 201 | MONDO: associated_with.mondo 202 | gene2disease-doid: 203 | DOID: associated_with.doid 204 | chemical2disease-mondo: 205 | MONDO: associated_with.mondo 206 | chemical2disease-doid: 207 | DOID: associated_with.doid 208 | chemical2gene: 209 | NCBIGENE: associated_with.ncbigene 210 | disease2gene: 211 | NCBIGENE: associated_with.ncbigene 212 | disease2chemical-chembl: 213 | CHEMBL.COMPOUND: associated_with.chembl 214 | disease2chemical-chebi: 215 | CHEBI: associated_with.chebi 216 | -------------------------------------------------------------------------------- /hmdb/smartapi.yaml: -------------------------------------------------------------------------------- 1 | openapi: 3.0.0 2 | info: 3 | contact: 4 | email: help@renci.org 5 | name: Chris B. 6 | description: Scibite 7 | termsOfService: https://automat.renci.org 8 | title: Automat HMDB API 9 | version: '2.0' 10 | x-translator: 11 | component: KP 12 | team: 13 | - Ranking Agent 14 | servers: 15 | - description: Production server 16 | url: https://automat.renci.org/hmdb 17 | tags: 18 | - name: drug 19 | - name: gene 20 | - name: disease 21 | - name: automat 22 | - name: translator 23 | paths: 24 | "/gene/chemical_substance/{geneid}": 25 | get: 26 | summary: gene2chemical 27 | parameters: 28 | - description: Put NCBIGENE ID here, e.g. 1017 29 | example: NCBIGENE:1017 30 | in: path 31 | name: geneid 32 | required: true 33 | schema: 34 | type: string 35 | responses: 36 | '200': 37 | description: An association object 38 | x-bte-kgs-operations: 39 | - "$ref": "#/components/x-bte-kgs-operations/gene2chemical" 40 | "/chemical_substance/disease/{chebi}": 41 | get: 42 | summary: chemical2disease 43 | parameters: 44 | - description: Put CHEBI ID here, e.g. "CHEBI:661" 45 | example: CHEBI:661 46 | in: path 47 | name: chebi 48 | required: true 49 | schema: 50 | type: string 51 | responses: 52 | '200': 53 | description: An association object 54 | x-bte-kgs-operations: 55 | - "$ref": "#/components/x-bte-kgs-operations/chemical2disease" 56 | "/chemical_substance/gene/{chebi}": 57 | get: 58 | summary: chemical2gene 59 | parameters: 60 | - description: Put CHEBI ID here, e.g. "CHEBI:661" 61 | example: CHEBI:661 62 | in: path 63 | name: chebi 64 | required: true 65 | schema: 66 | type: string 67 | responses: 68 | '200': 69 | description: An association object 70 | x-bte-kgs-operations: 71 | - "$ref": "#/components/x-bte-kgs-operations/chemical2gene" 72 | "/disease/chemical_substance/{mondo}": 73 | get: 74 | summary: disease2chemical 75 | parameters: 76 | - description: Put DOID ID here, e.g. "DOID:123" 77 | example: DOID:123 78 | in: path 79 | name: mondo 80 | required: true 81 | schema: 82 | type: string 83 | responses: 84 | '200': 85 | description: An association object 86 | x-bte-kgs-operations: 87 | - "$ref": "#/components/x-bte-kgs-operations/disease2chemical" 88 | components: 89 | x-bte-kgs-operations: 90 | gene2chemical: 91 | - inputs: 92 | - id: NCBIGENE 93 | semantic: Gene 94 | outputs: 95 | - id: CHEMBL.COMPOUND 96 | semantic: ChemicalSubstance 97 | predicate: related_to 98 | source: hmdb 99 | parameters: 100 | geneid: NCBIGENE:{inputs[0]} 101 | supportBatch: false 102 | response_mapping: 103 | "$ref": "#/components/x-bte-response-mapping/gene2chemical-chembl" 104 | - inputs: 105 | - id: NCBIGENE 106 | semantic: Gene 107 | outputs: 108 | - id: CHEBI 109 | semantic: ChemicalSubstance 110 | predicate: related_to 111 | source: hmdb 112 | parameters: 113 | geneid: NCBIGENE:{inputs[0]} 114 | supportBatch: false 115 | response_mapping: 116 | "$ref": "#/components/x-bte-response-mapping/gene2chemical-chebi" 117 | gene2disease: 118 | - inputs: 119 | - id: NCBIGENE 120 | semantic: Gene 121 | outputs: 122 | - id: DOID 123 | semantic: Disease 124 | predicate: related_to 125 | source: hmdb 126 | parameters: 127 | geneid: NCBIGENE:{inputs[0]} 128 | supportBatch: false 129 | response_mapping: 130 | "$ref": "#/components/x-bte-response-mapping/gene2disease-doid" 131 | - inputs: 132 | - id: NCBIGENE 133 | semantic: Gene 134 | outputs: 135 | - id: MONDO 136 | semantic: Disease 137 | predicate: related_to 138 | source: hmdb 139 | parameters: 140 | geneid: NCBIGENE:{inputs[0]} 141 | supportBatch: false 142 | response_mapping: 143 | "$ref": "#/components/x-bte-response-mapping/gene2disease-mondo" 144 | chemical2gene: 145 | - inputs: 146 | - id: CHEBI 147 | semantic: ChemicalSubstance 148 | outputs: 149 | - id: NCBIGENE 150 | semantic: Gene 151 | predicate: related_to 152 | source: hmdb 153 | parameters: 154 | chebi: "{inputs[0]}" 155 | supportBatch: false 156 | response_mapping: 157 | "$ref": "#/components/x-bte-response-mapping/chemical2gene" 158 | chemical2disease: 159 | - inputs: 160 | - id: CHEBI 161 | semantic: ChemicalSubstance 162 | outputs: 163 | - id: DOID 164 | semantic: Disease 165 | predicate: related_to 166 | source: hmdb 167 | parameters: 168 | chebi: "{inputs[0]}" 169 | supportBatch: false 170 | response_mapping: 171 | "$ref": "#/components/x-bte-response-mapping/chemical2disease-doid" 172 | - inputs: 173 | - id: CHEBI 174 | semantic: ChemicalSubstance 175 | outputs: 176 | - id: MONDO 177 | semantic: Disease 178 | predicate: related_to 179 | source: hmdb 180 | parameters: 181 | chebi: "{inputs[0]}" 182 | supportBatch: false 183 | response_mapping: 184 | "$ref": "#/components/x-bte-response-mapping/chemical2disease-mondo" 185 | disease2gene: 186 | - inputs: 187 | - id: MONDO 188 | semantic: Disease 189 | outputs: 190 | - id: NCBIGENE 191 | semantic: Gene 192 | predicate: related_to 193 | source: hmdb 194 | parameters: 195 | mondo: "{inputs[0]}" 196 | supportBatch: false 197 | response_mapping: 198 | "$ref": "#/components/x-bte-response-mapping/disease2gene" 199 | disease2chemical: 200 | - inputs: 201 | - id: MONDO 202 | semantic: Disease 203 | outputs: 204 | - id: CHEMBL.COMPOUND 205 | semantic: ChemicalSubstance 206 | predicate: related_to 207 | source: hmdb 208 | parameters: 209 | mondo: "{inputs[0]}" 210 | supportBatch: false 211 | response_mapping: 212 | "$ref": "#/components/x-bte-response-mapping/disease2chemical-chembl" 213 | - inputs: 214 | - id: MONDO 215 | semantic: Disease 216 | outputs: 217 | - id: CHEBI 218 | semantic: ChemicalSubstance 219 | predicate: related_to 220 | source: hmdb 221 | parameters: 222 | mondo: "{inputs[0]}" 223 | supportBatch: false 224 | response_mapping: 225 | "$ref": "#/components/x-bte-response-mapping/disease2chemical-chebi" 226 | x-bte-response-mapping: 227 | gene2chemical-chebi: 228 | CHEBI: associated_with.chebi 229 | gene2chemical-chembl: 230 | CHEMBL.COMPOUND: associated_with.chembl 231 | gene2disease-mondo: 232 | MONDO: associated_with.mondo 233 | gene2disease-doid: 234 | DOID: associated_with.doid 235 | chemical2disease-mondo: 236 | MONDO: associated_with.mondo 237 | chemical2disease-doid: 238 | DOID: associated_with.doid 239 | chemical2gene: 240 | NCBIGENE: associated_with.ncbigene 241 | disease2gene: 242 | NCBIGENE: associated_with.ncbigene 243 | disease2chemical-chembl: 244 | CHEMBL.COMPOUND: associated_with.chembl 245 | disease2chemical-chebi: 246 | CHEBI: associated_with.chebi 247 | -------------------------------------------------------------------------------- /iPTMnet/smartapi.yaml: -------------------------------------------------------------------------------- 1 | openapi: 3.0.3 2 | info: 3 | description: >- 4 | This is an API for iPTMNet providing information about post-translational 5 | modifications (PTMs) combined from multiple sources and tools. 6 | version: '2.1.1' 7 | title: iPTMNet API 8 | contact: 9 | ## using contact info from https://research.bioinformatics.udel.edu/iptmnet/about/api 10 | name: Sachin Gavali 11 | email: saching@udel.edu 12 | termsOfService: https://research.bioinformatics.udel.edu/iptmnet/license 13 | x-translator: 14 | infores: "infores:iptmnet" 15 | component: KP 16 | team: 17 | - Service Provider 18 | biolink-version: "4.2.2" 19 | servers: 20 | - description: Encrypted Production server 21 | url: https://research.bioinformatics.udel.edu/iptmnet/api 22 | x-maturity: production 23 | tags: 24 | - name: translator 25 | paths: 26 | "/{id}/substrate": 27 | get: 28 | summary: Retrieve the list of PTM sites with the given substrate 29 | description: >- 30 | By passing a IPTMNet identifier, you can retrieve the list of PTM sites 31 | and annotations with that given substrate 32 | operationId: asSubById 33 | parameters: 34 | - name: id 35 | in: path 36 | description: The iPTMNet ID. Usually reuse UniProt Accession numbers. 37 | required: true 38 | schema: 39 | type: string 40 | example: "P24941" 41 | responses: 42 | '200': 43 | description: >- 44 | Set of tables for the PTM sites for each proteoform of the given 45 | protein 46 | ## while this is from the original swagger doc, it doesn't seem to match the actual response: 47 | ## an object where the keys are the protein IDs and the values are an array of objects. 48 | ## the objects have fields like residue, site, ptm_type, score, sources, enzymes, pmids 49 | # content: 50 | # application/json: 51 | # schema: 52 | # type: array 53 | # items: 54 | # type: object 55 | # properties: 56 | # form: 57 | # type: string 58 | # example: Q15796 59 | # table: 60 | # $ref: '#/definitions/substrate_table' 61 | # example: 62 | # - form: Q15796 63 | # table: 64 | # $ref: '#/definitions/substrate_table/example' 65 | # - form: Q15796-1 66 | # table: 67 | # - site: T8 68 | # type: Phosphorylation 69 | # enzyme: 70 | # id: 'PR:000026189' 71 | # type: pro_id 72 | # name: 'hMAPK3/iso:1/Phos:1' 73 | # score: 2 74 | # sources: 75 | # PRO: 'http://purl.obolibrary.org/obo/PR_Q15796' 76 | # PMIDs: 77 | # - 12193595 78 | '501': 79 | description: Not yet implemented. Need to find format. 80 | ## 1 operation 81 | x-bte-kgs-operations: 82 | - $ref: '#/components/x-bte-kgs-operations/is_substrate_of' 83 | ## not in original swagger doc 84 | "/{id}/as-enzyme": 85 | get: 86 | summary: Retrieve the list of PTM sites the given enzyme modifies 87 | description: >- 88 | By passing a IPTMNet identifier, you can retrieve the list of PTM sites 89 | and annotations with that given enzyme 90 | operationId: asEnzById 91 | parameters: 92 | - name: id 93 | in: path 94 | description: The iPTMNet ID. Usually reuse UniProt Accession numbers. 95 | required: true 96 | schema: 97 | type: string 98 | example: "P24941" 99 | responses: 100 | '200': 101 | description: >- 102 | Set of tables for the PTM sites that each proteoform of the given 103 | protein acts on 104 | content: 105 | application/json: 106 | schema: 107 | type: object 108 | '501': 109 | description: Not yet implemented. Need to find format. 110 | ## 1 operation 111 | x-bte-kgs-operations: 112 | - $ref: '#/components/x-bte-kgs-operations/has_substrate' 113 | components: 114 | x-bte-kgs-operations: 115 | ## chose to use Protein as category since they are catalyzing PTMs 116 | ## knowledge_level / agent_type: some info seems to be text-mined, some imported from curated databases 117 | ## ref: materials and methods https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753337/#SEC2title 118 | is_substrate_of: 119 | ## response: an object where the keys are the protein IDs and the values are an array of objects. 120 | ## the objects have fields like residue, site, ptm_type, score, sources, enzymes, pmids 121 | - supportBatch: false 122 | useTemplating: true ## flag to say templating is being used below 123 | inputs: 124 | - id: UniProtKB 125 | semantic: Protein 126 | parameters: 127 | ## no prefix on ID 128 | id: "{{ queryInputs }}" 129 | outputs: 130 | - id: UniProtKB 131 | semantic: Protein 132 | predicate: is_substrate_of 133 | ## use api-level source of "infores:iptmnet" for now 134 | ## future? use JQ-post-processing on "sources" field? 135 | ## "sources" is an array of objects 136 | ## each object has name/label/url 137 | ## not sure what all the possible values are though... 138 | knowledge_level: knowledge_assertion 139 | agent_type: not_provided 140 | response_mapping: 141 | "$ref": "#/components/x-bte-response-mapping/is_substrate_of" 142 | testExamples: 143 | - qInput: "UniProtKB:P24941" ## CDK2 144 | oneOutput: "UniProtKB:P50613" ## CDK7 145 | has_substrate: 146 | ## response: an object where the keys are the protein IDs and the values are an array of objects. 147 | ## the objects have fields like substrate, substrate_symbol, site, score, sources, pmids 148 | - supportBatch: false 149 | useTemplating: true ## flag to say templating is being used below 150 | inputs: 151 | - id: UniProtKB 152 | semantic: Protein 153 | parameters: 154 | ## no prefix on ID 155 | id: "{{ queryInputs }}" 156 | outputs: 157 | - id: UniProtKB 158 | semantic: Protein 159 | predicate: has_substrate 160 | ## use api-level source of "infores:iptmnet" for now 161 | ## see notes on is_substrate_of 162 | knowledge_level: knowledge_assertion 163 | agent_type: not_provided 164 | response_mapping: 165 | "$ref": "#/components/x-bte-response-mapping/has_substrate" 166 | testExamples: 167 | - qInput: "UniProtKB:P24941" ## CDK2 168 | oneOutput: "UniProtKB:P33991" ## MCM4 169 | x-bte-response-mapping: 170 | is_substrate_of: 171 | UniProtKB: enzymes.id 172 | ref_pmid: pmids ## array of strings 173 | has_substrate: 174 | UniProtKB: substrate 175 | ref_pmid: pmids ## array of strings 176 | -------------------------------------------------------------------------------- /litvar/smartapi.yaml: -------------------------------------------------------------------------------- 1 | openapi: 3.0.3 2 | info: 3 | version: 1.1.0 4 | title: LitVar API 5 | description: >- 6 | LitVar allows the search and retrieval of variant relevant information 7 | from the biomedical literature and shows key biological relations between a variant 8 | and its close related entities (e.g. genes, diseases, and drugs). The LitVar results 9 | are automatically extracted (with regular updates) from over 27 million PubMed 10 | articles as well as applicable full-text articles in PubMed Central. See 11 | https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/LitVar/api.html for details. 12 | termsOfService: https://www.ncbi.nlm.nih.gov/home/about/policies/ 13 | contact: 14 | name: Zhiyong Lu 15 | email: luzh@ncbi.nlm.nih.gov 16 | x-translator: 17 | infores: "infores:litvar" 18 | component: KP 19 | team: 20 | - Service Provider 21 | biolink-version: "4.2.2" 22 | servers: 23 | - url: https://www.ncbi.nlm.nih.gov/research/bionlp/litvar/api/v1 24 | description: Production server 25 | x-maturity: production 26 | tags: 27 | - name: variant 28 | - name: translator 29 | paths: 30 | "/entity/litvar/{variantid}": 31 | get: 32 | summary: This will allow you to retrieve information about a variant given its VarID. 33 | parameters: 34 | - name: variantid 35 | in: path 36 | example: "rs121913527##" 37 | description: rsid 38 | required: true 39 | schema: 40 | type: string 41 | responses: 42 | '200': 43 | description: publications mentioned the submitted variant 44 | x-bte-kgs-operations: 45 | - "$ref": "#/components/x-bte-kgs-operations/variant_located_in_gene" 46 | components: 47 | ## knowledge_level / agent_type: gene assignments seem to happen in automated build process 48 | ## https://www.ncbi.nlm.nih.gov/books/NBK21088/#_ch5_ch5_s4_ 49 | x-bte-kgs-operations: 50 | variant_located_in_gene: 51 | ## API cannot do the reverse operation 52 | - supportBatch: false 53 | useTemplating: true 54 | inputs: 55 | - id: DBSNP 56 | semantic: SequenceVariant 57 | parameters: 58 | variantid: "{{ queryInputs | rmPrefix() }}%23%23" ## no prefix 59 | outputs: 60 | - id: NCBIGene 61 | semantic: Gene 62 | predicate: is_sequence_variant_of 63 | source: "infores:dbsnp" 64 | knowledge_level: knowledge_assertion 65 | agent_type: automated_agent 66 | response_mapping: 67 | "$ref": "#/components/x-bte-response-mapping/variant_located_in_gene" 68 | testExamples: 69 | - qInput: "DBSNP:rs121913527" 70 | oneOutput: "NCBIGene:3845" ## KRAS 71 | ## another example input is rs1193171808 72 | ## raw query example: https://www.ncbi.nlm.nih.gov/research/bionlp/litvar/api/v1/entity/litvar/rs121913527%23%23 73 | x-bte-response-mapping: 74 | variant_located_in_gene: 75 | NCBIGene: gene.id ## no prefix 76 | ref_url: links.url 77 | -------------------------------------------------------------------------------- /mychem.info/jsonld_context/mychem_context.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context": { 3 | "drugbank.name": { 4 | "@id": "oban:has_property", 5 | "@type": "http://identifiers.org/drug.symbol/" 6 | }, 7 | "drugbank.targets.uniprot": { 8 | "@id": "oban:is_Target_of", 9 | "@type": "http://identifiers.org/uniprot/" 10 | }, 11 | "drugbank.accession_number": { 12 | "@id": "oban:has_property", 13 | "@type": "http://identifiers.org/drugbank/" 14 | }, 15 | "drugbank.carriers.uniprot": { 16 | "@id": "oban:is_Carrier_of", 17 | "@type": "http://identifiers.org/uniprot/" 18 | }, 19 | "drugbank.transporters.uniprot": { 20 | "@id": "oban:is_Transporter_of", 21 | "@type": "http://identifiers.org/uniprot/" 22 | }, 23 | "drugbank.enzymes.uniprot": { 24 | "@id": "oban:is_Enzyme_of", 25 | "@type": "http://identifiers.org/uniprot/" 26 | }, 27 | "drugbank.drug_interaction.drugbank-id": { 28 | "@id": "oban:interact_with", 29 | "@type": "http://identifiers.org/uniprot/" 30 | }, 31 | "drugbank.pathway.drugs.drugbank-id": { 32 | "@id": "oban:has_property", 33 | "@type": "http://identifiers.org/drugbank/" 34 | }, 35 | "drugbank.pathways.enzymes.uniprot-id": { 36 | "@id": "oban:has_property", 37 | "@type": "http://identifiers.org/uniprot_enzymes/" 38 | }, 39 | "drugbank.pharmacology.snp_effects.effect.gene-symbol": { 40 | "@id": "oban:has_property", 41 | "@type": "http://identifiers.org/hgnc.symbol/" 42 | }, 43 | "drugbank.pharmacology.snp_effects.effect.rs-id": { 44 | "@id": "oban:has_property", 45 | "@type": "http://identifiers.org/dbsnp/" 46 | }, 47 | "drugbank.pharmacology.snp_effects.effect.pubmed-id": { 48 | "@id": "oban:has_property", 49 | "@type": "http://identifiers.org/pubmed/" 50 | }, 51 | "drugbank.pharmacology.snp_effects.effect.uniprot_id": { 52 | "@id": "oban:has_property", 53 | "@type": "http://identifiers.org/uniprot_snp/" 54 | }, 55 | "drugbank.pharmacology.snp_adverse_drug_reactions.reactions.pubmed-id": { 56 | "@id": "oban:has_property", 57 | "@type": "http://identifiers.org/pubmed/" 58 | }, 59 | "drugbank.pharmacology.snp_adverse_drug_reactions.reactions.gene-symbol": { 60 | "@id": "oban:has_property", 61 | "@type": "http://identifiers.org/hgnc.symbol/" 62 | }, 63 | "drugbank.pharmacology.snp_adverse_drug_reactions.reactions.rs-id": { 64 | "@id": "oban:has_property", 65 | "@type": "http://identifiers.org/dbsnp/" 66 | }, 67 | "drugbank.pharmacology.snp_adverse_drug_reactions.reactions.uniprot_id": { 68 | "@id": "oban:has_property", 69 | "@type": "http://identifiers.org/uniprot_snp/" 70 | }, 71 | "pharmgkb.cross_references.clinicaltrials_gov": { 72 | "@id": "oban:has_property", 73 | "@type": "http://identifiers.org/clinicaltrials/" 74 | }, 75 | "pharmgkb.cross_references.drugbank": { 76 | "@id": "oban:has_property", 77 | "@type": "http://identifiers.org/drugbank/" 78 | }, 79 | "pharmgkb.cross_references.uniprotkb": { 80 | "@id": "oban:has_property", 81 | "@type": "http://identifiers.org/uniprot/" 82 | }, 83 | "chembl.pref_name": { 84 | "@id": "oban:has_property", 85 | "@type": "http://identifiers.org/drug.symbol/" 86 | }, 87 | "aeolus.drug_name": { 88 | "@id": "oban:has_property", 89 | "@type": "http://identifiers.org/drug.symbol/" 90 | }, 91 | "pubchem.cid": { 92 | "@id": "oban:has_property", 93 | "@type": "http://identifiers.org/pubchem.compound/" 94 | }, 95 | "unii.preferred_term": { 96 | "@id": "oban:has_property", 97 | "@type": "http://identifiers.org/drug.symbol/" 98 | }, 99 | "unii.rxcui": { 100 | "@id": "oban:has_property", 101 | "@type": "http://identifiers.org/rxcui/" 102 | }, 103 | "aeolus.drug_code": { 104 | "@id": "oban:has_property", 105 | "@type": "http://identifiers.org/rxcui/" 106 | }, 107 | "ginas.xrefs.RXCUI": { 108 | "@id": "oban:has_property", 109 | "@type": "http://identifiers.org/rxcui/" 110 | } 111 | } 112 | } 113 | -------------------------------------------------------------------------------- /mychem.info/jsonld_context/mychem_query_1.1.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context": { 3 | "@version": 1.1, 4 | "@base": "http://identifiers.org/inchikey/", 5 | "term": "http://biothings.io/terms/mychem/", 6 | "ont": "http://biothings.io/ontology/", 7 | "_id": "@id", 8 | "hits": { 9 | "@type": "@id", 10 | "@id": "term:has_annotation", 11 | "@context": { 12 | "_id": { 13 | "@type": "@id", 14 | "@id": "ont:isRelatedTo", 15 | "@context": { 16 | "@base": "http://identifiers.org/inchikey/" 17 | } 18 | } 19 | } 20 | } 21 | } 22 | } -------------------------------------------------------------------------------- /mychem.info/openapi_minimum.yml: -------------------------------------------------------------------------------- 1 | openapi: '3.0.0' 2 | info: 3 | version: '1.0' 4 | title: MyChem.info API 5 | description: >- 6 | Documentation of the MyChem.info Chemical Query web services. Learn more about 7 | [MyChem.info](http://mychem.info/) 8 | termsOfService: http://mychem.info/terms/ 9 | contact: 10 | name: Chunlei Wu 11 | x-role: responsible developer 12 | email: help@mychem.info 13 | x-id: 'https://github.com/newgene' 14 | x-translator: 15 | component: KP 16 | team: 17 | - Service Provider 18 | servers: 19 | - url: 'http://mychem.info/v1' 20 | description: 'Production server' 21 | tags: 22 | - name: chemical 23 | - name: drug 24 | - name: annotation 25 | - name: query 26 | - name: translator 27 | paths: 28 | /query: 29 | get: 30 | summary: 'Make chemical query and return matching chemical hits' 31 | parameters: 32 | - name: q 33 | in: query 34 | description: >- 35 | Query string. Examples "Fludara", "CHEMBI:63599", "DB01073". 36 | required: true 37 | x-valueType: 38 | - 'http://identifiers.org/rxcui/' 39 | - 'http://identifiers.org/chebi/' 40 | - 'http://identifiers.org/chembl/' 41 | - 'http://identifiers.org/drugbank/' 42 | - 'http://identifiers.org/iuphar.ligand/' 43 | - 'http://identifiers.org/kegg.drug/' 44 | - 'http://identifiers.org/kegg.compound/' 45 | - 'http://identifiers.org/pubchem.compound/' 46 | - 'http://identifiers.org/unii/' 47 | - 'http://identifiers.org/inchikey/' 48 | - 'http://identifiers.org/inchi/' 49 | - 'http://identifiers.org/uniprot/' 50 | schema: 51 | type: string 52 | responses: 53 | '200': 54 | description: 'A query response object with "hits" property' 55 | x-responseValueType: 56 | - path: _id 57 | valueType: 'http://identifiers.org/inchikey/' 58 | - path: cadd.gene.genename 59 | valueType: 'http://identifiers.org/uniprot/' 60 | - path: clinvar.rsid 61 | valueType: 'http://identifiers.org/drugbank/' 62 | - path: cadd.gene.gene_id 63 | valueType: 'http://identifiers.org/dbsnp/' 64 | - path: cadd.gene.feature_id 65 | valueType: 'http://identifiers.org/pubmed/' 66 | - path: cadd.gene.ccds_id 67 | valueType: 'http://identifiers.org/clinicaltrials/' 68 | - path: clinvar.uniprot 69 | valueType: 'http://identifiers.org/rxcui/' 70 | x-JSONLDContext: 71 | 'https://github.com/NCATS-Tangerine/translator-api-registry/blob/master/mychem.info/jsonld_context/mychem_context.json' 72 | '/drug/{drugid}': 73 | get: 74 | summary: 'For a given chemical id, return the matching chemical object' 75 | parameters: 76 | - name: drugid 77 | in: path 78 | description: >- 79 | DrugBank ID, InCHIKey, CHEBI ID, CHEMBL ID 80 | required: true 81 | x-valueType: 82 | - 'http://identifiers.org/inchikey/' 83 | schema: 84 | type: string 85 | responses: 86 | '200': 87 | description: 'A chemical object' 88 | x-responseValueType: 89 | - path: cadd.gene.genename 90 | valueType: 'http://identifiers.org/uniprot/' 91 | - path: clinvar.rsid 92 | valueType: 'http://identifiers.org/drugbank/' 93 | - path: cadd.gene.gene_id 94 | valueType: 'http://identifiers.org/dbsnp/' 95 | - path: cadd.gene.feature_id 96 | valueType: 'http://identifiers.org/pubmed/' 97 | - path: cadd.gene.ccds_id 98 | valueType: 'http://identifiers.org/clinicaltrials/' 99 | - path: clinvar.uniprot 100 | valueType: 'http://identifiers.org/rxcui/' 101 | x-JSONLDContext: 102 | 'https://github.com/NCATS-Tangerine/translator-api-registry/blob/master/mychem.info/jsonld_context/mychem_context.json' 103 | -------------------------------------------------------------------------------- /mygene.info/jsonld_context/mygene_context.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context": { 3 | "symbol": { 4 | "@id": "oban:has_property", 5 | "@type": "http://identifiers.org/hgnc.symbol/" 6 | }, 7 | "ensembl.gene": { 8 | "@id": "oban:has_property", 9 | "@type": "http://identifiers.org/ensembl.gene/" 10 | }, 11 | "ensembl.protein": { 12 | "@id": "oban:has_property", 13 | "@type": "http://identifiers.org/ensembl.protein/" 14 | }, 15 | "ensembl.transcript": { 16 | "@id": "oban:has_property", 17 | "@type": "http://identifiers.org/ensembl.transcript/" 18 | }, 19 | "go.CC.id": { 20 | "@id": "oban:has_property", 21 | "@type": "http://identifiers.org/go/" 22 | }, 23 | "go.CC.pubmed": { 24 | "@id": "oban:has_property", 25 | "@type": "http://identifiers.org/pubmed/" 26 | }, 27 | "go.MF.id": { 28 | "@id": "oban:has_property", 29 | "@type": "http://identifiers.org/go/" 30 | }, 31 | "go.MF.pubmed": { 32 | "@id": "oban:has_property", 33 | "@type": "http://identifiers.org/pubmed/" 34 | }, 35 | "go.BP.id": { 36 | "@id": "oban:has_property", 37 | "@type": "http://identifiers.org/go/" 38 | }, 39 | "go.BP.pubmed": { 40 | "@id": "oban:has_property", 41 | "@type": "http://identifiers.org/pubmed/" 42 | }, 43 | "generif.pubmed": { 44 | "@id": "oban:has_property", 45 | "@type": "http://identifiers.org/pubmed/" 46 | }, 47 | "interpro.id": { 48 | "@id": "oban:has_property", 49 | "@type": "http://identifiers.org/interpro/" 50 | }, 51 | "pathway.biocarta.id": { 52 | "@id": "oban:has_property", 53 | "@type": "http://identifiers.org/biocarta.pathway/" 54 | }, 55 | "pathway.kegg.id": { 56 | "@id": "oban:has_property", 57 | "@type": "http://identifiers.org/kegg.pathway/" 58 | }, 59 | "pathway.pharmgkb.id": { 60 | "@id": "oban:has_property", 61 | "@type": "http://identifiers.org/pharmgkb.pathways/" 62 | }, 63 | "pathway.reactome.id": { 64 | "@id": "oban:has_property", 65 | "@type": "http://identifiers.org/reactome/" 66 | }, 67 | "pathway.sympdb.id": { 68 | "@id": "oban:has_property", 69 | "@type": "http://identifiers.org/sympdb/" 70 | }, 71 | "pathway.wikipathways.id": { 72 | "@id": "oban:has_property", 73 | "@type": "http://identifiers.org/wikipathways/" 74 | }, 75 | "refseq.genomic": { 76 | "@id": "oban:has_property", 77 | "@type": "http://identifiers.org/refseq/" 78 | }, 79 | "refseq.protein": { 80 | "@id": "oban:has_property", 81 | "@type": "http://identifiers.org/refseq/" 82 | }, 83 | "refseq.rna": { 84 | "@id": "oban:has_property", 85 | "@type": "http://identifiers.org/refseq/" 86 | }, 87 | "uniprot.Swiss-Prot": { 88 | "@id": "oban:has_property", 89 | "@type": "http://identifiers.org/uniprot/" 90 | } 91 | } 92 | } -------------------------------------------------------------------------------- /mygene.info/jsonld_context/mygene_gene_1.1.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context": { 3 | "@version": 1.1, 4 | "@base": "http://identifiers.org/ncbigene/", 5 | "term": "http://biothings.io/terms/mygene/", 6 | "ont": "http://biothings.io/ontologies/", 7 | "_id": "@id", 8 | "symbol": { 9 | "@type": "@id", 10 | "@id": "ont:hasSymbol", 11 | "@context": { 12 | "@base": "http://identifiers.org/hgnc.symbol/" 13 | } 14 | }, 15 | "unigene": { 16 | "@type": "@id", 17 | "@id": "ont:correspondsToUniGene", 18 | "@context": { 19 | "@base": "http://identifiers.org/unigene/" 20 | } 21 | }, 22 | "uniprot": { 23 | "@type": "@id", 24 | "@id": "term:has_annotation", 25 | "@context": { 26 | "Swiss-Prot": { 27 | "@type": "@id", 28 | "@id": "ont:encodes", 29 | "@context": { 30 | "@base": "http://identifiers.org/uniprot/" 31 | } 32 | } 33 | } 34 | }, 35 | "ensembl": { 36 | "@type": "@id", 37 | "@id": "term:has_annotation", 38 | "@context": { 39 | "protein": { 40 | "@type": "@id", 41 | "@id": "ont:hasEnsemblProtein", 42 | "@context": { 43 | "@base": "http://identifiers.org/ensembl.protein/" 44 | } 45 | }, 46 | "gene": { 47 | "@type": "@id", 48 | "@id": "ont:hasEnsemblGene", 49 | "@context": { 50 | "@base": "http://identifiers.org/ensembl.gene/" 51 | } 52 | }, 53 | "transcript": { 54 | "@type": "@id", 55 | "@id": "ont:hasEnsemblTranscript", 56 | "@context": { 57 | "@base": "http://identifiers.org/ensembl.transcript/" 58 | } 59 | }, 60 | "translation": { 61 | "@type": "@id", 62 | "@id": "ont:hasEnsemblTranslation", 63 | "@context": { 64 | "@base": "http://identifiers.org/ensembl.translation/" 65 | } 66 | } 67 | } 68 | }, 69 | "pdb": { 70 | "@type": "@id", 71 | "@id": "on:has3DStructure", 72 | "@context": { 73 | "@base": "http://identifiers.org/pdb/" 74 | } 75 | }, 76 | "pathway": { 77 | "@type": "@id", 78 | "@id": "term:has_annotation", 79 | "@context": { 80 | "biocarta": { 81 | "@type": "@id", 82 | "@id": "term:has_annotation", 83 | "@context": { 84 | "id": { 85 | "@type": "@id", 86 | "@id": "ont:isParticipantIn", 87 | "@context": { 88 | "@base": "http://identifiers.org/biocarta.pathway/" 89 | } 90 | } 91 | } 92 | }, 93 | "kegg": { 94 | "@type": "@id", 95 | "@id": "term:has_annotation", 96 | "@context": { 97 | "id": { 98 | "@type": "@id", 99 | "@id": "ont:isParticipantIn", 100 | "@context": { 101 | "@base": "http://identifiers.org/kegg.pathway/" 102 | } 103 | } 104 | } 105 | }, 106 | "reactome": { 107 | "@type": "@id", 108 | "@id": "term:has_annotation", 109 | "@context": { 110 | "id": { 111 | "@type": "@id", 112 | "@id": "ont:isParticipantIn", 113 | "@context": { 114 | "@base": "http://identifiers.org/reactome/" 115 | } 116 | } 117 | } 118 | }, 119 | "wikipathways": { 120 | "@type": "@id", 121 | "@id": "term:has_annotation", 122 | "@context": { 123 | "id": { 124 | "@type": "@id", 125 | "@id": "ont:isParticipantIn", 126 | "@context": { 127 | "@base": "http://identifiers.org/wikipathways/" 128 | } 129 | } 130 | } 131 | }, 132 | "pharmgkb": { 133 | "@type": "@id", 134 | "@id": "term:has_annotation", 135 | "@context": { 136 | "id": { 137 | "@type": "@id", 138 | "@id": "ont:isParticipantIn", 139 | "@context": { 140 | "@base": "http://identifiers.org/pharmgkb.pathways/" 141 | } 142 | } 143 | } 144 | } 145 | } 146 | } 147 | } 148 | } -------------------------------------------------------------------------------- /mygene.info/jsonld_context/mygene_query_1.1.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context": { 3 | "@version": 1.1, 4 | "ont": "http://biothings.io/ontology/", 5 | "hits": { 6 | "@type": "@id", 7 | "@id": "term:has_annotation", 8 | "@context": { 9 | "_id": { 10 | "@type": "@id", 11 | "@id": "ont:hasGeneId", 12 | "@context": { 13 | "@base": "http://identifiers.org/ncbigene/" 14 | } 15 | }, 16 | "symbol": { 17 | "@type": "@id", 18 | "@id": "ont:hasSymbol", 19 | "@context": { 20 | "@base": "http://identifiers.org/hgnc.symbol/" 21 | } 22 | }, 23 | "taxid": { 24 | "@type": "@id", 25 | "@id": "ont:hasTaxonmyId", 26 | "@context": { 27 | "@base": "http://identifiers.org/taxonomy/" 28 | } 29 | } 30 | } 31 | } 32 | } 33 | } -------------------------------------------------------------------------------- /mygene.info/openapi_minimum.yml: -------------------------------------------------------------------------------- 1 | openapi: '3.0.0' 2 | info: 3 | version: '3.0' 4 | title: MyGene.info API 5 | description: >- 6 | Documentation of the MyGene.info Gene Query web services. Learn more about 7 | [MyGene.info](http://mygene.info/) 8 | termsOfService: http://mygene.info/terms/ 9 | contact: 10 | name: Chunlei Wu 11 | x-role: responsible developer 12 | email: help@mygene.info 13 | x-id: 'https://github.com/newgene' 14 | x-translator: 15 | component: KP 16 | team: 17 | - Service Provider 18 | servers: 19 | - url: 'http://mygene.info/v3' 20 | description: 'Production server' 21 | tags: 22 | - name: gene 23 | - name: annotation 24 | - name: query 25 | - name: translator 26 | paths: 27 | /query: 28 | get: 29 | summary: 'Make gene query and return matching gene hits' 30 | parameters: 31 | - name: q 32 | in: query 33 | description: >- 34 | Query string. Examples "CDK2", "NM_052827", "204639_at". The 35 | detailed query syntax can be found at 36 | http://docs.mygene.info/en/latest/doc/query_service.html 37 | required: true 38 | x-valueType: 39 | - 'http://identifiers.org/hgnc.symbol/' 40 | - 'http://identifiers.org/refseq/' 41 | - 'http://identifiers.org/unigene/' 42 | - 'http://identifiers.org/uniprot/' 43 | - 'http://identifiers.org/pdb/' 44 | - 'http://identifiers.org/biocarta.pathway/' 45 | - 'http://identifiers.org/kegg.pathway/' 46 | - 'http://identifiers.org/wikipathways/' 47 | - 'http://identifiers.org/pharmgkb.pathways/' 48 | - 'http://identifiers.org/reactome/' 49 | schema: 50 | type: string 51 | responses: 52 | '200': 53 | description: 'A query response object with "hits" property' 54 | x-responseValueType: 55 | - path: hits._id 56 | valueType: 'http://identifiers.org/ncbigene/' 57 | - path: hits.entrezgene 58 | valueType: 'http://identifiers.org/ncbigene/' 59 | - path: hits.symbol 60 | valueType: 'http://identifiers.org/hgnc.symbol/' 61 | - path: hits.taxid 62 | valueType: 'http://identifiers.org/taxonomy/' 63 | x-JSONLDContext: 64 | 'https://github.com/NCATS-Tangerine/translator-api-registry/blob/master/mygene.info/jsonld_context/mygene_context.json' 65 | '/gene/{geneid}': 66 | get: 67 | summary: 'For a given gene id, return the matching gene object' 68 | parameters: 69 | - name: geneid 70 | in: path 71 | description: >- 72 | Entrez or Ensembl gene id, e.g., 1017, ENSG00000170248. A retired 73 | Entrez Gene id works too if it is replaced by a new one, e.g., 74 | 245794 75 | required: true 76 | x-valueType: 77 | - 'http://identifiers.org/ncbigene/' 78 | - 'http://identifiers.org/ensembl/' 79 | schema: 80 | type: string 81 | responses: 82 | '200': 83 | description: 'A gene object' 84 | x-responseValueType: 85 | - path: symbol 86 | valueType: 'http://identifiers.org/hgnc.symbol/' 87 | - path: unigene 88 | valueType: 'http://identifiers.org/unigene/' 89 | - path: uniprot.Swiss-Prot 90 | valueType: 'http://identifiers.org/uniprot/' 91 | - path: pdb 92 | valueType: 'http://identifiers.org/pdb/' 93 | - path: pathway.biocarta.id 94 | valueType: 'http://identifiers.org/biocarta.pathway/' 95 | - path: pathway.kegg.id 96 | valueType: 'http://identifiers.org/kegg.pathway/' 97 | - path: pathway.reactome.id 98 | valueType: 'http://identifiers.org/reactome/' 99 | - path: pathway.wikipathways.id 100 | valueType: 'http://identifiers.org/wikipathways/' 101 | - path: pathway.pharmgkb.id 102 | valueType: 'http://identifiers.org/pharmgkb.pathways/' 103 | x-JSONLDContext: 104 | 'https://github.com/NCATS-Tangerine/translator-api-registry/blob/master/mygene.info/jsonld_context/mygene_context.json' 105 | -------------------------------------------------------------------------------- /myvariant.info/jsonld_context/myvariant_context.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context": { 3 | "cadd.gene.gene_id": { 4 | "@id": "oban:has_property", 5 | "@type": "http://identifiers.org/ensembl.gene/" 6 | }, 7 | "cadd.gene.feature_id": { 8 | "@id": "oban:has_property", 9 | "@type": "http://identifiers.org/ensembl.transcript/" 10 | }, 11 | "cadd.gene.genename": { 12 | "@id": "oban:has_property", 13 | "@type": "http://identifiers.org/hgnc.symbol/" 14 | }, 15 | "cadd.gene.ccds_id": { 16 | "@id": "oban:has_property", 17 | "@type": "http://identifiers.org/ccds/" 18 | }, 19 | "clinvar.uniprot": { 20 | "@id": "oban:has_property", 21 | "@type": "http://identifiers.org/uniprot/" 22 | }, 23 | "clinvar.omim": { 24 | "@id": "oban:has_property", 25 | "@type": "http://identifiers.org/omim/" 26 | }, 27 | "clinvar.rsid": { 28 | "@id": "oban:has_property", 29 | "@type": "http://identifiers.org/dbsnp/" 30 | }, 31 | "clinvar.rcv.accession": { 32 | "@id": "oban:has_property", 33 | "@type": "http://identifers.org/clinvar/" 34 | }, 35 | "clinvar.rcv.conditions.identifiers.omim": { 36 | "@id": "oban:has_property", 37 | "@type": "http://identifiers.org/omim/" 38 | }, 39 | "clinvar.rcv.conditions.identifiers.efo": { 40 | "@id": "oban:has_property", 41 | "@type": "http://identifiers.org/efo/" 42 | }, 43 | "clinvar.rcv.conditions.identifiers.orphanet": { 44 | "@id": "oban:has_property", 45 | "@type": "http://identifiers.org/orphanet/" 46 | }, 47 | "clinvar.gene.symbol": { 48 | "@id": "oban:has_property", 49 | "@type": "http://identifiers.org/hgnc.symbol/" 50 | }, 51 | "clinvar.gene.id": { 52 | "@id": "oban:has_property", 53 | "@type": "http://identifiers.org/hgnc/" 54 | }, 55 | "dbnsfp.rsid": { 56 | "@id": "oban:has_property", 57 | "@type": "http://identifiers.org/dbsnp/" 58 | }, 59 | "dbnsfp.genename": { 60 | "@id": "oban:has_property", 61 | "@type": "http://identifiers.org/hgnc.symbol/" 62 | }, 63 | "dbnsfp.clinvar.rs": { 64 | "@id": "oban:has_property", 65 | "@type": "http://identifiers.org/dbsnp/" 66 | }, 67 | "dbnsfp.ensembl.geneid": { 68 | "@id": "oban:has_property", 69 | "@type": "http://identifiers.org/ensembl.gene/" 70 | }, 71 | "dbnsfp.ensembl.proteinid": { 72 | "@id": "oban:has_property", 73 | "@type": "http://identifiers.org/ensembl.protein/" 74 | }, 75 | "dbnsfp.ensembl.transcriptid": { 76 | "@id": "oban:has_property", 77 | "@type": "http://identifiers.org/ensembl.transcript" 78 | }, 79 | "dbnsfp.uniprot.acc": { 80 | "@id": "oban:has_property", 81 | "@type": "http://identifiers.org/uniprot/" 82 | }, 83 | "dbsnp.rsid": { 84 | "@id": "oban:has_property", 85 | "@type": "http://identifiers.org/dbsnp/" 86 | }, 87 | "dbsnp.gene.symbol": { 88 | "@id": "oban:has_property", 89 | "@type": "http://identifiers.org/hgnc.symbol/" 90 | }, 91 | "dbsnp.gene.geneid": { 92 | "@id": "oban:has_property", 93 | "@type": "http://identifiers.org/hgnc/" 94 | }, 95 | "docm.ensembl_gene_id": { 96 | "@id": "oban:has_property", 97 | "@type": "http://identifiers.org/ensembl.gene/" 98 | }, 99 | "docm.default_gene_name": { 100 | "@id": "oban:has_property", 101 | "@type": "http://identifiers.org/hgnc.symbol/" 102 | }, 103 | "docm.genename": { 104 | "@id": "oban:has_property", 105 | "@type": "http://identifiers.org/hgnc.symbol/" 106 | }, 107 | "docm.pubmed_id": { 108 | "@id": "oban:has_property", 109 | "@type": "http://identifiers.org/pubmed/" 110 | }, 111 | "emv.gene.symbol": { 112 | "@id": "oban:has_property", 113 | "@type": "http://identifiers.org/hgnc.symbol/" 114 | }, 115 | "emv.gene.id": { 116 | "@id": "oban:has_property", 117 | "@type": "http://identifiers.org/hgnc/" 118 | }, 119 | "evs.rsid": { 120 | "@id": "oban:has_property", 121 | "@type": "http://identifiers.org/dbsnp/" 122 | }, 123 | "evs.gene.symbol": { 124 | "@id": "oban:has_property", 125 | "@type": "http://identifiers.org/hgnc.symbol/" 126 | }, 127 | "evs.gene.accession": { 128 | "@id": "oban:has_property", 129 | "@type": "http://identifiers.org/refseq/" 130 | }, 131 | "grasp.rsid": { 132 | "@id": "oban:has_property", 133 | "@type": "http://identifiers.org/dbsnp/" 134 | }, 135 | "grasp.publication.snpid": { 136 | "@id": "oban:has_property", 137 | "@type": "http://identifiers.org/dbsnp/" 138 | }, 139 | "gwassnps.rsid": { 140 | "@id": "oban:has_property", 141 | "@type": "http://identifiers.org/dbsnp/" 142 | }, 143 | "gwassnps.genename": { 144 | "@id": "oban:has_property", 145 | "@type": "http://identifiers.org/hgnc.symbol/" 146 | }, 147 | "gwassnps.pubmed": { 148 | "@id": "oban:has_property", 149 | "@type": "http://identifiers.org/pubmed/" 150 | }, 151 | "mutdb.rsid": { 152 | "@id": "oban:has_property", 153 | "@type": "http://identifiers.org/dbsnp/" 154 | }, 155 | "snpeff.lof.genename": { 156 | "@id": "oban:has_property", 157 | "@type": "http://identifiers.org/hgnc.symbol/" 158 | }, 159 | "snpeff.ann.genename": { 160 | "@id": "oban:has_property", 161 | "@type": "http://identifiers.org/hgnc.symbol/" 162 | }, 163 | "snpeff.nmd.genename": { 164 | "@id": "oban:has_property", 165 | "@type": "http://identifiers.org/hgnc.symbol/" 166 | } 167 | } 168 | } 169 | -------------------------------------------------------------------------------- /myvariant.info/openapi_full_temp.yml: -------------------------------------------------------------------------------- 1 | openapi: '3.0.0' 2 | info: 3 | version: '1.0' 4 | title: MyVariant.info API 5 | description: >- 6 | Documentation of the MyVariant.info Variant Query web services. Learn more about 7 | [MyVariant.info](http://myvariant.info/) 8 | termsOfService: http://myvariant.info/terms/ 9 | contact: 10 | name: Chunlei Wu 11 | x-role: responsible developer 12 | email: help@myvariant.info 13 | x-id: 'https://github.com/newgene' 14 | x-translator: 15 | component: KP 16 | team: 17 | - Service Provider 18 | servers: 19 | - url: 'http://myvariant.info/v1' 20 | description: 'Production server' 21 | tags: 22 | - name: variant 23 | - name: annotation 24 | - name: query 25 | - name: translator 26 | paths: 27 | /query: 28 | get: 29 | summary: 'Make variant query and return matching variant hits' 30 | parameters: 31 | - name: q 32 | in: query 33 | description: >- 34 | Query string. Examples "rs752396467", "possibly_damaging", "CDK7". 35 | required: true 36 | x-valueType: 37 | - 'http://identifiers.org/hgnc.symbol/' 38 | - 'http://identifiers.org/dbsnp/' 39 | - 'http://identifiers.org/ensembl.gene/' 40 | - 'http://identifiers.org/ensembl.transcript/' 41 | - 'http://identifiers.org/ensembl.protein/' 42 | - 'http://identifiers.org/ccds/' 43 | - 'http://identifiers.org/uniprot/' 44 | - 'http://identifiers.org/clinvar/' 45 | - 'http://identifiers.org/omim/' 46 | - 'http://identifiers.org/efo/' 47 | - 'http://identifiers.org/orphanet/' 48 | - 'http://identifiers.org/hgnc/' 49 | - 'http://identifiers.org/pubmed/' 50 | - 'http://identifiers.org/refseq/' 51 | - 'http://identifiers.org/clinicalsignificance/' 52 | - 'http://biothings.io/terms/drugname/' 53 | x-requestTemplate: 54 | - valueType: 'http://identifiers.org/hgnc.symbol/' 55 | template: cadd.gene.genename:{{input}} OR cgi.gene:{{input}} OR clinvar.gene.symbol:{{input}} OR dbnsfp.genename:{{input}} OR dbsnp.gene.symbol:{{input}} OR docm.genename:{{input}} OR emv.gene:{{input}} OR evs.gene.symbol:{{input}} OR snpeff.ann.genename:{{input}} 56 | - valueType: 'http://identifiers.org/dbsnp/' 57 | template: clinvar.rsid:{{input}} OR dbnsfp.rsid:{{input}} OR dbsnp.rsid:{{input}} OR evs.rsid:{{input}} 58 | - valueType: 'http://identifiers.org/ensembl.gene/' 59 | template: dbnsfp.ensembl.geneid:{{input}} OR cadd.gene.gene_id:{{input}} 60 | - valueType: 'http://identifiers.org/ensembl.transcript' 61 | template: dbnsfp.ensembl.transcriptid:{{input}} OR cadd.gene.feature_id:{{input}} 62 | - valueType: 'http://identifiers.org/ensembl.protein/' 63 | template: dbnsfp.ensembl.proteinid:{{input}} 64 | - valueType: 'http://identifiers.org/ccds/' 65 | template: cadd.gene.ccds_id:{{input}} 66 | - valueType: 'http://identifiers.org/uniprot/' 67 | template: dbnsfp.uniprot.acc:{{input}} 68 | - valueType: 'http://identifiers.org/omim/' 69 | template: clinvar.omim:{{input}} 70 | - valueType: 'http://identifiers.org/efo/' 71 | template: clinvar.rcv.conditions.identifiers.efo:{{input}} 72 | - valueType: 'http://identifiers.org/orphanet/' 73 | template: clinvar.rcv.conditions.identifiers.orphanet:{{input}} 74 | - valueType: 'http://identifiers.org/hgnc/' 75 | template: clinvar.gene.id:{{input}} OR dbsnp.gene.geneid:{{input}} 76 | - valueType: 'http://identifiers.org/pubmed/' 77 | template: civic.evidence_items.source.pubmed_id:{{input}} OR docm.pubmed_id:{{input}} OR gwassnps.pubmed:{{input}} 78 | - valueType: 'http://identifiers.org/clinicalsignificance/' 79 | template: clinvar.rcv.clinical_significance:{{input}} 80 | - valueType: 'http://biothings.io/terms/drugname/' 81 | template: civic.evidence_items.drugs.name:{{input}} 82 | schema: 83 | type: string 84 | responses: 85 | '200': 86 | description: 'A query response object with "hits" property' 87 | x-responseValueType: 88 | - path: _id 89 | valueType: 'http://identifiers.org/hgvs/' 90 | x-JSONLDContext: 91 | 'https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/myvariant.info/jsonld_context/myvariant_query_1.1.json' 92 | '/variant/{variantid}': 93 | get: 94 | summary: 'For a given variant id, return the matching variant object' 95 | parameters: 96 | - name: variantid 97 | in: path 98 | description: >- 99 | Variant HGVS ID, dbSNP ID 100 | required: true 101 | x-valueType: 102 | - 'http://identifiers.org/hgvs/' 103 | - 'http://identifiers.org/dbsnp/' 104 | x-requestTemplate: 105 | - valueType: 'http://identifiers.org/hgvs/' 106 | template: /variant/{{input}} 107 | - valueType: 'http://identifiers.org/dbsnp/' 108 | template: /variant/{{input}} 109 | schema: 110 | type: string 111 | responses: 112 | '200': 113 | description: 'A variant object' 114 | x-responseValueType: 115 | - path: cadd.gene.genename 116 | valueType: 'http://identifiers.org/hgnc.symbol/' 117 | - path: clinvar.rsid 118 | valueType: 'http://identifiers.org/dbsnp/' 119 | - path: cadd.gene.gene_id 120 | valueType: 'http://identifiers.org/ensembl.gene/' 121 | - path: cadd.gene.feature_id 122 | valueType: 'http://identifiers.org/ensembl.transcript/' 123 | - path: cadd.gene.ccds_id 124 | valueType: 'http://identifiers.org/ccds/' 125 | - path: clinvar.uniprot 126 | valueType: 'http://identifiers.org/uniprot/' 127 | - path: clinvar.rcv.accession 128 | valueType: 'http://identifiers.org/clinvar/' 129 | - path: clinvar.rcv.conditions.identifiers.omim 130 | valueType: 'http://identifiers.org/omim/' 131 | - path: clinvar.rcv.conditions.identifiers.efo 132 | valueType: 'http://identifiers.org/efo/' 133 | - path: clinvar.rcv.conditions.identifiers.orphanet 134 | valueType: 'http://identifiers.org/orphanet/' 135 | - path: clinvar.gene.id 136 | valueType: 'http://identifiers.org/hgnc/' 137 | - path: dbnsfp.ensembl.proteinid 138 | valueType: 'http://identifiers.org/ensembl.protein/' 139 | - path: docm.pubmed_id 140 | valueType: 'http://identifiers.org/pubmed/' 141 | - path: evs.gene.accession 142 | valueType: 'http://identifiers.org/refseq/' 143 | - path: clinvar.rcv.clinical_significance 144 | valueType: 'http://identifiers.org/clinicalsignificance/' 145 | - path: civic.evidence_items 146 | valueType: 'http://biothings.io/concepts/clinical_evidence/' 147 | - path: civic.evidence_items.drugs.name 148 | valueType: 'http://biothings.io/terms/drugname/' 149 | x-JSONLDContext: 150 | 'https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/myvariant.info/jsonld_context/myvariant_variant_1.1.json' 151 | -------------------------------------------------------------------------------- /myvariant.info/openapi_minimum.yml: -------------------------------------------------------------------------------- 1 | openapi: '3.0.0' 2 | info: 3 | version: '1.0' 4 | title: MyVariant.info API 5 | description: >- 6 | Documentation of the MyVariant.info Variant Query web services. Learn more about 7 | [MyVariant.info](http://myvariant.info/) 8 | termsOfService: http://myvariant.info/terms/ 9 | contact: 10 | name: Chunlei Wu 11 | x-role: responsible developer 12 | email: help@myvariant.info 13 | x-id: 'https://github.com/newgene' 14 | x-translator: 15 | component: KP 16 | team: 17 | - Service Provider 18 | servers: 19 | - url: 'http://myvariant.info/v1' 20 | description: 'Production server' 21 | tags: 22 | - name: variant 23 | - name: annotation 24 | - name: query 25 | - name: translator 26 | paths: 27 | /query: 28 | get: 29 | summary: 'Make variant query and return matching variant hits' 30 | parameters: 31 | - name: q 32 | in: query 33 | description: >- 34 | Query string. Examples "rs752396467", "possibly_damaging", "CDK7". 35 | required: true 36 | x-valueType: 37 | - 'http://identifiers.org/hgnc.symbol/' 38 | - 'http://identifiers.org/dbsnp/' 39 | - 'http://identifiers.org/ensembl.gene/' 40 | - 'http://identifiers.org/ensembl.transcript/' 41 | - 'http://identifiers.org/ensembl.protein/' 42 | - 'http://identifiers.org/ccds/' 43 | - 'http://identifiers.org/uniprot/' 44 | - 'http://identifiers.org/clinvar/' 45 | - 'http://identifiers.org/omim/' 46 | - 'http://identifiers.org/efo/' 47 | - 'http://identifiers.org/orphanet/' 48 | - 'http://identifiers.org/hgnc/' 49 | - 'http://identifiers.org/pubmed/' 50 | - 'http://identifiers.org/refseq/' 51 | - 'http://identifiers.org/clinicalsignificance/' 52 | schema: 53 | type: string 54 | responses: 55 | '200': 56 | description: 'A query response object with "hits" property' 57 | x-responseValueType: 58 | - path: _id 59 | valueType: 'http://identifiers.org/hgvs/' 60 | - path: cadd.gene.genename 61 | valueType: 'http://identifiers.org/hgnc.symbol/' 62 | - path: clinvar.rsid 63 | valueType: 'http://identifiers.org/dbsnp/' 64 | - path: cadd.gene.gene_id 65 | valueType: 'http://identifiers.org/ensembl.gene/' 66 | - path: cadd.gene.feature_id 67 | valueType: 'http://identifiers.org/ensembl.transcript/' 68 | - path: cadd.gene.ccds_id 69 | valueType: 'http://identifiers.org/ccds/' 70 | - path: clinvar.uniprot 71 | valueType: 'http://identifiers.org/uniprot/' 72 | - path: clinvar.omim 73 | valueType: 'http://identifiers.org/omim/' 74 | - path: clinvar.rcv.accession 75 | valueType: 'http://identifiers.org/clinvar/' 76 | - path: clinvar.rcv.conditions.identifiers.omim 77 | valueType: 'http://identifiers.org/omim/' 78 | - path: clinvar.rcv.conditions.identifiers.efo 79 | valueType: 'http://identifiers.org/efo/' 80 | - path: clinvar.rcv.conditions.identifiers.orphanet 81 | valueType: 'http://identifiers.org/orphanet/' 82 | - path: clinvar.gene.id 83 | valueType: 'http://identifiers.org/hgnc/' 84 | - path: dbnsfp.ensembl.proteinid 85 | valueType: 'http://identifiers.org/ensembl.protein/' 86 | - path: docm.pubmed_id 87 | valueType: 'http://identifiers.org/pubmed/' 88 | - path: evs.gene.accession 89 | valueType: 'http://identifiers.org/refseq/' 90 | - path: clinvar.rcv.clinical_significance 91 | valueType: 'http://identifiers.org/clinicalsignificance/' 92 | x-JSONLDContext: 93 | https://github.com/NCATS-Tangerine/translator-api-registry/blob/master/myvariant.info/jsonld_context/myvariant_context.json 94 | '/variant/{variantid}': 95 | get: 96 | summary: 'For a given variant id, return the matching variant object' 97 | parameters: 98 | - name: variantid 99 | in: path 100 | description: >- 101 | Variant HGVS ID, dbSNP ID 102 | required: true 103 | x-valueType: 104 | - 'http://identifiers.org/hgvs/' 105 | - 'http://identifiers.org/dbsnp/' 106 | schema: 107 | type: string 108 | responses: 109 | '200': 110 | description: 'A variant object' 111 | x-responseValueType: 112 | - path: cadd.gene.genename 113 | valueType: 'http://identifiers.org/hgnc.symbol/' 114 | - path: clinvar.rsid 115 | valueType: 'http://identifiers.org/dbsnp/' 116 | - path: cadd.gene.gene_id 117 | valueType: 'http://identifiers.org/ensembl.gene/' 118 | - path: cadd.gene.feature_id 119 | valueType: 'http://identifiers.org/ensembl.transcript/' 120 | - path: cadd.gene.ccds_id 121 | valueType: 'http://identifiers.org/ccds/' 122 | - path: clinvar.uniprot 123 | valueType: 'http://identifiers.org/uniprot/' 124 | - path: clinvar.rcv.accession 125 | valueType: 'http://identifiers.org/clinvar/' 126 | - path: clinvar.rcv.conditions.identifiers.omim 127 | valueType: 'http://identifiers.org/omim/' 128 | - path: clinvar.rcv.conditions.identifiers.efo 129 | valueType: 'http://identifiers.org/efo/' 130 | - path: clinvar.rcv.conditions.identifiers.orphanet 131 | valueType: 'http://identifiers.org/orphanet/' 132 | - path: clinvar.gene.id 133 | valueType: 'http://identifiers.org/hgnc/' 134 | - path: dbnsfp.ensembl.proteinid 135 | valueType: 'http://identifiers.org/ensembl.protein/' 136 | - path: docm.pubmed_id 137 | valueType: 'http://identifiers.org/pubmed/' 138 | - path: evs.gene.accession 139 | valueType: 'http://identifiers.org/refseq/' 140 | - path: clinvar.rcv.clinical_significance 141 | valueType: 'http://identifiers.org/clinicalsignificance/' 142 | x-JSONLDContext: 143 | 'https://github.com/NCATS-Tangerine/translator-api-registry/blob/master/myvariant.info/jsonld_context/myvariant_context.json' 144 | -------------------------------------------------------------------------------- /ols/smartapi.yaml: -------------------------------------------------------------------------------- 1 | openapi: 3.0.3 2 | info: 3 | version: '1.0' 4 | title: Ontology Lookup Service API 5 | description: >- 6 | The OLS REST API provides access to key biological data from OLS. 7 | The services provide a unified interface to query information about ontology terms 8 | from GO (the Gene Ontology) and ECO (the Evidence & Conclusion Ontology), Gene 9 | Ontology annotations from the EBI's GOA database, and gene products (proteins 10 | from UniProt, RNA from RNAcentral and complexes from ComplexPortal). 11 | See https://www.ebi.ac.uk/ols/docs/api for more details. 12 | termsOfService: https://www.ebi.ac.uk/OLS/services 13 | contact: 14 | name: pharmgkb help desk 15 | x-role: responsible developer 16 | email: help@pharmgkb.org 17 | x-translator: 18 | infores: "infores:ols" 19 | component: KP 20 | team: 21 | - Service Provider 22 | biolink-version: "4.2.2" 23 | servers: 24 | - url: https://www.ebi.ac.uk/ols/api 25 | description: Production server 26 | x-maturity: production 27 | tags: 28 | - name: ontology 29 | - name: translator 30 | paths: 31 | "/ontologies/doid/children": 32 | get: 33 | summary: retrieve the children of specified ontology terms 34 | parameters: 35 | - name: id 36 | in: query 37 | description: Put Disease Ontology ID here, e.g. "DOID:0050686" 38 | required: true 39 | example: "DOID:0050686" 40 | schema: 41 | type: string 42 | responses: 43 | '200': 44 | description: A DISEASE Ontology annotation object 45 | x-bte-kgs-operations: 46 | - "$ref": "#/components/x-bte-kgs-operations/disease_has_subclass_disease" 47 | components: 48 | x-bte-kgs-operations: 49 | ## BIG NOTE: there is likely more data in this API, but want to add stuff that would be helpful for use cases, that we regularly update 50 | disease_has_subclass_disease: 51 | - supportBatch: false ## no batch support (get operation) 52 | useTemplating: true 53 | inputs: 54 | - id: DOID 55 | semantic: Disease 56 | parameters: 57 | id: "{{ queryInputs }}" ## HAS PREFIX (DOID) 58 | outputs: 59 | - id: DOID 60 | semantic: Disease 61 | predicate: superclass_of ## this is current biolink, same meaning as "has_subclass" 62 | source: "infores:disease-ontology" 63 | knowledge_level: knowledge_assertion 64 | agent_type: manual_agent 65 | response_mapping: 66 | "$ref": "#/components/x-bte-response-mapping/disease_has_subclass_disease" 67 | testExamples: 68 | - qInput: "DOID:10123" ## skin pigmentation disorder 69 | oneOutput: "MONDO:0007483" ## dyschromatosis symmetrica hereditaria 70 | x-bte-response-mapping: 71 | disease_has_subclass_disease: 72 | DOID: _embedded.terms.obo_id ## HAS PREFIX (DOID) 73 | -------------------------------------------------------------------------------- /openfda/jsonld_context/openfda_context.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context": { 3 | "results.patient.reaction.reactionmeddrapt": { 4 | "@type": "http://identifiers.org/drug_effect/", 5 | "@id": "oban:has_adverse_effect" 6 | }, 7 | "results.patient.drug.openfda.pharm_class_cs": { 8 | "@type": "http://identifiers.org/pharm_class/", 9 | "@id": "oban:belongs_to" 10 | } 11 | } 12 | } -------------------------------------------------------------------------------- /opentarget/smartapi.yaml: -------------------------------------------------------------------------------- 1 | openapi: 3.0.0 2 | info: 3 | version: '3.0' 4 | title: OpenTarget API 5 | description: The Opentarget API 6 | termsOfService: http://www.opentarget.org 7 | contact: 8 | name: opentarget help desk 9 | x-role: responsible developer 10 | email: help@opentarget.org 11 | x-translator: 12 | infores: "infores:open-target" 13 | component: KP 14 | team: 15 | - Service Provider 16 | biolink-version: "2.1.0" 17 | servers: 18 | - url: https://platform-api.opentargets.io/v3 19 | description: Production server 20 | x-maturity: production 21 | tags: 22 | - name: translator 23 | - name: opentarget 24 | paths: 25 | "/platform/public/evidence/filter": 26 | get: 27 | summary: retrieve evidence 28 | parameters: 29 | - name: target 30 | in: query 31 | description: ensembl gene id 32 | required: true 33 | example: ENSG00000088832 34 | schema: 35 | type: string 36 | - name: size 37 | in: query 38 | description: size of the output 39 | example: 100 40 | schema: 41 | type: integer 42 | - name: fields 43 | in: query 44 | description: the output field 45 | example: drug 46 | schema: 47 | type: string 48 | - name: datasource 49 | in: query 50 | description: the data source 51 | example: chembl 52 | schema: 53 | type: string 54 | responses: 55 | '200': 56 | description: A biosample object 57 | x-bte-kgs-operations: 58 | - "$ref": "#/components/x-bte-kgs-operations/gene_related_to_chemical" 59 | components: 60 | x-bte-kgs-operations: 61 | gene_related_to_chemical: 62 | - inputs: 63 | - id: ENSEMBL 64 | semantic: Gene 65 | outputs: 66 | - id: CHEMBL.COMPOUND 67 | semantic: SmallMolecule 68 | predicate: related_to 69 | source: "infores:chembl" 70 | parameters: 71 | target: "{inputs[0]}" 72 | datasource: chembl 73 | size: 100 74 | fields: drug 75 | supportBatch: false 76 | response_mapping: 77 | "$ref": "#/components/x-bte-response-mapping/gene_related_to_chemical" 78 | x-bte-response-mapping: 79 | gene_related_to_chemical: 80 | CHEMBL.COMPOUND: data.drug.id 81 | moleculeType: data.drug.molecule_type 82 | name: data.drug.molecule_name 83 | -------------------------------------------------------------------------------- /pharos/smartapi.yaml: -------------------------------------------------------------------------------- 1 | openapi: 3.0.0 2 | info: 3 | contact: 4 | email: help@renci.org 5 | name: Chris B. 6 | description: Scibite 7 | termsOfService: https://automat.renci.org 8 | title: Automat PHAROS API 9 | version: '2.0' 10 | x-translator: 11 | component: KP 12 | team: 13 | - Ranking Agent 14 | servers: 15 | - description: Production server 16 | url: https://automat.renci.org/pharos 17 | tags: 18 | - name: drug 19 | - name: gene 20 | - name: disease 21 | - name: automat 22 | - name: translator 23 | paths: 24 | "/gene/chemical_substance/{geneid}": 25 | get: 26 | summary: gene2chemical 27 | parameters: 28 | - description: Put NCBIGENE ID here, e.g. 1017 29 | example: NCBIGENE:1017 30 | in: path 31 | name: geneid 32 | required: true 33 | schema: 34 | type: string 35 | responses: 36 | '200': 37 | description: An association object 38 | x-bte-kgs-operations: 39 | - "$ref": "#/components/x-bte-kgs-operations/gene2chemical" 40 | "/gene/disease/{geneid}": 41 | get: 42 | summary: gene2disease 43 | parameters: 44 | - description: Put NCBIGENE ID here, e.g. 1017 45 | example: NCBIGENE:1017 46 | in: path 47 | name: geneid 48 | required: true 49 | schema: 50 | type: string 51 | responses: 52 | '200': 53 | description: An association object 54 | x-bte-kgs-operations: 55 | - "$ref": "#/components/x-bte-kgs-operations/gene2disease" 56 | "/chemical_substance/disease/{chebi}": 57 | get: 58 | summary: chemical2disease 59 | parameters: 60 | - description: Put CHEBI ID here, e.g. "CHEBI:661" 61 | example: CHEBI:661 62 | in: path 63 | name: chebi 64 | required: true 65 | schema: 66 | type: string 67 | responses: 68 | '200': 69 | description: An association object 70 | x-bte-kgs-operations: 71 | - "$ref": "#/components/x-bte-kgs-operations/chemical2disease" 72 | "/chemical_substance/gene/{chebi}": 73 | get: 74 | summary: chemical2gene 75 | parameters: 76 | - description: Put CHEBI ID here, e.g. "CHEBI:661" 77 | example: CHEBI:661 78 | in: path 79 | name: chebi 80 | required: true 81 | schema: 82 | type: string 83 | responses: 84 | '200': 85 | description: An association object 86 | x-bte-kgs-operations: 87 | - "$ref": "#/components/x-bte-kgs-operations/chemical2gene" 88 | "/disease/gene/{mondo}": 89 | get: 90 | summary: disease2gene 91 | parameters: 92 | - description: Put DOID ID here, e.g. "DOID:123" 93 | example: DOID:123 94 | in: path 95 | name: mondo 96 | required: true 97 | schema: 98 | type: string 99 | responses: 100 | '200': 101 | description: An association object 102 | x-bte-kgs-operations: 103 | - "$ref": "#/components/x-bte-kgs-operations/disease2gene" 104 | "/disease/chemical_substance/{mondo}": 105 | get: 106 | summary: disease2chemical 107 | parameters: 108 | - description: Put DOID ID here, e.g. "DOID:123" 109 | example: DOID:123 110 | in: path 111 | name: mondo 112 | required: true 113 | schema: 114 | type: string 115 | responses: 116 | '200': 117 | description: An association object 118 | x-bte-kgs-operations: 119 | - "$ref": "#/components/x-bte-kgs-operations/disease2chemical" 120 | components: 121 | x-bte-kgs-operations: 122 | gene2chemical: 123 | - inputs: 124 | - id: NCBIGENE 125 | semantic: Gene 126 | outputs: 127 | - id: CHEMBL.COMPOUND 128 | semantic: ChemicalSubstance 129 | predicate: related_to 130 | source: pharos 131 | parameters: 132 | geneid: NCBIGENE:{inputs[0]} 133 | supportBatch: false 134 | response_mapping: 135 | "$ref": "#/components/x-bte-response-mapping/gene2chemical-chembl" 136 | - inputs: 137 | - id: NCBIGENE 138 | semantic: Gene 139 | outputs: 140 | - id: CHEBI 141 | semantic: ChemicalSubstance 142 | predicate: related_to 143 | source: pharos 144 | parameters: 145 | geneid: NCBIGENE:{inputs[0]} 146 | supportBatch: false 147 | response_mapping: 148 | "$ref": "#/components/x-bte-response-mapping/gene2chemical-chebi" 149 | gene2disease: 150 | - inputs: 151 | - id: NCBIGENE 152 | semantic: Gene 153 | outputs: 154 | - id: DOID 155 | semantic: Disease 156 | predicate: related_to 157 | source: pharos 158 | parameters: 159 | geneid: NCBIGENE:{inputs[0]} 160 | supportBatch: false 161 | response_mapping: 162 | "$ref": "#/components/x-bte-response-mapping/gene2disease-doid" 163 | - inputs: 164 | - id: NCBIGENE 165 | semantic: Gene 166 | outputs: 167 | - id: MONDO 168 | semantic: Disease 169 | predicate: related_to 170 | source: pharos 171 | parameters: 172 | geneid: NCBIGENE:{inputs[0]} 173 | supportBatch: false 174 | response_mapping: 175 | "$ref": "#/components/x-bte-response-mapping/gene2disease-mondo" 176 | chemical2gene: 177 | - inputs: 178 | - id: CHEBI 179 | semantic: ChemicalSubstance 180 | outputs: 181 | - id: NCBIGENE 182 | semantic: Gene 183 | predicate: related_to 184 | source: pharos 185 | parameters: 186 | chebi: "{inputs[0]}" 187 | supportBatch: false 188 | response_mapping: 189 | "$ref": "#/components/x-bte-response-mapping/chemical2gene" 190 | chemical2disease: 191 | - inputs: 192 | - id: CHEBI 193 | semantic: ChemicalSubstance 194 | outputs: 195 | - id: DOID 196 | semantic: Disease 197 | predicate: related_to 198 | source: pharos 199 | parameters: 200 | chebi: "{inputs[0]}" 201 | supportBatch: false 202 | response_mapping: 203 | "$ref": "#/components/x-bte-response-mapping/chemical2disease-doid" 204 | - inputs: 205 | - id: CHEBI 206 | semantic: ChemicalSubstance 207 | outputs: 208 | - id: MONDO 209 | semantic: Disease 210 | predicate: related_to 211 | source: pharos 212 | parameters: 213 | chebi: "{inputs[0]}" 214 | supportBatch: false 215 | response_mapping: 216 | "$ref": "#/components/x-bte-response-mapping/chemical2disease-mondo" 217 | disease2gene: 218 | - inputs: 219 | - id: MONDO 220 | semantic: Disease 221 | outputs: 222 | - id: NCBIGENE 223 | semantic: Gene 224 | predicate: related_to 225 | source: pharos 226 | parameters: 227 | mondo: "{inputs[0]}" 228 | supportBatch: false 229 | response_mapping: 230 | "$ref": "#/components/x-bte-response-mapping/disease2gene" 231 | disease2chemical: 232 | - inputs: 233 | - id: MONDO 234 | semantic: Disease 235 | outputs: 236 | - id: CHEMBL.COMPOUND 237 | semantic: ChemicalSubstance 238 | predicate: related_to 239 | source: pharos 240 | parameters: 241 | mondo: "{inputs[0]}" 242 | supportBatch: false 243 | response_mapping: 244 | "$ref": "#/components/x-bte-response-mapping/disease2chemical-chembl" 245 | - inputs: 246 | - id: MONDO 247 | semantic: Disease 248 | outputs: 249 | - id: CHEBI 250 | semantic: ChemicalSubstance 251 | predicate: related_to 252 | source: pharos 253 | parameters: 254 | mondo: "{inputs[0]}" 255 | supportBatch: false 256 | response_mapping: 257 | "$ref": "#/components/x-bte-response-mapping/disease2chemical-chebi" 258 | x-bte-response-mapping: 259 | gene2chemical-chebi: 260 | CHEBI: associated_with.chebi 261 | gene2chemical-chembl: 262 | CHEMBL.COMPOUND: associated_with.chembl 263 | gene2disease-mondo: 264 | MONDO: associated_with.mondo 265 | gene2disease-doid: 266 | DOID: associated_with.doid 267 | chemical2disease-mondo: 268 | MONDO: associated_with.mondo 269 | chemical2disease-doid: 270 | DOID: associated_with.doid 271 | chemical2gene: 272 | NCBIGENE: associated_with.ncbigene 273 | disease2gene: 274 | NCBIGENE: associated_with.ncbigene 275 | disease2chemical-chembl: 276 | CHEMBL.COMPOUND: associated_with.chembl 277 | disease2chemical-chebi: 278 | CHEBI: associated_with.chebi 279 | -------------------------------------------------------------------------------- /quickgo/smartapi.yaml: -------------------------------------------------------------------------------- 1 | openapi: 3.0.3 2 | info: 3 | version: '1.0' 4 | title: QuickGO API 5 | description: >- 6 | The QuickGO REST API provides access to key biological data from QuickGO 7 | and GOA. The services provide a unified interface to query information about ontology 8 | terms from GO (the Gene Ontology) and ECO (the Evidence & Conclusion Ontology), 9 | Gene Ontology annotations from the EBI's GOA database, and gene products (proteins 10 | from UniProt, RNA from RNAcentral and complexes from ComplexPortal). 11 | See https://www.ebi.ac.uk/QuickGO/api/index.html for more details. 12 | termsOfService: https://www.ebi.ac.uk/QuickGO/services 13 | contact: 14 | name: pharmgkb help desk 15 | x-role: responsible developer 16 | email: help@pharmgkb.org 17 | x-translator: 18 | infores: "infores:ebi-quick-go" 19 | component: KP 20 | team: 21 | - Service Provider 22 | biolink-version: "4.2.2" 23 | servers: 24 | - url: https://www.ebi.ac.uk/QuickGO/services 25 | description: Production server 26 | x-maturity: production 27 | tags: 28 | - name: ontology 29 | - name: translator 30 | paths: 31 | "/ontology/go/terms/{goid}/children": 32 | get: 33 | summary: retrieve the children of specified ontology terms 34 | parameters: 35 | - name: goid 36 | in: path 37 | description: Put Gene Ontology ID here, e.g. "GO:0000082" 38 | required: true 39 | example: "GO:0000082" 40 | schema: 41 | type: string 42 | responses: 43 | '200': 44 | description: A gene ontology annotation object 45 | x-bte-kgs-operations: 46 | - "$ref": "#/components/x-bte-kgs-operations/ma_has_subclass_ma" 47 | components: 48 | x-bte-kgs-operations: 49 | ## BIG NOTE: there is likely more data in this API, but want to add stuff that would be helpful for use cases, that we regularly update 50 | ma_has_subclass_ma: 51 | - supportBatch: false 52 | useTemplating: true 53 | inputs: 54 | - id: GO 55 | semantic: MolecularActivity 56 | parameters: 57 | goid: "{{ queryInputs | replPrefix('GO') }}" ## has prefix (GO) 58 | outputs: 59 | - id: GO 60 | semantic: MolecularActivity 61 | predicate: superclass_of ## this is current biolink, same meaning as "has_subclass" 62 | source: "infores:go" 63 | knowledge_level: knowledge_assertion 64 | agent_type: manual_agent 65 | response_mapping: 66 | "$ref": "#/components/x-bte-response-mapping/ma_has_subclass_ma" 67 | testExamples: 68 | - qInput: "GO:0000082" ## G1/S transition of mitotic cell cycle 69 | oneOutput: "GO:2000045" ## regulation of G1/S transition of mitotic cell cycle 70 | x-bte-response-mapping: 71 | ma_has_subclass_ma: 72 | GO: results.children.id ## has prefix (GO) 73 | ## commenting out because data-processing / biolink-modeling issues 74 | # "biolink:original_predicate": results.children.relation 75 | -------------------------------------------------------------------------------- /reactome/jsonld_context/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/4c76bc60d3a8dbdb7d8a761d2f988be9088cab67/reactome/jsonld_context/.DS_Store -------------------------------------------------------------------------------- /reactome/jsonld_context/protein_interaction_context.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context": { 3 | "entities.interactors.acc": { 4 | "@id": "oban: interacts with", 5 | "@type": "http://identifiers.org/uniprot/" 6 | } 7 | } 8 | } -------------------------------------------------------------------------------- /reactome/jsonld_context/reactome_context.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context": { 3 | "BlackBoxEvent": { 4 | "@id": "oban:has_black_box_event", 5 | "@type": "http://identifiers.org/reactome/" 6 | }, 7 | "Pathway": { 8 | "@id": "oban:has_pathway", 9 | "@type": "http://identifiers.org/reactome/" 10 | } 11 | }, 12 | "Reaction": { 13 | "@id": "oban:has_reaction", 14 | "@type": "http://identifiers.org/reactome/" 15 | } 16 | } 17 | } -------------------------------------------------------------------------------- /reactome/jsonld_context/reactome_lower_context.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context": { 3 | "stId": { 4 | "@id": "oban:has_lower_pathway", 5 | "@type": "http://identifiers.org/reactome/" 6 | }, 7 | "displayName": { 8 | "@id": "oban: has_lower_pathway", 9 | "@type": "http://identifiers.org/pathway.name/" 10 | } 11 | } 12 | } -------------------------------------------------------------------------------- /robokop_extend/smartapi.yaml: -------------------------------------------------------------------------------- 1 | openapi: '3.0.0' 2 | info: 3 | version: "1.0" 4 | contact: 5 | email: patrick@covar.com 6 | name: Patrick Wang 7 | url: robokop.renci.org 8 | description: An API for answering biomedical questions 9 | termsOfService: https://robokop.renci.org/termsofservice/ 10 | title: ROBOKOP 11 | servers: 12 | - url: 'https://robokop.renci.org/api' 13 | description: 'Production server' 14 | tags: 15 | - name: translator 16 | - name: reasoner 17 | 18 | paths: 19 | '/simple/expand/chemical_substance/{chemical_id}/disease_or_phenotypic_feature/': 20 | get: 21 | summary: 'retrieve diseases related to chemical' 22 | parameters: 23 | - name: chemical_id 24 | in: path 25 | description: >- 26 | chembl id 27 | required: true 28 | example: "CHEMBL:CHEMBL744" 29 | schema: 30 | type: string 31 | responses: 32 | '200': 33 | description: 'A association object' 34 | x-bte-response-mapping: 35 | $ref: '#/components/x-bte-response-mapping/chemical-disease' 36 | x-bte-kgs-operations: 37 | treats: 38 | $ref: '#/components/x-bte-kgs-operations/treats' 39 | contraindication: 40 | $ref: '#/components/x-bte-kgs-operations/contraindication' 41 | '/simple/expand/gene/{gene_id}/gene_family/': 42 | get: 43 | summary: 'retrieve gene family related to gene' 44 | parameters: 45 | - name: gene_id 46 | in: path 47 | description: >- 48 | hgnc id 49 | required: true 50 | example: "HGNC:1771" 51 | schema: 52 | type: string 53 | responses: 54 | '200': 55 | description: 'A association object' 56 | x-bte-response-mapping: 57 | $ref: '#/components/x-bte-response-mapping/gene-genefamily' 58 | x-bte-kgs-operations: 59 | partOf: 60 | $ref: '#/components/x-bte-kgs-operations/partOf' 61 | '/simple/expand/gene/{gene_id}/chemical_substance/': 62 | get: 63 | summary: 'retrieve chemicals related to gene' 64 | parameters: 65 | - name: gene_id 66 | in: path 67 | description: >- 68 | hgnc id 69 | required: true 70 | example: "HGNC:1771" 71 | schema: 72 | type: string 73 | responses: 74 | '200': 75 | description: 'A association object' 76 | x-bte-response-mapping: 77 | $ref: '#/components/x-bte-response-mapping/gene-chemical' 78 | x-bte-kgs-operations: 79 | associatedWith: 80 | $ref: '#/components/x-bte-kgs-operations/associatedWith' 81 | components: 82 | x-bte-kgs-operations: 83 | treats: 84 | inputs: 85 | - id: chembl 86 | semantic: ChemicalSubstance 87 | outputs: 88 | - id: mondo 89 | semantic: DiseaseOrPhenotypicFeature 90 | parameters: 91 | chemical_id: "CHEMBL:{input1}" 92 | supportBatch: false 93 | response-mapping: 94 | $ref: '#/components/x-bte-response-mapping/chemical-disease' 95 | contraindication: 96 | inputs: 97 | - id: chembl 98 | semantic: ChemicalSubstance 99 | outputs: 100 | - id: mondo 101 | semantic: DiseaseOrPhenotypicFeature 102 | parameters: 103 | chemical_id: "CHEMBL:{input1}" 104 | supportBatch: false 105 | response-mapping: 106 | $ref: '#/components/x-bte-response-mapping/chemical-disease' 107 | partOf: 108 | inputs: 109 | - id: hgnc 110 | semantic: Gene 111 | outputs: 112 | - id: panther 113 | semantic: GeneFamily 114 | parameters: 115 | chemical_id: "HGNC:{input1}" 116 | supportBatch: false 117 | response-mapping: 118 | $ref: '#/components/x-bte-response-mapping/gene-genefamily' 119 | associatedWith: 120 | inputs: 121 | - id: hgnc 122 | semantic: Gene 123 | outputs: 124 | - id: chembl 125 | semantic: ChemicalSubstance 126 | parameters: 127 | chemical_id: "HGNC:{input1}" 128 | supportBatch: false 129 | response-mapping: 130 | $ref: '#/components/x-bte-response-mapping/gene-chemical' 131 | x-bte-response-mapping: 132 | chemical-disease: 133 | "@context": http://schema.org 134 | "@type": ChemicalSubstance 135 | bts:chembl: treats.source_id 136 | bts:treats: 137 | "@type": DiseaseOrPhenotypicFeature 138 | bts:mondo: treats.mondo 139 | bts:source: treats.source_database 140 | bts:pubmed: treats.publications 141 | "$input": bts:chembl 142 | "$source": robokop 143 | bts:contraindication: 144 | "@type": DiseaseOrPhenotypicFeature 145 | bts:mondo: contraindicated_for.mondo 146 | bts:source: contraindicated_for.source_database 147 | bts:pubmed: contraindicated_for.publications 148 | "$input": bts:chembl 149 | "$source": robokop 150 | gene-genefamily: 151 | "@context": http://schema.org 152 | "@type": Gene 153 | bts:hgnc: part_of.source_id 154 | bts:partOf: 155 | "@type": GeneFamily 156 | bts:panther: part_of.panther 157 | bts:source: part_of.source_database 158 | bts:pubmed: part_of.publications 159 | "$input": bts:hgnc 160 | "$source": panther 161 | gene-chemical: 162 | "@context": http://schema.org 163 | "@type": Gene 164 | bts:hgnc: literature_co-occurrence.source_id 165 | bts:associatedWith: 166 | "@type": ChemicalSubstance 167 | bts:chembl: literature_co-occurrence.chembl 168 | bts:source: literature_co-occurrence.source_database 169 | "$input": bts:hgnc 170 | "$source": robokop 171 | -------------------------------------------------------------------------------- /scibite/smartapi.yml: -------------------------------------------------------------------------------- 1 | --- 2 | openapi: 3.0.0 3 | info: 4 | contact: 5 | email: help@renci.org 6 | name: Chris B. 7 | description: Scibite 8 | termsOfService: https://automat.renci.org 9 | title: Automat CORD19 Scibite API 10 | version: '2.0' 11 | x-translator: 12 | component: KP 13 | team: 14 | - Ranking Agent 15 | servers: 16 | - description: Production server 17 | url: https://automat.renci.org/cord19-scibite 18 | tags: 19 | - name: drug 20 | - name: gene 21 | - name: disease 22 | - name: automat 23 | - name: translator 24 | paths: 25 | "/gene/chemical_substance/{geneid}": 26 | get: 27 | summary: gene2chemical 28 | parameters: 29 | - description: Put NCBIGENE ID here, e.g. 1017 30 | example: NCBIGENE:1017 31 | in: path 32 | name: geneid 33 | required: true 34 | schema: 35 | type: string 36 | responses: 37 | '200': 38 | description: An association object 39 | x-bte-kgs-operations: 40 | - "$ref": "#/components/x-bte-kgs-operations/gene2chemical" 41 | "/gene/disease/{geneid}": 42 | get: 43 | summary: gene2disease 44 | parameters: 45 | - description: Put NCBIGENE ID here, e.g. 1017 46 | example: NCBIGENE:1017 47 | in: path 48 | name: geneid 49 | required: true 50 | schema: 51 | type: string 52 | responses: 53 | '200': 54 | description: An association object 55 | x-bte-kgs-operations: 56 | - "$ref": "#/components/x-bte-kgs-operations/gene2disease" 57 | "/chemical_substance/disease/{chebi}": 58 | get: 59 | summary: chemical2disease 60 | parameters: 61 | - description: Put CHEBI ID here, e.g. "CHEBI:661" 62 | example: CHEBI:661 63 | in: path 64 | name: chebi 65 | required: true 66 | schema: 67 | type: string 68 | responses: 69 | '200': 70 | description: An association object 71 | x-bte-kgs-operations: 72 | - "$ref": "#/components/x-bte-kgs-operations/chemical2disease" 73 | "/chemical_substance/gene/{chebi}": 74 | get: 75 | summary: chemical2gene 76 | parameters: 77 | - description: Put CHEBI ID here, e.g. "CHEBI:661" 78 | example: CHEBI:661 79 | in: path 80 | name: chebi 81 | required: true 82 | schema: 83 | type: string 84 | responses: 85 | '200': 86 | description: An association object 87 | x-bte-kgs-operations: 88 | - "$ref": "#/components/x-bte-kgs-operations/chemical2gene" 89 | "/disease/gene/{mondo}": 90 | get: 91 | summary: disease2gene 92 | parameters: 93 | - description: Put DOID ID here, e.g. "DOID:123" 94 | example: DOID:123 95 | in: path 96 | name: mondo 97 | required: true 98 | schema: 99 | type: string 100 | responses: 101 | '200': 102 | description: An association object 103 | x-bte-kgs-operations: 104 | - "$ref": "#/components/x-bte-kgs-operations/disease2gene" 105 | "/disease/chemical_substance/{mondo}": 106 | get: 107 | summary: disease2chemical 108 | parameters: 109 | - description: Put DOID ID here, e.g. "DOID:123" 110 | example: DOID:123 111 | in: path 112 | name: mondo 113 | required: true 114 | schema: 115 | type: string 116 | responses: 117 | '200': 118 | description: An association object 119 | x-bte-kgs-operations: 120 | - "$ref": "#/components/x-bte-kgs-operations/disease2chemical" 121 | components: 122 | x-bte-kgs-operations: 123 | gene2chemical: 124 | - inputs: 125 | - id: NCBIGENE 126 | semantic: Gene 127 | outputs: 128 | - id: CHEMBL.COMPOUND 129 | semantic: ChemicalSubstance 130 | predicate: related_to 131 | source: scibite 132 | parameters: 133 | geneid: NCBIGENE:{inputs[0]} 134 | supportBatch: false 135 | response_mapping: 136 | "$ref": "#/components/x-bte-response-mapping/gene2chemical-chembl" 137 | - inputs: 138 | - id: NCBIGENE 139 | semantic: Gene 140 | outputs: 141 | - id: CHEBI 142 | semantic: ChemicalSubstance 143 | predicate: related_to 144 | source: scibite 145 | parameters: 146 | geneid: NCBIGENE:{inputs[0]} 147 | supportBatch: false 148 | response_mapping: 149 | "$ref": "#/components/x-bte-response-mapping/gene2chemical-chebi" 150 | gene2disease: 151 | - inputs: 152 | - id: NCBIGENE 153 | semantic: Gene 154 | outputs: 155 | - id: DOID 156 | semantic: Disease 157 | predicate: related_to 158 | source: scibite 159 | parameters: 160 | geneid: NCBIGENE:{inputs[0]} 161 | supportBatch: false 162 | response_mapping: 163 | "$ref": "#/components/x-bte-response-mapping/gene2disease-doid" 164 | - inputs: 165 | - id: NCBIGENE 166 | semantic: Gene 167 | outputs: 168 | - id: MONDO 169 | semantic: Disease 170 | predicate: related_to 171 | source: scibite 172 | parameters: 173 | geneid: NCBIGENE:{inputs[0]} 174 | supportBatch: false 175 | response_mapping: 176 | "$ref": "#/components/x-bte-response-mapping/gene2disease-mondo" 177 | chemical2gene: 178 | - inputs: 179 | - id: CHEBI 180 | semantic: ChemicalSubstance 181 | outputs: 182 | - id: NCBIGENE 183 | semantic: Gene 184 | predicate: related_to 185 | source: scibite 186 | parameters: 187 | chebi: "{inputs[0]}" 188 | supportBatch: false 189 | response_mapping: 190 | "$ref": "#/components/x-bte-response-mapping/chemical2gene" 191 | chemical2disease: 192 | - inputs: 193 | - id: CHEBI 194 | semantic: ChemicalSubstance 195 | outputs: 196 | - id: DOID 197 | semantic: Disease 198 | predicate: related_to 199 | source: scibite 200 | parameters: 201 | chebi: "{inputs[0]}" 202 | supportBatch: false 203 | response_mapping: 204 | "$ref": "#/components/x-bte-response-mapping/chemical2disease-doid" 205 | - inputs: 206 | - id: CHEBI 207 | semantic: ChemicalSubstance 208 | outputs: 209 | - id: MONDO 210 | semantic: Disease 211 | predicate: related_to 212 | source: scibite 213 | parameters: 214 | chebi: "{inputs[0]}" 215 | supportBatch: false 216 | response_mapping: 217 | "$ref": "#/components/x-bte-response-mapping/chemical2disease-mondo" 218 | disease2gene: 219 | - inputs: 220 | - id: MONDO 221 | semantic: Disease 222 | outputs: 223 | - id: NCBIGENE 224 | semantic: Gene 225 | predicate: related_to 226 | source: scibite 227 | parameters: 228 | mondo: "{inputs[0]}" 229 | supportBatch: false 230 | response_mapping: 231 | "$ref": "#/components/x-bte-response-mapping/disease2gene" 232 | disease2chemical: 233 | - inputs: 234 | - id: MONDO 235 | semantic: Disease 236 | outputs: 237 | - id: CHEMBL.COMPOUND 238 | semantic: ChemicalSubstance 239 | predicate: related_to 240 | source: scibite 241 | parameters: 242 | mondo: "{inputs[0]}" 243 | supportBatch: false 244 | response_mapping: 245 | "$ref": "#/components/x-bte-response-mapping/disease2chemical-chembl" 246 | - inputs: 247 | - id: MONDO 248 | semantic: Disease 249 | outputs: 250 | - id: CHEBI 251 | semantic: ChemicalSubstance 252 | predicate: related_to 253 | source: scibite 254 | parameters: 255 | mondo: "{inputs[0]}" 256 | supportBatch: false 257 | response_mapping: 258 | "$ref": "#/components/x-bte-response-mapping/disease2chemical-chebi" 259 | x-bte-response-mapping: 260 | gene2chemical-chebi: 261 | CHEBI: associated_with.chebi 262 | gene2chemical-chembl: 263 | CHEMBL.COMPOUND: associated_with.chembl 264 | gene2disease-mondo: 265 | MONDO: associated_with.mondo 266 | gene2disease-doid: 267 | DOID: associated_with.doid 268 | chemical2disease-mondo: 269 | MONDO: associated_with.mondo 270 | chemical2disease-doid: 271 | DOID: associated_with.doid 272 | chemical2gene: 273 | NCBIGENE: associated_with.ncbigene 274 | disease2gene: 275 | NCBIGENE: associated_with.ncbigene 276 | disease2chemical-chembl: 277 | CHEMBL.COMPOUND: associated_with.chembl 278 | disease2chemical-chebi: 279 | CHEBI: associated_with.chebi 280 | -------------------------------------------------------------------------------- /scigraph/smartapi.yaml: -------------------------------------------------------------------------------- 1 | openapi: 3.0.0 2 | info: 3 | contact: 4 | email: help@renci.org 5 | name: Chris B. 6 | description: Scibite 7 | termsOfService: https://automat.renci.org 8 | title: Automat CORD19 Scigraph API 9 | version: '2.0' 10 | x-translator: 11 | component: KP 12 | team: 13 | - Ranking Agent 14 | servers: 15 | - description: Production server 16 | url: https://automat.renci.org/cord19-scigraph 17 | tags: 18 | - name: drug 19 | - name: gene 20 | - name: disease 21 | - name: automat 22 | - name: translator 23 | paths: 24 | "/gene/chemical_substance/{geneid}": 25 | get: 26 | summary: gene2chemical 27 | parameters: 28 | - description: Put NCBIGENE ID here, e.g. 1017 29 | example: NCBIGENE:1017 30 | in: path 31 | name: geneid 32 | required: true 33 | schema: 34 | type: string 35 | responses: 36 | '200': 37 | description: An association object 38 | x-bte-kgs-operations: 39 | - "$ref": "#/components/x-bte-kgs-operations/gene2chemical" 40 | "/gene/disease/{geneid}": 41 | get: 42 | summary: gene2disease 43 | parameters: 44 | - description: Put NCBIGENE ID here, e.g. 1017 45 | example: NCBIGENE:1017 46 | in: path 47 | name: geneid 48 | required: true 49 | schema: 50 | type: string 51 | responses: 52 | '200': 53 | description: An association object 54 | x-bte-kgs-operations: 55 | - "$ref": "#/components/x-bte-kgs-operations/gene2disease" 56 | "/chemical_substance/disease/{chebi}": 57 | get: 58 | summary: chemical2disease 59 | parameters: 60 | - description: Put CHEBI ID here, e.g. "CHEBI:661" 61 | example: CHEBI:661 62 | in: path 63 | name: chebi 64 | required: true 65 | schema: 66 | type: string 67 | responses: 68 | '200': 69 | description: An association object 70 | x-bte-kgs-operations: 71 | - "$ref": "#/components/x-bte-kgs-operations/chemical2disease" 72 | "/chemical_substance/gene/{chebi}": 73 | get: 74 | summary: chemical2gene 75 | parameters: 76 | - description: Put CHEBI ID here, e.g. "CHEBI:661" 77 | example: CHEBI:661 78 | in: path 79 | name: chebi 80 | required: true 81 | schema: 82 | type: string 83 | responses: 84 | '200': 85 | description: An association object 86 | x-bte-kgs-operations: 87 | - "$ref": "#/components/x-bte-kgs-operations/chemical2gene" 88 | "/disease/gene/{mondo}": 89 | get: 90 | summary: disease2gene 91 | parameters: 92 | - description: Put DOID ID here, e.g. "DOID:123" 93 | example: DOID:123 94 | in: path 95 | name: mondo 96 | required: true 97 | schema: 98 | type: string 99 | responses: 100 | '200': 101 | description: An association object 102 | x-bte-kgs-operations: 103 | - "$ref": "#/components/x-bte-kgs-operations/disease2gene" 104 | "/disease/chemical_substance/{mondo}": 105 | get: 106 | summary: disease2chemical 107 | parameters: 108 | - description: Put DOID ID here, e.g. "DOID:123" 109 | example: DOID:123 110 | in: path 111 | name: mondo 112 | required: true 113 | schema: 114 | type: string 115 | responses: 116 | '200': 117 | description: An association object 118 | x-bte-kgs-operations: 119 | - "$ref": "#/components/x-bte-kgs-operations/disease2chemical" 120 | components: 121 | x-bte-kgs-operations: 122 | gene2chemical: 123 | - inputs: 124 | - id: NCBIGENE 125 | semantic: Gene 126 | outputs: 127 | - id: CHEMBL.COMPOUND 128 | semantic: ChemicalSubstance 129 | predicate: related_to 130 | source: scigraph 131 | parameters: 132 | geneid: NCBIGENE:{inputs[0]} 133 | supportBatch: false 134 | response_mapping: 135 | "$ref": "#/components/x-bte-response-mapping/gene2chemical-chembl" 136 | - inputs: 137 | - id: NCBIGENE 138 | semantic: Gene 139 | outputs: 140 | - id: CHEBI 141 | semantic: ChemicalSubstance 142 | predicate: related_to 143 | source: scigraph 144 | parameters: 145 | geneid: NCBIGENE:{inputs[0]} 146 | supportBatch: false 147 | response_mapping: 148 | "$ref": "#/components/x-bte-response-mapping/gene2chemical-chebi" 149 | gene2disease: 150 | - inputs: 151 | - id: NCBIGENE 152 | semantic: Gene 153 | outputs: 154 | - id: DOID 155 | semantic: Disease 156 | predicate: related_to 157 | source: scigraph 158 | parameters: 159 | geneid: NCBIGENE:{inputs[0]} 160 | supportBatch: false 161 | response_mapping: 162 | "$ref": "#/components/x-bte-response-mapping/gene2disease-doid" 163 | - inputs: 164 | - id: NCBIGENE 165 | semantic: Gene 166 | outputs: 167 | - id: MONDO 168 | semantic: Disease 169 | predicate: related_to 170 | source: scigraph 171 | parameters: 172 | geneid: NCBIGENE:{inputs[0]} 173 | supportBatch: false 174 | response_mapping: 175 | "$ref": "#/components/x-bte-response-mapping/gene2disease-mondo" 176 | chemical2gene: 177 | - inputs: 178 | - id: CHEBI 179 | semantic: ChemicalSubstance 180 | outputs: 181 | - id: NCBIGENE 182 | semantic: Gene 183 | predicate: related_to 184 | source: scigraph 185 | parameters: 186 | chebi: "{inputs[0]}" 187 | supportBatch: false 188 | response_mapping: 189 | "$ref": "#/components/x-bte-response-mapping/chemical2gene" 190 | chemical2disease: 191 | - inputs: 192 | - id: CHEBI 193 | semantic: ChemicalSubstance 194 | outputs: 195 | - id: DOID 196 | semantic: Disease 197 | predicate: related_to 198 | source: scigraph 199 | parameters: 200 | chebi: "{inputs[0]}" 201 | supportBatch: false 202 | response_mapping: 203 | "$ref": "#/components/x-bte-response-mapping/chemical2disease-doid" 204 | - inputs: 205 | - id: CHEBI 206 | semantic: ChemicalSubstance 207 | outputs: 208 | - id: MONDO 209 | semantic: Disease 210 | predicate: related_to 211 | source: scigraph 212 | parameters: 213 | chebi: "{inputs[0]}" 214 | supportBatch: false 215 | response_mapping: 216 | "$ref": "#/components/x-bte-response-mapping/chemical2disease-mondo" 217 | disease2gene: 218 | - inputs: 219 | - id: MONDO 220 | semantic: Disease 221 | outputs: 222 | - id: NCBIGENE 223 | semantic: Gene 224 | predicate: related_to 225 | source: scigraph 226 | parameters: 227 | mondo: "{inputs[0]}" 228 | supportBatch: false 229 | response_mapping: 230 | "$ref": "#/components/x-bte-response-mapping/disease2gene" 231 | disease2chemical: 232 | - inputs: 233 | - id: MONDO 234 | semantic: Disease 235 | outputs: 236 | - id: CHEMBL.COMPOUND 237 | semantic: ChemicalSubstance 238 | predicate: related_to 239 | source: scigraph 240 | parameters: 241 | mondo: "{inputs[0]}" 242 | supportBatch: false 243 | response_mapping: 244 | "$ref": "#/components/x-bte-response-mapping/disease2chemical-chembl" 245 | - inputs: 246 | - id: MONDO 247 | semantic: Disease 248 | outputs: 249 | - id: CHEBI 250 | semantic: ChemicalSubstance 251 | predicate: related_to 252 | source: scigraph 253 | parameters: 254 | mondo: "{inputs[0]}" 255 | supportBatch: false 256 | response_mapping: 257 | "$ref": "#/components/x-bte-response-mapping/disease2chemical-chebi" 258 | x-bte-response-mapping: 259 | gene2chemical-chebi: 260 | CHEBI: associated_with.chebi 261 | gene2chemical-chembl: 262 | CHEMBL.COMPOUND: associated_with.chembl 263 | gene2disease-mondo: 264 | MONDO: associated_with.mondo 265 | gene2disease-doid: 266 | DOID: associated_with.doid 267 | chemical2disease-mondo: 268 | MONDO: associated_with.mondo 269 | chemical2disease-doid: 270 | DOID: associated_with.doid 271 | chemical2gene: 272 | NCBIGENE: associated_with.ncbigene 273 | disease2gene: 274 | NCBIGENE: associated_with.ncbigene 275 | disease2chemical-chembl: 276 | CHEMBL.COMPOUND: associated_with.chembl 277 | disease2chemical-chebi: 278 | CHEBI: associated_with.chebi 279 | -------------------------------------------------------------------------------- /stanford_kp/smartapi.yaml: -------------------------------------------------------------------------------- 1 | openapi: '3.0.0' 2 | info: 3 | version: '1.0' 4 | title: Stanford BioSample API 5 | description: >- 6 | The Stanford biosample API 7 | termsOfService: http://www.stanford.edu 8 | contact: 9 | name: stanford help desk 10 | x-role: responsible developer 11 | email: help@stanford.edu 12 | servers: 13 | - url: 'http://api.kp.metadatacenter.org' 14 | description: 'Production server' 15 | tags: 16 | - name: translator 17 | - name: stanford 18 | 19 | paths: 20 | '/biosample/search': 21 | get: 22 | summary: 'retrieve biosample information' 23 | parameters: 24 | - name: q 25 | in: query 26 | description: >- 27 | query 28 | required: true 29 | example: "biolink:Disease=MONDO:0007256" 30 | schema: 31 | type: string 32 | - name: limit 33 | in: query 34 | description: size of the output 35 | example: 200 36 | schema: 37 | type: integer 38 | responses: 39 | '200': 40 | description: 'A biosample object' 41 | x-bte-response-mapping: 42 | - $ref: '#/components/x-bte-response-mapping/disease-biosample' 43 | - $ref: '#/components/x-bte-response-mapping/cellline-biosample' 44 | x-bte-kgs-operations: 45 | diseaseAssociatedWithBiosample: 46 | $ref: '#/components/x-bte-kgs-operations/diseaseAssociatedWithBiosample' 47 | clAssociatedWithBiosample: 48 | $ref: '#/components/x-bte-kgs-operations/clAssociatedWithBiosample' 49 | '/biosample/{sampleid}': 50 | get: 51 | summary: 'retrieve biosample information' 52 | parameters: 53 | - name: sampleid 54 | in: path 55 | description: >- 56 | the SAMD biosample ID 57 | required: true 58 | example: "SAMD00005006" 59 | schema: 60 | type: string 61 | responses: 62 | '200': 63 | description: 'A biosample object' 64 | x-bte-response-mapping: 65 | $ref: '#/components/x-bte-response-mapping/biosample' 66 | x-bte-kgs-operations: 67 | biosampleAssociatedWithDisease: 68 | $ref: '#/components/x-bte-kgs-operations/biosampleAssociatedWithDisease' 69 | components: 70 | x-bte-kgs-operations: 71 | diseaseAssociatedWithBiosample: 72 | inputs: 73 | - id: mondo 74 | semantic: DiseaseOrPhenotypicFeature 75 | outputs: 76 | - id: samd 77 | semantic: Biosample 78 | parameters: 79 | q: "biolink:Disease={input1}" 80 | supportBatch: false 81 | response-mapping: 82 | $ref: '#/components/x-bte-response-mapping/disease-biosample' 83 | clAssociatedWithBiosample: 84 | inputs: 85 | - id: clo 86 | semantic: CellLine 87 | outputs: 88 | - id: samd 89 | semantic: Biosample 90 | parameters: 91 | q: "biolink:CellLine={input1}" 92 | supportBatch: false 93 | response-mapping: 94 | $ref: '#/components/x-bte-response-mapping/cellline-biosample' 95 | biosampleAssociatedWithDisease: 96 | inputs: 97 | - id: samd 98 | semantic: Biosample 99 | outputs: 100 | - id: mondo 101 | semantic: DiseaseOrPhenotypicFeature 102 | parameters: 103 | sampleid: "{input1}" 104 | supportBatch: false 105 | response-mapping: 106 | $ref: '#/components/x-bte-response-mapping/biosample' 107 | x-bte-response-mapping: 108 | disease-biosample: 109 | "@context": http://schema.org 110 | "@type": DiseaseOrPhenotypicFeature 111 | bts:mondo: mondo 112 | bts:diseaseAssociatedWithBiosample: 113 | - "@type": Biosample 114 | bts:samd: data.biosampleAccession 115 | bts:organism: data.oorganism 116 | bts:age: data.attributes.age 117 | bts:sex: data.attributes.sex.name 118 | bts:cellline: data.attributes.cell_line.name 119 | "$input": bts:mondo 120 | "$source": NCBI Biosample Database 121 | cellline-biosample: 122 | "@context": http://schema.org 123 | "@type": CellLine 124 | bts:clo: clo 125 | bts:clAssociatedWithBiosample: 126 | - "@type": Biosample 127 | bts:samd: data.biosampleAccession 128 | bts:organism: data.oorganism 129 | bts:age: data.attributes.age 130 | bts:sex: data.attributes.sex.name 131 | bts:cellline: data.attributes.cell_line.name 132 | "$input": bts:clo 133 | "$source": NCBI Biosample Database 134 | biosample: 135 | "@context": http://schema.org 136 | "@type": Biosample 137 | bts:samd: samd 138 | bts:biosampleAssociatedWithDisease: 139 | - "@type": DiseaseOrPhenotypicFeature 140 | bts:mondo: data.attributes.Disease.mondo 141 | bts:organism: data.attributes.organism 142 | bts:age: data.attributes.age 143 | bts:sex: data.attributes.sex.name 144 | bts:cellline: data.attributes.cell_line.name 145 | "$input": bts:samd 146 | "$source": NCBI Biosample Database -------------------------------------------------------------------------------- /tests.py: -------------------------------------------------------------------------------- 1 | import unittest 2 | import os.path 3 | import json 4 | import pprint 5 | 6 | import requests 7 | import yaml 8 | 9 | 10 | def get_api_metadata_by_url(url, as_string=False): 11 | try: 12 | res = requests.get(url) 13 | except requests.exceptions.Timeout: 14 | return {"success": False, "error": "URL request is timeout."} 15 | except requests.exceptions.ConnectionError: 16 | return {"success": False, "error": "URL request had a connection error."} 17 | if res.status_code != 200: 18 | return {"success": False, "error": "URL request returned {}.".format(res.status_code)} 19 | else: 20 | if as_string: 21 | return res.text 22 | else: 23 | try: 24 | metadata = res.json() 25 | # except json.JSONDecodeError: # for py>=3.5 26 | except ValueError: # for py<3.5 27 | try: 28 | metadata = yaml.load(res.text) 29 | except (yaml.scanner.ScannerError, 30 | yaml.parser.ParserError): 31 | return {"success": False, 32 | "error": "Not a valid JSON or YAML format."} 33 | return metadata 34 | 35 | 36 | def get_api_metadata_by_path(file_path, as_string=False): 37 | if os.path.exists(file_path): 38 | with open(file_path) as in_f: 39 | if as_string: 40 | metadata = in_f.read() 41 | else: 42 | try: 43 | metadata = json.load(in_f) 44 | except ValueError: 45 | in_f.seek(0) 46 | try: 47 | metadata = yaml.load(in_f) 48 | except (yaml.scanner.ScannerError, 49 | yaml.parser.ParserError): 50 | return {"success": False, 51 | "error": "Not a valid JSON or YAML format."} 52 | return metadata 53 | else: 54 | return {"success": False, "error": "Invalid metadata file path \"{}\".".format(file_path)} 55 | 56 | 57 | def get_api_metadata(metadata_src, as_string=False): 58 | if isinstance(metadata_src, str) and metadata_src: 59 | if metadata_src.startswith('http') or metadata_src.startswith('ftp'): 60 | return get_api_metadata_by_url(metadata_src, as_string=as_string) 61 | else: 62 | return get_api_metadata_by_path(metadata_src, as_string=as_string) 63 | else: 64 | return {"success": False, "error": "Invalid metadata field value."} 65 | 66 | 67 | def validate_api_metadata(metadata_src): 68 | VALIDATE_API = 'https://smart-api.info/api/validate' 69 | metadata = get_api_metadata(metadata_src, as_string=True) 70 | if isinstance(metadata, dict) and metadata.get('success', None) is False: 71 | return metadata 72 | if len(metadata) >= 1024*1024*10: 73 | return {"success": False, "error": "Metadata is too big, should be < 10M."} 74 | res = requests.post(VALIDATE_API, data=metadata.encode('utf-8')) 75 | # if metadata_src.startswith('http') or metadata_src.startswith('ftp'): 76 | # metadata_url = metadata_src 77 | # else: 78 | # metadata_url = "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/" 79 | # metadata_url += metadata_src 80 | # res = requests.get(VALIDATE_API, {'url': metadata_url}) 81 | valid = res.json() 82 | return valid 83 | 84 | 85 | class TestAPIRegistry(unittest.TestCase): 86 | def setUp(self): 87 | with open("./API_LIST.yml") as in_f: 88 | self.api_d = yaml.load(in_f) 89 | 90 | def test_api_list(self): 91 | self.assertTrue("APIs" in self.api_d) 92 | api_li = self.api_d["APIs"] 93 | for api in api_li: 94 | self.assertTrue("metadata" in api, 95 | "Missing \"metadata\" in this API entry:\n" + pprint.pformat(api)) 96 | 97 | def test_api_metadata(self): 98 | api_li = self.api_d["APIs"] 99 | for api in api_li: 100 | metadata = get_api_metadata(api['metadata']) 101 | api_title = metadata.get('info', {}).get('title', '') 102 | self.assertFalse(metadata.get('success', None) is False, 103 | "Fail to retrieve metadata:\n" + 104 | "\tmetadata: {}\n\tAPI: {}\n\tError: {}".format(api['metadata'], api_title, metadata.get("error", ''))) 105 | self.assertTrue(metadata.get('tags', None), 106 | "Missing required \"tags\" field in the metadata content.\n" + 107 | "\tAPI: {}".format(api_title)) 108 | self.assertTrue('translator' in [t['name'] for t in metadata['tags']], 109 | "Requires \"translator\" as one of tags in the metadata content.\n" + 110 | "\tAPI: {}".format(api_title)) 111 | 112 | valid = validate_api_metadata(api['metadata']) 113 | self.assertTrue(valid.get('valid', False), 114 | "Validation Error.\n" + 115 | "\tAPI: {0}\n\tError: {1}".format(api_title, valid.get('error', ''))) 116 | 117 | 118 | if __name__ == '__main__': 119 | unittest.main() 120 | -------------------------------------------------------------------------------- /text_mining/autogenerate_co-occurrence_smartapi.py: -------------------------------------------------------------------------------- 1 | TYPE_ID_MAPPING = { 2 | "ChemicalSubstance": "CHEBI", 3 | "Cell": "CL", 4 | "BiologicalProcess": "GO", 5 | "CellularComponent": "GO", 6 | "MolecularActivity": "GO", 7 | "PhenotypicFeature": "HP", 8 | "Disease": "MONDO", 9 | "Gene": "NCBIGENE", 10 | "Protein": "PR", 11 | "SequenceFeature": "SO", 12 | "AnatomicalEntity": "UBERON", 13 | "OrganismTaxon": "NCBITaxon" 14 | } 15 | 16 | 17 | def generate_individual_x_bte_operation(input_type, output_type): 18 | return { 19 | input_type + '-' + output_type: [ 20 | { 21 | "inputs": [ 22 | { 23 | "id": TYPE_ID_MAPPING[input_type], 24 | "semantic": input_type 25 | } 26 | ], 27 | "outputs": [ 28 | { 29 | "id": TYPE_ID_MAPPING[output_type], 30 | "semantic": output_type 31 | } 32 | ], 33 | "parameters": { 34 | "q": "subject." + TYPE_ID_MAPPING[input_type] + ':"{inputs[0]}"' + " AND object.type:" + output_type, 35 | "fields": "object,association", 36 | "size": 1000 37 | }, 38 | "predicate": "related_to", 39 | "response_mapping": { 40 | "$ref": '#/components/x-bte-response-mapping/' + output_type 41 | }, 42 | "source": "Text Mining KP", 43 | "supportBatch": False 44 | } 45 | ] 46 | } 47 | 48 | def generate_individual_x_bte_reverse_operation(input_type, output_type): 49 | return { 50 | input_type + '-' + output_type + '-reverse': [ 51 | { 52 | "inputs": [ 53 | { 54 | "id": TYPE_ID_MAPPING[input_type], 55 | "semantic": input_type 56 | } 57 | ], 58 | "outputs": [ 59 | { 60 | "id": TYPE_ID_MAPPING[output_type], 61 | "semantic": output_type 62 | } 63 | ], 64 | "parameters": { 65 | "q": "object." + TYPE_ID_MAPPING[input_type] + ':"{inputs[0]}"' + " AND subject.type:" + output_type, 66 | "fields": "subject,association", 67 | "size": 1000 68 | }, 69 | "predicate": "related_to", 70 | "response_mapping": { 71 | "$ref": '#/components/x-bte-response-mapping/' + output_type + "-reverse" 72 | }, 73 | "source": "Text Mining KP", 74 | "supportBatch": False 75 | } 76 | ] 77 | } 78 | 79 | 80 | def generate_x_bte_operations(): 81 | res = {} 82 | for k in TYPE_ID_MAPPING.keys(): 83 | for v in TYPE_ID_MAPPING.keys(): 84 | res.update(generate_individual_x_bte_operation(k, v)) 85 | res.update(generate_individual_x_bte_reverse_operation(k, v)) 86 | return res 87 | 88 | 89 | def generate_x_bte_operations_refs(): 90 | res = [] 91 | for k in TYPE_ID_MAPPING.keys(): 92 | for v in TYPE_ID_MAPPING.keys(): 93 | res.append({ 94 | "$ref": "#/components/x-bte-kgs-operations/" + k + '-' + v 95 | }) 96 | res.append({ 97 | "$ref": "#/components/x-bte-kgs-operations/" + k + '-' + v + '-reverse' 98 | }) 99 | return { 100 | "x-bte-kgs-operations:": res 101 | } 102 | 103 | 104 | def generate_individual_x_bte_response_mapping(output_type): 105 | return { 106 | output_type: { 107 | "ngd": "hits.association.ngd", 108 | TYPE_ID_MAPPING[output_type]: "hits.object." + 109 | TYPE_ID_MAPPING[output_type] 110 | } 111 | } 112 | 113 | def generate_individual_x_bte_response_mapping_reverse(output_type): 114 | return { 115 | output_type + '-reverse': { 116 | "ngd": "hits.association.ngd", 117 | TYPE_ID_MAPPING[output_type]: "hits.subject." + 118 | TYPE_ID_MAPPING[output_type] 119 | } 120 | } 121 | 122 | 123 | def generate_x_bte_response_mappings(): 124 | res = {} 125 | for k in TYPE_ID_MAPPING.keys(): 126 | res.update(generate_individual_x_bte_response_mapping(k)) 127 | res.update(generate_individual_x_bte_response_mapping_reverse(k)) 128 | return res 129 | 130 | 131 | def to_yaml(json_doc, output_file): 132 | import yaml 133 | with open(output_file, 'w') as file: 134 | documents = yaml.dump(json_doc, file) 135 | -------------------------------------------------------------------------------- /text_mining/x_bte_operations.yml: -------------------------------------------------------------------------------- 1 | 'x-bte-kgs-operations:': 2 | c -------------------------------------------------------------------------------- /text_mining/x_response_mapping.yml: -------------------------------------------------------------------------------- 1 | AnatomicalEntity: 2 | UBERON: hits.object.UBERON 3 | ngd: hits.association.ngd 4 | AnatomicalEntity-reverse: 5 | UBERON: hits.subject.UBERON 6 | ngd: hits.association.ngd 7 | BiologicalProcess: 8 | GO: hits.object.GO 9 | ngd: hits.association.ngd 10 | BiologicalProcess-reverse: 11 | GO: hits.subject.GO 12 | ngd: hits.association.ngd 13 | Cell: 14 | CL: hits.object.CL 15 | ngd: hits.association.ngd 16 | Cell-reverse: 17 | CL: hits.subject.CL 18 | ngd: hits.association.ngd 19 | CellularComponent: 20 | GO: hits.object.GO 21 | ngd: hits.association.ngd 22 | CellularComponent-reverse: 23 | GO: hits.subject.GO 24 | ngd: hits.association.ngd 25 | ChemicalSubstance: 26 | CHEBI: hits.object.CHEBI 27 | ngd: hits.association.ngd 28 | ChemicalSubstance-reverse: 29 | CHEBI: hits.subject.CHEBI 30 | ngd: hits.association.ngd 31 | Disease: 32 | MONDO: hits.object.MONDO 33 | ngd: hits.association.ngd 34 | Disease-reverse: 35 | MONDO: hits.subject.MONDO 36 | ngd: hits.association.ngd 37 | Gene: 38 | NCBIGene: hits.object.NCBIGene 39 | ngd: hits.association.ngd 40 | Gene-reverse: 41 | NCBIGene: hits.subject.NCBIGene 42 | ngd: hits.association.ngd 43 | MolecularActivity: 44 | GO: hits.object.GO 45 | ngd: hits.association.ngd 46 | MolecularActivity-reverse: 47 | GO: hits.subject.GO 48 | ngd: hits.association.ngd 49 | OrganismTaxon: 50 | NCBITaxon: hits.object.NCBITaxon 51 | ngd: hits.association.ngd 52 | OrganismTaxon-reverse: 53 | NCBITaxon: hits.subject.NCBITaxon 54 | ngd: hits.association.ngd 55 | PhenotypicFeature: 56 | HP: hits.object.HP 57 | ngd: hits.association.ngd 58 | PhenotypicFeature-reverse: 59 | HP: hits.subject.HP 60 | ngd: hits.association.ngd 61 | Protein: 62 | PR: hits.object.PR 63 | ngd: hits.association.ngd 64 | Protein-reverse: 65 | PR: hits.subject.PR 66 | ngd: hits.association.ngd 67 | SequenceFeature: 68 | SO: hits.object.SO 69 | ngd: hits.association.ngd 70 | SequenceFeature-reverse: 71 | SO: hits.subject.SO 72 | ngd: hits.association.ngd 73 | 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