From 60e481f3c9029176facac7ed24856a37bc0648ce Mon Sep 17 00:00:00 2001 From: YaphetKG Date: Fri, 18 Sep 2020 08:37:52 -0400 Subject: [PATCH] Adding some of automat's servers in the repo. --- API_LIST.yml | 10 ++ hgnc_automat/smartapi.yaml | 205 ++++++++++++++++++++++++++++++ intact_automat/smartapi.yaml | 240 +++++++++++++++++++++++++++++++++++ 3 files changed, 455 insertions(+) create mode 100644 hgnc_automat/smartapi.yaml create mode 100644 intact_automat/smartapi.yaml diff --git a/API_LIST.yml b/API_LIST.yml index f7f06116..3de77640 100644 --- a/API_LIST.yml +++ b/API_LIST.yml @@ -91,3 +91,13 @@ APIs: translator: - returnjson: true notes: "" + + - metadata: hgnc_automat/smartapi.yaml + transator: + - returnjson: true + notes: "" + + - metadata: intact_automat/smartapi.yaml + transator: + - returnjson: true + notes: "" diff --git a/hgnc_automat/smartapi.yaml b/hgnc_automat/smartapi.yaml new file mode 100644 index 00000000..8cd787ff --- /dev/null +++ b/hgnc_automat/smartapi.yaml @@ -0,0 +1,205 @@ +openapi: 3.0.0 +info: + contact: + email: help@renci.org + name: Yaphet K + x-id: https://github.com/yaphetKG + x-role: responsible developer + description: HGNC gene family and gene relationships + termsOfService: https://automat.renci.org + title: Automat HGNC API + version: '2.0' +servers: +- description: Production server + url: https://automat.renci.org/hgnc +tags: +- name: gene +- name: geneFamily +- name: translator +- name: biothings +paths: + /gene/gene_family/{NCBIGene}: + get: + parameters: + - description: Put NCBIGene ID here, e.g. "NCBIGene:3539" + example: "NCBIGene:3539" + in: path + name: NCBIGene + required: true + schema: + type: string + responses: + '200': + description: An association object + summary: + gene to gene family + x-bte-kgs-operations: + - $ref: '#/components/x-bte-kgs-operations/gene2geneFamily' + tags: + - gene + - geneFamily + /gene_family/gene/{HGNC.FAMILY}: + get: + parameters: + - description: Put HGNC.FAMILY ID here, e.g. "HGNC.FAMILY:353" + example: "HGNC.FAMILY:353" + in: path + name: HGNC.FAMILY + required: true + schema: + type: string + responses: + '200': + description: An association object + summary: + organism taxon to gene + x-bte-kgs-operations: + - $ref: '#/components/x-bte-kgs-operations/geneFamily2gene' + tags: + - gene + - geneFamily + /predicates: + get: + description: Returns an object where outer keys represent source types with second + level keys as targets. And the values of the second level keys is the + type of possible edge typesthat connect these concepts. + summary: List of available concepts with thier relating predicates. + operationId: get_predicates + parameters: [] + responses: + "200": + description: OK + content: + application/json: + schema: + type: object + example: + chemical_substance: + gene: + - directly_interacts_with + tags: + - translator + + /reasonerapi: + get: + description: Returns a list of question templates that can be used to query this + plater instance/ + operationId: get_question_templates + summary: returns TRAPI query messages possible to run in the server. + parameters: [] + responses: + "200": + description: OK + content: + application/json: + schema: + type: object + example: + - query_graph: + nodes: + - id: n1 + type: gene + - id: n2 + type: chemical_substance + edges: + - id: e0 + source_id: n1 + target_id: n2 + type: is_affected_by + tags: + - translator + post: + description: Given a question graph return question graph plus answers. + operationId: post_question + summary: Post a TRAPI query and get answers back. + requestBody: + description: Reasoner api question. + content: + application/json: + schema: + type: object + example: + query_graph: + nodes: + - id: n1 + type: gene + - id: n2 + type: chemical_substance + edges: + - id: e0 + source_id: n1 + target_id: n2 + type: is_affected_by + required: true + responses: + "200": + description: OK + content: + application/json: + schema: + type: object + example: + query_graph: + nodes: + - id: n1 + type: gene + - id: n2 + type: chemical_substance + edges: + - id: e0 + source_id: n1 + target_id: n2 + type: is_affected_by + results: + - edge_bindings: [] + node_bindings: [] + knowledge_graph: + nodes: + - id: n1's DB ID + name: n1 has name + - id: n2's DB ID + name: n2 has name + edges: + - id: e0's DB ID + name: e0 has name + tags: + - translator +components: + x-bte-kgs-operations: + gene2geneFamily: + - inputs: + - id: NCBIGene + semantic: Gene + outputs: + - id: HGNC.FAMILY + semantic: GeneFamily + parameters: + ncbigene: '{inputs[0]}' + predicate: in_taxon + response_mapping: + $ref: '#/components/x-bte-response-mapping/gene2geneFamily' + source: hgnc + supportBatch: false + geneFamily2gene: + - inputs: + - id: HGNC.FAMILY + semantic: GeneFamily + outputs: + - id: NCBIGene + semantic: gene + parameters: + ncbitaxon: '{inputs[0]}' + predicate: part_of + response_mapping: + $ref: '#/components/x-bte-response-mapping/geneFamily2gene' + source: hgnc + supportBatch: false + + x-bte-response-mapping: + gene2geneFamily: + HGNC.FAMILY: + part_of.hgnc.family + geneFamily2gene: + NCBIGene: + part_of.ncbigene + diff --git a/intact_automat/smartapi.yaml b/intact_automat/smartapi.yaml new file mode 100644 index 00000000..4e459114 --- /dev/null +++ b/intact_automat/smartapi.yaml @@ -0,0 +1,240 @@ +openapi: 3.0.0 +info: + contact: + email: help@renci.org + name: Yaphet K + x-id: https://github.com/yaphetKG + x-role: responsible developer + description: IntAct provides a freely available, open source database system and analysis tools for molecular interaction data. + termsOfService: https://automat.renci.org + title: Automat Intact API + version: '2.0' +servers: +- description: Production server + url: https://automat.renci.org/intact +tags: +- name: gene +- name: organismTaxon +- name: translator +- name: biothings +paths: + /gene/organism_taxon/{NCBIGene}: + get: + parameters: + - description: Put NCBIGene ID here, e.g. "NCBIGene:273" + example: "NCBIGene:273" + in: path + name: NCBIGene + required: true + schema: + type: string + responses: + '200': + description: An association object + summary: + gene to organism taxon + x-bte-kgs-operations: + - $ref: '#/components/x-bte-kgs-operations/gene2organismTaxon' + tags: + - gene + - organismTaxon + /organism_taxon/gene/{NCBITaxon}: + get: + parameters: + - description: Put NCBIGene ID here, e.g. "NCBITaxon:9606" + example: "NCBITaxon:9606" + in: path + name: NCBITaxon + required: true + schema: + type: string + responses: + '200': + description: An association object + summary: + organism taxon to gene + x-bte-kgs-operations: + - $ref: '#/components/x-bte-kgs-operations/organismTaxon2gene' + tags: + - gene + - organismTaxon + /gene/gene/{NCBIGene}: + get: + parameters: + - description: Put NCBIGene ID here, e.g. "NCBIGene:273" + example: "NCBIGene:273" + in: path + name: NCBIGene + required: true + schema: + type: string + responses: + '200': + description: An association object + summary: + gene to gene + x-bte-kgs-operations: + - $ref: '#/components/x-bte-kgs-operations/gene2gene' + tags: + - gene + /predicates: + get: + description: Returns an object where outer keys represent source types with second + level keys as targets. And the values of the second level keys is the + type of possible edge typesthat connect these concepts. + operationId: get_predicates + parameters: [] + summary: List of available concepts with thier relating predicates. + responses: + "200": + description: OK + content: + application/json: + schema: + type: object + example: + chemical_substance: + gene: + - directly_interacts_with + tags: + - translator + + /reasonerapi: + get: + description: Returns a list of question templates that can be used to query this + plater instance/ + operationId: get_question_templates + parameters: [] + summary: returns TRAPI query messages possible to run in the server. + responses: + "200": + description: OK + content: + application/json: + schema: + type: object + example: + - query_graph: + nodes: + - id: n1 + type: gene + - id: n2 + type: chemical_substance + edges: + - id: e0 + source_id: n1 + target_id: n2 + type: is_affected_by + tags: + - translator + post: + description: Given a question graph return question graph plus answers. + operationId: post_question + summary: Post a TRAPI query and get answers back. + requestBody: + description: Reasoner api question. + content: + application/json: + schema: + type: object + example: + query_graph: + nodes: + - id: n1 + type: gene + - id: n2 + type: chemical_substance + edges: + - id: e0 + source_id: n1 + target_id: n2 + type: is_affected_by + required: true + responses: + "200": + description: OK + content: + application/json: + schema: + type: object + example: + query_graph: + nodes: + - id: n1 + type: gene + - id: n2 + type: chemical_substance + edges: + - id: e0 + source_id: n1 + target_id: n2 + type: is_affected_by + results: + - edge_bindings: [] + node_bindings: [] + knowledge_graph: + nodes: + - id: n1's DB ID + name: n1 has name + - id: n2's DB ID + name: n2 has name + edges: + - id: e0's DB ID + name: e0 has name + tags: + - translator +components: + x-bte-kgs-operations: + gene2organismTaxon: + - inputs: + - id: NCBIGene + semantic: Gene + outputs: + - id: NCBITaxon + semantic: OrganismTaxon + parameters: + ncbigene: '{inputs[0]}' + predicate: in_taxon + response_mapping: + $ref: '#/components/x-bte-response-mapping/gene2organismTaxon' + source: inact + supportBatch: false + gene2gene: + - inputs: + - id: NCBIGene + semantic: Gene + outputs: + - id: NCBIGene + semantic: Gene + parameters: + ncbigene: '{inputs[0]}' + predicate: directly_interacts_with + response_mapping: + $ref: '#/components/x-bte-response-mapping/gene2gene' + source: inact + supportBatch: false + organismTaxon2gene: + - inputs: + - id: NCBITaxon + semantic: organismTaxon + outputs: + - id: NCBIGene + semantic: gene + parameters: + ncbitaxon: '{inputs[0]}' + predicate: in_taxon + response_mapping: + $ref: '#/components/x-bte-response-mapping/organismTaxon2gene' + source: inact + supportBatch: false + + x-bte-response-mapping: + gene2organismTaxon: + NCBITaxon: + in_taxon.ncbitaxon + organismTaxon2gene: + NCBIGene: + in_taxon.ncbitaxon + gene2gene: + NCBIGene: + directly_interacts_with.ncbigene