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Welcome to the BigGIM_Parser wiki!

Workflow from KG to TRAPI API:

tables of KG -> Parser -> Biothing API (index; ) --> SmartAPI/BiothingsAPI YAML with x-bte annotation Node -> predicates -> Node (edge attribute: ) source: array of sources; attribute: array of attributes; no space

Things that need to be fixted: Change biolink:supporting_data_sources to supporting_data_sources; publications: array Biothings aspect qualifier: need to be in biolink models? aspect_qualifier: change from gene expression to expression Qualifier should not be in the edge attributes. [should be discussed] remove all sources from edge attributes; [in the future]

atrribute_type_id: biolink:p_value value_type_id: P-value;

change request body according to the new updates.

YAML editing: gene-physicallyInteracts-gene: ## https://biothings.ncats.io/biggim_drugresponse_kp/query?q=association.edge_label:"biolink:physically_interacts_with" ## 888994 records
- supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: - id: NCBIGene #input gene ids semantic: Gene # categories of input requestBodyType: object requestBody: body: >- { "q": [ {{ queryInputs | addPrefix('NCBIGene') | wrap( '["' , '","biolink:physically_interacts_with"]') }} ], #ids for input "scopes": ["subject.NCBIGene", "association.edge_label"] #categories of input } parameters: fields: object.NCBIGene,association.edge_attributes,sources # returned field size: 1000 #limit the maximum return record outputs: - id: NCBIGene semantic: Gene predicate: physically_interacts_with response_mapping: "$ref": "#/components/x-bte-response-mapping/ncbigene-object" #This is defined at the end of the YAML # testExamples: # - qInput: "NCBIGene:9282" ## MED14. #Testing inputs # oneOutput: "NCBIGene:55588" ## MED29 gene-physicallyInteracts-gene-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: - id: NCBIGene semantic: Gene requestBodyType: object requestBody: body: >- { "q": [ {{ queryInputs | addPrefix('NCBIGene') | wrap( '["' , '","biolink:physically_interacts_with"]') }} ], "scopes": ["object.NCBIGene", "association.edge_label"] } parameters: fields: subject.NCBIGene,association.edge_attributes size: 1000 outputs: - id: NCBIGene semantic: Gene predicate: physically_interacts_with response_mapping: "$ref": "#/components/x-bte-response-mapping/ncbigene-subject"