Multiomics-BigGIM-DrugResponse API updates

[gloriachin]

Yaml file has been revised according to the guidance from Colleen. The update includes adding sources in the parameters and x-bte-response-mapping section. @colleenXu Could you help to check it whether the updates fit with the current BET system?

[gloriachin]

API endpoint: https://biothings.transltr.io/biggim_drugresponse_kp YAML file: https://github.com/gloriachin/BigGIM_Parser/tree/main/BET_YAML Paser directory: https://github.com/gloriachin/BigGIM_Parser/

An example of one record: https://biothings.transltr.io/biggim_drugresponse_kp/association/Gene_biolink:associated_with_resistance_to_SmallMolecule_Input_DrugResponse_expr_auc_gdsc_08312022.csv_149182

[colleenXu]

@gloriachin

First: I think issues in this github repo have traditionally been for BioThings API deployments, and not for SmartAPI yaml editing. It think it's up to @erikyao and @newgene whether they want to have issues like this here....but I advise making these issues in the repo the registered yaml is in.

Second: do you have permission to make a branch/fork of the translator-api-registry repo? If you modify the registered yaml there, it's easier to compare / track / merge changes (and merging to update the registered yaml will happen once all instances are on TRAPI 1.4). So I suggest doing this and making a PR in that repo...

[gloriachin]

@colleenXu I revised the yaml file in a fork of translator-api-registry repo.

[colleenXu]

@gloriachin

It's good that a forked file has been made to contain the TRAPI-1.4-support-specific changes. We can connect BTE's instances that are on TRAPI-1.4 to that forked file, even though it's not fully fixed yet.

One issue: the field you added, association.sources appears to not exist in the API. You should be adding the JSON-notation-path of the field that contains the TRAPI 1.4 sources data.

[gloriachin]

Here is an example of the record: ⊖{ "_id": "Gene_biolink:associated_with_resistance_to_SmallMolecule_Input_DrugResponse_expr_auc_gdsc_08312022.csv_5509", "_score": 2.4046109, "attributes": ⊖[ ⊖{ "attribute_type_id": "EDAM:data_0951", "attributes": ⊖[ ⊖{ "attribute_type_id": "NCIT:C53236", "description": "Spearman Correlation Test was used to extract the association", "value": "NCIT:C53249", "value_type_id": "biolink:id" } ], "value": 0.0008900739749078, "value_type_id": "EDAM:data_1669" }, ⊖{ "attribute_type_id": "biolink:supporting_study_size", "value": 14 }, ⊖{ "attribute_type_id": "biolink:dataset", "value": "GDSC" }, ⊖{ "attribute_type_id": "biolink:publications", "value": "PMID:27397505" }, ⊖{ "attribute_type_id": "biolink:subject_aspect_qualifier", "value": "Gene expression" }, ⊖{ "attribute_type_id": "biolink:object_aspect_qualifier", "value": "AUC" }, ⊖{ "attribute_source": "infores:biothings-multiomics-biggim-drugresponse", "attribute_type_id": "biolink:context_qualifier", "value": "MONDO:0004056" } ], "object": ⊖{ "id": "pubchem.compound:5284616", "name": "AZD7762", "pubchem_compound": "pubchem.compound:5284616", "type": "SmallMolecule", "xref": "https://pubchem.ncbi.nlm.nih.gov/compound/5284616" }, "predicate": "biolink:associated_with_resistance_to", "sources": ⊖[ ⊖{ "resource_id": "infores:biothings-multiomics-biggim-drugresponse", "resource_role": "primary_knowledge_source" }, ⊖{ "resource_id": "infores:gdsc", "resource_role": "biolink:supporting_data_source" } ], "subject": ⊖{ "NCBIGene": "NCBIGene:729522", "id": "NCBIGene:729522", "name": "AACSP1", "type": "Gene", "xref": "https://www.ncbi.nlm.nih.gov/gene/729522" } },

[colleenXu]

Looks like this issue has been addressed: It was about x-bte annotation, and a series of x-bte annotation updates were made May + June 2023. The update to TRAPI 1.4 with sources was done in August 2023