RTX
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RTXteam
Software repo for Team Expander Agent (Oregon State U., Institute for Systems Biology, and Penn State U.)
TRAPI 1.3 recommends but does not require that we provide a meta_knowledge_graph for ARAX that is a union of all of its KPs' meta_knowledge_graphs: https://github.com/NCATSTranslator/ReasonerAPI/commit/e2ed87aa4f02dac55dcbd8eac7e190b8c188fbdd maybe this union meta KG...
I'm following the instructions here to try to get my local ARAX UI going (doing testing for #1871): https://github.com/RTXteam/RTX/wiki/Dev-info#setting-up-local-ui and this is what my `config.js` looks like: ``` // API...
For the following query: ``` { "message": { "query_graph": { "edges": { "e0": { "subject": "n1", "object": "n0", "predicates": [ "biolink:contributes_to" ] }, "e1": { "subject": "n2", "object": "n1", "predicates":...
From Jenn Hadlock: Would it be possible to add new predicates from 2.4.8? Basazin Belhu (Bassa) For instance, my team updated the predicate to "associated_with_increased_likelihood" and associated_with_decreased_likelihood". I could not...
For this query: ``` add_qnode(id=MONDO:0001475, key=n0) add_qnode(category=biolink:Protein, key=n1, is_set=true) add_qedge(subject=n0, object=n1, key=e0) add_qnode(category=[biolink:Drug], key=n2) add_qedge(subject=n1, object=n2, key=e1) expand(edge_key=e0) expand(edge_key=e1) overlay(action=fisher_exact_test,subject_qnode_key=n0,virtual_relation_label=F1,object_qnode_key=n1,filter_type=top_n,value=50) overlay(action=fisher_exact_test,subject_qnode_key=n1,virtual_relation_label=F2,object_qnode_key=n2,filter_type=top_n,value=50) overlay(action=compute_ngd, virtual_relation_label=N2, subject_qnode_key=n0, object_qnode_key=n2) overlay(action=predict_drug_treats_disease, virtual_relation_label=P1, subject_qnode_key=n2, object_qnode_key=n0) resultify()...
Will get example from @dkoslicki and post it here
For this query: ``` add_qnode(ids=[UMLS:C0220914,CHEMBL.COMPOUND:CHEMBL2108117,HMDB:HMDB0304735], categories=[biolink:ChemicalEntity], key=n0) add_qnode(key=n1) add_qedge(key=e0,subject=n0,object=n1,predicates=biolink:affects) expand() overlay(action=compute_ngd, virtual_relation_label=N1, subject_qnode_key=n0, object_qnode_key=n1) overlay(action=fisher_exact_test,subject_qnode_key=n0,virtual_relation_label=F1,object_qnode_key=n1) resultify() filter_results(action=limit_number_of_results, max_results=100) ``` I am getting the following error: `Object node with qnode key...
this stems from #1876 right now the script that generates the test triples file uses the KG2c Neo4j, which means it can't be part of the KG2c build process. ideally...
I've noticed this when running `test_ARAX_expand.py`, that the log includes messages like `2022-07-07T15:11:05.177757 INFO: [] Result was stored with id 231. It can be viewed at https://arax.ncats.io/?r=231` Going to https://arax.ncats.io/?r=231,...
Validation of TRAPI 1.3 Responses is currently failing, e.g.: https://arax.ncats.io/NewFmt/?r=54172 because we are validating TRAPI 1.3 messages against the TRAPI 1.2 schema Because the SRI-maintained TRAPI validator cannot validate against...