Open chunyuma opened 1 year ago
The action "chemical_gene_regulation_graph_expansion" has been added into ARAX_infer. Please see the instruction in the Document. I also added a few tests in test suites. But some of them have an error described below:
@amykglen and @edeutsch, I tried to add qualifiers
in the query graph but got an error: ERROR: [UnknownQEdgeProperty] QueryGraph edge 'r_edge' has an unexpected property 'qualifiers'. This property is not understood and therefore processing is halted, rather than answer an incompletely understood query.
Here is an example. It seems like the query graph currently doesn't allow to have qualifiers
.
yes, query graphs have qualifier_constraints
, not qualifiers
. see the TRAPI documentation:
https://github.com/NCATSTranslator/ReasonerAPI/blob/master/docs/reference.md#qedge-
Thanks @amykglen. Now all chemical_gene_regulation_graph_expansion
tests pass.
One more question: What is the function of .filled
method in the query_graphedges[key] ?
sorry @chunyuma, I missed your question back in February! QEdge.filled
is just a variable that we use within ARAX to signal to Resultify whether a given QEdge has already been processed/expanded. This allows Resultify to tell whether a given QEdge simply had no answers vs. answers haven't even been looked for, which in turn allows it to resultify partially-expanded queries (as needed in #1848)
@chunyuma what is the status on this item?
Triage from 6/28 AHM: focus first on DrugConflator & g() function before going after this one. Recall remaining TODOs are:
affects
directions makes sense (eg. if "upregulate" the "up regulate something that upregulates" is acceptable, but not "upregulate something that downregulates")
This issue summarizes the steps to integrate action
chemical_gene_regulation_graph_expansion
into ARAX_infer:increase gene activity while the other for
decrease ...`)creativeCRG.py
) Note:CRG
means "Chemical regulates gene".ARAX_infer
,infer_utilities.py
,RTX_Configuration.py
,config_dbs.json
,ARAX_expander.py
andARAX_database_manager.py
arax-databases.rtx.ai
server