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OHDSI / KnowledgeBase

Source code used to develop the OHDSI knowledge base of sources with information relevant for assessing assocations between drugs and health outcomes of interest.
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Incorrect Evidence Link Out #59

Closed ericaVoss closed 8 years ago

ericaVoss commented 9 years ago

@rkboyce the EVIDENCE_LINKOUT for AERS_REPORT_COUNT is to a pubmed article.

SELECT *
FROM DRUG_HOI_EVIDENCE
WHERE DRUG_HOI_RELATIONSHIP = '1363053-137829'
678452;"1363053-137829";"aers_report_count";t;5;9807;"http://www.ncbi.nlm.nih.gov/pubmed/22422992";"COUNT"
678453;"1363053-137829";"aers_report_PRR";t;5;0.952024246779733;"http://www.ncbi.nlm.nih.gov/pubmed/22422992";"AERS_PRR"
rkboyce commented 9 years ago

That is the linkout I intended because we don't have operationalized a way to 'drill down' into FAERS. For further development of this resource, we might look closely at the OpenFDA API into FAERS: https://open.fda.gov/drug/event/

What do you think?

ericaVoss commented 9 years ago

Well, if we get Vigibase, AERS will not be necessary and we already have traction with Vigibase. Maybe it isn't worth it building this functionality now.

Are the PubMed URLs you are passing are they even applicable? If not, I would just say the link out is NULL.

rkboyce commented 9 years ago

OpenFDA could still be interesting because any meaningful interaction with Vigibase is going to require a license which allot of academics will not be able to afford. So, lets hold on to the thought anyway.

rkboyce commented 9 years ago

We should also explore OpenPHACTs:

OpenPHACTS v.1.5 has just added AERS: https://dev.openphacts.org/docs/1.5

Also noticed their pathway explorer. Here's an example: https://explorer2.openphacts.org/compounds/pathways?uri=http%3A%2F%2Fidentifiers.org%2Fhmdb%2FHMDB00099

In general, there is probably a great deal of synergy between this project and OpenPHACTS

rkboyce commented 8 years ago

This needs to get fixed in the next update of LAERTES so that the WebApi drill down calls function consistently.