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NCATS-Tangerine / biolink-beacon

Monarch Biolink Knowledge Beacon implementation (as a Python Flask application)
MIT License
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Ensure all relevant Biolink data is getting pulled #8

Open mbrush opened 7 years ago

mbrush commented 7 years ago

At present there seem to be a significant number of statements from Biolink that are not making it into the aggregator. One issue is the fact that associations lacking a relation are not pulled, but this should be resolved on the Biolink end soon (see #7).

This is likely not the only cause of the problem, as there are examples of statements that have relations in Monarch. e.g. ALS phenotype annotations have asserted relationship (has_phenotype) but are not returned by tk.bio.

@kshefchek has made a preliminary fix at level of Monarch solr index that is not yet in production - it may be worth setting the beacon aggregator to pull from beta to see if fix propagates from solr through biolink and into the aggregator. We should evaluate once the fix is propagated to tk.bio.

kshefchek commented 7 years ago

The phenotype issue is likely the casing issue described here: https://github.com/NCATS-Tangerine/biolink-beacon/issues/7

RichardBruskiewich commented 7 years ago

I'm suspecting some platform timeout issues. I'm close to partially resolving some of these issues. Lo and behold, more data is being retrieved. Once I get the next production prototype out the door, I'll systematically revisit issues such as this to figure out what is going on?