Erica Wood
Erica Wood
New error due to #280: ``` + /home/ubuntu/kg2-venv/bin/python3 /home/ubuntu/kg2-code/update_version.py --increment_minor /home/ubuntu/kg2-build/kg2-version.txt KG2 version: 2.8.4 + /home/ubuntu/kg2-venv/bin/python3 -u /home/ubuntu/kg2-code/filter_kg_and_remap_predicates.py --dropNegated --dropSelfEdgesExcept interacts_with,regulates,inhibits,increase /home/ubuntu/kg2-code/predicate-remap.yaml /home/ubuntu/kg2-code/kg2-provided-by-curie-to-infores-curie.yaml /home/ubuntu/kg2-code/curies-to-urls-map.yaml /home/ubuntu/kg2-build/kg2.json /home/ubuntu/kg2-build/kg2-simplified.json /home/ubuntu/kg2-build/kg2-version.txt /home/ubuntu/kg2-venv/lib/python3.7/site-packages/rdflib_jsonld/__init__.py:12: DeprecationWarning: The...
Essentially, the big problem is that some nodes `provided_by` field is a string rather than a list. We should investigate this further at a later date, because this fix is...
I am working on figuring out where this is stored in the MySQL dump, since it is stored under "Target Predictions" on each compound's page (ex. https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL112/). Since the [given](https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/chembl_33_schema.png)...
GitHub's table function is useful for testing queries, so I am going to use it (pardon the volume of comments here) ``` select * from predicted_binding_domains as pbd inner join...
``` select * from predicted_binding_domains as pbd inner join activities as act on pbd.activity_id=act.activity_id inner join chembl_id_lookup as cil on cil.entity_id=act.molregno inner join binding_sites as bs on pbd.site_id=bs.site_id where cil.chembl_id="CHEMBL10";...
This query is pretty promising but also returns a lot of documents and `inactive` or `empty` targets: ``` select * from predicted_binding_domains as pbd inner join activities as act on...
If we constrain the entity type to "TARGET", we get the same number of rows, because `chembl_id_lookup` duplicates ID's for each type. ``` select * from predicted_binding_domains as pbd inner...
After spending a while looking through the MySQL database, I decided to reach out to the ChEMBL help desk: > I am working on ETLing ChEMBL's "Target Prediction" (that's the...
That is definitely what they are saying with this. It would be a lot of work to bring in the predictions through a Docker image. I'm not sure if it...
We can't close this issue out yet because, while trying to build using the merged JSON Lines code (#321), 100G worth of `binlog.*` files were created despite having ``` [mysqld]...