Comments (5)
@pgaudet It does indeed seem not to be in the final neo.obo
:
grep -c P06019 neo.obo
0
Okay, so let's peek at what's happening inside the "build" process. It exists in the upstream file:
grep -c P06019 uniprot_reviewed.gpi.tmp
1
It does not exist in the filtered version:
grep -c P06019 filtered_uniprot_reviewed.gpi.tmp
0
Okay, so why is it getting filtered? Looking at the line in the upstream source:
UniProtKB P06019 repc Repressor protein c repc|c|Mup01 protein taxon:10677 RefSeq:NP_050605.1|EMBL:AF083977 db_subset=Swiss-Prot|taxon_name=Escherichia phage Mu|proteome=gcrpCan
Looking through the code of the simple filter, it seems I coded in a regexp that was a little too aggressive, meaning that in some cases, taxon IDs that started with a "1" would get unnecessarily filtered. I've applied a fix that I believe will work.
Assuming it gets through the testing (starting now), we can either wait until the outage in two weeks to apply the change or coordinate an earlier time with @vanaukenk .
from neo.
Testing locally, it looks like we've bumped up the number of entities to 1625034 (from 1565994) and we now have the ones that were missing.
$ grep P06019 neo.obo
id: UniProtKB:P06019
With no further action, this will go into production next week.
from neo.
Sounds good, thanks for debugging this.
Pascale
from neo.
Next step: check at the next Noctua release next Friday May 27th
from neo.
I can now find P06019
Thanks!
from neo.
Related Issues (20)
- RNAcentral IDs incorrectly use OBO PURL namespace HOT 5
- Isoform display in label (originally on the visual tool) HOT 4
- Transient Xenbase issue dropped GPI file HOT 1
- unresolved IDs HOT 10
- Xenbase identifiers are not correct getting labels (in NEO?) HOT 5
- Some e.coli entries not found HOT 18
- In some cases bad identifiers are getting into the load HOT 5
- Ecoli data is gone from NEO as the upstream source changed HOT 13
- add additional species names to gene labels HOT 6
- Add FB Developmental and Anatomy Ontology HOT 14
- Unknown reduction in entities in NEO build HOT 15
- Add some minimal QC to the NEO pipeline HOT 14
- Some Reactome Identifiers are not resolving HOT 11
- NEO GOlr / Solr load does not use "modern" loader, so does not build all closures for "modern" AmiGO
- Xenbase entities do not seem to propagate to the NEO build from the Xenbase GPI HOT 6
- Would like phage proteins to be available HOT 2
- Request to load more phage proteins HOT 2
- Many ChEBI chemicals not available for metabolic models HOT 17
- Clarify and implement rules on inclusion of RNA gene products / RNA central HOT 4
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from neo.