Comments (6)
pgaudet
commented on September 27, 2024
Species names are still not being displayed in Noctua.
For example, Taxon:42789 & model: http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=gomodel%3A6494e2e900000134
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balhoff
commented on September 27, 2024
This seems to be controlled by the script https://github.com/geneontology/neo/blob/master/gpi2obo.pl. When it is called by the Makefile, a species code needs to be passed to be appended to the gene product name. There seems to be some unfinished work related to handling virus names here:
Lines 41 to 68 in b1a1039
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kltm
commented on September 27, 2024
(Quiet shoutout to geneontology/project-management#52)
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pgaudet
commented on September 27, 2024
Trying to quote @kltm
How the date gets in:
- takes the GPI file, and convert it into an obo and load it
- the GPI files are species-specific and the species 4-letter code is inserted at the processing of the GPI file to .obo.
- therefore, GPI files with more than one species cannot include a species code and include the taxon ID
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kltm
commented on September 27, 2024
Noting that this seems to be the "next step" referred to in #77. Essentially, we stopped there before getting to this point.
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Related Issues (20)
- RNAcentral IDs incorrectly use OBO PURL namespace HOT 5
- Isoform display in label (originally on the visual tool) HOT 4
- Some IDs we expect are not found in Noctua HOT 5
- 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 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
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- 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
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- 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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