ncbitaxon

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Travis Job - should it run or not?

2

Travis file was removed: https://github.com/obophenotype/ncbitaxon/pull/32 > remove .travis.yml which didn't seem to be doing anything useful Is it necessary to have a travis job for NCBITAXON?

matentzn

The current code in #30 can be configured to generate only classes with a given set of `tax_id`s. By adding one more pass through `nodes.dmp` we could find all the...

jamesaoverton

As far as I can tell, we have never included obsolete taxa in our `ncbitaxon.owl`. (There's nothing obvious in the old code, and `grep owl:deprecated ncbitaxon.owl` returns nothing.) `taxdmp.zip` includes...

jamesaoverton

Check OBO Dashboard results

1

See http://obo-dashboard-test.ontodev.com/ncbitaxon/dashboard.html Fix all issues, OR if there are false positives, report back to ticket: https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1076 It's not clear we can have meaningful text definitions

cmungall

Plan on regular (scripted?) releases?

6

Is there any plan/idea/need to get this updated on a regular basis?

bjonnh

add namespace

1

@cmungall would it be possible to add the namespace to the header of the ncbi taxon file? our loaders are unable to load without the namespace. thanks, Yvonne

ybradford

authority missing from taxa

2

From @MariaALaporte Seems to be failing when there is >1 authority per taxon? Examples http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=16&lvl=3&lin=f&keep=1&srchmode=1&unlock -> Worked, the authority is present in the ncbitaxon.owl file http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=36746&lvl=3&p=mapview&p=has_linkout&p=blast_url&p=genome_blast&lin=f&keep=1&srchmode=1&unlock -> Didn’t work, the...

cmungall

Use both SCHPO (deprecated) and SCHPM (preferred) in the taxon checker

3

So that older GAF files with the previous taxon ID 284812 go through the same screening as SCHPM 4896: N=Schizosaccharomyces pombe

selewis

red tile fish (ncbi taxon:270562)

6

Annotation to GO:0006265 (DNA topological change) should be true Tested with http://owlservices.berkeleybop.org/isClassApplicableForTaxon?format=txt&idstyle=obo&id=GO:0006265&taxid=NCBITaxon:270562

selewis