OBOFoundry
Practice for referring to taxa not in NCBI Taxon?
@bionicjules has a number of taxa he wants to refer to that are not in NCBI taxonomy. Is there any consistent way people deal with this?
In Phenoscape we use the Vertebrate Taxonomy Ontology (VTO) which has many taxa not in NCBI. This was assembled from a few different taxonomy sources, including NCBI, but the pipeline for building it is kind of stale. And it only includes vertebrates. We have a plan for moving to an OWL taxonomy based on the Open Tree of Life taxonomy, which has a better supported pipeline for continuous integration from several taxonomic sources. It also covers all of life. I made a start on tools for producing the OWL but it won't really be a priority to complete until sometime next year.
I have used VTO for Cetacea (can’t remember why) but went back to NCBI for the sake of uniformity. But the majority of animals used for experimentation, for many reasons, are overwhelmingly invertebrates. So we are left with the NCBI taxonomy. I’m surprised that the genome of Sepia nemoralis hasn’t been sequenced since it is so common. I am aware of the OTL taxonomy which I have used to map out a skeletal phylogeny which has just the essential relationships for my ontology (I simply want to arrange species in some sort of logical relationship - my main interest is in physiology, behaviour, morphology and functions in general). It looks as if I’ll have to wait and do an update in a year or so.
Thanks Julian
On 6 Jun 2017, at 19:08, Jim Balhoff [email protected] wrote:
In Phenoscape we use the Vertebrate Taxonomy Ontology (VTO) which has many taxa not in NCBI. This was assembled from a few different taxonomy sources, including NCBI, but the pipeline for building it is kind of stale. And it only includes vertebrates. We have a plan for moving to an OWL taxonomy based on the Open Tree of Life taxonomy https://devtree.opentreeoflife.org/about/taxonomy-version/ott3.0, which has a better supported pipeline for continuous integration from several taxonomic sources. It also covers all of life. I made a start on tools for producing the OWL but it won't really be a priority to complete until sometime next year.
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@bionicjules are you sure NCBITaxon will not work for your purposes? Note that it doesn't need to be sequenced to be in the NCBI Taxonomy, it only needs to have some sequence associated with it.
Your snail is in NCBI taxonomy, and in the corresponding ontology:
- https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=28835
- http://purl.obolibrary.org/obo/NCBITaxon_28835
Do you have a list of the taxa you need that are not in NCBI? Another possibility that works across inverts to would be to use EOL URIs
If the snail you refer to is Cepaea, it is one of the most studied of all snails, an early subject of genetic studies! The list of apparently ontologically orphaned taxa is below:
Glaphyrella trebouxiodes Neomeris annulata Notomegabalanus algicola Machilinus casasecai Machilinus spinifrontis Petrobius maritimus Rufocephalus sp. Cyclochila australasiae Entimus imperialis Myathropa florea Mallophora ruficauda Baryscapus galactopus Opisthobranchia Sepia nemoralis Acropora reticulata Antipathes salix
Not many, considering, but there are some common species amongst that lot.
On 6 Jun 2017, at 19:39, Chris Mungall [email protected] wrote:
@bionicjules https://github.com/bionicjules are you sure NCBITaxon will not work for your purposes? Note that it doesn't need to be sequenced to be in the NCBI Taxonomy, it only needs to have some sequence associated with it.
Your snail is in NCBI taxonomy, and in the corresponding ontology:
https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=28835 https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=28835 http://purl.obolibrary.org/obo/NCBITaxon_28835 http://purl.obolibrary.org/obo/NCBITaxon_28835 Do you have a list of the taxa you need that are not in NCBI? Another possibility that works across inverts to would be to use EOL URIs
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I can say that while FoodOn adopts NCBITaxon wherever possible, we now have need for many plant cultivars that are at sub-species level and no NCBITaxon IDs exists for them. We have taken up a solution where we use WikiData to reuse or add cultivars/varietals, and use wikiidata URI's directly. So we expect a combination of NCBITaxon and Wikidata to meet all our taxonomic needs. (WikiData of course can map to NCBITaxon on demand). Getting new entries into WikiData turned out to be pretty easy.
From OBO Operations meeting 2025-09-30:
James O points out that IEDB has a long list of transgenic mice that NCBI won’t add, it is a good idea to link to other things like WikiData, but there may be other problems due to axiom injections (we would be adding subclass axioms to an external term, the WikiData term); Updating NCBI Taxon with WikiData may be problematic too ; WikiData is probably a good idea but may need further discussion.
Other taxonomy resources: International Committee on Taxonomy of Viruses (ICTV)
Should we recommend WikiData and ICTV going forward to teams who have similar problems? Consensus so far is that this needs more discussion.
The Vertebrate Breed Ontology extends NCBItaxon for human made breeds such as cattle; perhaps they also started accepting mouse strains.
