Practice for referring to taxa not in NCBI Taxon?

[alanruttenberg]

@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?

[balhoff]

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.

[bionicjules]

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 notifications@github.com 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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[cmungall]

@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

[bionicjules]

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 notifications@github.com 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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[cmungall]

Have you tried contacting them? info@ncbi.nlm.nih.gov

[nlharris]

Is this still something that needs to be addressed?

[jamesaoverton]

This is still important and we do not have a resolution.