Re: [Obo-taxonomy] NCBITaxon

[Peter Midford]

Chris,

           Agree with adding ono-taxonomy.   Pulling updates from the Jenkins page is fine with me, though it looks like it hasn't been run since January either.

Heiko, I'd like to hear more about this obsoleting and merging of NCBI IDs.  I think a lot of us have assumed these were stable, so this is a concern.  Do you have some examples?

-Peter

On Dec 13, 2013, at 12:45 PM, Chris Mungall <cjmu...@lbl.gov> wrote:

I think we should take this to the obo-taxonomy group

On Fri, Dec 13, 2013 at 9:44 AM, Heiko Dietze <hdi...@lbl.gov> wrote:

Hello,

the version IRI seems to be correct. The last build from the ncbitaxon source files in the SVN was in January.
All recent changes have been updates to the slim files, which have been generated from the main tax file.

As for automation, my biggest concern is the ID strategy of the NCBI. They seem to obsolete and merge IDs quite frequently. This might throw off the automation/release process on our site.

regards,

Heiko

On 12/13/13 8:28 AM, Chris Mungall wrote:

Heiko, was that January we made the last change?

Seems so, unless the versionIRI is wrong:
http://purl.obolibrary.org/obo/ncbitaxon/2013-01-24/ncbitaxon.owl

Peter, we make regular builds here, but we don't actually release them:
http://build.berkeleybop.org/job/build-ncbitaxon/

Do you want to check that the latest fits your purposes?

We should probably have a regular release - synced with NCBI? Maybe
slower (changes in the taxonomy potentially has big impacts downstream)?
What do you think?


On Thu, Dec 12, 2013 at 6:51 PM, Peter Midford <peter....@gmail.com

<mailto:peter.midford@gmail.com>> wrote:

    Hi Chris,
                     I may be the last person you would expect to be
    requesting this, but could you run an update on the OWL version of
    NCBITaxon?  I've been using it for some spider behavior projects and
    it looks like it was last updated in January (or am I looking at the
    wrong modification date?)

    Thanks,

    Peter

[Heiko Dietze]

Hello Peter,

this is an excerpt from the NCBI taxonomy FAQ, see here:
http://www.ncbi.nlm.nih.gov/books/NBK54428/

"... Taxa are occasionally removed from the taxonomy database
(particularly internal nodes, during a taxonomic revision) ... "

They provide a file with deleted ids, but the sheer number of these
deletions blew up the OWL translation. We only include alt_ids, and do
not create obsolete classes for the deleted ones.

So it is possible that taxon ids might vanish from the OBO (or OWL)
file, due to them being deleted.
We noticed this, when we tried to regenerate the slim files from the
last run, there were a few taxon ids which were no longer used.

regards,

Heiko

On 12/13/13 12:33 PM, Peter Midford wrote:
> Chris,
> Agree with adding ono-taxonomy. Pulling updates from the
> Jenkins page is fine with me, though it looks like it hasn't been run
> since January either.
>
> Heiko, I'd like to hear more about this obsoleting and merging of NCBI
> IDs. I think a lot of us have assumed these were stable, so this is a
> concern. Do you have some examples?
>
> -Peter
>
> On Dec 13, 2013, at 12:45 PM, Chris Mungall <cjmu...@lbl.gov

> <mailto:cjmu...@lbl.gov>> wrote:
>
>> I think we should take this to the obo-taxonomy group
>>
>>
>> On Fri, Dec 13, 2013 at 9:44 AM, Heiko Dietze <hdi...@lbl.gov
>> <mailto:hdi...@lbl.gov>> wrote:
>>
>> Hello,
>>
>> the version IRI seems to be correct. The last build from the
>> ncbitaxon source files in the SVN was in January.
>> All recent changes have been updates to the slim files, which have
>> been generated from the main tax file.
>>
>> As for automation, my biggest concern is the ID strategy of the
>> NCBI. They seem to obsolete and merge IDs quite frequently. This
>> might throw off the automation/release process on our site.
>>
>> regards,
>>
>> Heiko
>>
>>
>> On 12/13/13 8:28 AM, Chris Mungall wrote:
>>
>> Heiko, was that January we made the last change?
>>
>> Seems so, unless the versionIRI is wrong:

>> http://purl.obolibrary.org/__obo/ncbitaxon/2013-01-24/__ncbitaxon.owl

>> <http://purl.obolibrary.org/obo/ncbitaxon/2013-01-24/ncbitaxon.owl>
>>
>> Peter, we make regular builds here, but we don't actually
>> release them:

>> http://build.berkeleybop.org/__job/build-ncbitaxon/

>> <http://build.berkeleybop.org/job/build-ncbitaxon/>
>>
>> Do you want to check that the latest fits your purposes?
>>
>> We should probably have a regular release - synced with NCBI?
>> Maybe
>> slower (changes in the taxonomy potentially has big impacts
>> downstream)?
>> What do you think?
>>
>>
>> On Thu, Dec 12, 2013 at 6:51 PM, Peter Midford

>> <peter....@gmail.com <mailto:peter....@gmail.com>
>> <mailto:peter.midford@gmail.__com

>> <mailto:peter....@gmail.com>>> wrote:
>>
>> Hi Chris,
>> I may be the last person you would expect
>> to be
>> requesting this, but could you run an update on the OWL
>> version of
>> NCBITaxon? I've been using it for some spider behavior
>> projects and
>> it looks like it was last updated in January (or am I
>> looking at the
>> wrong modification date?)
>>
>> Thanks,
>>
>> Peter
>>
>>
>>
>

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