Re: [Obo-taxonomy] NCBI taxonomy update

[Chris Mungall]

We need to set up a monthly pipeline

On 9 Jul 2014, at 13:29, Melanie Courtot wrote:

> Hi Chris,
>
> How is the OWL version of the NCBI taxonomy updated?
> For example I was trying to get
> http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1232152,
> but Ontofox returns nothing.
>
> Cheers,
> Melanie

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[Pankaj Jaiswal (OSU)]

Did this one get dropped? Looks like there are no recent updates.
http://www.obofoundry.org/cgi-bin/detail.cgi?id=ncbi_taxonomy

Pankaj

[Peter Midford]

It appears that the Jenkins build hasn't been run recently either:
http://build.berkeleybop.org/job/build-ncbitaxon/

-Peter

[Chris Mungall]

Version 2014-07-11 is now available from standard PURLs

We are now ready to go with our original plan of monthly releases, thanks to Heiko and James for getting the code and system in place. Here's how it works, for anyone interested. The Jenkins job is manually triggered by someone with relevant permissions.

http://build.berkeleybop.org/job/build-ncbitaxon/

If the build is successful, the contents will be deployed in http://www.berkeleybop.org/ontologies/ncbitaxon/ around midnight PT. No one should bookmark this URL however, always use the purls as described here http://www.obofoundry.org/wiki/index.php/NCBITaxon:Main_Page

I suggest as release managers myself, Peter Midford and James Overton. All the RM does is click the button on Jenkins, on the first of every month, or shortly thereafter. We can be flexible here - if people want more or less frequent speak up on this list.

Note that one issue with the current system is that NCBI sometimes removes IDs, and we aren't tracking these. If resources permit we could have a more labor intensive release process whereby the RM does a test build, makes a diff, announces it on this list. However, I can't commit to this myself.

We could also try and coordinate this more with NCBI but I don't have the bandwidth for this myself at the moment.

On Wed, Jul 9, 2014 at 4:58 PM, Pankaj Jaiswal (OSU) <jais...@science.oregonstate.edu> wrote:

Did this one get dropped? Looks like there are no recent updates.
http://www.obofoundry.org/cgi-bin/detail.cgi?id=ncbi_taxonomy

Pankaj

On 07/09/2014 4:54 PM, Chris Mungall wrote:

We need to set up a monthly pipeline

On 9 Jul 2014, at 13:29, Melanie Courtot wrote:

Hi Chris,

How is the OWL version of the NCBI taxonomy updated?
For example I was trying to get
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1232152,
but Ontofox returns nothing.

Cheers,
Melanie

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[Melanie Courtot]

That sounds fantastic - thanks for all your work on this. 

I am planning on liaising with the NCBI folks at some point with respect to some missing IDs; my supervisor Fiona is already talking to them about other unrelated things, and I'll be following up. Some serovars we deal with for food borne diseases are not available in the NCBI taxonomy as they haven't been sequenced yet, so we'd like to either (1) get NCBI to add those (2) get them to give us an ID range to add them. I'm not sure if they'd be willing to do the addition, as their mandate is specifically for sequenced organisms. However, I don't really want to assign my own specific IDs, so I was thinking maybe a reserved ID range within the NCBI namespace could be an option - and then we could build this as an extension of the NCBItax.owl file. If any of you has experience with that type of issue feedback is welcome. 

In any case, I anticipate I'll be talking to them soon-ish, and I'm happy to discuss the coordination of the OWL release (and include others in this discussion). Is there existing history/people you have been in touch with?

Cheers,

Melanie

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Mélanie Courtot

Research associate

Brinkman Lab, MBB Department, Simon Fraser University, 

Hsiao lab, BC Public Health Microbiology & Reference Laboratory,

Rm SSB7121, 8888 University Drive

Burnaby, BC, Canada, V5A 1S6

[Peter Midford]

Works for me.  I would be willing to participate in experimenting with test builds to tracked deleted IDs (though I suspect these are less common for multicellular taxa). 

-Peter

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[Chris Mungall]

What would happen once the serovars do get sequenced? Would NCBI use
your IDs?

The ID range thing seems complicated and fraught with difficulties. I
don't like the ID of having a n NCBITaxon ID that isn't backed by
something on the NCBI database/website. There's a precedent for using
your own ID space here, e.g. paleo databases.

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[Trish Whetzel]

If this is a matter of generating a diff of ontology IDs across sequential versions I can probably help out since the task sounds very similar to ID diffs I'm doing related to updating NIFSTD by comparing module files to bridge files.

Trish

[Melanie Courtot]

Ideally yes - after sequencing, NCBI would use those IDs. Though I agree with your assessment and I don't think that's ideal either. What is the paleo databases experience? 

My issues with assigning my own ID is that (1) assigning tax IDs is really out of scope for us, so I'd prefer having a way to not have to do it (2) we already know that those will get deprecated when sequencing happens; though I guess we could always state the equivalence.

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