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[bioontology-support] Updating Rat strain ontology

Paul R Alexander palexander at stanford.edu
Mon Nov 5 13:13:01 PST 2012


Rajni,

You will need to point to the OBO file directly, not just the directory on the ftp site where the OBO file is located. I updated the metadata for you to point to ftp://rgd.mcw.edu/pub/ontology/rat_strain/rat_strain.obo. If that isn't correct, please login and make the change to the correct version.

This change should get picked up when we do our nightly check for new ontology versions, meaning that the new version of Rat Strain should be available late tonight or tomorrow morning (PST).

Paul


On Nov 5, 2012, at 11:11 AM, "Nigam, Rajni" <rnigam at mcw.edu> wrote:

> Hi,
>  
> I did add the URL for our ftp files in the ontology location but still the files are not pulled up to your website could you please look into this and let me know if I have to do something else to facilitate this.
>  
> Regards,
>  
> Rajni
>  
> From: Nigam, Rajni 
> Sent: Friday, October 26, 2012 2:16 PM
> To: 'Trish Whetzel'
> Subject: RE: Updating Rat strain ontology
>  
> Ok Done, please let me know if it doesn’t work!
>  
> Rajni
>  
> From: Trish Whetzel [mailto:whetzel at stanford.edu] 
> Sent: Thursday, October 25, 2012 10:51 PM
> To: Nigam, Rajni
> Subject: Re: Updating Rat strain ontology
>  
> Hi Rajni, 
>  
> They are automatically pulled nightly from a subdirectory within "http://rgd.mcw.edu". We are also able to pull from a FTP site as well. To change this for the Rat Strain Ontology, login and go to Rat Strain Ontology summary page (http://bioportal.bioontology.org/ontologies/1150). Presumably you have Admin rights to update the ontology metadata and therefore will see a drop-down menu titled "Admin". Click on "Edit Ontology Information" and then in the section "ontology Location" select "URL" and add the URL for the FTP location that the latest version of the RS ontology is found.
>  
> Best, 
> Trish 
>  
>  
>  
> On Oct 24, 2012, at 12:20 PM, Nigam, Rajni wrote:
>  
> 
> Hi Trish,
>  
> I am looking at Clinical measurement Ontology http://bioportal.bioontology.org/ontologies/1583 Measurement Method Ontologyhttp://bioportal.bioontology.org/ontologies/1584 and Experimental Condition Ontologyhttp://bioportal.bioontology.org/ontologies/1585 that are housed and developed at RGD http://rgd.mcw.edu/ .
>  
> Could you please tell me how these ontologies are updated at NCBO? If you all directly download it from our  ftp filesftp://rgd.mcw.edu/pub/ontology/ then is it possible for you to please add Rat Strain Ontologyhttp://bioportal.bioontology.org/ontologies/1150 to that list too, as we have the latest version of it in our website.
>  
> Could you please tell me how frequently do you all take these from our website?
>  
> Thanks,
>  
>  
> Rajni
>  
>  
> Rajni Nigam 
> Scientific Curator 
> Rat Genome Database 
> (http://.rgd.mcw.edu) 
> Medical College of Wisconsin 
> 8701 Watertown Plank Road 
> Milwaukee, WI 53226
>  
> Phone: (414) 456 7508 
> email: rnigam at mcw.edu
>  
>  
>  
>  
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> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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