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[bioontology-support] BioPortal Ontology IDs

Trish Whetzel whetzel at
Fri Dec 19 17:13:38 PST 2008

Hi Lynn,


Attached is the NCBO favicon. Does this work?




From: Lynn Fink [mailto:jlfink at] 
Sent: Tuesday, December 16, 2008 9:31 PM
To: Trish Whetzel
Subject: Re: BioPortal Ontology IDs


Yes, I think the favicon size would work. This is what appears on Windows
windows in the upper left corner to brand the program. It would go on the
ontology download window.

On 12/16/08 9:13 PM, "Trish Whetzel" <whetzel at> wrote:

I'll see what I can do with this. Trying to envision the title bar, do you
mean as the size of a favicon?

Sent from my iPhone

On Dec 16, 2008, at 6:19 PM, Lynn Fink <jlfink at> wrote:

Hi Trish,

Do you have an icon that we can use in the add-in? We need one that is 16
pixels square for the title bar and then another that is a bit smaller
(waving hands) than the one on your web site ( <> ) -
whatever you think would look best in a Windows dialog box. No worries if
this is difficult.


On 12/15/08 6:46 PM, "Trish Whetzel" <whetzel at
<mailto:whetzel at> > wrote:


From: Lynn Fink [mailto:jlfink at <mailto:jlfink at> ] 
Sent: Monday, December 15, 2008 6:36 PM
To: Nigam Shah
Cc: Trish Whetzel
Subject: Re: BioPortal Ontology IDs

Here are some screenshots of the two instances in which we use NCBO
ontologies. Let me know if you want more detail. If anyone at the meeting is
interested in testing the add-in, please tell them to mail biolit at
<mailto:biolit at>  (or me).

Thanks for your support.


On 12/11/08 3:22 PM, "Nigam Shah" <nigam at
<mailto:nigam at> > wrote:
Hi Lynn,

Would it be possible for you to share a slide on BioLit and the Microsoft
Word Plugin that you mentioned? The reason I ask is that we have our NCBO
project meeting next week (Tue/Wed) and I'd like to highlight the work you
are doing and how you are using our services. A couple of NIH officers and
all our collaborating R01 projects will be present .. so will hit a good

Let me know.


On Tue, Dec 9, 2008 at 5:29 PM, Lynn Fink <jlfink at
<mailto:jlfink at> > wrote:

Ohhh! I get it now. Sorry about that. :) Great news. I'll make the
appropriate changes.

Good to know the add-in is getting some publicity. I hope people like it.
Maybe you guys would like to test it out? We should have something
distributable mid-month.

Also great about the taxonomy ontology.

Thanks, you guys are awesome.

On 12/9/08 5:22 PM, "Trish Whetzel" <whetzel at
<mailto:whetzel at> > wrote:

> Hi Lynn,
> The ontology IDs are stable, however when a new version of the ontology is
> loaded then that version of the ontology has a new identifier for that
> version. In the XML below (based on
<> ), the value 1070
is for
> all versions of Biological process, while the value 38995 is for version
> of Biological process.
> <ontology>
> <id>38995</id>
> <ontologyId>1070</ontologyId>
> <displayLabel>Biological process</displayLabel>
> ?<description>
> A controlled vocabulary of gene and gene product attributes related to
> biological process.
> </description>
> <abbreviation>GO</abbreviation>
> <format>OBO</format>
> <internalVersionNumber>102</internalVersionNumber>
> <versionNumber>1.376</versionNumber>
> <versionStatus>production</versionStatus>
> <contactName>Gene Ontology</contactName>
> <contactEmail>">go at</contactEmail>
<mailto:go at>  <go at
<mailto:go at> > 
> <statusId>3</statusId>
> ?<categoryIds>
> <int>2806</int>
> </categoryIds>
> <dateCreated class="sql-timestamp">2008-12-09 02:32:10.0</dateCreated>
> </ontology>
> BTW, I am at the Microsoft eScience conference and Tony Hey mentioned your
> Word plugin during his closing remarks - very cool work! If you would be
> to include a link and/or logo back to BioPortal that would be great.
> I also wanted to let you know that the issue with the NCBI taxonomy has
> resolved and will be able to be loaded in the next version of BioPortal,
> scheduled to be released in early January. The question regarding the Cell
> Type ontology is in the queue; my   aim is to clarify that by the end of
> week.
> Cheers,
> Trish
>> -----Original Message-----
>> From: Lynn Fink [mailto:jlfink at <mailto:jlfink at> ]
>> Sent: Tuesday, December 09, 2008 2:29 PM
>> To: Trish Whetzel; nigam at <mailto:nigam at> 
>> Subject: BioPortal Ontology IDs
>> Hi Trish and Nigam,
>> I have a question about the stability of the ontology IDs. I was
>> assuming
>> they were going to be stable, but it appears I may be wrong. For
>> example,
>> "Biological process" used to be 38612 and is now 1070.
>> What I need to do is download certain ontologies periodically using
>> software
>> and I was hardcoding the ID. Obviously, this won't work if the IDs
>> change,
>> so I was wondering if there are plans to keep them constant.
>> Specifically, I want to download these for two programs. One is the
>> BioLit
>> project that Nigam heard about last year - parsing full-text papers to
>> find
>> words from some ontologies, updated weekly or so. The other is a
>> Microsoft
>> Word 2007 Add-in that does the same thing, but as an author is writing a
>> document. BioLit will be fairly easy to change, but the Add-in is more
>> problematic. (We would be happy to include a logo and link from the
>> config
>> panel to BioPortal if you are interested.)
>> Cheers,
>> Lynn
>> --
>> Lynn Fink, Ph.D.
>> University of California, San Diego
>> Skaggs School of Pharmacy and Pharmaceutical Sciences
>> 9500 Gilman Drive
>> La Jolla, CA 92093-0444 USA
>> +1-858-822-1897

Lynn Fink, Ph.D.
University of California, San Diego
Skaggs School of Pharmacy and Pharmaceutical Sciences
9500 Gilman Drive
La Jolla, CA 92093-0444 USA

Lynn Fink, Ph.D.
University of California, San Diego
Skaggs School of Pharmacy and Pharmaceutical Sciences
9500 Gilman Drive
La Jolla, CA 92093-0444 USA

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