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Re: Minutes for Scientific Discourse call

From: Tim Clark <twclark@nmr.mgh.harvard.edu>
Date: Wed, 31 Mar 2010 07:22:05 -0400
Cc: Helen Parkinson <parkinson@ebi.ac.uk>, Michael Miller <mmiller@teranode.com>, "M. Scott Marshall" <marshall@science.uva.nl>, HCLS <public-semweb-lifesci@w3.org>
Message-Id: <9928E985-071B-4E9D-8004-38A17362A1EA@nmr.mgh.harvard.edu>
To: jiezheng@pcbi.upenn.edu
Thanks very much, Jie!

Tim

On Mar 24, 2010, at 9:07 PM, jiezheng@pcbi.upenn.edu wrote:

> Hi All,
> 
> I have made the mapping between MO and OBI/OBO ontologies and posted the mapping
> files on MGED ontology page. You can find the links in the mapping section of
> page
> http://mged.sourceforge.net/ontologies/MGEDontology.php
> 
> The mapping were made based on the definition. We found it should be more
> accurate to map the terms based on how they were used in the MAGE-TAB files.
> This work is in progress. I will update the MO to OBI mapping file soon and
> distribute the link.
> 
> Thanks,
> 
> Jie
> 
> 
> Quoting Helen Parkinson <parkinson@ebi.ac.uk>:
> 
>> Hi all,
>> 
>> let me clarify. OBI is at release 1.0
>> 
>> 1. EFO imports parts of OBI that we need for ArrayExpress, we will continue to use EFO in ArrayExpress, as it has added terms and relations between terms that exist nowhere else - cell types, to cell lines for example. And it has some terms that are imported from e.g. the cell type ontologu EFO is an application ontology and will persist as we need it in our GUIs. You can see our paper on this here:
>> 
>> http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq099
>> 
>> 2. Where we import terms from OBI - or any other ontology we retain their namespace as recommended by OBI foundry. As more terms are in OBI we will import them.
>> 
>> 3. My colleague Jie Zheng is in the process of mapping MO to OBI and when this is complete we will import more terms from OBI into EFO, but EFO will still be used for the foreseeable future by ArrayExpress. You can think of EFO as an application ontology, or view on OBI and many other ontologies.
>> 
>> 4. Where ontology terms imported into EFO have an authoritative source e.g. Chebi we use their namespace and where they are from non authoritative sources, for example there is no obo foundry ontology and many competing ontologies we assign our own ids and will continue to do so
>> 
>> Happy to answer any questions.
>> 
>> best regards
>> 
>> Helen
>> 
>> 
>> 
>> 
>> 
>> Michael Miller wrote:
>>> hi all,
>>> 
>>> some comments on the minutes.
>>> 
>>> "Possible overlaps with EFO ontology from EBI and OBI"
>>> 
>>> if i understand correctly, EFO was created because OBI was not finalized
>>> yet and ArrayExpress at EBI is a live gene expression data repository and
>>> the curators needed an ontology they could use.  i believe their plan is
>>> to move to OBI or update EFO to reflect the relationship of terms in EFO
>>> to terms in OBI.
>>> 
>>> "MGED may be part of OBI now"
>>> 
>>> MGED (www.mged.org) is a non-profit organization.  What is being referred
>>> to as MGED on the HCLS web site is a predecessor to OBI which should be
>>> called the MGED Ontology, also referred to as MO, that came out of an MGED
>>> effort.  OBI is to replace MO.
>>> 
>>> cheers,
>>> michael
>>> 
>>> Michael Miller
>>> Principal Software Developer
>>> www.teranode.com
>>> 
>>> 
>>>> -----Original Message-----
>>>> From: public-semweb-lifesci-request@w3.org [mailto:public-semweb-
>>>> lifesci-request@w3.org] On Behalf Of M. Scott Marshall
>>>> Sent: Wednesday, March 24, 2010 12:31 PM
>>>> To: HCLS
>>>> Subject: Minutes for Scientific Discourse call
>>>> 
>>>> Minutes for the Scientific Discourse call last Monday can be found at:
>>>> http://www.w3.org/2010/03/22-hcls-minutes.html
>>>> 
>>>> Sudeshna has distilled them nicely onto the wiki:
>>>> http://esw.w3.org/HCLSIG/SWANSIOC/Meetings/2010-3-22_Conference_Call
>>>> 
>>>> Cheers,
>>>> Scott
>>>> 
>> 
> 
> 
> 
> 
> 
> 
Received on Wednesday, 31 March 2010 11:22:39 GMT

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