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Re: Minutes for Scientific Discourse call

From: Helen Parkinson <parkinson@ebi.ac.uk>
Date: Wed, 24 Mar 2010 22:06:56 +0000
Message-ID: <4BAA8D00.2070006@ebi.ac.uk>
To: Michael Miller <mmiller@teranode.com>
CC: "M. Scott Marshall" <marshall@science.uva.nl>, HCLS <public-semweb-lifesci@w3.org>, Jie Zheng <jiezheng@pcbi.upenn.edu>
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, 24 March 2010 22:08:30 GMT

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