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Re: Minutes for Scientific Discourse call

From: Jim McCusker <mccusker@gmail.com>
Date: Wed, 31 Mar 2010 09:51:42 -0400
Message-ID: <s2w68084f3e1003310651m966e6b91k9c7f81bc7588df2@mail.gmail.com>
To: jiezheng@pcbi.upenn.edu
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>
Is this just classes, or are properties mapped as well?

Jim

On Wed, 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
>>>>
>>>>
>>
>
>
>
>
>


-- 
Jim
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.mccusker@yale.edu | (203) 785-6330
http://krauthammerlab.med.yale.edu

PhD Student
Tetherless World Constellation
Rensselaer Polytechnic Institute
mccusj@cs.rpi.edu
http://tw.rpi.edu
Received on Wednesday, 31 March 2010 13:52:35 GMT

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