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Re: Minutes for Scientific Discourse call

From: Jim McCusker <mccusker@gmail.com>
Date: Wed, 31 Mar 2010 11:02:27 -0400
Message-ID: <p2p68084f3e1003310802i84cf8831i2b8f14de12aa0245@mail.gmail.com>
To: Jie Zheng <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>
Thanks. I have been using classes and properties from MGED Ontology in
magetab2magerdf (http://magetab2magerdf.googlecode.com), and was hoping to
move to an OBI-based mapping sooner rather than later. You can see an
example at
http://magetab2rdf.googlecode.com/svn/trunk/magetab2magerdf/examples/E-MEXP-986.rdf

You will note that I am using an extension of MO which includes classes and
properties for things like Comments, ProtocolApplications, and other items
that are missing from MO. Any advice on if those items exist in OBI would be
helpful.

Thanks,
Jim

On Wed, Mar 31, 2010 at 10:47 AM, Jie Zheng <jiezheng@pcbi.upenn.edu> wrote:

> Hi Jim,
>
> We are only working on classes and instances but properties now. Most of
> mapped classes have logical definition (use OBI properties) in OBI. We will
> map properties when classes/instances mapping are done. If you have any use
> cases that used MO properties, please let me know. I can check whether it
> can map to any OBI one.
>
> Thanks,
>
> Jie
>
> Jim McCusker wrote:
>
>> Is this just classes, or are properties mapped as well?
>>
>> Jim
>>
>> On Wed, Mar 24, 2010 at 9:07 PM, <jiezheng@pcbi.upenn.edu <mailto:
>> 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
>>    <mailto: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 <http://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 <http://www.teranode.com>
>>
>>
>>
>>                -----Original Message-----
>>                From: public-semweb-lifesci-request@w3.org
>>                <mailto:public-semweb-lifesci-request@w3.org>
>>                [mailto:public-semweb- <mailto:public-semweb->
>>                lifesci-request@w3.org
>>                <mailto: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 <mailto:james.mccusker@yale.edu> | (203) 785-6330
>>
>> http://krauthammerlab.med.yale.edu
>>
>> PhD Student
>> Tetherless World Constellation
>> Rensselaer Polytechnic Institute
>> mccusj@cs.rpi.edu <mailto:mccusj@cs.rpi.edu>
>> http://tw.rpi.edu
>>
>
>


-- 
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 15:03:21 GMT

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