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Re: Minutes for Scientific Discourse call

From: Jim McCusker <mccusker@gmail.com>
Date: Wed, 31 Mar 2010 17:09:13 -0400
Message-ID: <r2n68084f3e1003311409q49177a52r8027e25af0b51db7@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>, Chris Stoeckert <stoeckrt@pcbi.upenn.edu>
The terms I use (as opposed to classes, like BioSource, Experiment,
Hybridization, etc.) are picked up through the Term Sources listed in the
MAGE-TAB files.

Jim

On Wed, Mar 31, 2010 at 12:12 PM, Jie Zheng <jiezheng@pcbi.upenn.edu> wrote:

> Thanks. I will check your use case later. Now Dr. Chris Stoeckert (my
> supervisor) and I are working on MO terms that were used in the microarray
> experiments which stored in ArrayExpress. Most of the terms used in those
> studies have been added into OBI. If you have other terms needed including
> those out of scope of MGED ontology, you can either provide the list to me
> or check OBI first and submit needed terms to OBI tracker items directly (
> http://sourceforge.net/tracker/?group_id=177891&atid=886178).
>
> I will post latest mapping file later today and let you know the link.
>
>
> Thanks,
>
> Jie
>
> Jim McCusker wrote:
>
>> 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<mailto:
>> 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>
>>        <mailto: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>
>>           <mailto: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>
>>        <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>
>>        <http://www.teranode.com>
>>
>>
>>
>>                       -----Original Message-----
>>                       From: public-semweb-lifesci-request@w3.org
>>        <mailto:public-semweb-lifesci-request@w3.org>
>>                       <mailto:public-semweb-lifesci-request@w3.org
>>        <mailto:public-semweb-lifesci-request@w3.org>>
>>                       [mailto:public-semweb- <mailto:public-semweb->
>>        <mailto:public-semweb- <mailto:public-semweb->>
>>                       lifesci-request@w3.org
>>        <mailto:lifesci-request@w3.org>
>>                       <mailto: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>
>>        <mailto: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>
>>        <mailto: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 <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 21:10:05 GMT

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