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Re: Minutes for Scientific Discourse call

From: Jim McCusker <mccusker@gmail.com>
Date: Thu, 1 Apr 2010 00:14:09 -0400
Message-ID: <r2i68084f3e1003312114ld4d2ba63t2d23ba39ed44ca4a@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>
A quick scan of my source code gives me the concepts in the attached file
(all local names relative to MO).

Jim

On Wed, Mar 31, 2010 at 9:12 PM, Jie Zheng <jiezheng@pcbi.upenn.edu> wrote:

> Hi Jim,
>
> I have updated the MO to OBI mapping file and check in soureforge.net.
> However, I got trouble to update the MGED ontology website hosted by
> sourceforge.net. Will try it later and send email if I made it. Sorry
> about it since I will take 2 week vacations from tomorrow.
>
> If you like, you can send me the terms you used and I can check whether
> they are in OBI.
>
>
> Thanks,
>
> Jie
>
> Jim McCusker wrote:
>
>> 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<mailto:
>> 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
>>    <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>
>>         <mailto: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>>
>>               <mailto: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>>
>>                  <mailto: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>
>>               <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>
>>               <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-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->>
>>               <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>>
>>                              <mailto: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>>
>>               <mailto: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>>
>>               <mailto: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>
>>        <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 Thursday, 1 April 2010 04:15:04 GMT

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