Re: Minutes for Scientific Discourse call

[jie zheng]

I quickly look through the terms you listed in the attached file. Most 
of them are MO terms. Moving MO to OBI, we may model the microarray 
experiments in the different way. The MO properties will be replaced by 
relations in RO. I will think about it and let you know what OBI 
properties can be used to replace the MO ones.

Jie
Jim McCusker wrote:
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 <jiezh...@pcbi.upenn.edu 
<mailto:jiezh...@pcbi.upenn.edu>> wrote:

    Hi Jim,

    I have updated the MO to OBI mapping file and check in
    soureforge.net <http://soureforge.net>. However, I got trouble to
    update the MGED ontology website hosted by sourceforge.net
    <http://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
        <jiezh...@pcbi.upenn.edu <mailto:jiezh...@pcbi.upenn.edu>
        <mailto:jiezh...@pcbi.upenn.edu
        <mailto:jiezh...@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>
         
         <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
               <jiezh...@pcbi.upenn.edu
        <mailto:jiezh...@pcbi.upenn.edu>
        <mailto:jiezh...@pcbi.upenn.edu <mailto:jiezh...@pcbi.upenn.edu>>
               <mailto:jiezh...@pcbi.upenn.edu
        <mailto:jiezh...@pcbi.upenn.edu>
               <mailto:jiezh...@pcbi.upenn.edu
        <mailto:jiezh...@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,
               <jiezh...@pcbi.upenn.edu
        <mailto:jiezh...@pcbi.upenn.edu>
        <mailto:jiezh...@pcbi.upenn.edu <mailto:jiezh...@pcbi.upenn.edu>>
                      <mailto:jiezh...@pcbi.upenn.edu
        <mailto:jiezh...@pcbi.upenn.edu>
               <mailto:jiezh...@pcbi.upenn.edu
        <mailto:jiezh...@pcbi.upenn.edu>>>
                      <mailto:jiezh...@pcbi.upenn.edu
        <mailto:jiezh...@pcbi.upenn.edu>
               <mailto:jiezh...@pcbi.upenn.edu
        <mailto:jiezh...@pcbi.upenn.edu>>
                      <mailto:jiezh...@pcbi.upenn.edu
        <mailto:jiezh...@pcbi.upenn.edu>
               <mailto:jiezh...@pcbi.upenn.edu
        <mailto:jiezh...@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 <parkin...@ebi.ac.uk
        <mailto:parkin...@ebi.ac.uk>
               <mailto:parkin...@ebi.ac.uk <mailto:parkin...@ebi.ac.uk>>
                      <mailto:parkin...@ebi.ac.uk
        <mailto:parkin...@ebi.ac.uk> <mailto:parkin...@ebi.ac.uk
        <mailto:parkin...@ebi.ac.uk>>>
                         <mailto:parkin...@ebi.ac.uk
        <mailto:parkin...@ebi.ac.uk>
               <mailto:parkin...@ebi.ac.uk
        <mailto:parkin...@ebi.ac.uk>> <mailto:parkin...@ebi.ac.uk
        <mailto:parkin...@ebi.ac.uk>
               <mailto:parkin...@ebi.ac.uk
        <mailto:parkin...@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>
                      <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>
                      <http://www.teranode.com>



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               <mailto:lifesci-requ...@w3.org
        <mailto:lifesci-requ...@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.mccus...@yale.edu
        <mailto:james.mccus...@yale.edu>
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               --         Jim
               --
               Jim McCusker
               Programmer Analyst
               Krauthammer Lab, Pathology Informatics
               Yale School of Medicine
               james.mccus...@yale.edu
        <mailto:james.mccus...@yale.edu>
        <mailto:james.mccus...@yale.edu <mailto:james.mccus...@yale.edu>>
               <mailto:james.mccus...@yale.edu
        <mailto:james.mccus...@yale.edu>
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        <mailto:james.mccus...@yale.edu>>> | (203) 785-6330
               http://krauthammerlab.med.yale.edu

               PhD Student
               Tetherless World Constellation
               Rensselaer Polytechnic Institute
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        -- 
        Jim
        --
        Jim McCusker
        Programmer Analyst
        Krauthammer Lab, Pathology Informatics
        Yale School of Medicine
        james.mccus...@yale.edu <mailto:james.mccus...@yale.edu>
        <mailto:james.mccus...@yale.edu
        <mailto:james.mccus...@yale.edu>> | (203) 785-6330
        http://krauthammerlab.med.yale.edu

        PhD Student
        Tetherless World Constellation
        Rensselaer Polytechnic Institute
        mcc...@cs.rpi.edu <mailto:mcc...@cs.rpi.edu>
        <mailto:mcc...@cs.rpi.edu <mailto:mcc...@cs.rpi.edu>>
        http://tw.rpi.edu





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

PhD Student
Tetherless World Constellation
Rensselaer Polytechnic Institute
mcc...@cs.rpi.edu <mailto:mcc...@cs.rpi.edu>
http://tw.rpi.edu