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Re: Minutes for Scientific Discourse call

From: jie zheng <jiezheng@pcbi.upenn.edu>
Date: Thu, 01 Apr 2010 04:01:39 -0400
Message-ID: <4BB452E3.4030109@pcbi.upenn.edu>
To: Jim McCusker <mccusker@gmail.com>
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>
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 <jiezheng@pcbi.upenn.edu 
> <mailto:jiezheng@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
>         <jiezheng@pcbi.upenn.edu <mailto:jiezheng@pcbi.upenn.edu>
>         <mailto: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>
>          
>          <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>>
>                <mailto: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>>>
>                       <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
>         <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>>>
>                          <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
>         <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>
>                       <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>
>
>
>
>                                      -----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
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>                <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>>
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>         <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->>>
>                       <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>>>
>                                      <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
>         <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>>>
>                       <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
>         <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>>>
>                       <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 <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>>
>                <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
Received on Thursday, 1 April 2010 08:02:21 GMT

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