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Re: Minutes for Scientific Discourse call

From: Jie Zheng <jiezheng@pcbi.upenn.edu>
Date: Wed, 31 Mar 2010 21:12:25 -0400
Message-ID: <4BB3F2F9.3020905@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>
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
Received on Thursday, 1 April 2010 01:13:15 GMT

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