- From: Jim McCusker <mccusker@gmail.com>
- Date: Thu, 1 Apr 2010 00:14:09 -0400
- 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>
- Message-ID: <r2i68084f3e1003312114ld4d2ba63t2d23ba39ed44ca4a@mail.gmail.com>
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
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Received on Thursday, 1 April 2010 04:15:04 UTC