- From: Jim McCusker <mccusker@gmail.com>
- Date: Wed, 31 Mar 2010 17:09:13 -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: <r2n68084f3e1003311409q49177a52r8027e25af0b51db7@mail.gmail.com>
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> 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). > > 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>> 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>>> 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>>>: >> >> >> >> 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>) 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> >> >> >> >> -----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- <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>>] 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>> | (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 Wednesday, 31 March 2010 21:10:05 UTC