RE: MGED/FuGO. was: Re: BioRDF [Telcon]: slides for the UMLS presentation

Hi Kei,

> My question is that can we use FuGO or FuGO-OM or other ontologies ..

Quick note, there is no FuGO-OM, just FuGO.  There is FuGE-OM (and its
generated FuGE-ML) which is a UML model, quite a different animal.

If you go to the "Available Actions" box there is a "View MAGE-ML"
button.  Click that and you will see a MAGE-ML document that has already
been rather nicely annotated using the MGED Ontology.  What MAGE-OM
does, and this is reflected in the MAGE-ML of course, is allows
references into an ontology to associate a UML class instance in the
MAGE-ML with annotations from an ontology.  You'll see the
<OntologyEntry> elements for the BioMaterial classes and
ExperimentDesign classes that use <OntologyEntry> and its nested
elements to reference into an Ontology.  The power of references is that
the entire ontology doesn't have to be used, only the relevant terms
referenced in the XML, and any appropriate ontology can be used, not
just the MGED Ontology.

    <OntologyEntry category="ExperimentDesignType"
value="subclassification" description="Group of assays that are related
as a subclassification experiment">
      <OntologyReference_assn>
        <!--  inDatabase=true, dbId=20526, uniqueId=20526,
modified=false, attributeModified=false 
        --> 
        <DatabaseEntry accession="#ExperimentDesignType"
URI="http://mged.sourceforge.net/ontologies/MGEDontology.php#ExperimentD
esignType">
          <Database_assnref>
            <Database_ref identifier="MO" /> 
          </Database_assnref>
        </DatabaseEntry>
      </OntologyReference_assn>
    </OntologyEntry>

After the information has been downloaded into a local datastore
(MAGE-ML is intended to only exchange information, not be used
directly), a user can run whatever applications they want on the
information, including ontology inference machines that can go out to
the referenced ontologies.

cheers,
Michael

> -----Original Message-----
> From: kei cheung [mailto:kei.cheung@yale.edu] 
> Sent: Tuesday, June 06, 2006 10:34 AM
> To: Miller, Michael D (Rosetta)
> Cc: Alan Ruttenberg; donald.doherty@brainstage.com; 
> wilbanks@creativecommons.org; Daniel Rubin; 
> public-semweb-lifesci@w3.org; Matthew Cockerill
> Subject: Re: MGED/FuGO. was: Re: BioRDF [Telcon]: slides for 
> the UMLS presentation
> 
> 
> Hi Michael et al.,
> 
> Karen Skinner (of NIDA) has once pointed me to the following public 
> microarray experiment related to the study of Parkinson's Disease
> 
> http://arrayconsortium.tgen.org/np2/viewProject.do?action=view
> Project&projectId=61
> 
> 
> My question is that can we use FuGO or FuGO-OM or other ontologies 
> (MGED-OWL) to describe this experiment (or part of it)? This 
> might also 
> serve as a Parkinson use case study for the ontology working group.
> 
> Cheers,
> 
> -Kei
> 
> Miller, Michael D (Rosetta) wrote:
> 
> >Hi All,
> >
> >  
> >
> >>Thanks for pointing us to FuGO. To me, it seems like that the FuGO 
> >>community is currently defining an upper ontology that can be 
> >>universally used to describe different types of genomic/proteomic 
> >>experiments including microarray experiments. 
> >>    
> >>
> >
> >This, I believe, is their goal.
> >
> >  
> >
> >>but 
> >>there is no 
> >>example use for microarray experiments. 
> >>    
> >>
> >
> >To actually describe microarray experiments (and proteomics, 
> etc.), it
> >is expected that this will be done through extensions of 
> FuGE-OM, a UML
> >model that takes experiences from MAGEv1 and PEDRo (and others) to
> >create an object model that describes what is basic to all biological
> >based experiments.  MAGEv2 will extend this model.
> >
> >One goal of FuGO is:
> >
> >"The purpose of this ontology is to support the consistent 
> annotation of
> >functional genomics experiments, regardless of the 
> particular field of
> >study."
> >
> >So it is unlikely at this point that there will be a class
> >"Hybridization" or "FeatureExtraction" in the ontology but there is
> >likely to be terms that describe particular ways of doing a
> >hybridization or feature extraction.
> >
> >FuGO is still at an early stage, see http://fugo.sourceforge.net/ for
> >how someone can contribute.
> >
> >cheers,
> >Michael
> >
> >  
> >
> >>-----Original Message-----
> >>From: public-semweb-lifesci-request@w3.org 
> >>[mailto:public-semweb-lifesci-request@w3.org] On Behalf Of 
> kei cheung
> >>Sent: Tuesday, June 06, 2006 9:52 AM
> >>To: Alan Ruttenberg
> >>Cc: donald.doherty@brainstage.com; 
> >>wilbanks@creativecommons.org; 'Daniel Rubin'; 
> >>public-semweb-lifesci@w3.org; 'Matthew Cockerill'
> >>Subject: Re: MGED/FuGO. was: Re: BioRDF [Telcon]: slides for 
> >>the UMLS presentation
> >>
> >>
> >>
> >>Hi Alan,
> >>
> >>Thanks for pointing us to FuGO. To me, it seems like that the FuGO 
> >>community is currently defining an upper ontology that can be 
> >>universally used to describe different types of genomic/proteomic 
> >>experiments including microarray experiments. There is a draft OWL 
> >>version of FuGO 
> >>(http://fugo.sourceforge.net/ontology/FuGO.owl). A list 
> >>of use case uses is also shown at: 
> >>http://fugo.sourceforge.net/ontologyInfo/ontology.php, but 
> >>there is no 
> >>example use for microarray experiments. So it might be 
> worthwhile to 
> >>take a look at how FuGO can be used to describe microarray 
> >>experiments 
> >>(at least at a high level).
> >>
> >>Cheers,
> >>
> >>-Kei
> >>
> >>Alan Ruttenberg wrote:
> >>
> >>    
> >>
> >>>On Jun 5, 2006, at 9:15 PM, kc28 wrote:
> >>>
> >>>      
> >>>
> >>>>It might be time to think about how to convert mged ontology or 
> >>>>mage-ml into RDF/OWL. The following are two related articles:
> >>>>
> >>>>http://www.nature.com/msb/journal/v2/n1/full/msb4100052.html
> >>>>http://www.nature.com/nbt/journal/v23/n9/full/nbt0905-1095.html
> >>>>
> >>>>Cheers,
> >>>>
> >>>>-Kei
> >>>>        
> >>>>
> >>>As I understand it, this is the nature of the FuGO project: 
> >>>http://fugo.sourceforge.net/
> >>>They have an upcoming workshop
> >>>http://www.ebi.ac.uk/microarray/General/Events/FuGO2006/index.html
> >>>
> >>>-Alan
> >>>
> >>>
> >>>      
> >>>
> >>
> >>
> >>
> >>    
> >>
> >
> >
> >  
> >
> 
> 
> 
>

Received on Tuesday, 6 June 2006 18:57:52 UTC