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RE: [Obo-relations] FuGE, Ontologies, NINDS Microarray, GENSAT, ABA, and AD

From: Miller, Michael D (Rosetta) <Michael_Miller@Rosettabio.com>
Date: Mon, 4 Jun 2007 18:04:01 -0700
To: "Kei Cheung" <kei.cheung@yale.edu>
cc: "William Bug" <William.Bug@DrexelMed.edu>, "Smith, Barry" <phismith@buffalo.edu>, "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>, samwald@gmx.at, public-semweb-lifesci@w3.org, obo-relations@lists.sourceforge.net, "Paul Spellman" <spellman@bdgp.lbl.gov>, "Shrikant Mane" <shrikant.mane@yale.edu>
Message-ID: <E1HvNT7-0006gU-Ls@aji.w3.org>

hi kai,

> I think these are related subjects

well, as we've seen, everything is related to everything else, but,
specifically, there's obviously the need for people to be able to not
only compare microarray experiments for similarities but all types of
system biology experiments, one interesting use case (among many) is
comparing proteomic results with gene expression results for the same
set of subjects.

> Before going into further 
> detail about how to convert NINDS microarray data into OWL ...

one item i was unclear on was what the scope of conversion of microarray
data into OWL you have in mind.  my take on this, as i said previously,
is that in MAGE and eventually in MAGEv2, the actual performance of the
microarray experiment and the results are captured in the XML schema
generated from the UML model.  there is also the ability to annotate,
using the ontology package, all the objects in the XML document.  it's
this annotation i believe can be easily translated into RDF or OWL,
based on the early version of the OMG Ontology Metamodel.  the rest of
the document is easily comparable with other documents at the XML or UML
level.

cheers,
michael

> -----Original Message-----
> From: Kei Cheung [mailto:kei.cheung@yale.edu] 
> Sent: Saturday, June 02, 2007 7:26 AM
> To: Miller, Michael D (Rosetta)
> Cc: William Bug; Smith, Barry; Kashyap, Vipul; 
> samwald@gmx.at; public-semweb-lifesci@w3.org; 
> obo-relations@lists.sourceforge.net; Paul Spellman; Shrikant Mane
> Subject: Re: [Obo-relations] FuGE, Ontologies, NINDS 
> Microarray, GENSAT, ABA, and AD
> 
> Hi Michael, Bill, Barry, et al.,
> 
> I think these are related subjects (see the modified title and 
> discussion below). I also copied this email to the Yale PI 
> (Dr. Shrikant 
> Mane) who is one of the PI's of the NINDS microarray 
> consortium (Yale is 
> among one of the four centers in the consortium) in the hope of 
> initiating an interaction between the consortium and 
> SWHCLS/ontology/MGED groups. I'm also trying to practice TBL's "Web 
> Science" synergizing different communities. Before going into further 
> detail about how to convert NINDS microarray data into OWL , 
> we should 
> probably step back and see what we might accomplish.
> 
> Since our HCLS paper (http://www.biomedcentral.com/1471-2105/8/S3/S2) 
> and Banff demo (http://esw.w3.org/topic/HCLS/Banff2007Demo) 
> centered on 
> a use case of Alzheimer Disease (AD), for the fun of it, I searched 
> using the keyword "Alzheimer Disease" to see if there are any AD 
> microarray data stored in the NINDS microarray consortium repository. 
> It's not a surprise that I found a number of neuroscience microarray 
> projects that have to do with the study of AD. Below is the 
> URL pointing 
> to the description of one of the AD microarray projects.
> 
> http://arrayconsortium.tgen.org/np2/viewProject.do?action=view
> Project&projectId=110
> 
> As you can see the content is structured and I think can be converted 
> into an OWL ontology. More interestingly, it seems to have some 
> annotation errors. For example, if you look at the following 
> field/value 
> pairs:
> 
> organ/tissue type: blood
> organ region: adrenal medulla
> 
> According to the description of the project (e.g., experimental 
> procedure and design), I think they should be:
> 
> organ/tissue type: brain
> organ region: entorhinal cortex
> 
> Basically, this microarray project generated differential gene 
> expression profiling data for neurons containing 
> neurofibrillary tangles 
> and normal neurons from the entorhinal cortex of AD cases (mid-stage).
> 
> Even more interestingly, one can integrate such gene expression data 
> with other types of gene expression data (e.g., image-based gene 
> expression data) stored in other repositiories. For example, 
> if you go 
> to GENSAT, you can find what genes are expressed in a given 
> brain region 
> (e.g., entorhinal cortex).
> 
> http://braininfo.rprc.washington.edu/Scripts/indexothersite.as
> px?ID=150&type=h&term=entorhinal_area&thterm=Entorhinal%20Cort
ex&city=Bethesda&country=USA&institue=NCBI,%20National%20Library%20of%>
20Medicine&namesite=GENSAT&URL=http://www.ncbi.nlm.nih.gov/pro
> jects/gensat/index.cgi?cmd=searchhjsAMPgene_name=hjsAMPgene_sy
m=hjsAMPage=anyhjsAMPexp_tech=anyhjsAMPplane=anyhjsAMPregion=Entorhinal+
CortexhjsAMPcell=anyhjsAMPl> evel=anyhjsAMPfmt=gene
> 
> Of course, similar integration can be performed with other 
> image-based 
> gene expression repositories such as Allen Brain Atlas.
> 
> Cheers,
> 
> -Kei
> 
> Miller, Michael D (Rosetta) wrote:
> 
> > hi bill and kei,
> >  
> > i've changed the subject, since this is moving away from 
> the original 
> > topic.
> >  
> > "Yes - you are right, of course - right now the TGEN infrastructure 
> > for the consortium is committed to providing MAGE-ML instances [1]."
> >  
> > that's great.
> >  
> > "the FuGE-stk [2] will provide a means to "convert" MAGE-ML 
> to FuGE-ML"
> >  
> > not exactly, the folks (myself included) that worked on 
> FuGE but with 
> > a focus on microarrays are working on MAGEv2 and there is a 
> commitment 
> > to provide a way to translate to/from MAGEv1 <-> MAGEv2.  at the 
> > minimum this would be a mapping but if there is time and resources 
> > available, this would also have an implementation in the 
> MAGEstk v2. 
> >  
> > MAGEv2 is being built on top of FuGE as an extension to add in 
> > microarray specific classes (extending Data as ArrayDesign, 
> > DesignElementData, etc, Material as Array, QPCRPlate, etc, and 
> > DimensionElement as DesignElement extended by Feature, 
> Reporter, and 
> > CompositeElement).
> >  
> > we have not been quite as organized as the MAGEv1 effort so 
> the work 
> > doesn't have a high visibility yet, plus we have been working on 
> > MAGE-TAB, a simplified, spreadsheet version of the MAGE-OM model.
> >  
> > i'm hoping we can get back on track soon, we are not that far from 
> > completion, perhaps the NIH or BIRN microarray folks would 
> be willing 
> > to host a MAGEv2 meeting? (note, this would have little to do with 
> > ontology development!)
> >  
> > "many of the experts working on FuGE .. are looking for 
> assistance in 
> > how to make use of ontologies when representing microarray 
> data in a 
> > FuGE instance"
> >  
> > yes, but note that this has nothing to do with ontology 
> modeling per 
> > se but simply the best way to model ontology annotation for the 
> > objects of a FuGE document.  in essence, a FuGE object, such as a 
> > Material that represents a rat or the Investigation itself, becomes 
> > either implicitly or explicitly an Individual of the 
> desired classes 
> > from whatever ontologies that are appropriate.  it then 
> inherits the 
> > properties of those classes (if there are any) and can specify slot 
> > instances.  it is anticipated that OBI will be usable for 
> most of the 
> > basic annotation then, perhaps, specialized ontologies in 
> the domain 
> > of the particular investigation can annotation more exactly.
> >  
> > most specifically, information and relationships of these 
> > referenced classes would not be in the FuGE document, just the 
> > information necessary to look them up in the ontology itself.
> >  
> > we modeled the FuGE ontology package from the Individual 
> diagram of an 
> > early draft of OMG's Ontology Definition MetaModel (ODM).  that 
> > section was actually explicitly dropped from the final 
> version of the 
> > ODM because it had problems with OWL Full (and perhaps DL), but we 
> > anticipate that the vast majority of desired ontology 
> annotation can 
> > be captured via this model.
> >  
> > temporal and containment/association relationships are actually 
> > intended to be captured by the FuGE objects (the flow of 
> Material and 
> > Data through ProtocolApplications, the various associations between 
> > FuGE classes)
> >  
> > "there is both an eye toward - and a need for - automatic 
> conversion"
> >  
> > interestingly enough, if one can generate MAGEv1 to capture the 
> > details of the microarray experiment, one could also use FuGE to 
> > export the Material/BioSource individuals as stand alone with the 
> > ontology annotation and tie them together via the 
> identifier attribute.
> >  
> > "may require a MAGE-ML import into a FuGE DDL database - 
> then export 
> > from the database - I'm not clear on this yet"
> >  
> > since MAGE-ML has an in-memory model and FuGE does also, then it 
> > should be just as easy to auto-generate bridging code based on a 
> > mapping between the two in-memory models as to have to write to a 
> > database first (which requires the same mapping!).
> >  
> > also note that the application/database doesn't have to be 
> based on a 
> > FuGE DDL database, it simply needs to be able to import MAGE-ML and 
> > export FuGE.  i would be out of work if it did.
> >  
> > cheers,
> > michael
> >  
> > Michael Miller
> > Lead Software Developer
> > Rosetta Biosoftware Business Unit
> > www.rosettabio.com
> >
> >     
> --------------------------------------------------------------
> ----------
> >     *From:* public-semweb-lifesci-request@w3.org
> >     [mailto:public-semweb-lifesci-request@w3.org] *On Behalf Of
> >     *William Bug
> >     *Sent:* Thursday, May 31, 2007 7:36 PM
> >     *To:* Kei Cheung
> >     *Cc:* Smith, Barry; Kashyap, Vipul; samwald@gmx.at;
> >     public-semweb-lifesci@w3.org; 
> obo-relations@lists.sourceforge.net
> >     *Subject:* Re: [Obo-relations] Advancing translational research
> >     with the Semantic Web (Not clear about definition of
> >     <is_location_of_process>)
> >
> >     Hi Kei,
> >
> >     Yes - you are right, of course - right now the TGEN 
> infrastructure
> >     for the consortium is committed to providing MAGE-ML 
> instances [1].
> >
> >     My understanding from speaking with FuGE folks is that the the
> >     FuGE-stk [2] will provide a means to "convert" MAGE-ML 
> to FuGE-ML
> >     (may require a MAGE-ML import into a FuGE DDL database - then
> >     export from the database - I'm not clear on this yet).  
> Since many
> >     of the FuGE model developers were a part of the MGED MAGE model
> >     development project, there is both an eye toward - and 
> a need for
> >     - automatic conversion. As FuGE is intended to cover ALL of
> >     functional genomics beyond microarray alone, there's a bit more
> >     abstraction in the data model and some more specific 
> parts of the
> >     model will likely not be needed for microarray data.
> >
> >     I'm not completely clear on how automatic it will be, but folks
> >     such as Michael Miller who have contributed to the HCLS IG list
> >     before would certainly be able to give us the most comprehensive
> >     answer to that question that is available at this time.
> >
> >     One example I found recently is out of the 
> bioinformatics unit at
> >     Newcastle U. - the Centre for Integrated System Biology of Aging
> >     and Nutrition [3] [4].  In addition to being one of the first
> >     public systems based on the Milestone 3 release of FuGE & the
> >     FuGE-stk, it has a means of transferring data from the
> >     ArrayExpress backend - maxdLoad2 [5].  Since the latter 
> system is
> >     capable of importing MAGE-ML instances, this provides a 
> route via
> >     which one can get from MAGE-ML to FuGE-ML.
> >
> >     Of course, we could skip the FuGE step and just look at 
> how to use
> >     OBI and other OBO Foundry ontologies to create a SemWebTech
> >     repository for NIH Neuroscience Microarray Consortium 
> data as is -
> >     in MAGE-ML or in the backend model - akin to the ones 
> Alan et al.
> >     have set up for the HCLS demo at the NeuroCommons.  We 
> are working
> >     with annotating MAGE-based microarray data within MouseBIRN as
> >     well, so it would be wonderful, if there were some way 
> for this to
> >     be included.  One of the goals of what we are doing for 
> microarray
> >     data in BIRN is to stay in sync with the consortium in 
> such a way
> >     so as to make it possible for us to query consortium data - and
> >     visa versa.  There are some folks on BIRN whose are also
> >     associated with the consortium (I believe the Autism groups
> >     recently added to BIRN are participants of the consortium).
> >
> >     Do you know whether others on the consortium - or TGEN itself -
> >     are working on this task?  We might want to have a call that
> >     includes some of the core informatics folks in the 
> consortium, in
> >     addition to yourself.
> >
> >     Cheers,
> >     Bill
> >
> >
> >     [1] 
> http://arrayconsortium.tgen.org/np2/public/dataAndAnalysisPolicies.jsp
> >     [2] http://fuge.sourceforge.net/dev/index.php
> >     [3] http://www.cisban.ac.uk/cisbanDPI.html
> >     [4] 
> http://www.cs.ncl.ac.uk/research/pubs/trs/abstract.php?number=1016
> >     [5] http://www.cisban.ac.uk/resources.html
> >
> >     On May 31, 2007, at 10:05 PM, Kei Cheung wrote:
> >
> >>     Hi Bill,
> >>
> >>     Thanks for describing the evolution of MGED into FuGO. As I
> >>     understand it, the consortium's microarray data can be exported
> >>     in MAGE-ML (XML) format. Would it be possible to convert it to
> >>     the FuGE format?
> >>
> >>     Cheers,
> >>
> >>     -Kei
> >>
> >>     William Bug wrote:
> >>
> >>>     Barry beat me to the punch here - 
> >>>     BUT - 
> >>>     I would not want to miss out on the specific value of the
> >>>     proposal Kei has made.
> >>>
> >>>     I believe looking closely at how the OBI representation of
> >>>     microarray-associated instruments, protocols, reagents, data
> >>>     artifacts, algorithms, etc. - could be put to use in 
> describing
> >>>     some of the data being produced for the NIH Neuroscience
> >>>     Microarray Consortium that you are contributing to, 
> Kei.  As you
> >>>     may already know, many of the experts working on FuGE 
> (grown out
> >>>     of MAGE which used the MGED Ontology as its shared semantic
> >>>     framework) are looking for assistance in how to make use of
> >>>     ontologies when representing microarray data in a FuGE
> >>>     instance.  As you also probably know, the original
> >>>     FuGE-associated ontology, FuGO, has expanded its 
> domain to cover
> >>>     all forms of biomedical investigation (Ontology of Biomedical
> >>>     Investigation - aka the OBI that Barry cited).  This 
> was a part
> >>>     of the evolution of FuGO as it began to participate in the OBO
> >>>     Foundry AND make a commitment to use BOTH the OBO Relations
> >>>     ontology and BFO.
> >>>
> >>>     With that in mind - and considering the NIH Neuroscience
> >>>     Microarray Consortium is committed to providing array data in
> >>>     FuGE format - it could be very helpful both to understand how
> >>>     OBI can be used to provide a formal semantic representation of
> >>>     important experimental provenance information AND how 
> SemWebTech
> >>>     in general could be used to provide a more flexible - and
> >>>     query-able - framework in which to access this 
> semantic information.
> >>>
> >>>     Cheers,
> >>>     Bill
> >>>
> >>>     On May 31, 2007, at 9:21 PM, Kei Cheung wrote:
> >>>
> >>>>
> >>>>     Smith, Barry wrote:
> >>>>
> >>>>>     At 08:52 PM 5/31/2007, Kei Cheung wrote:
> >>>>>
> >>>>>>     Hi Barry,
> >>>>>>
> >>>>>>     Welcome to the SWHCLS list. Such a discussion reminds me of
> >>>>>>     the Nature paper: "Are the current ontologies in 
> biology good
> >>>>>>     ontologies?"
> >>>>>>     
> (http://www.nature.com/nbt/journal/v23/n9/full/nbt0905-1095.html).
> >>>>>>     The paper uses the MGED (microarray) ontology to illustrate
> >>>>>>     some of the ontological issues. I'm just curious 
> how the BFO
> >>>>>>     principles and practice can help make such a microarray
> >>>>>>     ontology more ontologically sound and therefore 
> more machine
> >>>>>>     readable.
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>     We are already working on it:
> >>>>>
> >>>>>     http://obi.sf.net
> >>>>>
> >>>>>     BS
> >>>>>
> >>>>     That's great! I hope we can develop some real use case of it.
> >>>>
> >>>>     -Kei
> >>>>
> >>>>
> >>>
> >>>
> >>>
> >>>     Bill Bug
> >>>     Senior Research Analyst/Ontological Engineer
> >>>
> >>>     Laboratory for Bioimaging  & Anatomical Informatics
> >>>     www.neuroterrain.org
> >>>     Department of Neurobiology & Anatomy
> >>>     Drexel University College of Medicine
> >>>     2900 Queen Lane
> >>>     Philadelphia, PA    19129
> >>>     215 991 8430 (ph)
> >>>     610 457 0443 (mobile)
> >>>     215 843 9367 (fax)
> >>>
> >>>
> >>>     Please Note: I now have a new email - 
> William.Bug@DrexelMed.edu
> >>>     <mailto:William.Bug@DrexelMed.edu>
> >>>
> >>>
> >>>
> >>>
> >>
> >>
> >
> >     Bill Bug
> >     Senior Research Analyst/Ontological Engineer
> >
> >     Laboratory for Bioimaging  & Anatomical Informatics
> >     www.neuroterrain.org
> >     Department of Neurobiology & Anatomy
> >     Drexel University College of Medicine
> >     2900 Queen Lane
> >     Philadelphia, PA    19129
> >     215 991 8430 (ph)
> >     610 457 0443 (mobile)
> >     215 843 9367 (fax)
> >
> >
> >     Please Note: I now have a new email - William.Bug@DrexelMed.edu
> >     <mailto:William.Bug@DrexelMed.edu>
> >
> >
> >
> >
> 
> 
> 
> 
Received on Tuesday, 5 June 2007 01:04:23 GMT

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