- From: Kei Cheung <kei.cheung@yale.edu>
- Date: Wed, 06 Jun 2007 16:04:56 -0400
- To: "Miller, Michael D (Rosetta)" <Michael_Miller@Rosettabio.com>
- 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>
Hi Michael, Sorry, I'm a little bit behind reading/responding emails these days. Please see my response below. Miller, Michael D (Rosetta) wrote: > 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. > Web science I think is about relating many things including communities and people. I gave a few slides to Dr. Mane in the hope that he would be able convince folks to think about SW at the NINDS Microarray Consortium meeting which will be held within a couple of days. It's great that you mentioned proteomic data. I used GENSAT only as an example, but we can extend to other types of data including proteomic data. In addition to NINDS microarray center, Yale has a neuroproteomic center funded by NIDA (National Institute on Drug Abuse). We are actually planning to correlate gene expression data with protein expression data. >> 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. > At this point, we don't need to worry about the measurement data (which is enormous). We can start with experiment and sample annotation. "Are current ontologies in biology good ontologies?". I hope, as a community, we can prove that they are. Cheers, -Kei > 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 Wednesday, 6 June 2007 20:05:06 UTC