- From: William Bug <William.Bug@DrexelMed.edu>
- Date: Thu, 31 May 2007 22:41:14 -0400
- To: public-semweb-lifesci hcls <public-semweb-lifesci@w3.org>, obo-relations@lists.sourceforge.net, OBI Developers <obi-devel@lists.sourceforge.net>
- Cc: Kei Cheung <kei.cheung@yale.edu>, Barry Smith <phismith@buffalo.edu>, Vipul Kashyap <VKASHYAP1@PARTNERS.ORG>, Matthias Samwald <samwald@gmx.at>, Allyson Lister <a.l.lister@newcastle.ac.uk>
- Message-Id: <D35617B5-E69D-4494-A8F0-D78BE72282B2@DrexelMed.edu>
P.S.: Allyson Lister who participates on the Newcastle U. project I cited below is also a very active participant on the OBI project. http://www.cisban.ac.uk/staff.html P.P.S.: Sorry for the cross-posting, but I believe there are others on the OBI developer list who might be interested in this specific discussion. On May 31, 2007, at 10:36 PM, William Bug wrote: > 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 > > > > 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
Received on Friday, 1 June 2007 02:38:57 UTC