- From: William Bug <William.Bug@DrexelMed.edu>
- Date: Thu, 31 May 2007 22:44:02 -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: <D1A66FFA-2983-4CC5-8749-6C62E6644D26@DrexelMed.edu>
P.P.S.: Oops - forgot to mention this Newcastle U. project has also implemented use of LSID, which is obviously of great interest to this list. On May 31, 2007, at 10:41 PM, William Bug wrote: > 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 > > > > 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 02:41:47 UTC