[Bioperl-l] Offering to help

Kevin Clancy kpclancy at hotmail.com
Thu Mar 5 00:49:35 EST 2009


Hi Guys
You might also want to check out Ontologies  for Biomedical Investigations - OBI
http://obi-ontology.org/page/Main_Page
I've been following this thread and am intreagued by the use of roles in Moose. So if I have a defined ontology with classes, each of which has roles, can that be dropped into the Moose framework?
The main reason for asking is that a lot of work has gone into OBI including normalizing the ontology to others in the national center for biomedical ontologies http://bioontology.org/ and obo foundry http://www.obofoundry.org/. having some of this ontological work extended into the behaviour of the Bio* languages would be an interesting extension of these projects. My main concern with FuGE is that I don't know how compatable it is with these communities. 
kevin

> Date: Tue, 3 Mar 2009 14:05:22 -0600
> From: kanzure at gmail.com
> To: awitney at sgul.ac.uk
> CC: cjfields at illinois.edu; bioperl-l at lists.open-bio.org; kanzure at gmail.com
> Subject: Re: [Bioperl-l] Offering to help
> 
> On Tue, Mar 3, 2009 at 12:49 PM, Adam Witney wrote:
> > On 3 Mar 2009, at 17:21, Bryan Bishop wrote:
> >> On Tue, Mar 3, 2009 at 11:14 AM, Chris Fields wrote:
> >>> For a Moose-based bioperl implementation I suggest a separate repo
> >>> completely.  We're using svn currently on dev.open-bio.org, though I and
> >>> a
> >>> few others are also using git.  I'm neutral on the matter but it's
> >>> possible
> >>> the consensus may be to keep everything in the open-bio svn repo (not
> >>> everyone has git or uses it).
> >>
> >> Yes, I've been figuring that the protocols work should be done in a
> >> separate repository for now anyway, I just haven't got around to
> >> starting the code, although with XML::Simple it should be easier or
> >> quicker to do than I'm making it out to be. Part of the issue is that
> >> there needs to be some good thought put into what exactly the schema
> >> should be or how exactly to represent the information, which I've
> >> always had a little bit of anxiety over. It would be fantastic if I
> >> could somehow come up with an easy format and a wizard creation tool
> >> front-end for something like protocol-online.org, since all of those
> >> protocols truly deserve to be in some sort of microformat, whether
> >> CLP-ML or something based off of YAML. Maybe I'll post a thread soon
> >> outlining what a discussion would have to go over to make sure there's
> >> no shooting of self in the foot, to come up with that relatively
> >> mature API or microformat, and see what others on the list have to say
> >> about it? My background is more computer science than bioinformatics
> >> and biology (even though I've been in biology labs longer (strange)),
> >> so it would be great to get some support on that front.
> >
> > The FuGE folks have modeled Protocols as part of their object model. I
> > haven't looked at it recently but it is supposed to be fairly generic for
> > any kind of protocol. We have used the MAGE (FuGE's almost predecessor)
> > version of Protocol within our database for several years and it covers most
> > cases.
> >
> > The FuGE project pages can be found here:
> >
> > http://fuge.sourceforge.net/
> >
> > Maybe that would be a good place to start?
> 
> Thanks Adam, I hadn't seen that before. I glanced over their API documentation.
> 
> http://fuge.sourceforge.net/dev/V1Final/FuGEv1-refManual.html#Action
> 
> So, it looks like they are defining individual steps with an ordinal
> number (which is good), also equipment via make and model tags. One of
> the ideas that I have been working on is the concept of instructions
> being "solved" by equipment: so you can either execute a PCR protocol
> by manually dunking test tubes into warm and cold baths, or you can
> use a thermocycler or microfluidic chip using some standardized
> interface. This is also the same problem that "semantic web" advocates
> have to put up with: UDDI, WSDL, B2B, "service discovery", etc.,
> without overly restricting the standards to the point that nobody can
> do anything new. But anyway, getting off track.
> 
> There is a link to "example files"- which is broken-
> http://fuge.sourceforge.net/dev/V1Final/Instances/
> 
> Although this one does work:
> http://fuge.sourceforge.net/presentation/master_example.xml
> though it might be too meta for me :-).
> 
> Ultimately I'd like to come up with a system that I can dump into EXPO
> (like The Robot Scientist) but also into a human readable format
> (comparably, instructables?).
> 
> http://expo.sf.net/
> videos: http://www.aber.ac.uk/compsci/Research/bio/robotsci/video/
> 
> - Bryan
> http://heybryan.org/
> 1 512 203 0507
> 
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