Chris,
Many thanks for bringing this up! This is good news for me and I'm very much encouraged to move forward with the suggestions. We have been aware of the tool for some time now but I have not had the chance to follow up with Christine on this. As you know I'm technically challenged on this matter and so I have to consult with Todd and Jim on what our local group should do next.
Christine, is the tool available for us to try out? We would like to work with you on this. Perhaps I can call you directly and talk more in detail on how we can pursue possible collaboration?
I very much look forward to any progress we can achieve here. FMA in OWL is long due!
Thanks!
Onard
From: "Chris Mungall" <cjmu...@lbl.gov>
To: fma-ow...@googlegroups.com, "Alan Ruttenberg" <alanrut...@gmail.com>, "Christine Golbreich" <Christine...@univ-rennes1.fr>
Cc: "Harry Stewart Hochheiser" <har...@pitt.edu>, "Melissa Haendel" <hae...@ohsu.edu>, "Todd Detwiler" <d...@u.washington.edu>, "Jim Brinkley" <brin...@u.washington.edu>, "mej...@u.washington.edu Mejino" <mej...@u.washington.edu>, "zooinfo...@gmail.comTravillian" <zooinfo...@gmail.com>
Dear Cornelius
I'm very happy to hear from you. Happy New Year 2013.
I absolutely miss what these words about me and my attitude refer to :
" ... particularly whether Christine will play the ball. What would happen if she maintains her old attitude"
Can you please be more explicit ?
Hi Chris and all
Chris, thank you very much for your email to the list and also for sending the paper. I'm happy to get it :-) , I even did not have it.
There is a 2 weeks Christmas break here in France. I'm waiting for talking with my French colleagues, as soon as everybody is back (hopefully from tomorrow). I hope to answer in more details if possible next. Meanwhile, see below my first impressions/reactions
Some questions for Christine:
- do you intend to keep extending this tool and making regular releases, or do you consider this project done?
do you mean regular releases of the tool or of the FMA in OWL ?
- the project is absolutely not done, it's a first (second) step, there is still much to do and the tool might / should be improved and extended
- it's also still necessary to debug the FMA before using it in real applications. Reasoning with OWL may help to fix some errors but it's a hard and time consuming work which needs means.
- a loop and regular feedback should be achieved
- alignment between FMA and SNOMED-CT is another important issue
etc.
All this requires means.
Unfortunately, on my side further development is being stuck nearly since 2 or 3 years, mainly because of lack of fundings and people availability. I already said it several times.
- would you be willing to make some changes to make the OWL compliant with OBO Foundry guidelines? This would include using the numeric identifier in the IRI, reusing standard annotation properties and object properties.
- I'm open to all changes that are possible and make sense. A possibility might be perhaps to add new options to the tool, for example to choose using the numeric identifier.
- What do you mean "reusing standard annotation properties and object properties" ?
- are you aware of the OCDM project, and have you tried using the tool to generate an OWL version of OCDM?
I have not tried. What is the exact connection between OCDL and FMA ? Are they concretely linked ?
the FMA-OWLizer tool is specific to FMA
- Regarding the other questions about the tool, of course I want to make it available to everybody to try it, it was the initial goal/intent of this tool.
- Regarding collaboration, as always, I'm personally completely open to any collaboration of * any * type that may help to progress (as much as I can). But for years now the recurrent problem is to have strengths. I'm still looking for a concrete means to make it in practice.
As some of you remember, in the past, aiming at collaborating for improving the FMA, I had submitted (as PI) several NIH R01 collaborative proposals for grants. The last one was “Relating Neuroimaging Data to Human Diseases”, submitted together with NCBO, BIRN, Drexel University, Manchester University (I. Horrocks) and others. Onard Mejino and Pr. Cornelius Ross supported the project and were involved as consultants for University of Washington. Unfortunately, all these attempts were unsuccessful.
After our 2009 meeting I had also tried to launch the idea to submit again together a new proposal, if I remember well mainly focused on
- FMA revision and conversion to OWL 2 or extension,
- Align, integrate the FMA and SNOMED-CT OWL 2 ontologies (relevant anatomical modules).
- Use reasoners for KE of FMA and SNOMED-CT
- Indexing and answering queries on EMR
I contacted then several persons ( University of Washington, if I remember well) asking them to be the PI, but nobody was available and nothing happened next.
Today, things have progressed in many areas, and there are many new pressing things to do. I'm still available to contribute.
All ideas, suggestions and proposals are welcome !
Best regards,
Christine
Here's a copy of the paper
Chris,
Many thanks for bringing this up! This is good news for me and I'm very much encouraged to move forward with the suggestions. We have been aware of the tool for some time now but I have not had the chance to follow up with Christine on this. As you know I'm technically challenged on this matter and so I have to consult with Todd and Jim on what our local group should do next.
Christine, is the tool available for us to try out? We would like to work with you on this. Perhaps I can call you directly and talk more in detail on how we can pursue possible collaboration?