Re: [CDAO-discuss] project plan teleconference

[Rutger V. <R....@re...>]

Sure, what's the best place for that?

On Wed, Nov 9, 2011 at 5:48 PM, Hilmar Lapp <hl...@ne...> wrote:
> Rutger -
>
> can you document your query needs as a use-case on the wiki? I think it's
> important to retain this and other cases for continuous validation.
>
>        -hilmar
>
> On Nov 8, 2011, at 10:38 AM, Rutger Vos wrote:
>
>>> I also feel that some of these are not difficult to address - e.g., it is
>>> not hard to envision new subclasses to provide alternative forms of data
>>> to be used in the matrix representation. E.g., the matrix representation
>>> already allows compound characters that can be used to provide a sequence
>>> as a single entity (instead of breaking it down into smaller characters).
>>> We also need to remember that an ontology is not a data format (thus
>>> succinctness is not one criteria to drive its design) - it should provide
>>> whatever level of detail one desires to annotate any existing source of
>>> data.
>>
>> I certainly agree with your point that an ontology is not a data
>> format, but verbosity is still an issue: if we transformed all of
>> TreeBASE's NeXML to CDAO/RDF it would become, to the best of my
>> knowledge, the biggest public triple store currently in use in the
>> life sciences (I'm basing this on the presentations of Jerven Bolleman
>> from UniProt). In other words, it will not scale. Also, we really do
>> want to be able to find out with a relatively simple SPARQL query
>> whether a matrix/alignment is DNA, RNA, Protein, or something else
>> without too many joins and interpretation of the used alphabet.
>>
>> Rutger
>>
>>> On 11/8/11 3:57 AM, "Rutger Vos" <R....@re...> wrote:
>>>
>>>> Hey Jim,
>>>>
>>>> thanks for pushing this. I think it's crucial that CDAO continues to
>>>> be under development. At the BioHackathon in Kyoto I spent my time
>>>> working on improving the NeXML-to-CDAO stylesheet and on querying
>>>> CDAO/RDF graphs to extract known objects (taxa, trees, matrices) out
>>>> of it.
>>>>
>>>> I discovered some inconvenient design decisions in terms of the
>>>> verbosity of the generated RDF and the circumlocution in which certain
>>>> important facts are expressed (e.g.: how do I find out the data type
>>>> of a character state matrix through a SPARQL query? This is
>>>> surprisingly hard to do in CDAO).
>>>>
>>>> I would be happy to share these findings on the call as I feel it is
>>>> important that these issues are addressed in the run up to, or at, the
>>>> HIP meetings.
>>>>
>>>> Best wishes,
>>>>
>>>> Rutger
>>>>
>>>> On Tue, Nov 8, 2011 at 4:16 AM, Jim Balhoff <ba...@ne...> wrote:
>>>>>
>>>>> Hi all,
>>>>>
>>>>> Arlin has suggested that we hold a conference call to talk about the
>>>>> future of CDAO, organizing development, and finding funding. I think
>>>>> this is a great idea and I have created a Doodle poll to help find a
>>>>> time when everyone who is interested is available:
>>>>>
>>>>> http://www.doodle.com/5mv7m5mmywsv5sxf
>>>>>
>>>>> If you would like to participate in this discussion, please fill out
>>>>> your availability in that poll (note that time zone support is enabled,
>>>>> so you can view the times for your area). After a couple of days I'll
>>>>> let everyone know when the call will be, and the number to call.
>>>>>
>>>>> Anyone interested in the future of CDAO is welcome to join in. Let us
>>>>> know how CDAO in its current form has been useful (or not), and how it
>>>>> can be improved for future use-cases.
>>>>>
>>>>> Best regards,
>>>>> Jim
>>>>>
>>>>> ____________________________________________
>>>>> James P. Balhoff, Ph.D.
>>>>> National Evolutionary Synthesis Center
>>>>> 2024 West Main St., Suite A200
>>>>> Durham, NC 27705
>>>>> USA
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Dr. Rutger A. Vos
>>>> School of Biological Sciences
>>>> Philip Lyle Building, Level 4
>>>> University of Reading
>>>> Reading, RG6 6BX, United Kingdom
>>>> Tel: +44 (0) 118 378 7535
>>>> http://rutgervos.blogspot.com
>>>
>>>
>>>
>>
>>
>>
>> --
>> Dr. Rutger A. Vos
>> School of Biological Sciences
>> Philip Lyle Building, Level 4
>> University of Reading
>> Reading, RG6 6BX, United Kingdom
>> Tel: +44 (0) 118 378 7535
>> http://rutgervos.blogspot.com
>>
>>
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>
> --
> ===========================================================
> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================
>
>
>
>



-- 
Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
Reading, RG6 6BX, United Kingdom
Tel: +44 (0) 118 378 7535
http://rutgervos.blogspot.com