Re: Dec 14 HCLSIG TC Minutes

Hi Eric,

I think NCI Metathesaurus really should be placed under BioONT, if we  
are to properly communicate how the BioONT & DSE TFs overlap.   
Perhaps BioCyc could be replaced by NCI MT.  Given the domain we are  
covering, its important for NN to stay, I believe.

What do others think?

Cheers,
Bill

On Dec 18, 2006, at 7:04 AM, Eric Neumann wrote:

>
> For Clinical Trials (DSE):
>
> - CDISC (Clinical Data Onformation Standards Consortium)
> - RCRIM (HL7 clinical trials)
> - NCI Metathesaurus
> - FDA's JANUS database
>
>
> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org on behalf of William Bug
> Sent: Sun 12/17/2006 11:26 PM
> To: Joanne Luciano
> Cc: kc28; Alan Ruttenberg; W3C HCLSIG
> Subject: Re: Dec 14 HCLSIG TC Minutes
>
> Hi Joanne,
>
> I like what you are trying to achieve in this figure, and I think you
> do it well in a very small amount of space.
>
> I've added just a quick "key" to the right-hand side, to give readers
> a more concrete sense of what community resources the 4 Task Forces
> have been focused on integrating.  This should obviously not be
> exhaustive, just examples to give folks a concrete sense of what each
> task force has been examining.  I provided examples for BioONT and
> BioRDF drawn from the paper.  I'd leave it to those who know better
> than I what public resources fall under the purview of DSE & ACPP.
>
> Just my $0.02.
>
> Cheers,
> Bill
>
> ?
>
> On Dec 17, 2006, at 10:10 PM, Joanne Luciano wrote:
>
>>
>> Please provide feedback on the figure too.
>>
>> Joanne
>>
>> On Dec 17, 2006, at 2:53 PM, kc28 wrote:
>>
>>>
>>> Hi Joanne,
>>>
>>> I'll work with Alan and others based on your suggestions.
>>>
>>> Thanks,
>>>
>>> -Kei
>>>
>>> Joanne Luciano wrote:
>>>
>>>> Hi Kei,
>>>>
>>>> I made my edits on the google page this morning, so this becomes
>>>> a  belated request for deadline extension.
>>>>
>>>> Included here:
>>>>
>>>> 1.3.2. Standards as Applications of Semantic Web Technologies
>>>> (Joanne)
>>>>
>>>>
>>>> There is a tacit assumption within the Semantic Web community
>>>> that  every type of data sets and ontologies will be
>>>> interoperable. The  reality is that a multitude of different
>>>> conceptualisations and  formal representation of data exist. A
>>>> key part of the Health and  Life Sciences SIG's vision is that
>>>> standards need to be established  and accepted sufficiently
>>>> widely within the community so as to allow  that necessary
>>>> interoperability between data sets, application and  workflows. A
>>>> relatively early effort in this direction was the BioPAX
>>>> initiative [REFS] which aimed to provide a common framework for
>>>> the  disparate data sources and multiple conceptualisations of
>>>> cellular  pathways. Its major success was in increasing public
>>>> awareness and  persuading a community of researchers that the
>>>> integration of data  was possible and would result in major
>>>> research and discovery  advantages. It highlighted the multiple
>>>> conceptualizations existing  within the domain of cellular
>>>> pathways and made people aware of the  significant investment
>>>> needed to achieve interoperability at not only  a syntactic level
>>>> but also at a semantic one. A considered critique  of the effort
>>>> with suggestions of the way forward is presented in  [REF to
>>>> Luciano and Stevens] in this issue.
>>>>
>>>> In the medium term future, the efforts for standardization need
>>>> a  much more careful analysis of the user requirements so as to
>>>> be able  to get the end users (wet lab scientists) to buy into
>>>> the approach  and its benefits. A greater understanding is needed
>>>> both of the  conceptualisations needed which will be reflected in
>>>> a number of  ontologies and the boundary which lies between what
>>>> is possible and  useful in OWL based ontologies given the
>>>> capabilities of the current  generation of reasoners, and on the
>>>> other hand the ambitions and   needs of clinical researchers to
>>>> integrate and interpret their data.
>>>>
>>>> The HCLSIG has an interesting role in the SW community because
>>>> potentially there is a far greater commitment to resourse
>>>> curation  and the need for standard formats and data integration,
>>>> thus making  it a much more likely candidate for being a poster
>>>> child for the  success of Semantic Web technologies.
>>>>
>>>> Added to Section 2:
>>>>
>>>>
>>>> The following figure shows the respective relationship between
>>>> the  different task forces and their role in the bench to bedside
>>>> vision.
>>>>
>>>>
>>>> ------------------------------------------------------------------- 
>>>> -
>>>> ----
>>>>
>>>>
>>>> and added my contributions to the section at the bottom:
>>>>
>>>>
>>>> JL Joanne Luciano, Havard Medical School, Universtity of
>>>> Manchester  (UK), BioPathways Consortium, BioPAX
>>>>
>>>> Affiliation:
>>>>
>>>> JL Joanne Luciano, Havard Medical School, Universtity of
>>>> Manchester  (UK), BioPathways Consortium, BioPAX
>>>>
>>>> To Acknowledgment
>>>>
>>>> (after Kei's) JL was supported by NSF grant IIS-0542041.
>>>>
>>>> ---Joanne
>>>>
>>>>
>>>> On Dec 15, 2006, at 10:58 AM, Kei Cheung wrote:
>>>>
>>>>>
>>>>> Just want to add that the google doc editing deadline is 12:00
>>>>> am  (mid-night EST), Dec 15. If people still need a little bit
>>>>> more  time, please let us know as soon as possible. We might be
>>>>> able to  extend it to 12:00 noon, Saturday Dec 16 (but not
>>>>> anymore since the  deadline is very close).
>>>>>
>>>>> Thanks,
>>>>>
>>>>> -Kei
>>>>>
>>>>> Alan Ruttenberg wrote:
>>>>>
>>>>>>
>>>>>> Correction: Helen, Vipul will send whatever they haven't
>>>>>> integrated  into the googledoc to Alan over the weekend for
>>>>>> integration. Alan  will edit and send to Kei at weekend's end.
>>>>>>
>>>>>> -Alan
>>>>>>
>>>>>> On Dec 14, 2006, at 6:14 PM, Eric Neumann wrote:
>>>>>>
>>>>>>> [NEW] ACTION: Content will be moved off from googleDoc to
>>>>>>> Word  COB  Dec 15; to be serially edited by Alan, Helen,
>>>>>>> Vipul, and  returned  to Kei Dec 20. [recorded in http://
>>>>>>> www.w3.org/ 2006/12/14-hcls- minutes.html#action01 <http://
>>>>>>> www.w3.org/ 2006/12/14-hcls- minutes.html#action01> ]
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>> Joanne Luciano, PhD
>>>> Predictive Medicine, Inc.
>>>> 45 Orchard Street
>>>> Belmont MA 02478-3008
>>>> Email: jluciano@predmed.com
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>
>> Joanne Luciano, PhD
>> Predictive Medicine, Inc.
>> 45 Orchard Street
>> Belmont MA 02478-3008
>> Email: jluciano@predmed.com
>>
>>
>>
>>
>
> 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