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Re: [BIONT] Telcon minutes

From: William Bug <William.Bug@DrexelMed.edu>
Date: Thu, 11 Jan 2007 05:20:50 -0500
Message-Id: <2629C914-3F01-4840-AC07-B1DA18E8A65D@DrexelMed.edu>
Cc: "w3c semweb hcls" <public-semweb-lifesci@w3.org>
To: "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>
Hi All,

I again apologize for having missed this important discussion due to  
conflicting commitments.

I wanted to add just a few brief comments to the discussion points  
listed in the minutes:

16:09:09 [Don]
     What is the goal of BIONT? (DD)
16:11:05 [Don]
     Goal is not a demo per se. It's to create artifacts listed on  
the BIONT wiki. (VK)

BB: Specifically targeting support for the Use Cases being pursued  
collectively by all the Task Forces, correct?  If so, a demo that  
includes BioONT efforts is implied, since the Use Cases will lead to  
a demo.

16:16:03 [Don]
     When we say best practices developing ontologies...isn't NCBO  
doing this? (TC)
16:16:37 [Don]
     NCBO's goal is to provide tools and technologies to support the  
collaborative process. (VK)

Exactly.  And they have as their mandate to be maximally inclusive  
both in terms of artifacts they distribute to the community and  
practices pursued across the community.  Mark Musen discusses some of  
the complexities of dealing with these differing views & practices in  
biomedical ontology development in his presentation from this 2005  
Biomedical Ontology-driven Informatics meeting from 2005 (http:// 
ontology.buffalo.edu/wg6/), as do the presentation by several others  
at this meeting (e.g., Chris Chute [http://mayoresearch.mayo.edu/mayo/ 
research/staff/chute_cg.cfm] from Mayo Clinic whose LexGrid system  
[http://informatics.mayo.edu/LexGrid/index.php?page=tnt] needs to  
support this fact in the context of providing lexicon+ontology  
support for the NCI caBIG project, as does their related Open  
Terminology Services (OTS) project [http://www.ncbi.nlm.nih.gov/ 
entrez/query.fcgi? 
db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=14728514&query_hl=1&i 
tool=pubmed_docsum] which I believe has been absorbed into LexGrid as  
their implementation of the HL7 Common Terminology Service [http:// 
informatics.mayo.edu/LexGrid/index.php?page=projects]).

Having said this, the OBO Foundry IS promoting a collection of best  
practices which appear to have been distilled from the experience of  
the Gene Ontology Consortium, the Stanford Medical Informatics group,  
the IFOMIS center's efforts in regards to the various applications to  
which the BFO foundational ontology has been put in the biomedical  
domain, and several other community biomedical concept-mapping,  
classification, and ontology development efforts. I do think it is  
extremely important we stay abreast of those ontologies being  
collected in the OBO Foundry (e.g., BFO, PATO, OBI, etc.) and the  
various applications where they are being used.

16:16:56 [Don]
     Look at experiences of the GO project. (VK)

BB: see above comment - plus I would strongly recommend taking a look  
at the slides contributed by Suzi Lewis & Michael Ashburner (two of  
the GO founding PIs) to the presentation "Principles for Building  
Biomedical Ontologies" listed at the GO educational resource page  
(http://www.geneontology.org/GO.teaching.resources.shtml?all).

16:17:34 [Don]
     Is this more of a group self help effort? (TC)

BB: I'm not certain I understand what Tim means here but would love  
to know more about the discussion that took place regarding this  
comment.

...
...
...

16:21:24 [Don]
     We could compile experiences integrating data using existing  
open source ontologies such as FMA. (VK)

I have an Anatomical Informatics bibliography I've compiled over the  
years that includes nearly all the applications to which FMA has been  
applied of which I'm aware - along with other related anatomical  
ontology efforts such as those associated with the Edinburgh Mouse  
Atlas Project & the JAX/MGI/GO effort, if that could be of some use  
on this point.

16:28:56 [helen]
     start to put together data/ontology we have now, to see waht  
query/isses we can get out of these data

Exactly - to my mind, this is THE critical task BioONT needs to  
invest in - essentially the iterative process of honing ontology  
support for the Use Cases.

...
...
...

16:29:42 [Don]
     ACTION: Map ontologies to data sources (VK)

BB: see some of the issues I bring up in the Word file I've attached  
below

...
...
...

16:30:46 [Don]
     ACTION: Have teams with experience using ontologies to integrate  
data talk about...

BB: Great idea!

16:31:10 [vipul]
     ACTION: get feedback from various group on the issues that came  
up in developing ontologies and mapping to data

BB: I'd be glad to provide feedback based on ontology development &  
mapping data based on our BIRNLex work within the BIRN project.


Attached please find some very detailed descriptions of how to fully  
flesh out the required HCLSIG ontologies derived from our recent  
communal manuscript editing effort.  None of this made it into the  
final draft (where it really didn't belong anyway), so many may have  
not seen it all, but I would suggest we seek this level of due  
diligence to pull together references to the relevant, extant public  
knowledge sources covering the required domains.

The idea here is in order to be maximally useful to the BioRDF  
effort, the ACPP effort, the efforts in the publishing task force,  
and other tasks forces as they pursue supporting the Use Cases, we  
should try to link to all the unique, community resources relevant to  
the entities and relations we need to cover.  I would also want to  
spend more time reviewing this with Matthias to determine how many of  
these relevant links can be derived directly from his bio-zen work,  
as well as discussing with Kei and others within BioRDF the ways in  
which they may have already established some of these links.

As an additional thought to consider on this issue of supporting  
ontologies, I would suggest we consider pursuing a manuscript to  
describe how we've been approaching this task - one highlighting the  
BioONT ontology artifacts and our means of incorporating appropriate,  
extent community ontologies and related knowledge resources.  It  
would center around the Use Cases and describe some of the issues  
that have come up as we've worked to support the formal semantic  
framework/ontology requirements for all of the other HCLSIG Task  
Forces.  Pursuing such a manuscript would probably assist in further  
specifiying the BioONT commitment to all the other task forces, as well.

Cheers,
Bill




On Jan 9, 2007, at 1:35 PM, Kashyap, Vipul wrote:

> are available at: http://www.w3.org/2007/01/09-hcls-irc
>
>
>
> ---Vipul
>
>
>
> =======================================
>
> Vipul Kashyap, Ph.D.
>
> Senior Medical Informatician
>
> Clinical Informatics R&D, Partners HealthCare System
>
> Phone: (781)416-9254
>
> Cell: (617)943-7120
>
> http://www.partners.org/cird/AboutUs.asp?cBox=Staff&stAb=vik
>
>
>
> To keep up you need the right answers; to get ahead you need the  
> right questions
>
> ---John Browning and Spencer Reiss, Wired 6.04.95
>
>
>
> THE INFORMATION TRANSMITTED IN THIS ELECTRONIC COMMUNICATION IS  
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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 Thursday, 11 January 2007 10:21:25 UTC

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