HCLSIG/PharmaOntology/Meetings/2010-03-25 Conference Call

Conference Details

* Date of Call: Thursday March 25 2010 
* Time of Call: 12:00pm - 1:00pm ET 
* Dial-In #: +1.617.761.6200 (Cambridge, MA) 
* Dial-In #: +33.4.89.06.34.99 (Nice, France) 
* Dial-In #: +44.117.370.6152 (Bristol, UK) 
* Participant Access Code: 42572 ("HCLS2"). 
* IRC Channel: irc.w3.org port 6665 channel #HCLS2 (see W3C IRC page for details, or see Web IRC) 
* Mibbit instructions: go to http://www.mibbit.com/chat and click the server link. Enter irc.w3.org:6665 into that box, enter a nickname, and enter #HCLS2 for the channel 
* Duration: 1h 
* Convener: Susie

Agenda

* TMO 
 - Data - Michel 
 - Ontology - Elgar, Colin 
 - Interface - Bosse 
 - Outreach - Michel, Colin, Chris 
* Inclusion/exclusion criterion - Michel, Bosse 
* Drug Ontology Update - Susie
* Other Outreach 
 - UPenn Translational Medicine (ITMIT) - Chris 
 - Other opportunites (AAAI) - Egon
 - Upcoming F2F - Susie
 - Email list - Susie
 - Indivo User Group Meeting - Susie
 - Journal of Biomedical semantics - Susie
* AOB

Minutes

Attendees: Chris, Julia, Joanne, Trish, Vagnoni, Elgar, Bosse, Conor, Susie

Apologies: Michel

<Joanne> Susie: Update on drug ontology - has made progress, spoken to others asking if this task makes sense, so far people like the idea, specifically Pistoia Alliance, as they are a Pharma Industry Aliance

<Joanne> Susie: discussions included the types of info to capture, such as small molecule to point to ChEBI, large molecule and structure activity, tox, and trials

<Joanne> Susie: and how likely it would be to scale up up the medicine for production

<Joanne> Susie: Offer to write up her interests - perhaps for BioOntologies SIG, looking for others to join

<Joanne> - talking form Harvard Business Review and open innovation

<Joanne> HBR Eric Bonabeau - Dec or Jan issue?

<Joanne> Question - would this be HC or pharma only / Susie replies - that it's focused on getting medicines to market

<Joanne> Susie: that there isn't sufficient information, also pharma looking to outsource, so idea would be a standard that would help academic and pharm. to exchange chemical info.

<Joanne> in a certain area and then there could be competitions for fee for service work

<Joanne> Susie: Aims to create a standard ontology that Eric Bonabeau would use. Also, for example, repositioning drugs

<Joanne> Susie will write up short paper - to be submitted to BioOntologies, with the thought of it becoming a poster

<Joanne> Elgar: brings up the question of the nature of our relationship with Pistoia

<Joanne> Susie: Pistoia - largely focused on biz challenges, and not implement

<Joanne> Change topic to TMO:

<Joanne> Elgar: not much since last week.

<Joanne> Elgar: Michel has made multiple changes - mostly took care of reports and classes, but no addition of new classes

<Joanne> Elgar: the larger issues are .... biomarker which are useful for clinical and ....

<Joanne> Elgar: orphaned classes, done need review

<Joanne> Elgar: ; couple of options on how to record annotations and comments

<Joanne> Elgar: SKOS,

<Joanne> Other than taking care of the orphaned classes, though beyond orphans, not much done

<Joanne> Trish: will add metadata to say TMO exists

<vagnoni> Trish: Ontologies are never done.

<vagnoni> Susie: Want to upload Drug Ontology into BioPortal. Make sure its tidied up before.

<vagnoni> Susie signs up Elgar to replace Collon as leader of Drug Ontology.

<vagnoni> Trish wants to know what mailing list to use. Where do we talk about an ontology?

<vagnoni> Susie says W3C to use hcls list. But it ends up going having side discussions through direct email.

<vagnoni> Susie lets focus more on the Drug Ontology, but make sure we have a great deal of momentum before we go to a different list.

<vagnoni> FYI When you post to the W3C mailing list, put a [group] tag so people can filter on what they are interested in.

<vagnoni> Elgar wants to have confirmation that his emails to the W3C ML reached it.

<vagnoni> Susie suggests just going to the W3C Website and checking. Not sure if there is another way.

<ElgarPichler> this is the link to the w3c semweb email archive: http://lists.w3.org/Archives/Public/public-semweb-lifesci/

<vagnoni> Susie wants to get feedback about how to increase energy for Drug Ontology Dev.

<vagnoni> Bosse doing work on interface.

<vagnoni> Discussion with Luke from Emerge Network with EHR and Rx DB.

<vagnoni> Access to 2m EHR rec and Genotype Subjects.

<vagnoni> Looking into solutions for better use of information.

<vagnoni> Chris thinks we can apply what we are doing to a clinical setting and show what we can do.

<vagnoni> RDFizing the data, hurdles querying the data, etc.

<vagnoni> ...Introduce semantic ontologies, translational ontology, standarding data across domains...

<vagnoni> ...to generate phenotype/genotype classifications on the EHR/Geneotype data.

<vagnoni> we have a small demo to show off how it works and then (step2) move onto real clinical data.

<vagnoni> ...Then folks would be impressed to use it.

<vagnoni> ...Potentially time consuming to get mired in RW applications too early in the game.

<vagnoni> (someone) says that having RW data will actually better drive the process then doing it hypothetically.

<bbalsa> Link to eMerge, https://www.mc.vanderbilt.edu/victr/dcc/projects/acc/index.php/Main_Page