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Date/Time: Thursday, December 8, 2011; 10-11 AM ET

Attendees

Brian Davis, Sherri de Coronado, Sharron Lewis, Stuart Turner, Troy Bleeker, Hua Min, Larry Wright

Agenda

  • OOR Update – Brian Davis (5 min)
  • Discuss and Review OOR “Sandbox”- Sherri De Coronado (10 min)
  • Roadshow
    • Discuss Updated Roles and Usecases – Brian Davis (15 min)
    • Discuss Ontology Requirements (Curation Questions)- Brian Davis (2 min)

Assigned To

Description

Due Date

Brian Davis

Contact Peter Yim for direction on CTS2 Version Control

12/08/2011

Sherri de Coronado

Contact Peter Yim to request SANDBOX access of OOR

12/08/2011

Sherri de Coronado

Mention the Plan Demo (Roadshow) during the TBPT Face-to-Face

12/07/2011

Brian Davis

contact Trish Whetzel for a list of BioPortal endusers

12/08/2011

Brian Davis

Send Densie Warzel the wiki link or doc so she can possibly update the Roadshow Usecase.

12/08/2011

Denise Warzel

Contact Diane Reeves to see if she has a list of questions for the Curators to make the decision of which terminology to use.

12/08/2011

Notes

OOR Update

  • Brian displayed the list of people who have downloaded Bioportal (Trish sent him the excel spreadsheet) He points out- these are the Bioinformatics player not actually scientific users – so it might be valuable for who we will actually get feedback from.
  • Peter Yim and his team are having problems --they received help – they call it virtual user appliance
  • Q. Do we know the people on the list are downloading them?
  • A. Brian - it doesn’t say but Trish wouldn’t know either.
  • AI: Trish could find out about the federation then we can maybe find out the actual people using it instead of just downloading.
  • AI: Sherri- Why there might be problems with federation issues
  • Maybe we could ask Peter Yim if they try to perform federation- Sherri said I guess we can’t go to far with the issue
  • Synchronization and different versions could be an issue – so GRID Services and the analytical services- the client server box.
  • The GRID API could be an issue where they have the same pointers – the API could be different
  • Q. Larry could do the same with the GRID API?
  • One of the issues could be the federated could be the source and their version – how do they know which one they are looking at
  • Q. How would we have a plan for the federation
  • A. Maybe we do want to discuss this with the ORR group – but we would want to include a LexEVS developer – they might not have the time now
  • AI: Sherri and Larry – List of what the issues could be for Bioportal (bullet points)
  • You can federate medata without having a federated repository.
  • AI: Sherri - Approach Peter Yim what he is thinking on what writing was done in terms of metadata for ontology
  • AI : Sherri and Troy could come up with a list of issues and talk about it next week.
  • Ontolog update meeting sent out the email today –
  • Michael was supposed to send a request for Sherri and Harold to speak on Dec 13th
  • Harold is out of country ?
  • AI Brian- Contact Mike Bennett to determine the OOR presentation status of Harold ahd Sherri
  • They talked a bit about the bioportal issues – one of their main issues is mapping among ontologies – especially in different languages --discuss issues at UniBremen (IKL)- they talked about a prototype call IAL. Everything is done is OWL they want to do things that are done in OWL
  • The mapping is somewhat limited – you can do it
  • Q. Are they looking to make UniBremen a commercial product
  • A. No open source
  • GUAH- Scemhama dot.org talked about – 4 major players come with a pre-standard how they can mark up the page – they said it would be an increase of 10%-200% more hits (google, yahoo) would find it – the hits would be more useful.
  • The google folks (GUAH) – said they would not take on the work- the Ontolog group was willing to provide additonal feedback to make it more useful
  • Sent the information to the caBIG facilators- if anyone wanted to get more hits they could research it

OOR SANDBOX

  • There is not a lot there
  • They have only a handful of ontologies-- a couple broken links- they have the frame work but nothing useful- don’t know how much experience we can get out of this- it looks a lot like Bioportal- doesn’t look like the community is using it
  • Its not clear to me - the relationship with the sandbox and Devbox- I think they are going to need more from the devbox.
  • They are trying to use NCBO as the core – as a more open source- goal is to try to make plugins for more things they want to use – so they can test plugins against it
  • Yes, that might be – thought it was more of community effort - not actually trying develop something – use case description ontology-
    +TBPT Feedback meeting +
  • Most people understood the benefit and headache of semantics – in reality even though people are using standards I still heard the different needs for mapping.
  • There are considerable needs for mapping- people don’t usnderstand what and when to use the different ontologies
  • Sherri recommended the BKC to help out – she then mentioned the roadshow that will help people understand the difference
  • There were several people that had issues with caDSR. Having to click too many times to get to the terminology they would like to more info.
  • Sherri asked for usecases so we can make more changes in the API when updating
  • Q There are so many standards how do you know which one to use – then talked about the sources and metathesaurus
  • Discussed to them about NCBO trying to put together a community
  • Q. Did you get names and numbers for the people that would benefit
  • A. Anna and Beth took notes – received one name – Andrew Brenchick. He probably has connections to the endusers. Also received contact from someone from TJU.
  • Dave Watson and Bill are working together and wrote a paper for the” Ideal Biorepository System” -working close with TBPT
  • Talks on Transcend-- very interesting to see all the work done at Vanderbilt- they have a whole department – 55 faculty and 500 people working on it, in some way. Biomedical information – they are doing everything including LP. Very interesting seeing how much work they are doing and good work.
  • So many standards that no one knows when and where
  • Q Is there mappings among standards that anyone has done? There is software out there
  • A. That is a good idea- topic map other than a concept map- you can use a resource to anyone that may want to add to it- they did do something like to for a NCSF grant. Topic map as a collaboration tool. We are asking what standards are important to the community that’s would be more helpful. I think it would be a good exercise for the community – describe something in a table
  • That would be very useful- because it’s so difficult to keep up with all the data – to keep the data and metadata straight
  • Also impressed how the medical field is progressing they are doing personalized practice

Updates and Script

  • Brian linked to the roadmap work regarding roles – reference the wiki – he suggested that the we concentrate on the middle three- they acutally made profiles of the stakeholders and copy the roles in the wiki – we could possibly use that – also copy the NCBO
  • What Sherri, Denise Brian did --they took the use cases and flushed it out a little bit in terms and put down what they think the requirements what the think the use cases would be – before we go out we can ask people about their requirements- there was a lot of good work in the SOA list
  • Sharron started reaching out to the workspace leads for discussion and info before presenting at their monthly teleconferences.
  • Q. We can ask If in 3b I-vii) ask the leads what they think?
  • A. Do you think the list is concrete enough? I do agree that is clearly the best way – but if you asked them in the abstract you don’t get a lot back – there has to be a better way- We can at least ask the WS lead s- if they can ask what they have
  • AI: Sharron ask the WS facilitator for list

Action Items

Assigned To

Description

Due Date

Brian Davis

Find out from Mike if Sherri and Harold could speak during later scheduled OOR meeting another time

12/15/2011

Trish Whetzel

Find out about the federation (Bioportal)then we can maybe find out the actual people using it instead of just downloading.

12/15/2011

Sherri de Coronado

Why there might be problems with federation issues

12/15/2011

Sharron Lewis

Ask the WS Facilitators for a list of possible Use Cases from their community

12/22/2011

Sherri and Troy

Come up with a list of issues (NCBO Bioportal)

12/15/2011

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