Notes from call:
- Next call will be January 10, due to holidays.

- There was enthusiasm for having the next OBI workshop in San Diego. Requests for more solid dates were made. We should pick a 3 day timeframe. Based on call participants, these would work well: Tentative dates: 2011, March 13-15, 19-21, 20-22 or 21-23. BP will apply for some basic funding.
Will send out a survey in a separate email

- Status of OBI release paper:
Chris is trying to look over it this week; will then pass on to Bjoern. Goal is to assess the necessary reviewer responses in light of what we have done since submission, and have a plan before the end of year. comments

- We went through the sourceforge tracker, and tackled several items. BP implemented those today.


(9:12 AM)  Bjoern: Philippe / Susanna, March: 14 -18 21-25
(9:13 AM)  Jess: Mar 14-18 is better for me
(9:13 AM)  Carlo: for eagle-i better 14.18
(9:17 AM)  Bjoern: http://obi-ontology.org/page/Workshop_OBI_San_Diego_2011
(9:19 AM)  Carlo: what about 14-16?
(9:19 AM)  Alan: 16-18 is Wed - Fri. I have at least one talk to give on the 16th.
(9:19 AM)  Alan: Perhaps Sun, Mon, Tues?
(9:19 AM)  Alan: 13th
(9:20 AM)  Carlo: well it works better not to have it on the 25th
(9:20 AM)  Carlo: before that everything is fine



(9:23 AM)  Alan: go to sourceforge
(9:23 AM)  Jess: The release is done, right?
(9:23 AM)  Alan: yes
(9:24 AM)  Jess: yay. :) Now the paper.
(9:24 AM)  Alan: was mail sent to user list?
(9:24 AM)  Jess: I think it was I just forgot for a sec.
(9:24 AM)  Bjoern: I don't think so
(9:24 AM)  Bjoern: obi-users, right?
(9:24 AM)  Jess: developers' list, yes.
(9:25 AM)  Alan: that's what I was asking
(9:26 AM)  Alan: btw, bioportal has managed to omit displaying definition editor for any of our terms
(9:26 AM)  Asiyah Lin: It's working here
(9:27 AM)  Alan: on a bright point, all our PURLs resolve to ontobee now
(9:27 AM)  Asiyah Lin: don't stop talk... please
(9:28 AM)  Carlo: Sorry, I have to leave. I have another call in two minutes. Talk to you soon
(9:28 AM)  Carlo: bye
(9:32 AM)  Alan: id is stable
(9:32 AM)  Alan: ok
(9:35 AM)  Jen: good
(9:36 AM)  Alan: looking
(9:38 AM)  Asiyah Lin: What about the forward primer and reverse primer as the subclasses of primer.
(9:38 AM)  Alan: ok
(9:39 AM)  Asiyah Lin: Do I need to submit a request in tracker?
(9:40 AM)  Bjoern: Asiyah, could you explain what you are asking?
(9:40 AM)  Bjoern: Can't hear
(9:40 AM)  Jen: faint
(9:41 AM)  Jen: better
(9:41 AM)  Bjoern: can anyone else hear her?
(9:41 AM)  Jen: faint but audible
(9:41 AM)  Asiyah Lin: what about now?
(9:41 AM)  Alan: hear that she is talking, but not what she is saying
(9:41 AM)  Bjoern: very very faint.
(9:41 AM)  Asiyah Lin: I will try to type
(9:42 AM)  Bjoern: ok
(9:43 AM)  Asiyah Lin: In the brucellosis ontology, we use forword primer and reverse primer as the subclasses of primer for modeling PCR
(9:43 AM)  Asiyah Lin: so that I think forward primer and reverse primer should be added into OBI
(9:44 AM)  Asiyah Lin: great
(9:44 AM)  Asiyah Lin: OK I should put my request in tracker then.
(9:45 AM)  Bjoern: True that a primer used as a forward primer in one experiment could be a reverse primer in another?
(9:45 AM)  Bjoern: substitute a ->amp; as a
(9:45 AM)  Bjoern: ?
(9:46 AM)  Jen: they are at left adn right end of amplicon
(9:46 AM)  Jen: you need both to define the sequence amplified
(9:46 AM)  Jen: yes
(9:47 AM)  Jen: you cannot change left and right and get anything meqningful
(9:47 AM)  Asiyah Lin: every PCR assay has a specific pair of primers
(9:47 AM)  Jen: +1 Asiyah
(9:48 AM)  Alan: we only have primer role currently
(9:48 AM)  Asiyah Lin: right, there is no primer even
(9:48 AM)  Asiyah Lin: will you consider to add the primer also?
(9:49 AM)  Asiyah Lin: I am submitting
(9:52 AM)  Bjoern: lost alan
(9:53 AM)  Jess: I gotta go folks, have fun. :)
(9:53 AM)  Alan: I did advocate it. But I think I lost that one.
(9:53 AM)  Bjoern: bye jess
(9:53 AM)  Alan: have we tried to get SO to change them?
(9:53 AM)  Asiyah Lin: It's a issue that need to a lots of discussion....
(9:55 AM)  Asiyah Lin: We might need to put some sequences into our ontology. and we are thinking the sequences should be in the description of the term or something else
(9:55 AM)  Alan: it just disconnected me
(9:55 AM)  Bjoern: AI for Bjoern: Figure email OBO foundry if there will be a unique name imposed.
(9:55 AM)  Alan: and I reconnected
(9:56 AM)  Alan: wondering whether there needs to be a "foundry unique label" metadata property
(9:56 AM)  Alan: can't see your screen
(9:56 AM)  Asiyah Lin: I can see
(9:57 AM)  Alan: ok. vyew lossage
(9:57 AM)  Alan: what are we discussing now?
(9:58 AM)  Alan: trust you
(9:58 AM)  Alan: (in this case ;-) )
(9:58 AM)  Alan: yes
(9:58 AM)  Alan: yes
(9:59 AM)  Jen: next two weeks
(9:59 AM)  Asiyah Lin: yes, your screen is not active.
(10:00 AM)  Jen: done
(10:00 AM)  Asiyah Lin: OK. I can copy
(10:00 AM)  Asiyah Lin: Happy new year!
(10:00 AM)  Jen: bye!

--
Bjoern Peters
Assistant Member
La Jolla Institute for Allergy and Immunology
9420 Athena Circle
La Jolla, CA 92037, USA
Tel: 858/752-6914
Fax: 858/752-6987
http://www.liai.org/pages/faculty-peters



--
Bjoern Peters
Assistant Member
La Jolla Institute for Allergy and Immunology
9420 Athena Circle
La Jolla, CA 92037, USA
Tel: 858/752-6914
Fax: 858/752-6987
http://www.liai.org/pages/faculty-peters