[Obi-devel] OBI Developer Call for May 20, 2013

[James A. Overton]

Hi everyone,

I'm chairing the call on Monday. We have quite a number of items to discuss:

1. Matt has a deadline, and wants to finish the discussion of CLO-OBI alignment:
- http://sourceforge.net/mailarchive/message.php?msg_id=30811056
2. We should discuss the email from Susanna-Assunta Sansone of Nature Publishing Group:
- http://sourceforge.net/mailarchive/forum.php?thread_name=5194CE6A.9040500%40gmail.com&forum_name=obi-devel
3. We should quickly review the workshop schedule: http://obi-ontology.org/page/Philly2013
4. I think we should review the discussion and status of "data item".
5. I saw Bill Duncan in Buffalo and we talked about his two tracker items. I now have a few more details, and I'd like to resolve them:
- http://sourceforge.net/tracker/?func=detail&aid=3610398&group_id=177891&atid=886178
- http://sourceforge.net/tracker/?func=detail&aid=3611768&group_id=177891&atid=886178

I'm probably missing something -- please let me know. But keep in mind that we'll already be short of time.

James



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[Melissa Haendel]

Hi all,

I may not make it on Monday as will be in transit. I've commented on Bill's two tracker items, but only based on what was currently in the tracker.

As for Susanna's email, I'm on board and have been in discussions with them to work on instance inclusion in ISA-Tab, which would fit well with OBI.

As for the CLO-OBI alignment late-breaking submission, we'll need to know who to include as authors.

Cheers,

Melissa

Dr. Melissa Haendel

Assistant Professor
Ontology Development Group, OHSU Library

http://www.ohsu.edu/library/

Department of Medical Informatics and Epidemiology
Oregon Health & Science University
hae...@ohsu.edu
skype: melissa.haendel

503-407-5970

[Matthew Brush]

Hi all.  Yes, I would like to use 15 minutes or so of the call to get final feedback on the CLO-OBI alignment work – as I am submitting an ICBO abstract on it due this week, and Oliver is submitting a JBMS paper on CLO due at the end of the month.  I will briefly recap what has been done so far, but the main issue we need to resolve is what ‘scales’ of cultured cell population classes are useful to represent, and how to define and label them.  At present we represent cultured cells/cell line cells at three levels –  as single cells, as experimental samples/populations, and as the ‘entire’ line – but we have yet to agree on the need and labels for these.  Resolving this will allow us to move ahead with the alignment work enough to get these papers out.  More in depth review of the new modeling can occur offline at a later date.

 

Best, Matt

 

Matthew H. Brush

Research Associate

OHSU Ontology Development Group

Department of Medical Informatics and Clinical Epidemiology

Oregon Health and Science University

phone :  919-452-6914

fax :  503-346-6815

bru...@ohsu.edu

[James A. Overton]

Hello everyone,

Here are my notes on today's call.

NOTE: May 27th is an American holiday, so there will be no OBI call. The next call will be on June 3rd.

James


Agenda:

1. Matt on CLO-OBI alignment
2. Email from Susanna-Assunta Sansone of Nature Publishing Group:
3. Workshop schedule: http://obi-ontology.org/page/Philly2013
4. We should also assign chairs.
5. Data item
6. Bill Duncan's dentistry tracker items

Note: we ran out of time for items 5 and 6.


1. Matt on CLO-OBI alignment

This discussion follows up on the April 13th call. There are some conference and journal deadlines coming up very soon. We need to decide:

1.1 What scales do we want to represent? Matt proposes: "cell cultures/lines" (OBI?), "cell line samples" (OBI?), "cultured cells" (CLO). He draws a parallel between the species/population/organism distinction, and has examples where each of these three representations would be useful for cultured cells, cell line samples, and entire cell lines.

The questions that remain are (a) where the terms should live, and (b) the best labels to give them. OBI might not be the best home, but there is ample precedent for OBI including terms that other ontologies later take over. Unfortunately we did not resolve these questions on the call.

1.2 Is the CLO term "cell line cell population" the same as OBI's "cell line sample"? Oliver says that the CLO term is meant to include populations that might be polluted or mixed with multiple types of cells. Matt points out that this is different from the OBI usage of "cell line sample", which is intended to be homogeneous. It is not immediately clear how "cell line cell population" should be related to "cell line sample".


2. Susanna-Assunta Sansone on the use of OBI by Nature Publishing Group

Susanna is located in Oxford and works with Philippe and Alejandra in one of her roles there. She is familiar with OBI. She also works on the new Scientific Data initiative from the Nature Publishing Group (http://www.nature.com/scientificdata/). On the call she summarized this as open access online data publishing. It is distinct from traditional publishing, focusing instead on publishing curated data sets so they can be easily reused and cited. Each data set will be described using a "data descriptor", which will have a structured part based on the ISA framework. Susanna's group is in the process of selecting the community standards to support and hiring their first curator for the project. The email she sent to the OBI list last week is an invitation to hear from various communities about their interest in the Scientific Data platform.

Based on her familiarity with OBI, its broad scope, and its active community, Susanna would like to see OBI used as the default terminology for the project. In response to questions from James and Chris, she clarified that she would like OBI to:

2.1 register interest in the Scientific Data project (by email, see Step 1 here: http://blogs.nature.com/scientificdata/2013/05/13/our-roadmap-to-engagement-your-call)
2.2 have someone "claim" the OBI entry on the BioSharing site, and commit to keeping that entry up-to-date

Alejandra pointed out that their work at ISA relies on the use of OBI terms, and this project extends that work. Philippe pointed out that collaboration would bring examples from a wide range of scientific investigations, which could enrich OBI. He also said that this highlights the urgency of settling the discussion of "data item" and related terms as soon as possible.

Bjoern has the role of "OBI contact person", so James will update him on today's discussion.


3. Workshop

The wiki page for the workshop has been updated: http://obi-ontology.org/page/Philly2013

Please follow the links and contribute to the Google Docs! Email James with your Google ID and he will give you editing privileges.


4. Chairs

Chris Stoeckert volunteered to chair the call on June 3rd.


We ran out of time for items 5 and 6.

[Susanna Sansone]

Many thanks, James.

Just a clarification on this please for the record.

> Susanna's group is in the process of selecting the community
> standards to support and hiring their first curator for the project.

It is NPG's Scientific Data that is in the process of hiring the first in-house curator.
I, as their consultant, also advise on community standards, curation matters.

> She is familiar with OBI.

Indeed, having be there from the onset in 2004; but over the years I left my team to contribute. Currently it is Philippe and Alejandra.

Many thanks again,
Susanna

-- 
Susanna-Assunta Sansone, PhD
uk.linkedin.com/in/sasansone

University of Oxford e-Research Centre
 Associate Director, PI and Team Leader
 isacommons.org | biosharing.org

Nature Publishing Group
 Consultant, Scientific Data
 www.nature.com/scientificdata
-- 

Hi all.  Yes, I would like to use 15 minutes or so of the call to get final feedback on the CLO-OBI alignment work � as I am submitting an ICBO abstract on it due this week, and Oliver is submitting a JBMS paper on CLO due at the end of the month.  I will briefly recap what has been done so far, but the main issue we need to resolve is what �scales� of cultured cell population classes are useful to represent, and how to define and label them.  At present we represent cultured cells/cell line cells at three levels �  as single cells, as experimental samples/populations, and as the �entire� line � but we have yet to agree on the need and labels for these.  Resolving this will allow us to move ahead with the alignment work enough to get these papers out.  More in depth review of the new modeling can occur offline at a later date.
 
Best, Matt
 
Matthew H. Brush
Research Associate
OHSU Ontology Development Group
Department of Medical Informatics and Clinical Epidemiology
Oregon Health and Science University
phone :  919-452-6914

[James A. Overton]

Thanks for the clarifications Susanna -- much appreciated. I myself am fairly new to OBI, so I wasn't clear on your past involvement.

James

>>> Hi all. Yes, I would like to use 15 minutes or so of the call to get final feedback on the CLO-OBI alignment work – as I am submitting an ICBO abstract on it due this week, and Oliver is submitting a JBMS paper on CLO due at the end of the month. I will briefly recap what has been done so far, but the main issue we need to resolve is what ‘scales’ of cultured cell population classes are useful to represent, and how to define and label them. At present we represent cultured cells/cell line cells at three levels – as single cells, as experimental samples/populations, and as the ‘entire’ line – but we have yet to agree on the need and labels for these. Resolving this will allow us to move ahead with the alignment work enough to get these papers out. More in depth review of the new modeling can occur offline at a later date.

[Bjoern Peters]

After reading Susanna's original email and going throug the notes from the call, I see no downsides to registering OBI on the BioSharing site; is that correct? As I was asked to do the registering (which is fine for me), I want to make sure that I am not overlooking any objections that may have been raised, so please let me know, or I will register by the next call. 

Thanks, 

- Bjoern

---

--

Bjoern Peters
Assistant Professor
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