Conference call developers agenda

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Call-in Information

Notes/Minutes of 2009


Conference Call Agenda Items

March 2017

Mar 6: James

February 2017

Feb 27: Bjoern

Feb 20: Jie

Feb 13: Becky

Feb 6: Gully

January 2017

Jan 30: Bjoern

Jan 23: Bjoern

Jan 16: Jie

Jan 9: Bjoern

Jan 2: no call

December 2016

Dec 26: no call

Dec 19: James

Dec 12: Chris

Dec 5: Bjoern

November 2016

Nov 28: Mathias

Nov 21: Chris

Nov 14: James

Nov 7: Mathias

October 2016

Oct 31: Bjoern

Oct 24: Jie

Oct 17: Gully - Progress on KeFed text mining and evidence extraction; Aspergillus use case

Oct 10: Chris

Oct 3: Bjoern

September 2016

All calls hosted by Bjoern - assay harmonization

August 2016

Aug 29: Gully

Aug 22: Jie

Aug 15: Chris

Aug 8: Becky

Aug 1: ICBO

July 2016

July 25: Chris

July 18: Gully

July 11: Jie

July 4: Cancelled due to Holiday

June 2016

June 27: Dan B.

June 20: Chris

June 13: James

June 6: Ramona

May 2016

May 30: Gully

May 23: Cancelled

May 16: Matt

May 9: Bjoern

May 2: Marcus

April 2016

April 25: Jie

April 18: Matt

April 11: James

April 4: Chris

March 2016

March 7: Bjoern

March 14: Bjoern

March 21: Asiyah

March 28: Gully

February 2016

February 29: Bjoern

February 22: James

February 15: Chris

February 8: Jie

February 1: Marcus

January 2016

Jan 25: James

Jan 18: Cancelled for Martin Luther King Day

Jan 11: Jie

Jan 4: Chris

December 2015

Dec 28: Cancelled for Christmas

Dec 21: Gully

Dec 14: Mathias

Dec 7: James

November 2015

Nov 30: Gully

Nov 23: Asiyah

Nov 16: Chris

Nov 9: Bjoern

Nov 2: Jie

October 2015

Oct 26: Asiyah

Oct 19: Gully

Oct 12: Chris

Oct 5: Bjoern

September 2015

Sept 28: James

Sept 21: Jie

Sept 14: Bjoern

Sept 7: cancelled for Labor Day

August 2015

Aug 31: cancelled

Aug 24: Asiyah

Aug 17: James

Aug 10: Gully

Aug 3: Jie

July 2015

July 27: ICBO - no call

July 20: James

July 13: Marcus

July 6: Chris

June 2015

June 29: Bjoern

June 22: Marcus - minutes

June 15: Sagar

June 8: Chris

June 1: Jie - Gully, presentation

May 2015

May 25: canceled (Holiday)

May 18: Bjoern

May 11: James

May 4: Chris

April 2015

April 27: Asiyah

April 20: tentatively cancel

April 13: Jie (joined by Ramona / BCO)

April 6: Bjoern

March 2015

March 30: Bjoern

March 23: James

March 16: Jie

March 9: Cancelled

March 2: Chris Stoeckert - Tracker items

February 2015

2/23 James Overton - Assay harmonization.

2/16 Chris Stoeckert - Tracker items

2/9 Bjoern Peters - Tracker items

2/2 Bjoern Peters

January 2015

1/26 Jie Zheng
1/19 cancelled due to US holiday
1/12 Chris Stoeckert
1/5 - Asiyah - Assay Harmonization

December 2014

12/29 - no call

12/27 - no call

12/15 Jie - OBI release, trackers

12/8 James - OBI trackers

12/1 Jie - assay review / term submissions

November 2014

11/24 Asiyah - Assay review

11/17 Bjoern

11/10 Bjoern

11/3 Bjoern

October 2014

October 27: Chris Stoeckert

October 20: James Overton

October 13: Jie Zheng

October 6: Cancelled due to ICBO meeting

September 2014

September 29: Asiyah Yu Lin

September 22: Heiner Oberkampf

September 15: James Overton

September 8: Jie Zheng

July 2014

July 28: Bjoern Peters - cancelled

July 21: Asiyah Yu Lin

July 14:

July 7:

June 2014

June 30: Jie Zheng

June 23: No call

June 16: James Overton

June 9: Alejandra Gonzalez-Beltran

June 2: Philippe Rocca-Serra

May 2014

May 26: no call Holiday

May 19: James Overton

May 12: Chris Stoeckert

May 5: Jie Zheng

April 2014

April 28: Bjoern Peters

April 21: no call

April 14: Chris Stoeckert

April 7: Philippe Rocca-Serra

Present: Bjoern, Jie, Alan, Randi, Heiner, Johannas, Alejandra, Myself,

1. Main Topic: IAO issue tracker item 157 (data item)

AR captured the elements of discussion in comments on the ticket.

Clarify the notion of 'data set' as child of 'data item' therefore, suggestion rename 'data set' to 'data item set' to indicate the aggregate nature of the entity in the class label but also work on an axiom: has_part min 2 'data item' but this raises issues with transitive property chain so suggestion to rely on 'has_member' relation instead which is safer.

Also, it was discussed that 'data item set' subtypes will have to be created if one requires more specificity with regarding to the nature of 'data item' making up the 'data item set'

so the following restriction: (has_part only ('mass measurement datum' or not ('measurement data item'))). could be used to define a 'mass measurement data (item) set'.

2. IAO tracker item 156 to be close via a commit implement the requested changes as document in the issue tracker

AI on James O.

3. OBI support page requires maintenance and upgrade

Reported by Barry Smith who submitted a tracker item AI on PRS to update. and link to obi-dev mailing list

4. OBI presence at ICBO:

Will be covered by a tutorial by James O. + BP

5. OBI release manuscript update

in BP 's hands, a week to 10 days are needed to do further edits

Next Call: April 14th same time Chair: Chris Stoeckert

Webex Chat:

from Philippe to Everyone: thx from Philippe to Everyone: from Philippe to Everyone: from IEDB Conferencing to Everyone: alan is joining from Philippe to Everyone: from jie to Everyone: replace 'datum' by 'data item' from jie to Everyone: I think last time we discussed and would like to keep JAR's notes from jie to Everyone: 'data set' is subClassOf 'data item' from jie to Everyone: but label should be datum label from jie to Everyone: to apply to a single datum from jie to Everyone: data item label might mislieading. it cannot apply to dataset from Philippe to Everyone: we had this discussion already a few years back from Philippe to Everyone: s/data set/data item set/ ? do we agree? from IEDB Conferencing to Everyone: I personally find nothing wrong with the current state of things, and don't believe making strong distinctions on datum / data item is particularly helpful. so I am quite because I just want to have this be over. from Philippe to Everyone: should we add an axiom on data item set, has_part min 2 (data item and is about some entity)) ? from jie to Everyone: has min 2 data item from jie to Everyone: has_member from jie to Everyone: I wll

March 2014

March 31: Jie Zheng

March 24: Bjoern Peters

March 17th: James Overton

March 10th: Chris Stoeckert

March 3rd: Jie Zheng

February 2014

February 24: Bjoern Peters

February 17: NO CALL (US Holiday)

February 10: Alejandra Gonzalez-Beltran

February 3: Philippe Rocca-Serra

January 2014

January 27: Matthias

January 20: No call - MLK day

January 13: Asiyah

January 6: Bjoern

December 2013

December 30: no call Xmas break

December 23: no call Xmas break

December 16: Philippe Rocca-Serra

December 9: Jie Zheng

December 2: Philippe Rocca-Serra

November 2013

November 4: Jennifer Fostel

October 2013

October 28: James Overton

October 21: James Overton

October 14: Bjoern Peters

October 7: James Overton

September 2013

September 30: Jie Zheng (preparation for OBI release)

September 23: Jie Zheng (review study design and assay related core terms)

September 16: Chris Stoeckert (review human subject enrollment related core terms)

September 9: James Overton (review data item related core terms)

September 2: US holiday, cancelled

August 2013

August 26: James Overton (review data item related core terms)

August 19: James Overton (review data item related core terms)

August 12: Jie Zheng

August 5: Chris Stoeckert

July 2013

July 29th: Bjoern Peters

July 22: James Overton

July 15th: Matthew Brush

July 1st: Melissa Haendel

June 2013

June 24th: Philippe Rocca-Serra

June 17th: James Overton

  • Data item discussion

June 10th: Jie Zheng

June 3rd: Chris Stoeckert

May 2013

May 6th: Bjoern Peters

May 13th:Philippe Rocca-Serra

May 20th: James Overton

April 2013

April 29th: Alejandra


April 22th: Matt

April 15th: James

April 8th: Oliver

April 1st: No call due to holiday in Europe

March 2013

March 25th: Bjoern

March 18th: Jie

March 11th: Alejandra

March 4th: Jie

February 2013

Feb 25th: Carlo

Feb 18th: Jennifer

Feb 11th: James

January 2013

Jan 28th: Bjoern

Jan 21: American Holiday -- Martin Luther King Day

Jan 14th: Jie - Call cancelled

Jan 7th: Carlo

December 2012

Dec 17th: James Overton

Dec 10th: Jie

Dec 3rd: Bjoern

November 2012

Nov 26th: Philippe

Nov 19th: Matt Call Notes

Nov 12: James Overton

Nov 5th: Philippe

October 2012

Oct 29th: Jie

Oct 22nd: Bjoern

Oct 15th : Matt Call Notes

Oct 7th: no call, holiday

September 2012

Sep 30th: James

Sep 24th: Jie

Sep 17th: Christian

Sep 10th: Melissa

August 2012

August 27th Christian (randi host)

August 20th James (randi host)

August 13th Bjoern

August 6th Jie

Notes from chat

July 2012

July 30th

July 23rd

July 16th

July 9th Chair: Jie

July 2nd Next Call Chair: CARLO

Possible future agenda: - -data item continued discussion -> resolution is needed -- OBI core terms -- OBI participation ICBO2012. - -OBI next release - -find volunteers for chairing the dev call until September Agenda additions: - Alan: Set up meeting with Clark and Parsia re: SBIR - Alan: Cross-talk on diagnosis textual entity. performing a diagnosis with OGMS

June 2012

25 June" Chair: Oliver

Attendees: Chris, Philippe, Alan, Christian, Jie, James, Carlo, Oliver (Chair)

Representation of 'predicted data' and 'measured data' - We have 'measurement datum' in IAO/OBI now. - We also have 'predicted data item': - Jie: We have 'data item' in CORE but not measurement datum

Philippe: - measurement unit label is different from a measurement unit in the same way a product label is not a product - We don't have measurement unit. We have measurement unit label. - 'mass unit' is imported from unit ontology and inserted under 'measurement unit label'. This is a problem. A unit and a unit label are not the same. - what units are? - the issue i raise is that scalar measurement always compare to a standard scale - predicted data can be compared to measured data, out of some measurement assay. - Christian: out of some computation, does not have to compare to measured data.

Alan: - what does the predicted value 10.1 grams mean 1) need to say how "models" work 2) is_about points to a type rather than an instance

Christian raises the issue of a "real" measurement being associated with a model

Chris Stoeckert: - but in OBI we can restrict - no unicorns! - We are restricting our models to things that are real.

Christian Boelling: - the definition of iao:data item should be reviewed in any case: the truthfulness part of it, that I find problematic and a source of confusion. - Data items and truth: the current definition of data item states that an instance of iao:data item "…is an information content entity that is intended to be a truthful statement…" - In fact, a data item is *NOT* a statement (as the current definition suggests) and as such is neither true nor false. Rather, (representations of) data items are part of statements such as "mouse#1 - has weigth - 10 gram" expressed in some suitable language (e.g.: OWL) with the last bit being an instance of data item. It is *this statement* which may be true or false; *not* the data item. -- propose the data item issue also for the IAO informal session at ICBO - Relevant posts:

Alan Ruttenberg: - keeping backwards compatible as we make the future changes - Another interpretation: the statement is: it is the case that 10 grams is a quality measurement of <that quality of the material entity> That can be true or false - those statements look like <subproperty of is about> <something>

OBI release: - May not be ready to have another release since no major improvements have been made compared to last version. - Alan: not ready in terms of updated measurement data representation - Consensus: may postpone this OBI release to after ICBO meeting

Oliver: We need to reserve at least one or two meetings for OBI tutorial, to be held on July 22nd, 2012, Graz, Austria:

18 June Chair: Philippe

Attending: Carlo Torniai, Marcus Chibucos, Jie Zheng, Yu Lin, Oliver He, Alan Ruttenberg, Bjoern Peters, Randi Vita, Chris Stoeckert,

Minutes: Overall goal: reorganize 'data item branch' to avoid redundant declaration as currently experienced.

proposal create 3 defined classes:

predicted data item: is_specified_output_of some 'prediction data transformation'

specified/planned/set data item: is_specified_output_of some 'planning'

measured data item: is_specified_output_of some "assay or measurement"


i. class naming:

'value specification' has been suggested to be rename 'value denotation', which was deemed more neutral. However, it is being argued that the term is misused.

-denotation (verb) = process that takes label/name and finds what it points to.(AR) -denotation (Noun) is the target of what is pointed to.(AR)

for context: denotation (noun):the literal or primary meaning of a word, in contrast to the feelings or ideas that the word suggests. [mass noun] the action of indicating or referring to something by means of a word, symbol, etc.. Philosophy the object or concept to which a term refers, or the set of objects of which a predicate is true.

denote (verb): be a sign of, indicate

No resolution as both the use of 'specification' and 'denotation' labels can be miscontrued.

"value specification/denotation" is just value + unit

ii. discussion on aboutness:

argument that predicted data item are about something different than measured data item (predicted water temperature would not be about water but a realizable entity Alan Ruttenberg's view) Are 'predicted water temperature' and 'measured water temperature" 'about' the same entity? (important note: it is assumed that the predictions result from a 'realistic model about an entity' which delivers values, which, by plan, should be compatible with reality). ->unresolved discussion:

points are made for thinking in terms of type versus instances to help clarifying the proposal:

predicted data (wouldbe)_about universal (universal/type level) measured data is_about a particular of the type (instance level)

AI: ->drill on this point over next call.

iii. discussion on comparison process associated with predicted data.

argument that predicted data item always need to be presented in the context of a comparison to actual measurement data. "prediction of temperature is about a realizable entity realized in a process in which when the conditions of the simuation obtain and a measurement of temperature is made, that temperature is compared to the predicted value and is approximately (or data item weasel word) correct " Christian Bolling argues that the comparison is a different and distinct step. (see his post)

11 June Chair: Philippe

May 2012

28 May No Call (US holiday)

21 May Chair: Oliver

Prepare the Ann Arbor OBI face-2-face workshop.

14 May Chair: Marcus

7 May Chair: James

April 2012

30 April Chair: Melissa

23 April Chair: Jie

16 April Chair: Jennifer Attending: CT,CS,JO,JZ,PRS,RV,JMF

OBI Core - we will use the terms identified as necessary by the majority of developers; JZ had identifed 14 terms, which with antecedents from logical definitions produces a list of about 100 terms. Other communities will create a slim / add terms

Other topics for F2F:

Manuscript - JZ, JMF to discuss with BP

Time/Domain Knowledge - BFO does not include

Specimen - JZ/JMF to set up call

OBI-ECO - JZ will present proposal next week

Use case/documentation/modeling - subteam of James, Jie, Randy, Jennifer to bring back to F2F

Statistics - OH will present proposal at the F2F

QTT - part of Evidence Code discussion

Data item - under discussion by IAO

Topics for next week: OBI-ECO proposal (JZ, MC)

9 April Chair: Marcus

2 April Chair: Chris

March 2012

26 March Chair: Jennifer

19 March Chair: Bjoern

12 March Chair: James

5 March Chair: Jie

February 2012

27 Feb Chair: Larissa

Attended: BP, LS, Jie, James Overton, Philippe, Chris Stoeckert, Melissa,Trish Whetzel, Marcus, Carlo, Zvita, Matthew Brush, Jen Fostel,
1. jie: A reprt from the subgroup meeting about phenotype assessment

AI: Jie - prepare and post a short report on the subgroup work.

Shortly report of RCN: Plant people are interested in modeling metadata using OBI framework. I am in contact for this. They are also thinking to collect experimental condition. OBI can help in providing terms in annotations. Currently, they really want us to help in "growth condition" (modeling and annotation).

Suggestion: subgroups should post short reports about their work and the results for the OBI dev. Subgroups activities should be better recognized and acknowledged.

On the related issue: people are having difficulty using OBI, e.g. developing annotation forms, contributing terms, alignning their existing ontology with OBI, etc. We need to think about better tutorial, regular help line, assistance, etc.

2. the Revision of the OBI organizational structure. 

The documents has been accepted by the majority (only 1 vote against). The document will beposted on-line.

There were worth considering comments on the document made. AI: LS - incorporate suggestions to improve the document and send an updated version to BP in a week.

AI: ALL -assign yourself to the tasks:

add new tasks if needed

3. Item  'purification' from the tracker has been closed; new class 'purified material' added.

20 Feb No meeting; Holiday

13 Feb Chair: Jennifer

6 Feb Chair: Melissa

January 2012

30 Jan Chair: Carlo

23 Jan Chair: Bjoern

16 Jan No call. MLK day

9 Jan Chair: Jie

 1. Transition to BFO2
 We decided to transit to BFO2 which is close to be officially released soon.
 * import the whole bfo.owl (light version)
 * MIREOT relations defined in ro.owl if needed

The reason we cannot make the release out due to one relation "towards" used in defining "molecular concentration". It may take a while to be in BFO 2. The term "molecular concentration" is in PATO scope and Chris Mungall agreed that the term should be in PATO. The term is not used by any other OBI terms. So, we decided to deprecate the term now for making the current release out. We will import the term from PATO when it is available since we used the term in the manuscript.

AI for Jie: release and keep track on it by contact Alan and Chris.

 2. OBI organizational structure
 We went through documents and defined who are 'active developers'. Please give your comments on:
 * do we need a benevolent dictator?
 * list the tasks and add your name to those you'd like contribute to on the page:

December 2011

19 Dec Chair: Bjoern

12 Dec Chair: Jie

5 Dec Chair: Carlo

November 2011

28 Nov Chair: Marcus

 * Label role related terms
 * OBI core terms

21 Nov Chair: Jie

 * OBI manuscript (focus on OBI core)
 * OBI core (AI for All)
 * OBI release (Around Dec 10th)
 * Phenotype (Contact Chris Mungall, AI for Marcus)
 * Label role related terms (AI for Matt)

14 Nov Cancelled

7 Nov Chair: Jennifer

 Phenotype discussion

October 2011

31 Oct Chair: Chris

* phenotype discussion

24 Oct Chair: Bjoern

* molecular tracer/label discussion

17 Oct Chair: Carlo

* review OBI workshop action items

10 Oct No call - preparation for Philly workshop

3 Oct Chair: Bjoern

* decide on implementing label edits (so far consensus seems to be to implement what I emailed, but use 'tracer' instead of 'label' 
* Conference planning
* Jie presentation on Ontology views

September 2011

26 Sep Chair: Jie

19 Sep Chair: Melissa

12 Sep Chair: Carlo

5 Sep US - Holiday

August 2011

29 Aug Chair: Bjoern

- OBI foundry re-review
- OBI paper
- workshop planning
- Tracker items, including recent exchanges on DNA sequencing and organisms

22 Aug Chair: Jie

15 Aug Chair: Chris

Grant planning 

8 Aug Chair: Bjoern

Grant planning 
Release status
Chairs for next calls
OBI community view - Dealing with community specific labels
OBI slim
OBI planning - what are the next steps 
OBI workshop - set a date and location
OBI paper - application section

1 Aug Chair: Bjoern

ICBO review

July 2011

25 July Chair: Bjoern

ICBO presentations

18 July Chair: Bjoern

ICBO presentations

11 July Chair: Jie

June 2011

27 June Chair: Chris

20 June Chair: Bjoern

13 June Chair: Carlo

6 June Chair: Bjoern

May 2011

23 May Chair: Philippe

- Minutes
- Present: Anita,Jessica,Melissa,Bjoern,Jie,Marcus,Matt,Philippe
- Excused: Alan
- 1. OBI manuscript: roadmap
        Comment by Jessica: possible lack of information for newcomer -> need for a tutorial
               o. Action Item: creation of a tutorial and use case -> documention to point as supplementary material
        Input from Anita ( and Marcus (recent presentation to the GO) updates                
              i.Action Item Anita to update table of projects using OBI for annotation purposes.
              ii. include statement about ECO consuming OBI (possibly in discussion section)
              Marcus to take lead on this and, when done, pass on to Bjoern.
              iii. Some level of redundancy between some of the example in Applications of OBI.
              ->possible need to fuse and relevant parties will be contacted as necessary.

              iv. Sanity check against latest OBI release 
              i.e. check that all classes/relations mentioned in the manuscript match strictly with class 
              definitions (textual and formal).
              Note: process is painfull so should be done only once, when manuscript has solidified. 	
- 2. Class metadata:

OBI seems happy with current metadata but would not oppose changes provided work and interoperability with other resources is not disrupted.

- 3. Discussion on Datum (follow Asiyah post about dose, thread with Alan)

Bjoern restated the issue which can be decomposed as follows:

There are different problems: i. time problems (translating weeks / months etc.) ii.age problems (time from when) iii. measurement datum vs. quality iv. measurement datum vs. specification datum

points i and ii seem to cover a need from Anita, Melissa, Jessica but it is noted that might be out of scope (point i)

The current layout is an attempt to create a solution which would cover datum resulting from a measuring process and those datum corresponding to recommandations,directives ( use a solution of 20x TBE) and would be generic enought to avoid duplication of hierarchy.

all points require more work -> calls to be dedicated to this.

Question: Why is point 4 necessary since, in OBI, we assumed 'canonical realization' of protocol specification.

Possible explanation: The specification will state 20xTBE, the experiment relying on that solution will *not* test that the solution has the right titer (assumption is the manufacturer did its job and there is no decay of the solution). Therefore, these 2 type of data /information datum may justify distinguishing them.

- 4. no time to discuss term submissions

16 May Chair: Chris

Given we hope the release will be out by then, the next priority would be the paper, any polishing needed for a paper-specific release, and Melissa's been following up on the genotype work/discussion/terms from the workshop earlier this year to incorporate those.

9 May Chair: Jessica - Release issues: 1) IAO and OBI coordinated releases: Jie to talk to Alan and get a decision on that in the next two days. It should be ok to release OBI with references to the October release of IAO but want to check. 2) There are still 8 uncurated terms, which will be noted in the Release notes. 3) There are 3 "meta-data complete" terms which are actually missing definitions; those will be fixed as they can be and noted in the Release notes otherwise.

- Aiming for a release on Friday, because no one can edit the obi.owl files and add new terms until that's done and it's holding things up for everyone.

- there will be another release for the paper.

- Manuscript: Philippe needs to incorporate his changes into the Applications of OBI.docx in the repository. Bjoern put a Manuscript 2011 document in the repository. To edit it, the consensus is to check the manuscript out, send an email to the list locking it, use track changes, re-check it back into SVN when done and send an email letting folks know, just like when working on the .owl files.

2 May Chair: Anita

- Manuscript update (Use case finalized)
- Release (done?)

April 2011

25 April Chair: Bjoern

18 April Chair: Carlo

- Update on the release (Jie)

- Update on the OBImanuscript (Bjoern)

- Service implementation (Carlo)

- ICBO OBI tutorial (status of the website, recruiting, Assigning AIs)

11 April Chair: Jie

- imported terms

 PATO - merged terms (will add their labels and definitions in old version PATO in OBI manually, AI for Jie)
 PRO - changed IRI, OBO -> OWL and PRO -> PR (will double check and contact Protein ontology people if it is true, AI for Bjoern)

- Chromatography device / Chromatography instrument (decide to merge the terms, not for this release)

- other release related issues (fixed during the call)

4 April Chair: Bjoern

- Definition format

 Definition of A which is a subclass of B
 1. a B in which ...
 2. A is a B in which ...
 3. is a B in which ...
    - should use option 1

- Use of 'only' or 'some'

 For example, 'protein complex' has_part 'protein'
  'protein complex' has_part some 'protein' or 'protein complex' has_part only 'protein'?
    - should use some (transitive issue)

March 2011

28 March Chair: Bjoern P

Follow up San Diego workshop
Preparation ICBO tutorial
New Chairs

21 March No call, San Diego workshop

14 March Chair: Bjoern P

Finalize Agenda of San Diego workshop

IEDB - complex assays vs. study designs

7 March Chair: Jie Z

Agenda of San Diego workshop

MGED ontology experimental design

The request terms have been added in ExpDesign.owl under 'study design'

ExpDesign.owl has been checked in SVN:

February 2011

28 February Chair: Bjoern P

21 February - holiday -

14 February Chair: Jessica T

7 February Chair: Carlo T

- Review eagle-i related topics proposed for the OBI workshop and identify action items to be 
   done  between now and then
- Review/refine the Workshop agenda and topic priority
- Update on OBI tutorial at ICBO
- Review agenda and chairs for next calls

January 2011

31 January Chair: Philippe RS

- San Diego workshop: registration and public component? 
- manuscript vote decision
- setting milestones in preparation of the meeting (OBI review and OBI coverage)

24 January Chair: Jie Z Discussion of some SO related terms needed for annotations of functional genomics experiments.

  - genetic characteristics information (MO:individualGeneticCharacteristics)
  - genotype information (MO:genotype)
  - Allele information (MO:Allele)
  - genetic background information

17 January - holiday

10 January Chair: Bjoern P

- assign next call chairs
- update for OBI release paper
- update Meeting in San Diego
- continuation of term discussion

December 2010

20 December Chair: Bjoern P

- status of OBI release paper - Meeting in San Diego - continuation of term discussion

13 December Chair: Jie Z

Attending: BP, HP, CT, PRS, JZ, AR

- status of OBI release paper

 Chris or Bjoern will go through the paper first and address the reviewer's comments

- Two terms related to 'strain' are decided to be added into OBI

 selectively maintained organism
 selective organism creation objective

- discussion about 'genotype' related terms

 happy with 'genotype information' discussed on Nov 29 dev call 
 debate on 'genetic material'. Propose to continue the discussion on next call

6 December Chair: Jessica T

Present: Cognitive Paradigm Ontology

November 2010

29 November Chair: Jie Z

Attending: MH, AR, CS, CT, JT, JZ

- status of OBI release

 plan to submit to Bioportal this week

- discussion about 'genotype'

 proposed to add two new terms: 1. genetic material, 2. genotype information

22 November Chair: Bjoern P

- name for this OBI release - what we would like to include in the release notes - progress of OBI paper - MO terms if we have time

15 November Chair: Jennifer F Attending: AR, CS, CT, JF, JZ Topic: age measurement datum

age measurement assay: An assay that measures the duration of temporal interval of a process that is part of the life of the bearer, where the initial time point of the measured process is close, in some sense, to the beginning of some transitional state of the bearer such as birth or when planted.

note: life of bearer doesn't imply organism

note: this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature

note: note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet.

note: age as a quality is dubious;; we plan to revisit

note: stages in development are currently handled with controlled vocabulary, such as 2-somite stage

age measurement assay realizes some evaluant role and has_specified_output some 'age measurement datum'

age measurement datum is_specified_output of some age measurement assay and is_quality_measure_of some age

8 November Chair: Chris S

- MO term submissions, review of services

1 November Chair: Carlo T.

- services

Agenda and notes: 1) Update about OBI release 2) Follow-up on eagle-i services

Attendees: Carlo Torniai Bjoern Peters Melissa Hendel Jessica Turner Jennifer Fostel


We briefly discuss about the status of OBI release and it seems that we are at the final stage with Alan reviewing the latest files Jie posted.

Discussion about services: - We discussed about aligning the current service classes (under planned process) in eagle-i to what is in OBI related to service provider/consumer role. We all agreed that instead of proliferation of roles we would like to identify for each of the current classes of services in eagle-i ( which are aligned with what NIF has) a process (starting from what is in OBI) and then have services as defined/inferred [process provided as service]

AI: Melissa and Carlo will go through the service classes and OBI processes to assess if there is the need to add processes to Then e can discuss in the next OBI call the best way to define services.

Jessica Turner we will presenting her Cognitive Process ontology in one of the call in November in order to asses what should go in OBI/ what to import form OBI.

October 2010

25 October Chair: Jie Z.

1. release process / issues

 external ontologies: import or include in the obi.owl, will send email about it

2. obsolete policy

 deprecated terms before Philly release will be removed from obi.owl permenantly

3. continue discussion of MO requested terms

 Six MO requested terms have been agreed to be added into OBI, details see the tracker

18 October Chair: Chris S

11 October Chair: Bjoern P

4 October Chair: Alan R

September 2010

27 September Chair: Jie Z

Canceled due to low attendance(JZ and JF)

OBI release 2010_08_19 clean up, see:

20 September COORD CALL - Chair: Bjoern P

- workshop planning (San Diego 2011)
- paper
- call schedule (back to Mondays weekly?) + chairs (only those that have time)
- community view of OBI (if we have time)

15 September Chair: Philippe R

13 September Chair: Alan R

8 September Chair: Helen P

6 September Labor day - no call

1 September Chair: Chris S

August 2010

30 August Chair: Jennifer F

* JZ proposal for tutorial for adding terms to OBI discussed and approved; see e-mail.
* No call Sept 6 - holiday

23 August Chair: Bjoern P

16 August Chair Jie Z

* Gathering requirements for the Protege Change Analysis plugin
* Curation status of OBI classes

9 August Chair: Bjoern P - Coord Call

* Release Progress Update
* Proposal for 'binding assays'

2 August Chair: Oliver H

July 2010

No call during the summer break

June 2010

30 June

Chair: Carlo


28 June

Chair: Alan


23 June

Chair: Chris

-- Agenda:

21 June

Chair: Philippe


16 June

Chair: Helen Parkinson


14 June

Chair: Bjoern Peters


9 June

Chair: Oliver He


7 June

Chair: Jie Present: JZ, DD, CS, PRS, JT, JF, MH


1. Dirk's time and space use case

- relation 'precedes'used to relate the ordered processes

- time, such as 1.5 sec, 'is duration of' a process

- issue: how to represent one process repeated many times

possible solution: there will be 10 instances of the same specification, have a counting process, count = 10, or process has frequence/rate = 10

AI for PRS: contact Barry to check the status of rate/frequence relation that they are working on

- need some spatial terms used to describe a stimulus location relative to a subject

2. Chris and Jie's knockout mouse model

- background and overview, no enough time to go through the diagram, leave for next call

2 June - part coord call

Chair: James Malone


May 2010

May 31 Memorial Day USA

No call.

May 26

Chair:Chris Stoeckert

  • Generate the list of dev call chair for next round.

May 24

Chair: Alan Ruttenberg

May 19

Chair: Carlo T.


(1) Brief update on the QTT for eagle-i and NIF devices

(2) Follow up on time representation: How to say that Process A occurred before Process B / repeat Process A / etc.

CT, JZ, JF were attending. For QTT device it would be nice if somebody can review the current owl in the SVN (Helen? Bjoern?) so that we can have feedback in the next call. As for repetition of process the email thread on the dev list has been definitely useful for representing a repetition of a process. We didn't make anyway any decision except to have the two agenda items discussed again in the next call.

May 17

Chair: Philippe Rocca-Serra on call: JT, CT, JF questions raised: how to say Process A occurred before Process B / repeat Process A / etc.

May 12

coord call

Chair: Bjoern Peters

  • status of Nat. Biotech paper
  • release of OBI at BioPortal
  • Coordination with other OBO ontologies: e.g., SO (for genotypes genomes, IDO (for host etc.)
  • 2011 ICBO workshop - what would we like to do?

May 10

Chair: Jie Zheng

Present: JF, CT, OH, JZ, BP, LS, AR, CS, JT, MH, DD

(1) Carlo will give an update on the instrument pattern and branch being developed for Eagle-i

AI for CT: send device spreed sheet files to OBI

AI for CT and MH: provide at least textual definition for functions (The logical definition of functions are not required now.)

Devices and related functions will be reviewed and added into separate OWL file.

"Part of device" class was proposed to be added into OBI in previous dev call. The "has_part" relation can solve this issue. So, there is no necessary to add the term.

(2) Discuss the reviewer comments on the accepted SIG paper (Oliver)

OH: first draft of final version and will address the reviewers issues in the discussion section

AR: address the provenance issue

(3) Progress on using Protege 4.1 (Alan)

Worked in Mac, need volunteer to test it in PC

AI for JZ and AR: test it on PC

(4) Time and space issues (Dirk)

Discuss some use cases of using time

May 5

Chair:Oliver He

Present: JZ, BP, MH, JM, JF, AR, CT, LS, YH

(1) SO-related terms: We discussed different options to represent mouse gene knockout.

AI: Jie is going to modify the figure by including some tentative relations.

(2) OBI main manuscript update: the letter to Nature Biotechnology was finalized during the call. Bjoern is going to email out the letter soon.

(3) host and host of immune response: the host role will go to IDO. The term 'host of immune response' may not be a good ontology term, since it is indeed an immune response of some organism that bears the host role.

May 3 - May bank holiday Europe

April 2010

April 28

Chair: James Malone

Went through AI from Vancouver

April 26 Chair: JF On the call: CT, JZ, JT, LS, JF, JM

JT: Scales update. working with AR on handedness. also working on age, gender, diagnosis. AI to bring diagnosis to dev call when ready for discussion

JZ: acrylamide gel question; incorrect definition and differs from agarose gel in inferred hierarchy change definition: a processed material resulting from the polymerization of acrylamide with TEMED in some buffer solution add: is_specified_output_of some polymerization has_part acrylamide (or has grain acrylamide?)

also change definition of agarose gel to: a processed material resulting from the polymerization of agarose after heating agarose suspended in some buffer solution

consider X part_of device Z if X has a function then X is a device itself X and Z can had same or differing functions X does not inherit function of Z; Z does not inherit function from X if X does not have function then it is not a device, but is still part_of a device X can exist without Z; in some cases Z can function without X consider adding defined class under processed material 'part of device' -> processed material and is_part_of some device

editing (thanks, JZ!): plate holder used to classify under measurement device; changed function to position function bead parent class is not considered to be device; some bead children could be NMR probe should have measurement function; added post-call

deferring instrument to later call, once devices are all classifying properly we suspect centra web version does not permit the person using it to be promoted to co-presenter or to share screen

April 21 on the call: HP, CT, CS, JZ, JF; chairing: HP/JF

HP has previously checked material entity, processed material that should be devices

device = processed material with some function using this function to move asserted device classes to sub-classes. e.g. measurement device

analog-to-digital converting device -> signal conversion function also info processing function Faraday cage -> isolation function heating block, cooling device, hyb station -> temperature control function light source -> light supply function liquid handler -> transfer function cell-culture incubator -> temperature control function and atmosphere control function

did not have sufficient info to add function to Brucker Sample Rail system

platform was discussed previously and a decision made to deprecate it; CS will send an e-mail

electrically-powered device was added at workshop and may include everything; we decided to deprecate it; HP will send e-mail

we found under chromatography: chromatography has chromatography column, chromatography device (frits, jackets), chromatography instrument (pump, detector) why is column not a device?

There is the general issue: how to consider things that are part of an instrument or a device and have function by being a part. What is the general guideline here?

reagents are devices bearing reagent role

1. We reviewed the AI from the Vancouver workshop - see summary here

2. We started to work through the tracker items rated 9. Edited items commented in wiki, file to be checked back in shortly

3. Work in progress

AI: need a function for all the devices which currently don't have logical defs - HP will do a quick pass and make sure what we have to date makes sense. CT will report later on Eagle-i progress with this pattern. Discussion on electrically powered device not being fine grained for use - everything can be maded electrical by hooking it up to a motor.

AI: JZ will start implementation page for groups using obi and email when she is done to deal with AI from Vancouver, suggestion to cross link to reviewer comments google doc

AI:JT and AR have been working offline on handedness assays and scales for measuring same check in IAO handedness and comment tracker item

AI: re services and training in OBI - ask AR to update relevant ticket with the design pattern in progress when ready

Weds chair is James, he may not make it due to volanic ash, Jennifer will be the backup.

April 19

Chair: Helen P.

1. review vancouver workshop action items

tracker, open and sorted by priority

1. We reviewed the AI from the Vancouver workshop - see summary here

2. We started to work through the tracker items rated 9. Edited items commented in wiki, file to be checked back in shortly

3. Work in progress

AI: need a function for all the devices which currently don't have logical defs - HP will do a quick pass and make sure what we have to date makes sense. CT will report later on Eagle-i progress with this pattern. Discussion on electrically powered device not being fine grained for use - everything can be maded electrical by hooking it up to a motor.

AI: JZ will start implementation page for groups using obi and email when she is done to deal with AI from Vancouver, suggestion to cross link to reviewer comments google doc

AI:JT and AR have been working offline on handedness assays and scales for measuring same check in IAO handedness and comment tracker item

AI: re services and training in OBI - ask AR to update relevant ticket with the design pattern in progress when ready

Weds chair is James, he may not make it due to volanic ash, Jennifer will be the backup.

April 14

Chair: BP, coord call. Agenda: Modification of OBI organizing structure (see email from BP on 3/30)

April 12

Chair: JF

Yongqun He,Jie Zheng, Carlo Torniai, Jennifer Fostel, Jessica Turner, Allen, Alan Rutenberg attending

In Oliver's use case we identified:

(A) Study Design specifies the independent variables (correspond to experimental factors) In use case, these include strain, vaccine type, pathogen, age, etc. This corresponds to experimental (textual) hypothesis "I think that age, pathogen, vaccine type, etc. will impact vaccine protection."

(B) The Study Design Execution includes: (1) planned process - curation of literature

in use case this means (a) identify corpus of papers, (b) read the papers and (c) collect data: quantification of qualities (e.g. age, strain) + measurements (e.g. CFU reduction)

(2) data transformation - discretization (convert e.g. continuous ages into "young" and "old" categories) (3) select a subset of experimental factors to test using statistical hypothesis test such as ANOVA, predictive model, etc. specify this subset in process (4) receive p_values for each experimental factor tested as output from statistical test (5) interpret to support / refute hypothesis

add data transformation "discretization process" to tracker specified input = continuous data specified output = categorical/nominal data objective = convert continuous data to categorical / nominal data

we plan to add to agenda for next call

April 7

Chair: JF Discussion of Oliver's vaccine use case, in particular the link between data from assay, data in a dataset and ANOVA.

ANOVA design: input is (measurement) data and grouping data, ANOVA test carries out statistical analysis, and produces results (possibly a data set of features; possibly a test of hypothesis (null or experimental))

The input data is the dependent variable, the grouping data are independent variable(s).

The ANOVA tests the null hypothesis, which is different from hypothesis in general; Larissa is writing a paper about hypothesis and will distribute once ready. Larissa also points out ontoDM. ANOVA is one of DM methods in ontoDM.

following the call YH and JF had additional discussion about the specific use case; see e-mail from JF 4/7/2010, notes from today's call.

April 5

Chair: BP

March 2010

March 31

Chair: RB

March 29

Chair: SAS

  • CT illustrate item ID: 2974764, providing a service process for Eagle-i
    • according to AR 'training' can be included, but training as a service should not because there are trainings that are not services; on the same token 'DNA sequencing' and 'providing access' should be added as processes, not as services.
    • in OBI we could keep it general, e.g. providing service to realize service provider role achieve providing service objective; 'DNA sequencing service' could be either defined by eagle-i or at the instance level.

AI: Alan to provide one example worked out in the file for all to review and agree by next call on Wed (ideally)

    • note that 'DNA sequencing service', 'DNA sequencing training service' were added into OBI during the workshop as test; once agrement is reached changes to these may be needed
    • 'education, teaching and training' roles may not fit into OBI, perfectly, but it in absence of a relevant reference ontology these will stay in OBI

March 24 - No call, workshop

March 22 - No call, workshop

March 17

Note UK attendees call is at 3pm (US stays the same) Chair: JM (swapped with HP)

March 15

Note UK attendees call is at 4pm (US stays the same)

Chair: HP (swapped with JM)

* Review workshop agenda
* VO use case update - cases/Vaccine_usercase_Vancouver2010.ppt?
* tracker terms

March 10 Chair: BP (semi-coord call)

  • Bjoern presents IEDB export use case
  • Coord call - outreach action items

March 8

  • Oliver and Allen present Vaccine use case

AI: we will map Vaccine parameters into existing OBI terms and come up with new ones if needed (we think most are covered). BP/PRS offered to help

AI: OH will produce a design pattern for modelling anova with the parameters as inputs and outputs.

Docs in svn: cases/Vaccine_usercase_Vancouver2010.ppt?revision=2773

All welcome to the VO call tomorrow which will continue this discussion: VO meeting at 11:00 am EST on Skype

March 3

Chair: AR

  • OBI workshop: attendees list, presentations, agenda

March 1

Chair: MC

Action items:

  • AI for AR: take discussion with Oliver, Larisa, Jie, Dirk (JBMS figures)
  • AI for Jie: mireot ChEBI terms in, try and find more information to help ChEBI add the 2 missing compounds
  • AI for JF: clean up hierarchy under label
  • AI for MC/Jie: send use case of "dye"
  • AI for JM: create tracker item for specimen (circular definition)


I/ JBMS paper figures AR: I looked at the text. I don't think there need to be changes.

CS: if the originators of the use case are happy then it's fine with me and I suspect with everyone else.

AI for AR: take discussion with Oliver, Larisa, Jie, Dirk

II/ Jie's terms requests

1. Label compounds

2. Labeled RNA, Labeled DNA (related to a labeling process)

3. Terms related to a storage process

4. Plan specification or objective specification terms

Items 1, 2 seem to be solved easily. I'd like to discuss those terms first.

Item 4 may need some time. Chris and I have generated design patterns for those terms. The details have been attached to the tracker item. The attached file is DesignType-20100215.xls. If possible, I suggest you can check the file before our discussion.

1. ChEBI terms

How to submit terms to ChEBI: successful use of tracker (AR, MC, BP). submission tool: (PRS)

a) mireoting chebi terms: all attendees ok. AI for Jie: mireot those in, try and find more information to help ChEBI add the 2 missing compounds. (AR: Link: for the fluors that cites the patents. Jie, would you mind adding this to the tracker, and if we send back to chebi, to include this info?)

b) label/dye role

Consensus: mireot chebi terms, add label role to the relevant ones for now. Clean up label hierarchy and if we keep dye role we'll add the restriction there AI for JF: clean up hierarchy under label AI for MC/Jie: send use case of "dye"

2. labeled RNA, labeled DNA

consensus: have labeled material as output of labeling process, with subclasses such as labeled RNA, labeled DNA...: we wouldn't have sub processes labeling RNA process (process not very interesting for OBI)

CS use case: labeled RNA: take input as RNA, enzymatic process -> copies which have fluo tag and hybridize hat to reporters on an array. output = quantification of DNA or RNA species

AR: labeling done uniformely to DNA or RNA, chemical modification to produce new substance MC: specimen in MA: solution of labeled oligonucleotide you throw on your array

JM: side issue: definition of specimen circular. AI for JM: create tracker item

BP adding labeled specimen and labeled RNA specimen to file

3. Terms related to a storage process

4. Plan specification or objective specification terms

Items 1, 2 seem to be solved easily. I'd like to discuss those terms first.

Item 4 may need some time. Chris and I have generated design patterns for those terms. The details have been attached to the tracker item. The attached file is DesignType-20100215.xls. If possible, I suggest you can check the file before our discussion.

February 2010

February 24th, 2010 (Wed) - Chair BP

1. Jie has produced a SDRF in OBI use case, she will check into svn and notify when done.

2. We will add term requests from Jie, starting Monday 1 March 2010

3. We will edit the core file, if we run into problems will be resolved at the workshop

4. Chair list has rotated again. please check dates for conflicts and arrange a swap/substitute. See here:

February 22th, 2010 (Mon) - Chair LS

Attended: BP, MC, JM, LS, JT, AR, PRS, JZ

  • Report from OBOF meeting:

to be in OBOF, OBI needs independent users, min 2 DBs

include this into the agenda for f2f meeting?

AI: BP will put slides from OBOF

  • Broken reasoning on current file:

Alan will look into it and give recommendations

4 options were proposed:

1 - discuss each item on a call - no one agreed

2 - review by 2-3 OBI people - not very popular either

3 - assign ID and remove if there is something wrong - popular option

4 - let eagle-i do that, need training - popular option combine 3+4 - very popular option

5 - they build on obi in sep owl file and bring it to us for review

AI: add to agenda on wiki for f2f - have obi slims for tests option 5

AI: Alan to try separate files

  • What do we need before the OBI meeting in Vancouver?
  • Do we need to change the figure captions in the OBI/JBMS paper?

AI: LS make minor changes to captions, send the text, contact the Editors

AI: keep for the next call

  • AI from the previous call

February 17th, 2010 (Wed) - no call - OBOF meeting

February 15th, 2010 (Mon) - no call - OBOF meeting and US holidays

February 10th, 2010 (Wed) - Chair BP - Coord Call

February 8th, 2010 (Mon) - Chair AR

February 3rd, 2010 (Wed) - Chair PRS

February 1st, 2010 (Mon) - Chair SAS

January 2010

January 27th, 2010 (Wed) - Chair JF Attendees: MC, JZ, JF call canceled due to minimal attendance.

January 25th, 2010 (Mon) - Chair JZ

Attendees: AR, MC, JF, PRS, JM

1. term submission policy

The term submission section refers to the quick ID proposal which was never finalized/implemented (, and use the old branches file system which is now obsolete.

Decide to move forward with this proposal (and assign people to work on it) or decide that it doesn't fit our needs anymore and update the wiki accordingly.

 No use case for Quick ID proposal now. Put it as low priority. QTT might supercede this in the future.
 Term submission: go with tracker items.

2. Material type related terms needed by MO

3. invesitigation/study result (this tracker item related to JBMS paper)

4. MIREOT of UO terms
Alan has posted a proposal

5. other tracker items if we have time left

 Comments were added into the tracker items.

January 20th, 2010 (Wed) - Chair CS 1. survival assessment: edit process issues - Submitted by Chris/Jie, no assignee.

2. review analyte assays - Submitted by Alan, assigned to Bjoern If I remember correctly this was deemed as pretty straightforward during last call - any update?

3. obsolete terms needed by MO - Submitted by Jie, assigned to Helen

Note that out of the tracker items above, 2 relate to application of our deprecation policy. Is there any issue with the application of the policy, linked to editing or else?

4. validated information - Submitted by Melanie, assigned to Chris. Some comments from Bjoern.

5. MIREOT of UO terms - Submitted by Jie, no assignee. Status is "awaiting formal proposal from Alan" - I think we reached agreement and the scripts have been updated accordingly, so this should be fairly straightforward.

6. MIREOT ChEBI deoxyribonucleic acid and ribonucleic acid under nucleic acid instead of molecular entity

January 18th, 2010 (Mon) - Chair MC - call canceled - US holiday

January 13th, 2010 (Wed) - Chair BP - coord call

January 11th, 2010 (Mon) - Chair JM

We discussed the agenda for the Vancouver meeting. There was a suggestion that we might use this meeting perform a lot of outreach activities, e.g. inviting external groups along and give them a short course on how to use OBI, how to construct terms, QTT, MIREOT, IAO and so on. There was also a suggestion that we might charge a small fee for registration to help cover some costs.

January 6th, 2010 (Wed) - Chair HP

(1) decision for dates Vancouver workshop -

(2) Priority 7 Tracker items

January 4th, 2010 (Mon) - Chair OH

Attendees: OH, BP, JM, JT, HP, CT, MC

(1) OBI chair list: The previous order can be used. AI: OH will update the page and re-use previous order.

(2) Terms related to MO ( The long-term goal of the MGED ontology (MO) is to have it replaced by OBI in the future. The defs need reworking. It's possible to break down some of these into design patterns for QTT (quick terms template) tool. We also discussed other issues, such as ways to define mouse strains (e.g., C57 inbred mouse). Chris will think more about different choices.

AI: Jie, Hp will see if we can develop patterns and use QTT tool.

(3) AI: HP will work with MH (Melissa Haendel) to get defs for her terms and we will see if these are QTT. Working with BRO will be an agenda item for the next coord call.

(4) The JBMS paper is basically accepted. We need to make the final update and submission by Jan 20th (LSS is the corresponding author).

AI: Oliver will add some more OBI background to the paper to address a reviewer's comment; Oliver will put together a few sentences of discussion about granularity in the paper based on today's discussion.

AI: Jessica will do a final sanity check after OH makes his changes.

AI: OH will coordinate the getting figs for the JBMS paper in consistent format.

(5) Workshop status - 22nd March is a preferred week. Need to close the doodle by Wed.

December 2009

December 16, 2009 - Chair PRS

December 14, 2009 - Chair AR

December 9, 2009 - Chair BP - coord call - Vote on 'communicating author' for release manuscript (currently BP).

December 7, 2009 - Chair SAS

December 2, 2009 - Chair JM

November 2009

November 30, 2009 - Chair JF on the call: HP, BP, JM, JZ, JT, CC, JF

AI JZ: Post policy of editor / curator notes to wiki Postpone discussion on policy for making changes to policy until later call MGED Ontology: JZ has mapped terms, CS, HP and JM have reviewed; will import into OBI 1.0

Tracker items: Manuscript: BP has received last minute edits which are good and which he will incorporate Title: The Ontology for Biomedical Investigations seems to win

James Malone: i closed a couple of dt related ones Helen Parkinson: I closed a lot of fixed things.

Focus of discussion: immortal cell tracker items: 2894003, 2892283, 2906085 In OBI now: immortalized cell line; output of: cell line immortalization and establishing a cancer cell line immortalized cell line has grain (some or only) immortal cell

cell culture: a cell culture is a material entity consisting of a population of cells that is maintained in vitro; children: clonal cell culture, primary cell culture, cell line culture

in general a cell line culture is considered to be homogeneous, stardardized, named, something which can be obtained reproducibly. it will have an original tissue source and associated history of being made immortal through natural, disease or in-vitro process

a primary cell culture is not homogeneous, generally not immortal, and not a cell line culture

added two processes to OBI: cell line immortalization has specified output some immortalized cell line culture

establishing a cancer cell line has specified input some immortal cell has specified output some immortalized cell line culture

immortal cell: a cell derived from a multicellular organism that has the potential to replicate indefinitely

AI JF: add tracker item summarizing discussion, diferentiating clonal cell culture, other terms.

- CS: curator note/editor note
- What is our consortium process to modify established policy (deprecation policy, metadata policy)?
Some options:
1) we need to have a formal vote with approval of quorum of core-dev,
2) we publish proposed modifications and if no objection under 2 weeks we go ahead
3) we publish proposed modifications and if objection go to vote
- Should OBI 1.0 cover MGED terms?
Plan to mireot terms
Plan to add new terms
- Tracker items with priority 7

November 25, 2009 - Chair JZ Present: CS, JF, AR
Canceled due to too few people

- CS: curator note/editor note
- What is our consortium process to modify established policy (deprecation policy, metadata policy)?
Some options:
1) we need to have a formal vote with approval of quorum of core-dev,
2) we publish proposed modifications and if no objection under 2 weeks we go ahead
3) we publish proposed modifications and if objection go to vote
- Should OBI 1.0 cover MGED terms?
Plan to mireot terms
Plan to add new terms
- Tracker items with priority 7

November 23, 2009 - Chair CS
Plan is to go through pririty 7 tracker plans. What MC wrote for last call still holds. i.e.
- don't forget to check/update your tracker items before the call (at least those that are priority 7 and up)
- if there is anything you want to add/update/modify for the next release please create a new tracker item with priority 7.
The tracker is available at

please send in all review comments for fig 5 (the fucoidan study figure) so we can finalize it

November 18, 2009 - Chair MC

Agenda: - don't forget to check/update your tracker items before the call (at least those that are priority 7 and up) - if there is anything you want to add/update/modify for the next release please create a new tracker item with priority 7. The tracker is available at

1. Next OBI meeting AI: HP will email again re OBI meeting and volunteers needed to coord only

2. Next OBI release - 1.0 Create tracker items 7 for what we want to finish - don't have to be done for 1.0 - but will set priorities (do not use anymore priority 8 and 9) 1.0: comes out with published manuscript. Target end of January.

After 1.0, aiming at monthly releases. Will need Jie's help.

3. manuscript AI: BP will send a reminder for the authorship google doc. He sent 4 reminders (valid email addresses) - 5 or 6 no reply -> if no response no inclusion in author list BP: manuscript done (unless for emergency edits today, or huge mistake detected very late by Bjoern). He will send out final version (FYI) by next Wednesday.

4. deprecation policy reminder that this is now fully enforced. See

5. discussion about curated/validated/edited AI for Alan - start discussion on tracker or dev list (whichever he prefers) about "biocuration" => see email sent by Alan on the obi-dev list.

November 16, 2009 - Chair HP

- coord concerns? (as no call on Veterans day): users email for release, next OBI meeting
- Release progress, setting next priorities
- Paper progress, - Reminder that outstanding paper reviews are due by Weds 19th Nov
- Tracker items 9,8,7

November 11, 2009 - Veterans Day - no call

November 9, 2009 - Chair RB - Action Items (full details sent to -devel list)

- [Helen/Bjoern] to put together spreadsheet of terms missing definitions and pass to AR to incorporate into release candidate

-[not sure who was going to do this fix] BIRN/NIFSTD: BIRN is dead; but is BioPortal; needs change of ID

-[BP] will recieve updated Figure 5 and edit as required for clarity and consistancy

-[BP] wil circulate submission-ready manuscript when missing definitions added, Figure 5 fixed,

-[All] please continue to use existing tracker numbering until manuscript submitted

-[PRS: Create tracker item Obsoluete diluted; Will discuss with PATO

-[All] No more editing for this release after above is dealt with ; go back to normal editing of obi.owl

-[Jie] Fix Table so it publication ready (remove extra sheets, etc.)

-[release team] Release process: editor notes and curator notes wil be dictated by release time

-[HP] Will fix release notes; need comments now or hold your peace

October 2009

Chair: AR - use of 'hypothesis' in SIG paper - journal switch for release paper - cleanup terms of RC1

October 28, 2009

Chair: OH

Attendees: Bjoern, Jie, Melanie, Helen, Alan, Chris, James, Oliver

In today's OBI dev call, the main task was still to go through tracker items 9 and 8, which are high priorities for the main OBI release paper. Many items in these two categories have been discussed, and eventually closed, reassigned, or downgraded.

We have also discussed the policy for the JBMS paper authorship. The final agreement agreed by all attendees in today's OBI call is that we will include all the authors signed up on the web page: including their names and affiliations. In the end of the author line, we will include the name "the OBI consortium". The OBI consortium will also be listed in the section of acknowledgements.

October 26, 2009'

Chair: RB

- rc1.0 - agreement on what this will contain needed see email of 21/10 after workshop

- Tracker items - 9

- Tracker items - 8

- Release progress (due Nov 5th)

- IAO updates progress

October 21 2009

No call clean up meeting

October 19, 2009

No call cleanup meeting

October 14 2009

Coord call (brief, Chair: BP)

- Parasite Experiment Ontology: satya sahoo
- Sending periodic message to obi-users list

Dev call Chair: MC

Agenda: finalize agenda for cleanup meeting

prioritize on:

- removal of _unclassified place holders - need volunteers - e.g. JM/HP for dt, JF/HP for roles
- role - needs the most work has placeholder class, use the review
- code needed for release - volunteers to work on that e.g. strip ed notes, update cur status - MC/AR
- typo clean up
- tracker items
- other?

October 12, 2009

Chair: BP

paper link

Agenda: task assignment for cleanup meeting

Review IEDB use case - BP

Review DT use case - JM

Text for CT use case in paper is out of date, (aspirin etc)

October 7, 2009'

Chair: HP

Call summary 7 Oct 09

1. We have now completed enough detail for the clinical trials use case to support the original aim - to show the breadth of OBI vs the glucose use case which shows depth

2. We discussed what we need to complete and in what granularity, remaining issues are

   2.1 Statistical test - discussion on what are the inputs and we 

don't have enough info in the paper on what the test was. AR and JF will work offline to model what they think is going on

   2.2 Hypothesis - we understand this to be 'fucoidan may have 

anticoagulant activity in vivo. result is a small stat sig effect of AT3 anticoagulant effect, author interpretation indicates no useful clinical effect.

   2.3 Modelling the dosing regime - we decided to do this using day 

processes instances, with subparts, and these will be related using preceded by. AR will work on this.

We understand that

we will not model time triggers now we do not need instances for all patients, one representative for each group is enough we will not work on this use case in Philly, but working on it later is desirable

3. 12 October we will review the IEDB use case, and the DT one. All will look at the paper in advance. BP will present the IEDB one, JM will present the DT one. We are hoping to have a screenshot from NCBO for the last use case. If we don't get this we will need to work around.

4. Next week 12 Oct the chair will be Bjoern. As he is presenting if would help I can chair again.

October 5, 2009


September 2009

September 30. 2009

Chair:JZ Present: AR, BP, JM, RB, HP, JF, MC, YH, LS

1. Progress on SIG paper

  • which use cases should be used in the paper
  • assign at least 2 people for each use case
  Oliver will propose the plan for working on the use cases for SIG paper and organize a call to work on the SIG use cases.
  Will go case by case together to reach the consistency for all the use cases. 
  The proposed order is Oliver's use case first, then laris's then Dirk's.

2. epitope: ?role/disposition/quality/other

  Want to change it like "epitope realizable entity" later.
  BP and AR will improve the definitions so they are clearer.

3. glucose figure for OBI paper

  • shall we change "portion of blood" to "blood specimen"? (JF's answer: NO)
  add labels in legend
  change 'portion of blood' to 'blood specimen'
  change the relation of blood and tube filled with blood from 'part_of' to 'contained_in'   

4. Clinical trials use case

  BP: We want to model the process of an assay measured data item (output of assay) which is input to 
  a 'statistical hypothesis test' which has as an outpt a p-value. Based on the p-value, the authors reach 
  a conclusion that it is significant or not. 
  will continue discussion in the next dev call

5. Tacker items

September 28, 2009'

Chair: JM

  • Progress on paper - BP
  • progress on SIG paper
  • clinical trials use case (paper now available)
 * AR to present changes
 Alan has been working on adding some additional classes and instance to the investigation use case file.
 JF: we are using terms a bit carelessly.  placebo is not synonymous with all negative controls; i had not thought subject was a thing but a role
 AR: modeled in detail now, but we may generalize e.g. "informing/communication" process and have different participants/ information entities
 JF: distinction for this use case between pill and capsule prob not needed, though details are likely useful
 It was clear from the work Alan has done that we do not know how to limit the scope of the use cases we are 
 building and when we have satisfied them. As such will endeavour to draw up a list of competency questions 
 which we will use to determine when we have satisfied our use case.
 AI: AR will doc the classes defined in terms of instances as a design pattern
 AI: JF to draw up list of competency questions for the clinical trial use case for Wed call

September 23 2009

Chair: CS Attending: CS, MC, HP, JF, JZ, BP

Clinical Trials use case continues:

Continued discussion focussing on the Study Design Execution.

 - decision to not put the level of detail in the figure for the antithrombin-III (AT3) analyte assay as shown 
   in the glucose assay since it will already be in the paper and need to keep use case figure simple.
 - edited OBI file to include discussion.
 AI: HP has checked out file and incorporating discussion from today and Monday
 - decision to add classes to main file for fucoidan, guar gum, and AT3 so that we could create instances in OBI-use case file.
   -- fucoidan and AT3 are not in ChEBI so should submit. 
   -- from Wikipedia:
 AI: Submit fucoidan and antithrombin-III terms to ChEBI
 - likely need a blood collection tube (as opposed to flow cytometer collection tube) but for now may use 
   generic tube entered for glucose assay.
 - model AT3 assay as analyte assay with analyte = AT3.
   -- output of assay is measurement. Need to sort out what are the units and make sure in OBI.
 AI: JF will track down units needed
 - in OBI use case, created instance of a fucoidan treated homo sapiens and guar gum treated homo sapiens.
   -- will likely need to create more but this is a start
 - issue with modeling treatment. Options are as a generic treatment or as subparts of a process. 
   JF strongly prefers the latter but we need a way to link inputs and outputs to describe the same person get successive treatments.
 AI: AR will model by Sept. 28 (as discussed on previous call) or we go with generic treatment approach.
 - need to capture data transformation of collection of measurements from the AT3 assay.
   -- They used a statistical test (i.e., generated a P-value) but not clear which test (don't want to say t-test if don't know for sure). 
 AI: JF will check on test

September 21 2009

Chair: HP

1. 2 papers issue resolved OH, LSS coordinating. Please submit use cases to

1A. Main paper progress - BP

1B. Glucose use case paper figure

2. Work on clinical trials use case

- summary of progress

3. Priority 9 tracker items:

  • drug role has been modified, no progress on approved drug (not urgent for use case) HP
  • ISA-TAB use case - PRS
  • IAO part of paper - AR
  • Clin trials use case fig - JF - progress on this?
  • Action spec - needs more info for AR
  • mixtures of chemicals in Chebi - BP

September 16 2009 Dev Call - chair RB

1. Resolve issues with 2 papers, vote on call, or wiki Vote here Sig_paper_vote

2. Continue with clinical trial use case updated slides -

2.1 trials type - revise to parallel design and intervention design. Reference design is wrong and should be disjoint with parallel design. HP.

September 14 2009

Present: HP (Chair), JM, AR, CC, JF, JZ, CS, MC, PRS

1. SIG paper

Oliver's offered to work on this, but we need to make a decision as these are now in same time frame. Various views expressed:

Option A. We work on both papers, we proposed asking Oliver to coordinate the work on the SIG paper

Option B. We work on the main OBI paper and don't do the SIG

Option C. We work on the SIG paper and defer main paper.

AI: Add to Wednesday's discussion as neither BP or OH were on the call and if necessary vote on the wiki.

2. Clinical trial use case

Slides were edited (rather than OWL file) and will be checked in to sf.

AI: PRS suggested we should liase with the OCI/OCRE re: clinical terms and he'll follow up with OCRE (OCI is inactive at present) (after 2 weeks due to other work) to see what their status is. AR suggested check OGMS. In the meantime we will add terms as we need them for this use case Alan Ruttenberg: OCRE:

1. study design was unresolved last week. We discussed adding single blind trial design and decided that this should be defined in terms of the process rather than adding a new term. There are still then multiple study design terms that describe the use case and we need all of these still.

2. Drug role - def. reviewed, agreed that it's too tight now and will be relaxed so we can use it in this use case. We will add a new defined class which is 'approved drug role' - output of some approval process which will work for the original def of drug role.

AI: HP will redefine drug role more generally for this use case - DONE AI: approved drug role needs to be added as does approval process - HP will create tracker item

3. excluded study participant role - this is now in a placeholder _under discussion. We decided that we don't need to assign roles here, and this role will be deprecated and not used in the use case. JM modified slides.

AI:deprecate excluded study part role - DONE

4. study participant role - discussion on whether this is needed, in a workshop FG and others expressed the view that this be deprecated. It's not used and we will use study subject instead.

AI: HP will dep. this term and repoint the obsoleted 'potential study participant role' to 'study subject' - DONE

5. Person/Homo sapiens, discussion that these are instances of Homo sapiens and not people. Agreed, we'll use Homo sapiens in this use case

6. Discussion on how we can label the two groups - treated and untreated. There's no role for this only 'study treatment group' which refers to both those treated with the query or active compound vs. the control one. These can be modelled as processes but we have no process terms for these yet. Not completed.

7. Suggestion by JF that 'study population role' be deprecated, there are more specific roles which can be logically defined.

AI: HP will deprecate this term. - DONE and child terms asserted under role

September 9 2009 Coord Call - chair BP

  - Person can't be resolved AR will not be on call
  - DT clustering edits for manuscript not made yet, tho no objections - issues with reasoning HP

September 7 2009 Dev Call - chair JZ - canceled due to US holiday

September 2 2009 Dev Call - chair MC agenda: tracker items, obsolete classes, ontie merge

1. ONTIE merge issues Should be logged under the OBI tracker and assigned to Bjoern

2. obsolete classes: Proposal to delete those before 1.0 Concerns that those obsolete classes sometimes record design decision, and that we should ensure we don't loose that information Best place for design decisions is not in obsolete classes, but we will keep obsolete classes information somewhere

AI for JM: email dev list with proposal DL: 2 weeks (next dev call) for objection

3. Tracker items

  • isa tools use case - wait on PRS
  • person/homo sapiens

duplicate classes have been cleaned up. discussion deferred until next dev call

  • paragraph about clustering

AI for HP: redraft this paragraph - DL next call

Jennifer asked her graphics group to work on figure.

  • Manuscript

We would like to have an OWL file as supplemental material for each use case. Jennifer's could be done during the calls. Supplementary table: should be updated at the end of writing process - after clean up meeting, before RC

  • Clarification for editing process regarding manuscript: use cases section will be emailed to BP directly. Edits to whole document go through editing queue.

AI for MC: write instructions on how to create a new OWL file, BP to try and use instructions to create file. DL next call

August 2009

August 31 2009 Dev Call - chair YH (Oliver)

Attendants: JF, BP, YH (Oliver), MC, AR, HP, CS, CC.

NOTES: 1. ONTIE merging: ONTIE has been mergerd to OBI.

(1) However, the reasoner does not work well. We may need to contact Pellet developers. Pellet 2 ok in command line or P4. Pellet 1.5 doesn't work in P3 or command line. There should be a P4.1 version coming soon. We can switch to it once it is ready. However, we may need to take temporary pain to make it work now.

(2) A strategy to show ONTIE terms are generated by IEDB originally for epitope research may be needed. One strategy is to use the 'definition source' with the content 'IEDB'. It may be better than ID range.

AI for Alan: However, a new annot prop or another strategy may be needed. Alan will add a tracker item to iao to record such notification requests.

(3) All ONTIE terms will be included for OBI v1.0 release and will be assigned OBI IDs when releasing. Bjoern will make sure all ONTIE terms are curated well.

2. Manuscript will be submitted after clean up workshop.

3. NCBI taxonomy terms. Current taxnonomy terms in OBI are probably overloaded. OntoFox ( ) is a good program that will be used for possible cleanup. We will need do the following steps proposed by Alan and Oliver:

1) Collect leaf terms we want in OBI;

2) Run ontofox methods on these. Three OntoFox methods are available and all used for this run: includeNoIntermediaaries, includeSensibleIntermediaaries, and includeAllIntermediaaries.

3) Inspect all results for review. We will then decide which one will be used for OBI.

This will be implemented by Oliver's group.

We may need to generate disjoints among NCBITaxon terms, or this may need to be done by NCBITaxon itself.

4. OBI specific 'homo sapiens'. This term has different meaning compared to the NCBITaxon Homo sapiens. See: = usage of 'homo sapiens' It's more like person or organization that has legal entity role. So maybe it can be replaced with a name like 'legal entity' (this name may not be ideal, though). Currently we have ~15 cases where person and not homo sapiens could be used, devices, manufact. etc. AI for Helen or Bjoen (?): paste this issue into the tracker. We will discuss it next call.

5. Bjoern will remove 'has_output' in OBI.

6. AI for Alan: Clean up conferred qualities. Those would become defined material - eg irradiated becomes irradited material, i.e material output of irradiation process.

August 26 2009 Dev Call - chair JF

Atending: AR, BP, CS, JF, MC, HP, JZ

AIs from last call:

(1) review CS assay design template:

(2) review JZ list of terms in manuscript:

(3) documentation of discussion - email / tracker / calls emails - thread name is often not reflective of discussion, so important topics can be difficult to find / follow email format is virtually impossible to read once it is more that three deep - when should we trigger a summary? FG: tracker discussions are missed by folks not following tracker -> ask all interested people to follow tracker? complex issues cannot be easily discussed on paper / assigned to a single term in the tracker

AI: HP will summarize specified_in/output, and run it past FG. JZ was tasked with documenting e-mail threads in tracker

Ongoing: (4) Manuscript: Need OBI developers to take on unassigned items!

  • need to update figure 1 -> already in tracker
  • species neutrality. Mention as a big issue across OBO Foundry ontologies
  • Update logical definition of PBS buffer -> tracker
  • better example of objective specification. AR: goal is to take something someone else has written in a protocol
  • Redraw figure 2, replace 'depend ons' with 'inheres in'. -> JF tracker (error in fig 2)
  • clean up information processing/ data transformation -> tracker (clustering paragraph paper)
  • IAO section of paper
  • add glucometer to OBI for paper
  • person/Homo sapiens in OBI

(5) priority 9 tracker items

New items:

(6) hotel accomodation options for Cleanup Meeting Accommodation options Chris/Jie/Helen

(7) HP and PL performed useful review of Role branch -- several issues raised also occur in other branches; is there a review underway of other branches?

 (1) discussed CS assay design template:
 this is the place to document complex, generalizable decisions, e.g. analyte assay.  
 please add to sequencing example

 (2) documentation of discussion -> tracker
 AI from last call: HP summarize specified_in/output, and run it past FG; we have agreement

 (3) Clean up meeting will have a speaker phone
 hotel space:  evening of oct 17 may need to stay at airport and 
 CS will organize transport additional accomodation options in e-mail
 funding information - HP has funds on first come first served basis.

 (4) ms:
 a. changes to fig 2 acceptable; re-label taking sample -> taking specimen since this is more generic
 b. BP working on use cases:1 pp to introduce the problem pp #2 specifically formulates the use case /
 how OBI is used and figure to graphically display implementation in OBI
 c. HP: the content of the table is broken in 2 places, we need to fix the file or the use case; 
 missing use of spec input
 d. add note in text summarizing current state of implementation GenePattern
 e. AR will look at ONTIE/OBI
 f. BP to add terms from ms as defined classes; change regulatory agency to government regulator = 
 org or person that has role regulatory role; add scientific research funder as person or org 
 that has role funder role

 (5) cleanup mtg could have session on roles

 (6) Oliver is the next host

August 24 2009 Dev Call - chair CS Attending: HP, JF, CS, JZ, BP, AR

AIs from last call:

  • JZ has generated a table of terms mentioned in manuscript. This is checked into svn with the manuscript.

  • CS has drafted design template documentation for assays. Still needs work - please review and make suggestions for improvements

Documentation of email discussions: JZ was tasked with documenting email threads in the tracker but it's not clear if that's the best place to put it and how to capture these discussions that always tie nicely to a term or a single tracker item. It is clear that we need to document these somehow otherwise we are doomed to repeat the discussions and waste time and effort. Proposal is to use current discussion on has_participant and has_specified_input as test case. Once we have summary, we can figure out the best place to put it as an agenda item. AI: HP will summarize specified_in/output, and run it past FG. - Done, documented and resolved

Manuscript: BP has gone through the comments from other readers and addressed for the most part. We went through comments and either made changes or added items to tracker.

  • calculate # of classes & relations -> tracker
  • can use plural of terms in manuscript in order to make manuscript nice to read (also see tracker use of plurals in the manuscript).
  • need to update figure 1 -> already in tracker
  • species neutrality. Mention as a big issue across OBO Foundry ontologies
  • Update logical definition of PBS buffer -> tracker
  • better example of objective specification. AR: goal is to take something someone else has written in a protocol
  • Redraw figure 2, replace 'depend ons' with 'inheres in'. -> JF tracker (error in fig 2)
  • clean up information processing/ data transformation -> tracker (clustering paragraph paper)

Also did same thing for the table that JZ generated - i.e., made adjustments to manuscript or added to tracker. Revised version checked into to svn at end of call

  • IAO section of paper
  • add glucometer to OBI for paper
  • person/Homo sapiens in OBI

Need OBI developers to take on unassigned items!

August 19 2009 Dev Call - chair LS

  • Release progress
  • BP: I think we need and should not define many sub-objectives of assay,

but should simply rely on what the specified output is to define something like a sequencing assay

- Assays like Chip-seq or MeDip-seq should have a sequencing assay as a part, not classify as one.

- I agree with what Alan wrote below, specifically that it is hard to get the logical definitions right. That does not mean we should give up on them, but that we should try to develop uniform design patterns. I think calls are best suited to establish those, and we should have several before the clean up meeting.

  • continue with the tracker
  • JZ: Manuscript - Table with all terms in the manuscript + their OBI ID
* AI for Jie: OBI terms used in manuscript and their IDs -will be done this week.
* AI for Chris: a design template for sequencing assays. 
  BP adds quality - 'primary structure of macromolecule' is quality that should be in SO, added as a placeholder here  
  - sequence is info about a quality - from previous discussion with Chris Mungall. 
  - the spec output then for the seq assay is info about a quality 
  - this will be an IAO term for sequence needed as well. 
  can put design template here:
* AI (already done by Chris): put to the tracker sequence macromolecule, assign to BP.
* AI  - the same for methylation state

August 17 2009 Dev Call - chair JM

  • Release progress
  • Discussion of user deprecation docs - HP's AI from last call
* Old page has been repointed, google doc AI's have been extracted to page
* check for obsolete terms needs to be rolled into release process, tracker item added
* What constitutes a deprecated term discussion? for RC1.0 will the following mean that a class is deprecated:

  1. If RDFS labels are changed?
  2. If there are axiomatic changes? E.g. new necessary and sufficient conditions
  3. If there are new asserted parents - ie a class is moved
  4. If text definitions are changed?
  5. If a MIREOT term is obsoleted
  • Milestones check, OBI user docs and development docs need work
  • Reminder to sign up for cleanup tasks

August 12 2009 Coord Call - chair BP

  • Review of last action items (all done)
* new call schedule
* ICBO poster
* capture discussion on consortium consolidation on wiki
  • OBI meetings
* cleanup meeting in October 2009
* meeting early 2010
  • OBI release of 0.9, 1.0
* review tracker priority order: 9 influences writing, 
8 needs to be fixed to accompany  manuscript submisssion 
7 should be fixed before publication (during review process)
  • OBI manuscript
  • release process documentation.
*HP had an AI to transfer docs on AR's application to the wiki - still incomprehensible.

August 10 2009 Dev Call - chair RB

August 5 2009 Dev Call - chair JZ Present: BP, MC, JF, AR, RB, JM, HP

August 3 2009 Dev Call - chair JM

  • Canceled due to no enough people

July 2009

July 29 2009 Dev Call - chair YH (Oliver). Attendants: JF, YH, JZ, CS, JM, BP, HP, PR, AR

Agenda (1): All the remaining high priority tracker items have been discussed: Some items were closed during the talk. Some remain. Those that remain open and have priority of "9" include:

Item #1: 2829038 specified ... relations 2009-07-29 Note: The 'has specified ... ' relations might need cleanup and not refer to roles any more. A feedback from Larissa and the Relation branch is needed to close this item.

Item #2: 2828363 Raw Data vs Processed data 2009-07-28 Note: We need original data for data (e.g, microarray data) analysis. Currently, IAO and OBI disagree in terms of measured data. May need to create an assay measurement data item in OBI. May still keep 'assay' in OBI, and then IAO reference OBI assay. Since Alan was not late and not in the discussion, James will bring it up in next IAO call.

Item #3: 2827920 ONTIE term migration 2009-07-27 NOTE: ONTIE has terms (like ELISA assay) to be included in OBI as classes. The ONTIE database also contains many epitope data that will be OBI instances.

Item #4: 2827918 Include terms to allow query for Genepattern use case, 2009-07-27 NOTE: This item was not specifically discussed for closure. However, we discussed a lot about mireoting existing terms from other ontologies for ArrayExpress microarray data analysis. See below.

Item #5: 2613561 action specification, 2009-02-18 NOTE: This item was not discussed.

Item #6: 2100531 mixtures of chemicals in Chebi, 2008-09-08 NOTE: This item was not discussed.

Item #7: 1911447 release + documentation 2008-03-10 NOTE: Alan, Jie, and Melanie have put a lot of time in OBI release. Alan targets to debug and make the release process work by this weekend. Allen from Oliver's lab has also been asked to develop a more generic Java-based version for late OBI release. Allen is currently working on this. For OBI manuscript, now Melanie has it for review. Jen likes to re-join the review list.

Agendat (2): Helen indicates that ArrayExpress can suggest terms (typically tissues, parts, diseases, compounds) to MIREOT from other ontologies based on their EFO work. NOTE: we all agreed that many terms from well developed ontologies, such as CHEBI and FMA, can be mireoted. Ontologies should be ranked. It means that some terms from many ontologies may not mireoted. One solution is to put terms (such as disease related terms) that are not well defined in some seperate file or branches, and make notes for future cleanup.

(3) We need to start planning our next face to face OBI meeting. Chris voluteered Philly. NOTE: Current candidates: Phily, Stanford, Vancouver, and EBI. Many voted for Philly. Helen will check on Emerald funding from EBI. We may need to set up a doodle site for voting. About timing: all agreed that the paper should be submitted first before we meet next time. Nov-Jan is good timing.

(4) James raised a question about MIREOTing classes into OBI. We may need to make some policy in terms of what ontologies we should import terms from. Some ontologies that are not orthogonal may need to be excluded. NOTE: all agreed.

(5) A note from Helen: _cloning placeholder needs some work. Kevin Clancy and Bjoern had done quite a lot of work in this area. NOTE: Helen is going to do more work on this.

(6) Broken links in OBI: . Now, the download link ( ) in this page is pointed to: Note: the 2009-01-28 date is right. This is our most recent release. We need to generate a new release soon.

(7) DNA sequencing. Philippe has done some preliminary but nice work on including DNA sequencing in OBI. Discussions appeared to focus on how to make it more specifically and logically defined. Philippe has added DNA sequencing as a defined class. He also distinguished DNA sequencing by use of DNA ligase from DNA sequencing by use of DNA polymerase. DNA polymerase is already imported under protein complex. NOTE: not discussed.

(8) Where to add svn checkout instructions? Bjoern has laid out a very helpful and simple instruction. NOTE: We may need to add this in wiki and read me file. We also need to freeze old wiki and only work to new wiki. However, it was often hard to know which is new wiki and which is old.

July 27 2009 Dev Call - chair AR

July 22 2009 Dev Call - chair CS Canceled due to not enough people (many are at ICBO)

July 20 2009 Dev Call - chair LS Finished going through tracker list looking for blockers or items to close.

July 15 2009 Dev Call - chair MC Went through tracker list looking for blockers or items to close.

July 8 2009 Coord Call - chair BP

  • OBI poster for ICBO
  • Reducing the OBI consortium post-publication to active members only - including removing from SourceForge site
  • Reducing dev calls to every 2 weeks
  • Consolidation of OBI calls
  • Creating an Information processing ontology outwith OBI
  • Is OBI stalled? (Ryan wrote: It seems to me that OBI development has been somewhat stalled as of late. OBI seems to be just as fluid as it was two years ago, and releases are about as regular. If others agree, then what can we do to fix this? Perhaps identifying specific areas to focus efforts on and freezing these areas until 1.0 & paper is out once there is agreement might help?)

July 1 2009 Dev Call - chair CS

  • Consistency checks on OBI for release. Current status and plans moving forward. Use of reasoner.
  • When apply MIREOT? before merged .owl file created or after, or does it not matter?
  • Plans for ICBO poster
  • status of the manuscript. Who has it?
  • IAO calls to start Tuesday 9 to 10 am PST (weekly to start with, once every other week later on). Melanie would like to start those on the 7th of July, to allow time for clean-up before the ICBO tutorial. There is a tracker at:
  • OBI at ISMB - feedback?

June 2009

June 24 2009 Dev Call - JM and CS chaired Present: JM, CS, RB, AR, MC, JZ, OY

  • Discussion on linking data to its visualization as a report graph. In general, it was agreed that some data is input to some data visualization process where some report graph is output. Issue is with how to specify types of report graphs such as dot plots. One option based on earlier discussions (at the F2F workshop) are to create a specific process such as dot plot visualization with output dot plot - so create a visualization process for each type of report graph. The other option is to just use a general process and use something like description logic safe rules that are under development. The consensus was that DL safe rules are not mature enough yet and we should stick with the first option that we all understand.

AI: for JM to have a go at adding the data transformation visualization process, using the form has_input data and has_output graph report

  • Jie has started working on OBI release and running into some problems.

AI: MC and AR to help Jie with some release process issues

  • DIscussion on MIREOT of terms with regard to whether to just bring in the term, its parent, or up to the root. For example, does PATO:dead belong directly under 'quality' or under 'monadic quality of continuant'? Agreed that it is better to at least bring in parent so that term can be placed better in OBI but current script just brings in term and would take some effort to fix. Oliver has developed a site with input from Melanie and Alan that solves this problem (see OntoFox at

AI: Jie will try OntoFox for MIREOT of PATO terms into OBI.

June 17 2009 Dev Call - chair JM Present: JM, CS, RB, JF, MC, JZ, OY

  • Went spent most of call giving overview of items discussed and agreed from workshop, including discussion with Envo, use case issues from journal paper, sample, specimen, change to has_input/output relations, BFO 2.0 and working with IAO.
  • IAO work: Alan and Melanie are going to co-lead that ontology (in a similar way to lead editors in OBI branches) so we will be relying on them to initiate conference calls when necessary and follow up on/assign action items for things relating to IAO (as agreed at workshop).
  • Next Workshop: two suggestions from call were (all only possibles at moment) UPenn in January and tying it in with PSB meeting in Hawaii. We would welcome any other suggestions from people.
  • Reminder of next few call chairs given

June 03 2009 Developers Call - chair MC

  • call hosting: establish list of chairs
  • workshop agenda
  • OBI report for OBO Foundry meeting
  • manuscript

May 2009

May 27 2009 Developers Call - chair BP - Manuscript update - Workshop agenda - OBO foundry metrics feedback

May 20 2009 Developers Call - chair AR (BP substituted)

May 13 2009

Coordinators Call - chair BP

  • Manuscript update
  • Agenda for Face to Face meeting
  • restructuring of OBI coord / devel
  • Polymorphism community Michelle and Erick to relay Tina for the Consortium
  • Progress on only asserting Realizable_enitites, directly under the class realizable enity and not asserting classes under role, function or disposition. The current classes under function and role need to be moved and defined as generic realizable entities, removing the suffixes. This process has been endorsed by Barry as an acceptible way forward. For the specifics see Phil's paper, as its easier to follow than the email thread
  • How to use subversion: The purpose of subversion is to enable one document to be revisioned. You can roll back between revisions so nothing is lost and add tags to describe specfic version. In other words we should only ever have one copy of a document that gets revisioned, rather than multiple copies of the same document which has appeared under the release folder, for the release manuscript and the ismb paper. Can we svn:delete everything under the papers folder that is not the current document.

May 6 2009 Developers Call - chair AR notes

April 2009

April 29 2009 Developers Call - chair LS

April 22 2009 Developers Call - chair JF

April 15 2009 Developers Call - chair JM

April 8 2009 Coordinators Call - chair BP

April 1 2009 Developers Call - chair MC

March 2009

March 11 2009 Coordinators Call - chair BP

  • Discussion of authorship policy following the debate around co-authors on the Quick Terms paper

February 2009

February 25 2009 Developers Call - chair JM

February 11 2009 Coordinator call - chair BP

  • Desired changes for BFO
  • incorporating changes from workshop
  • tracking of action items from workshop
  • policy for 'generalization' of branches beyond OBI

January 2009

January 28st 2009 Developers call - chair BP

  • Overview of core terms

January 21st 2009 Developers call - chair JM

  • Core term discussion


  • Vancouver agenda


January 14th 2009 Coordinator call - chair BP

January 7th 2009 Developers call - chair FG

  • Core term discussion


December 2008

Dec 17, 2008 Developers call - chair JF

  • Welcome potential new developer Dirk Deron
  • Implementation of the quick term proposal

Dec 10, 2008 Coordinators call - chair BP

  • msi terms policy (in general, not just for msi terms - just easier to use those as example)
  • licensing of OBI and derived materials:
 * for the ontology itself: in TheRest.owl <dc:rights xml:lang="en">free, no license required.</dc:rights> Does that mean that anybody can take anything in OBI, do whatever they want with it, with no need for attribution?  
 * for the derived materials (posters, presentations, ...) : do we want to decide on maybe a creative common share-alike ?
  • syncing the author list on OBI consortium page with that in the release owl file.
  • Manuscript writing, results section: identification of core terms in each branch
  • Workshop planning

Dec 03, 2008 Developers call - chair MC

  • importing resources: what criteria?

Some concerns have been expressed that for example IAO doesn't meet our minimal metadata requirements.

  • release team - members

We are calling for volunteers to help out with the release, which at the moment is done by AR and MC.

  • OBI defined classes policy
  • roles/qualities for data
  • branch annotation: to keep?

November 2008

Nov 12, 2008 Coordinators call. Chair: BP

  • Identifier / Namespace policy issues - Alan
  • Any issues with manuscript writing?
  • Any concerns for OBI Winter 2009 workshop?

October 2008

Oct 22, 2008

  • Demo of use and application of restrictions in Protege
  • workshop issues

Oct 15, 2008

  • Any issues with manuscript writing?
  • Any concerns for OBI Winter 2009 workshop?

Oct 8, 2008

  • Contact with Expo
  • Contact with Vaccine Ontology
  • Community outreach in general (via Philippe, Susanna)
  • Any issues with manuscript writing?
  • Any concerns for OBI Winter 2009 workshop?
  • BioPortal demo and Usability study? (Trish)

Oct 1, 2008

  • OBI workshop: if attending add your name
  • OBI manuscript update - reminder deadline for first draft of section is Oct 31,
  • OBI in OBO and OLS - update on this
  • IAO: next release of OBI to happen during OWLED where will be the release team - we may not manage to integrate IAO into OBI before the november release.
  • use case: current status?
    • RS use case?
    • "global" use cases: have to be worked upon by submitting communities
    • "mini" use cases: simple examples to be worked upon inter-branches: e.g. the biomaterial branch started working on irradiated, the role branch works on a PCR use case with biomaterial and process branches...
  • Philippe's relation between "occurent" and "independent continuant" email

September 2008

Sep 8, 2008

  • Review progress on use case to date
  • Decide how to conclude this use case
  • Decide if we do more and how
  • Manuscript: Go through section assignments, turn open sections into milestones

Aug 15, 20, 22, 27, 29 - Use Case Calls

August 2008

Aug 13, 2008 Coordinators call. Chair: BP

Aug 6, 2008 Developers call. - Use Case

July 2008

July 16, 2008 Developers call. Chair: James Present: JM, JF, MC

  • Recapped OBI workshop outcomes to those not present at meeting
  • Awaiting result on data - cross branch concensus is crucial to proceed
  • AI: email coord and dev about change to calls over 4 weeks after 30th July
  • AI: Melanie to invite via google calander, JM, JF, MC and Alan to a Role call on Sample

July 2, 2008 Developers call. Chair: Philippe

June 2008

June 25, 2008 Developers call. Chair: Melanie

  • "browse OBI" button on top of our pages? pointing to our purl:
  • status of documentation
  • OBI funding and pictures for poster

currently: "This work is partially supported by grant funding from the National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health (R01EB005034, NIH P41 HG003619) and EC EMERALD project (LSHG-CT-2006-037686)"

  • ISMB attendees list
  • discontinue use of autoID plugin - easier to control ID assignment in one place
  • release process: don't forget to send your highlights for release notes
  • agenda items for workshop?

June 18, 2008 Developers call. Chair: Daniel Schober

  • Deadline for documentation - due today
  • Poster info from MC and JM
  • Reminder about release process (T-10 days) AR
  • (Bjoern's "Function - protocol applications" - discussion )
  • (Philippe and Daniel's use case - discussion )
  • Remove (Pseudo)-Redundance and experimental stuff from release file
    • E.g. now we have unmarked helper-bins such as OBI_function and PATO_quality as well as this (pseudo-)redundancy e.g. Protocol, Protocol_aplication, Protocol_application_role, _defined_protocol_aplication, all in the release file.
    • Does it make sense to release differrent views on the ontology, e.g. one with (for developers) and one without experimental stuff (for endusers/biologists)?
  • Check all inherited properties on correctness' as part of OBI checkup policy?
    • E.g. currently all instruments inherit an OBI: 'is_reagent_in' relation to 'protocol application' (asserted on the independent_continuant' class level). I think this is not very intuitive and it should be asserted deeper down the hierarchy or renamed in a more general wording so that it still applies to the leaf node level. Accordingly all inherited properties could be checked on applicability on the leaf node level. Use the properties view instead of the logics view to see all inherited relations.
  • What is the status of "help request for setting nested/composite restrictions in protege (e.g. material has_part (cell has_part virus))", and where is that documented ?

June 11, 2008

June 4, 2008

Alan example: 'material entity' and ro:has_part some (cell and (ro:has_part some virus)) Remember to put quotations around term labels with space in them - not had chance to look yet

  • To be included in next release (not this one, following one)
    • versioning of the release: number, date... (currently <owl:versionInfo xml:lang="en">1.0.530</owl:versionInfo>, 1.0 + SVN revision number)
    • sourceforge tracker Please review/update your items.

May 2008

May 28, 2008

May 21, 2008

  • Developers call. Chair: Jennifer
    • release status
    • function implementation
    • sourceforge tracker
    • clean up of TheRest.owl
    • deprecation policy

May 14, 2008

  • Coordinator call
    • distribution of OBI to external resources (Bioportal, OLS)
    • While creating the obi-users group I saw that you can get boxes for website for the list, there is even a "subscribe to the list". Maybe that's something we would want to add on our static webpage?
      • Maybe even a section "support" (we could update the resource page), which would group:
        • documentation under SVN
        • faq
        • release notes (purl-ed)
        • obi-users mailing list
        • resources (e.g. OBI logo)
    • Authorship on technical papers
    • Deadlines for branch development. When are they "done."

May 7, 2008

April 2008

April 30, 2008

  • Developers call. Chair: Bjoern
  • While creating the obi-users group I saw that you can get boxes for website for the list, there is even a "subscribe to the list". Maybe that's something we would want to add on our static webpage?

Maybe even a section "support", which would group:
- documentation under SVN
- faq
- release notes (purl-ed)
- obi-users mailing list

April 23, 2008

How to proceed with feature and has_feature (unassigned at the moment) - news from BS?

    • approval of automatic checks for release

note for additional correction: definition editor is a required metadata - could be defaulted to "OBI" when missing
do we want to keep our annotation properties underscore separated? (e.g. curation_status)

    • function report from Bill
    • conclusion to organization discussion (Bjoern)
    • "uses" branch - Jennifer

April 16, 2008

TBD as well authorship on documents relating to development of new features of OBI. E.g. mapping policy. How to proceed with new things to be added, e.g. deprecation policy

(April 9 call postponed - centra update incompatible with sound and mac users)

April 2, 2008

  • Developers call - Chair:Melanie
    • sourceforge tracker - ongoing votes
    • SVN reorganization
    • retire obi-plan-branch and obi-txcommit mailing-lists
    • normalized IDs have been assigned with releases: discuss deprecation policy

previously proposed was to move classes under obsolete, maybe adding an annotation property pointing to the previous parent

March 2008

Mar. 26, 2008

  • Developers call - Chair: James
    • ISMB abstract submission
    • if quorum present, quickly go over decisions from previous call and confirm them.

as a reminder:

1/ import policy

The import policy has been approved by all members present. It will be used from now on, with the reserve that it can be revised if any problem becomes apparent.

2/ update of minimal metadata page

Proposal to change the cardinality of definition_source to 1...n (instead of 1 currently). Attendees don't see any objection to do so, and leaving the curators free to put 1 or more sources. However, there had been previous objections by others who were not attending the call, so we think that this should be re-discussed.

3/ implementation of the obi-users list

Attendees agree on using Google groups. Again, there has been some objection before, so will need to be re-discussed. It would be nice to formalize the decision of using Google groups for our mailing-lists in the future. This has already been discussed and we thought it was agreed upon: due to recurrent problems with sourceforge lists, we would switch to google groups. We already mirrored the sourceforge mailing-lists on google for archiving purpose, and the latest lists (biomaterial, denrie, obi-owl) have been created under google.

4/ SVN and documentation

DT branch expressed the need for having a directory under SVN where to store for example spreadsheets for their branch. All attendees agree that there is no problem with that. We also agreed that we would like to have 2 distinct documentation directories, one for user documentation and one for development documentation. We could even have a link for the user documentation. This will be dealt with during SVN reorganization. Note: Liju commented that her branch already uses google doc and wishes to keep this, as there is a version control system. Everybody agreed that it is up to the branches to decide how to proceed, the DT proposal is for archiving of non-edited anymore documents for example.

5/ Function

In Vancouver it has been decided to let the Protocol Application branch define the function in the context of the protocol they create and where they specify the function of instruments. But function is more than just realizing a process, it also specifies the mode of participation of the bearer in the process. Bill point to a page on the wiki with examples :

There is still some confusion between role and function. Bill is in contact with "function gurus" to try and sort out things, and will come back to the instrument branch (who submitted functions) with more information as soon as possible.

The consensus (amongst attendees) is to clearly mention the function in the definition for the moment, and submit it under the tracker. Bill will liaise with Bjoern to see how to create processes and function, on the model "some independent continuant is the bearer of a function and participates in a process". The needed relations are already in OBO_REL.

6/ OBI wikipedia page

James proposed to create a wikipedia page for OBI, now that we enter a release cycle. All attendees agree.

    • last vote on the wiki regarding tracking system
    • use "clinical investigation" instead of "medical" on our website. (Alan tested a google search with "medical experiment")
    • SVN reorganization - proposal to be reviewed: could be implemented for next release, beginning of april.
    • What do we we do regarding import of non-obofoundry ontologies?

e.g., John Westbrook's ontology (PDBO.obo) is in OBO format and non-foundry, and DT would like to import some terms: do we convert to owl, then slurp in terms? can we use it if non foundry?

Note: Call time will be one hour earlier for those on GMT (this changes to BST on 30th March which is GMT+1hour)

Mar. 19, 2008

  • Developers call - Chair: Bill
    • Final review of import policy
    • Update of minimal metadata page

- do we want to keep definition_source with cardinality 1 or should we modify to 1..n?

    • mailing list for support: discuss implementation of the obi-users mailing-list as agreed on the coord call
    • DT branch would like to have a branch documentation directory under SVN to store their files
    • SVN structure - proposal for reorganization
    • Function branch - how to proceed?
    • OBI Wikipedia entry?

Mar. 12, 2008

  • Coordinators call
    • Proposal to add Alan as OBI project admin on sourceforge
    • ISMB abstract
    • Discuss publication policy.
    • OBO Foundry Associate Editor
    • Update on OBI votes

Mar. 5, 2008

Proposal to have a list of attendees and rotate for the chair position.
Chair role consists of:
- sending out the agenda at least one day before (and post it on the wiki),
- lead the discussions and ensure we keep on track on those,
- take the notes and post them (or liaise with Allyson/Melanie to have them posted)

    • Discuss use of svn properties (e.g. revision, date...)

TheRest.owl contains versionInfo 0.6.7

    • Officially retire the protege auto_id plug-in
    • Discuss our IDs policy

cf changes proposed with the release: - use of purl, e.g. - use of "/" as a separator instead of "#" - assign IDs to everything (including relations)

February 2008

Feb. 28, 2008

  • Developers call
    • Discuss implementation policy for votes that have been accepted on the 20th.

1. curation_status: new values - cardinality
2. definition_source: update of the annotation property file and all the branch files

    • Discuss release policy

1. Files have to be checked when committing into SVN
2. Various pre-releases check, J-8, J-3
3. email on dev if problems: the branches have to check/correct their respective files
4. If inconsistency/problem -> no release.

Feb. 20, 2008

  • Developers call
    • Discuss the use of the curation_status annotation property

We need to decide if we want to release all the terms, including their curation_status, and oducment it as suggested by Bill: "...expectation to be set would be that anything other than those with "review complete" should be considered likely to change place in hierarchy or have definition refined, or be obsoleted in the next release".
The other option is to release only terms with curation_status "complete" (name to be defined following vote), and not their annotation property curation_status. One issue is that ant term deemd "complete" which is an IS_A term curation "incomplete" will not be released. As described by Alan: "For instance, if a class has 'curation_status' 'review_complete', but one of its IS_A asserted graph ancestors is NOT 'review_complete', we'll not be able release that term, since we won't be able to construct its ancestor graph. This would also cause problems for classes using ObjectProperty relations. If one of the classes referred to in a class restriction are not 'review_complete', this would at least keep us from releasing that class with its restrictions. We'd need to simply leave the restrictions out. This might lead to a released, merged OBI that's considerably smaller than we all might expect"

see discussion thread at

DECISION: we agreed that for the moment we will release all the terms and their annotation properties. This might be modified in the future with progress made on OBI. Release notes will clearly state that the status of this release is "not to be used in production - things may (and probably will) change"

    • Organizations

How to deal with them. Who will take care of that branch? Should be independent?

DECISION: We will keep person and organization (in the sense of aggregate of person) under material. Organization is to be replaced by population. The role branch will create the necessary organization_roles for these to bear. The classes under material represent the physical part of the concept, and they bear roles representing the social status associated to these.
Side note: We had a discussion about how to represent for example "sigma". It has been decided that this would be an instance of reagent_supplier_role (or chemical_supplier) for example. Again, the role branch will create the appropriate classes.

    • Spatial regions

Instrument branch identified several terms that are spatial regions. These have been moved under spatial regions at the moment. What is the bfo status of this branch?

DECISION: discussion postponed until Alan/Bill on the call.

    • SVN tidyup, to have single folder for ontology. Suggested structure and assignment of task.

DECISION: Daniel volunteered to clean up SVN. He will circulate a proposal of action for this before modifying the current structure.

    • Sourceforge tracker review

AI for everybody: review the terms and assign them. By default, terms related to branch will be assigned to branch leaders. E.g., cohort_role will be assigned to Jennifer as leader of the role branch. Comments are to be posted on the tracker items when action is taken towards resolution.

Feb. 13, 2008

  • Coordinators call
    • AI:OBI coordinators should nominate 1 person to be OBO foundry associate editors
    • AI:Resolution of how to focus coordinators and also have useful community representation, and also to consider advisor input
    • Time and location for next workshop. Sept/ Oct in Hinxton with OBO Foundry? Or in summer in Boston (Science Commons)?
    • Update on deprecation policy from developers call
    • Authorship of the "big" OBI manuscript, as it has implications for efforts over the next months.

Feb. 6, 2008

  • Developers call
    • assign issues currently open on the sourceforge tracker to somebody.
    • AI:Deprecation policy will be discussed on next coordinators call to allow others to comments.
      • AR Proposal for discussion is that we use OBO foundry process
    • add an obsolete class. Issues with logical definitions and previous use of editor note for this
    • The proposal as topic on agenda
    • Road map to release

January 2008

Jan. 16, 2008

  • Developers call
    • Discuss use of Quality and PATO
    • Further discussion of resolving and documenting prolonged development issues (James, all)
    • Resolve citation vs source if major advocates are on call. (Daniel, Alan)
    • Use of annotation property (Melanie)

Jan. 9, 2008

  • Coordinators call
    • Community/Collaborative issues
      1. letter of support for PATO
      2. PDB community and workshop
      3. NCBI grant to evaluate and extend Collaborative Protege (D. Rubin, M. Musen, N. Noy)
    • Development issues
      1. Clean up wiki regarding the development policies methodology section (Frank)
      2. Proposal on using voting to solve ongoing discussions like analyte. (Melanie)
        • When an issue seems unsolvable (e.g. current analyte discussion) among the community, a community member can submit a request to the coordinating committee (CC) to put the issue to a vote.
        • The coordinating committee then decides to either put this issue to vote by the whole community, or alternatively can decide to solve the issue between coordinators (for example by voting only among members of the CC)
        • Voting should be open for at least a month (cf point 1.3.2 of the OBI Regs)
        • Voting behavior (either by CC members or by the whole community) will be made public (cf point 1.3.5 of OBI Regs)
      3. Questions for advisors (from last weeks developers call)
        • gaps in ontology coverage - e.g., no quantitative values (note: Alan Rector has way of doing this)
        • issues resolved or postponed in OBI, general use of roles
        • old issues with biomaterial:
          1. biomaterial hard to define: something of interest, biological origin?
          2. granularity (Frank, Matthew)
          3. multiple inheritance
        • General properties, eg definition, overall structure of OBI
        • uses cases/competency questions
          1. how to apply use cases and competency questions to OBI.
          2. question for advisors: given these questions and the current status of OBI are we ready?
          3. Want to solicit Robert and Frank to get new questions (relevant for use with NCIt, Mygrid, etc.) Frank (in the context of the Thesaurus) and curators are trying to do fair amount of logical definition. This will be the next step for OBI, put more logical definitions in. We should get his advice on that.

December 2007

Dec. 19, 2007

- finalize decision on space/underscore: no objections on that, so I propose that we definitively say we will use the space as a separator. We would need to update the wiki (maybe Daniel would volunteer as our "naming convention guru"  :-) ) and then we need to decide how we are going to modify the current terms. (per branch responsibility seems logical)

DECISION: Use space as separator.

- it would be nice also to get a general agreement on the following (which are non sensitive issues)

1. cardinality of definition_editor: in case we have several editors for a definition, do we put them all in one field (and with which separator?) or do we create distinct annotations. The instrument branch proposes to have several annotations (<definition_editor>Daniel Schober</definition_editor><definition_editor>Franck Gibson</definition_editor>...)

DECISION: Use 1:1 cardinality.

2. cardinality of definition_citation/source: same than above do we put everything in one field or do we separate, Again, the Instrument branch used the latter. (note: here I am not talking about the name source or citation, just the cardinality). The current cardinality on the minimal metadata page is 1 (, so would need to be changed

DECISION: Use 1:1 cardinality.

The above issues are just "technicalities" we need to agree on and that are currently holding us back in the curation work we are doing in Instrument and Data_transformation branches.

Then a few "problematic" issues:

- the annotation "curation_status" and its value "curation_complete". The instrument branch has bee using it to say "the term is clean" in the sense definition and metadata are ok. We used it in conjunction with other curation_status annotation, so for example a term cleaned but that we think might move in the hierarchy is curation_status complete and curation_status graph_position_temporary (the cardinality of curation_status on the minimal metadata page is 1...n) However, as Trish mentioned, for some people it actually means "term ready for release and won't (probably) move again". This is also a reasonable approach in the sense that moving a term in the hierarchy would probably imply modifying the definition as pointed out by James. Trish also proposed to have the cardinality of the curation_complete status set to one, which means using that value we would not be allowed to use any other curation_status in conjunction with it.

DECISION: Melanie, James, Bill and Alan will draw up list with definitions for use, cardinality will be 1:n

- the OBI IDs: some terms don't have any, and most of the time they are heterogeneous (between 2 and 10 digits for example). This seems to me to be an important issue, the IDs in the context of an ontology are very central as they represent the concept in the annotation made by our users. The proposal (James, Daniel and me) is that the lead editor of each branch takes care of that. We need uniform IDs, OBI_6digits, and we need to have the autoID files under SVN

FG: I can tidy up the wiki for the development policies/methodology section and remove duplication - Apologies I will be unable to attend the call but can someone let me know the outcome, thanks.

Dec. 12, 2007

November 2007

Nov. 21, 2007

  • Developers Call
    • Subversion + Protege Tutorial (Allyson, Daniel S., Melanie)

Nov. 14, 2007

Nov. 7, 2007

  • Developers Call
    • Providing formal definitions for low level terms. E.g., different models of the same type of instrument such as the different benchtop flow cytometers that Becton Dickinson makes.

October 2007

Oct. 31, 2007

  • Developers Call
    • metadata questions (Melanie, James)
      • metadata "definition_source": shall we annotate using definition_citation or dc: source? (definition_citation in Instrument branch, dc:source in data_transformation)
      • alternative_term_tags: tagging of alternative term depending on the community, how will it be implemented?
    • Branch reports.

Oct. 24, 2007

  • Developers Call
    • Jena script to automatically add required metadata elements to the OBI terms (Melanie)
    • Object hierarchy. Any update?
    • Branch reports.

Oct. 17, 2007

  • Developers Call
    • Minimal metada - which go in public release

Oct. 10, 2007

Oct. 3, 2007

  • Developers Call
    • Object hierarchy. Alan will summarize where the discussions stand on this issue.
    • Branch reports. Last week we heard about the Relations Branch. Any volunteers?

September 2007

Sept. 26, 2007

  • Developers Call
    • use case/competency questions (James)
    • PAG abstract (Bjoern)
    • Branch reports (??)
    • Naming conventions (Daniel)

Sept. 19, 2007

  • Developers Call
    • Call options
    • Presentation at PAG
    • Status of object hierarchy
    • derived classes

Sept. 12, 2007

  • Coordinators Call
    • Conference call set-up
    • Letter of support for MGED grant (Chris)
    • Stem cell community (Alan)
    • Mailing lists

August 2007

Aug 29, 2007

  • Developers Call
    • Daniel raised a number of issues (see "some glitches in OBI.owl" email) which could be discussed based on his request for comments.
    • Problems with sourceforge for mail lists - try Google groups?
    • PURL for OBI?

Aug 15, 2007

Aug 8, 2007

Aug 1, 2007

July 2007

July 25, 2007

  • No Developers Call

July 18, 2007

  • Developers Call

Conference call developers 2007 notes

    • unresolved non branch action items from the workshop and assign them to people and prioritise
18. Artefact object discussion. Two different hierarchies were  discussed. No resolution during meeting. These OWL files need to be  
posted and discussed during a dev call.
19. Inferred classes. We worked through an example and identified that exploring existing design pattern work is needed.  Discuss on  
dev call.
20. Update OBI to BFO1.1
23. Lot and material type - no resolution on this, needs further discussion on dev call
25. Issue of handling vendor reagents in OBI unresloved - needs more  discussion on dev. call

June 2007

June 27, 2007 Potentially last call before workshop (4th July is holiday)

  • Developers Call
  • Possible review branches:
    • Plan Branch
      • Status report link: here
    • Relations Branch
      • Status report link: here
    • Role Branch
      • Status report link: here

June 20, 2007

June 13, 2007

  • Coordinators Call
    • Discuss plans for the ISMB poster
    • Discuss workshop agenda
    • Lead editors for each branch - does each branch have one to coordinate the effort?

June 6, 2007

May 2007

May 30, 2007

  • Developers Call
    • Follow up on protege import bugs
    • CTO follow up, Jennifer Fostel/Richard S.
    • Discuss metadata annotation properties
      • example, needs better definition and should this be mandatory - Frank
    • Discuss Milestones in general, missed Milestones, tracking of Milestones etc.
    • Discuss upcoming June 1 milestone implications
    • Call Minutes can be found here

May 23, 2007

  • Developers Call
    • Branch wiki pages - James
    • Term Provenance - Trish
    • Motivation is to provide a method to filter terms for use in annotation applications.

May 16, 2007

  • Developers Call
    • Review Workflow for Branches development
    • Cross-branch issues
    • Function branch status (BB)
      • important cross-branch nexus
      • relations between BFO Function, Disposition, Role, and Process
      • BFO definitions for Function & Disposition problematic, complicated, and somewhat ambiguous
      • working on examples - see OBI Examples at bottom of OBI Function Branch Wiki page
      • specify process and independent continuants, as well as relevant continuant roles and qualities
      • reviewing articles on Function by IFOMIS researcher Ingvar Johannson - see Function manuscripts at foot of page

May 9, 2007

  • Coordinators Call
    • Core Developers?
    • Google group for OBI?
      • Any guidelines needed - final archive of document?
    • Postponed: Update on Coordinators - Ryan
    • Tentative: Policy for adding new communities - Susanna
    • Meet with NIH program officers Monday July 9 before Workshop starts?

May 2, 2007

  • Developers Call
    • OBI Workshop in July, update by Mervi
    • Policy to collect relations - Liju and Relations branch editors
    • Discussion of Richard's email on protocol application subtree (see email 4/27)

April 2007

April 25, 2007

  • Developers Call
    • OBI Branch files - generation and usage
      • Batch term loading code
    • Policy to collect relations?
    • SVN::Notify - preference for email list to post to
    • Annotation properties
      • definition_source, see DueCredit for implementation requirements
      • term provenance
    • tools/software directory for OBI SVN?

April 18, 2007

  • Developers Call
    • Update on discussion on representation of definition_source
    • Branch report - volunteers?
    • Vote on representation of ontology authors using dc:creator tag, 1 per author - All
    • Vote on information re:representing advisors - All

April 11, 2007

  • Coordinators Call
    • OBI Support for OBO Foundry paper
    • Vote on CARMEN Community
    • Combining branches GDC and Digital Entity
    • Level of modeling granularity of OBI - provide annotation terms or also provide a framework for a biomedical investigation
    • Follow-up/Summary from Dagsthul?
    • Confirm Editor-in-Chief role
    • Update on plans for 4th Workshop - Mervi
    • Term submission Milestone - Deadline vs Guideline?

April 4, 2007

March 2007

March 28, 2007

  • Developers Call - Cancelled

March 21, 2007

  • Developers Call
    • review timeline with triggers in OWL- Alan - Postponed
    • discuss remaining metadata annotation implementation issues, see email on File Format for batch loading for questions - All
    • discuss information on splitting OBI.owl file, which branch gets which subtrees as 'active' - All
    • discuss implementation ideas for definition_source, see DueCredit wiki page for requirements - All
    • managing terms proposed by communities with existing resources in production use, e.g. PSI, MGED, what information needs to be maintained by the branch editors - All

March 14, 2007

  • Coordinators Call
    • Discuss policy for due credit for work with ontology development, posters etc.
    • Milestone Deadlines, are these realistic?
      • Is there a need for branch editor? Some branches are doing so and 'editor-in-chief' to oversee the work of the branch groups?
    • Discuss viewpoint on representing information in OBI to fit the needs of the semantic web
    • Register permanent URL for OBI file? - see note from Chris Mungall/Bill Bug
    • Stable release of OBI planned for Oct, 2007 - which version of OWL? - Trish
    • Coordinator Participation - Ryan
    • Decide on meetings to submit OBI paper to (Outreach Milestone)
      • Page has been created at the Main Page (see 'Upcoming meetings - submit abstract' section)
    • Travel Fund email - Bjoern
    • OBI logo - is there a resolution on which version to display on site?
    • Vote on policy for web site maintenance - policy approved by project admins (Ally, Daniel, Trish, Daniel)

March 7, 2007

  • Developers Call
    • Finalize implementation of Workshop_San_Diego_2007_Metadata in OWL
    • Agree on string syntax representation of definition_source information - All
    • Review OWL representation of definition_source information as classes and instances - Alan
    • Present working implementation of timeline with triggers in OWL - Alan

February 2007

February 28, 2007

  • Developers Call
    • Finalize implementation of Workshop_San_Diego_2007_Metadata in OWL
    • Review OWL representation of definition_source information as classes and instances - demo OWL file needed
    • Discuss plans to split OBI file into 'branches'
    • Present working implementation of timeline with triggers in OWL - Alan

February 21, 2007

February 14, 2007

  • Coordinators Call
    • Travel Fund email
    • Discuss policy for due credit for work with ontology development, posters etc.
    • Vote on dividing into branches covering OBI scope, Branch development
    • Vote on policy for web site maintenance - policy being reviewed by OBI project admins
    • Remind Coordinators to sign-up for obi-advisors list
    • clean-up of OBI file following workshop - see email from Daniel,

February 7, 2007

January 2007

January 31, 2007

  • No call - OBI Workshop

January 24, 2007

  • Developers Call
    • Continue review of BFO

January 17, 2007

  • Developers Call
    • Review OBI classes that are siblings of BFO classes. Decide if we can re-tree them somewhere else without changing BFO structure. Follow up with BFO developers if agree that some have to stay as is.

January 10, 2007

  • Coordinators Call
    • Finalize Workshop Prep - Bjoern, All
    • Vote on inclusion of the Imaging Community
    • Development Policies regarding the obiwiki (Gilberto), SVN (Trish) and ontology file (Trish) - Agreement by All
    • Agree as to the information to send NCBO on OBI as required by the ~BioPortal - All
    • Agree that the FuGO Sourceforge project, SVN etc. will be left on Sourceforge - All
    • Status of OBI CC List at: [1] - All
    • Status of obi-advisors list - who should be subscribed to this list and is a change to the OBI Project Structure document needed? - All
    • Discuss new groups - ORegAnno( and Pazar(
    • Update on PATO meeting - Tina
    • Discuss policy for funding, specifically letters of support: All funding welcome - Bjoern
    • LoS Request from Barry

January 3, 2007

  • Developers Call
    • Finalize metadata annotation terms needed to replace the usage of the existing search tags
    • Discussion on other Workshop prep action items as needed [2]

December 2006

December 27, 2006

  • No Developers Call

December 20, 2006

  • No Developers Call

December 13, 2006

  • Coordinator Call
    • Discuss number of attendees at the workshop - Bjoern
    • Agree as to the information to send NCBO on OBI as required by the ~BioPortal - All
    • Agree that the FuGO Sourceforge project, SVN etc. will be left on Sourceforge - All, Postponed
    • Status of OBI CC List at: [3] - All, Postponed
    • Development Policies regarding the obiwiki, svn and ontology file - Gilberto - wiki, Trish - svn, Agreement by All, Postponed
    • Status of obi-advisors list - who should be subscribed to this list and is a change to the OBI Project Structure document needed? - All, Postponed
    • Update on PATO meeting - Tina, Postponed
    • Discuss policy for funding, specifically letters of support: All funding welcome - Bjoern
    • LoS Request from Barry
    • Vote on including the Clinical Trials 'community' into OBI - All
    • Prioritize Action Items for Workshop Prep - All
    • Discuss new group - ORegAnno( and Pazar( - All, Postponed

November 2006

November 8, 2006

  • Coordinator Call
    • Follow-up from ISMB
    • Questions regarding submitting OBI to OBO
    • Domain name for obiwiki
    • Vote on logo - see [4] for choices
    • SF Site - project admins and list admins
    • Note:Update Project Name/URL on web sites

October 2006

October 11, 2006

  • Coordinator Call
  • Agenda for January workshop - please add topic suggestions to Workshop San Diego 2007
  • Participants and modes of participation in workshop
  • Comments on New Logo
  • Decision as to when to announce move to developers list and start using the obi-devel list
  • BBSRC funding - link sent by Ljiu
  • Wrap-up of all docs from 2nd Workshop

September 2006

September 13, 2006

  • Coordinator Call
    • External participants (Alison Deckhut) at Workshop in San Diego
    • Vote on Project name change
    • Vote on Project Organization document
    • Vote on expanded project scope - more than Functional Genomics
    • Not able to attend:
      • Trish, Helen P, Susanna, Philippe

August 2006

August 23, 2006

  • Developers Call
    • Demo by Robert Stevens and Nick Drummond on Protege/OWL and how to generate machine managed multiple inheritance

August 16, 2006

  • Developers Call
    • Review items for further clean-up in OWL file from workshop
    • Plan continued devlopment of the ontology

August 12, 2006

  • FuGO Coordinators Call
    • General Business
      • Discuss project name change (All)
      • Discuss project structure, document proposed by Chris T (All)
      • Vote on addition of imaging working group to FuGO project (All)
      • Is further clean-up of the OWL file needed before posting, e.g. update version, release date, term identifiers (Class versus OBI versus FuGO? (All)
      • Discuss edits to Workshop Report (All)
      • Discuss plans for continuing the development of the ontology
      • Planning for next meeting: San Diego January / February 2007?
    • Coordinators Reports

July 2006

July 12, 2006

  • FuGO Coordinators Call
    • General Business
      • Finalize/Approve Workshop Schedule (All)
      • Reply to Allyson on definition paper (All)
      • Use of AutoID plugin during workshop? (Trish, All)
      • Decision to have a Developers Call on July 19 and if so what to discuss
      • Structure of FuGO project - how to best list the Communities and Coordinators on the FuGO web site (needs to be done before OMICS publication)
      • Structure of FuGO project - organizational structure for adding new Community Coordinators? (All)
      • Community Road Maps? (All)
      • Finalize content for DILS/JBB poster? (Susanna, All)
      • Discuss use of xml:lang attribute in FuGO file? (Daniel/Trish, All)
      • Update on interest in FuGO from the Yeast Community? (Chris T)
      • POSTPONED ITEM FOR WORKSHOP- Discuss Clincal Trial Ontology and how this effects the process and scope of FuGO (Barry Smith)
    • Coordinators Reports

July 5, 2006

  1. BIRNLex (imaging)
  2. PSI-MS (mass spec)

June 2006

June 28, 2006

  • FuGO Developers Call
    • Review Instrument Terms from the following Communities:
  1. Flow Cytometry
  2. Transcriptomics

June 21, 2006

  • FuGO Developers Call
    • Review ontology modeling proposal to indicate a "Factor"
    • Discuss plans to move forward with reviewing Intrument Terms

June 14, 2006

  • FuGO Coordinators Call
    • General Business
      • Discuss/Confirm 2nd FuGO Workshop Agenda ( - All
      • Decide on topics to address in next months Developers Calls (include Epitope Use Case) - All
      • Vote on MIACA as a collaborating community ( - All
      • Review Policy for managing tracker items - add URL to wiki, Managing FuGO Term Tracker - Trish
      • Review new FuGO web site design - Trish
      • Update on potential Collaboration with Yeast Community - Chris T.
    • Coordinators Reports

June 7, 2006

  • Review location of Factor terms

May 2006

May 31, 2006

  • Review plans for the 2nd FuGO Workshop
  • Review Modelling Proposal for indicating Factor terms
  • Review proposed location of factor terms

May 10, 2006

  • FuGO Coordinators Call
    • General Business
      • Discuss Community Road Maps
  1. do communities have these
  2. how do they fit OR diverge in development style of FuGO
  3. can these be posted on FuGO site
      • Post a How to Contribute wiki page?
      • Approve new members
      • Set-up time to confirm that CVS merge will work
      • Discuss plan for next months calls
      • Discuss when to review Epitope Use Case
      • Participation in upcoming " Biomedical Ontology in Action" November 8, 2006, Baltimore, Maryland, USA
    • Coordinator Reports
    • Chris - report from MGED Jamboree
    • Susanna, Trish, Chris, Dawn, Philippe, Daniel - Report from PSI meeting
    • Timeline for updating web sites to present/display correct name of FuGO, i.e. add Investigation to the long name
    • AOB

May 3, 2006

  • Review Study terms fro Toxicology community - Jennifer presenting

April 2006

April 26, 2006

  • Review Study terms from the Flow Cytometry Community - Ryan presenting

April 12, 2006

  • FuGO Coordinators Call
    • General Business
      • Developers Meeting schedule for April period (time between Coordinator calls) (All)
      • Addition of new communities (CS)
      • Ontology management items (All)
  1. agree as to idspace of FuGO
  2. policy for assigning and approving terms into FuGO as proposed through the tracker - universal and domain/technology specific
      • CVS policy - trunk and branches
      • Copyright of FuGO (TW)
      • Plans for next workshop - funding possibilities, proposed dates (CS, SS)
      • OMICS Special Issue (DF/SS)
    • Coordinators Reports
      • Community Coordinator Reports
      • CS - update from Ontology Immunology Workshop?
      • SS - update from Crop Sciences Workshop
      • CT - update from Genomes2Sytems Conference
      • CT - update on PSI preparations
      • Others - add as needed

April 5, 2006

  • FuGO Developers Call
    • Discuss terms proposed from Transcriptomics community
    • Discuss issue of Study and timeline