Workshop OBI Vancouver 2010 Mar

Summary of Action items and owners
extracted from page below

AI: Eagle-i to continue work on instruments in a sep file to present internally to obi pre-meeting. - DONE pending presentation on 10 May on call

AI: Fahim will identify Data Transformation related terms and coordinate with James to get those into OBI. Spreadsheet sent to Fahim, awaiting feedback from him.

AI: Fahim will identify a NIF representative to add/edit the obi.owl file with data transformation terms. - JM to follow up

AI: Eagle-i/NIF will work with Helen over the next several days on how to edit obi.owl DONE

AI: Jessica - Report back with 5 examples developer of scales (e.g., Sledae score) and how to model in OBI based on initial model developed during workshop - April 26 developer call IN PROGRESS

AI: Jessica - How to represent levels of scale into what data transformation are allowed coordinated with James/ Allan - Report back on April 26 developer call IN PROGRESS

AI: Trish will ensure BRO presentation will be put in OBI svn (March 28) - HP to ping Trish

AI: Melissa have identified instruments to be submitted to OBI on behalf of BRO (March 23) - s/sheet circulating for this

AI: Trish and Dave will coordinate with their groups to make OBI requests for terms (especially instruments) (Report back on OBI call April 30) - remind Trish add to agenda - added to agenda for call on monday 3rd May

AI: NIF to provide link to instrumentation doc (March 24) - DONE

AI: NIF will move the example processes to a shareable document and will work through the remaining list of ~95 instruments based on the results of the modelling done by Bjoern during the meeting (April 28)  - adding functions for the instruments and wil try and develop a branch for this for inclusion in OBI. Done by 26 April. IN PROGRESS

AI: Allen will place VO presentation in OBI svn - Hp will check.

AI: Alan R will give an example of time measurement data that measures the interval between two events such as vaccination and challenge. (report back at developer call April 28) - JM Will chase up Alan R

AI: Discussion on how community tags will be used related to in vivo etc, AR favours OWL2/P4, JM worked on a way to model community tags in OWL1/P3: This second approach doesn't work so we need OWL2/P4 (AI for AR to test as that becomes available) - James tested in OWL1/P3 - so can only be done in P4/OWL 2.

AI: Bjoern will put "Efficacy of treatment assay" and T-cell assay as a study design. This will done offline during the workshop - NOT DONE. HP will add a tracker item.

https://sourceforge.net/search/?group_artifact_id=886178&type_of_search=artifact&group_id=177891&words=efficacy

AI: Bjoern will do Colony forming units for Allen and IEDB.

NOT DONE - HP will remind Bjoern and add a tracker item. - Jie has imported colony forming unit per volume from UO into OBI as an instance of concentration unit, check if these are present.

AI: Bjoern will contact NBT, and based on discussions make a wiki vote page for this proposal (March 28) follow up on April 28 when Bjoern is back

AI: Every community representative is to provide implementation details for next year to be provided by next coordinator call - TO DO. Make a wiki page for this. May be a pre-existing google doc? PRS will send link http://docs.google.com/Doc?docid=0AaEXoAK_iKrtZGhnbXQ1azZfMjE0ZnhjeDlyY2I&hl=en -

AI: Bjoern will submit the following proposal for a vote & discussion on on the next coord call: Remove Coordinating group/developer distinction in OBI, only have "Contributors". These will self-identify to a community, and if they are able to speak for that community as to official policy. List of members will have "active flag" for current calendar year, as to if they are currently participating in OBI (e.g., we would track this no for 2010, then next year switch that to 2011) Votes will decided be by simple majority after 2 weeks.

IN PROGRESS

AI: Clean up the website communities as part of this process, once a way forward has been decided AI update: turn into active devs and alumni and remove communities element

NOT DONE

AI: Jie will add some terms for experimental design type through MIEROT and has a pattern for doing so (report back on a call April 28) IN PROGRESS

AI: James has student who will test slim and logical/slim and report back September 30

NOT DONE

AI: Eagle-i & NIF are going to add to a branched obi.owl and present their results at a appropriate devel call and then the changes will be merged

IN PROGRESS

AI: (Devices?) Articulate single inheritance hierarchy below convenience classes with initially trying to make all such children have necessary and sufficient branches. This will allow us to have Aristolean definitions in these single inheritance. BP will report back on BP's birthday May 18.

AI: Adding restriction to material_sampling (HP will try to resolve offline and report back April 28) - NO IDEA, read notes and return to this.

AI: reference substance role will be fixed by HP according to tracker notes - DONE. Was requested to map to molecular entity, agreeds is less precise and will use material entity. Related tracker item now closed.

(April 28) AI: Reagent role is deferred will decision what a device/reagent is - NOT DONE

AI: Review tracker items for items to 9 for release, as fixed by HP during meeting to be fixed before releases to be reviewed during calls

AI: Add level 9 items are required (All) AI: There will be a Vancouver2010 release by Jie once these items are fixed

Access
You can take a taxi from YVR airport (around 25-30$CAN) or use the new Skytrain line: http://www.translink.ca/en/Rider-Info/Canada-Line.aspx (around 8$CAN).

The Skytrain has a station in the airport, and stops at Broadway City Hall, 2 blocks away from the hotel: map

Venue
British Columbia Cancer Research Center (BCCRC) 675 West 10th Avenue Vancouver, BC V5Z 1L3, Canada

Monday to Wednesday meeting will be in boardroom on the first floor (go right when you enter building), the same location as in past years. On Thursday we move to the 12th floor meeting room (right our of elevator to end and then go right).

If you have any question regarding local organization please contact rbrinkman [at] bccrc.ca and mcourtot [at] gmail.com

Hotel discount code
A block booking has been made at the Holiday Inn Vancouver Centre (attention: there are several Holiday Inn in Vancouver - you want to book the Holiday Inn Vancouver Centre and *not* Vancouver Downtown) at the special rate: Deluxe Room			$ 99.00		single/double occupancy $ 15.00		additional person in room

All rates are subject to Provincial Sales Tax of 10% and Goods & Services Tax of 5% (subject to change).

Rooms from the Group Block, can be accessed by visiting the Holiday Inn website. On the left side of the main screen please fill in the Group Code Field with TEF and check availability. Holiday Inn Vancouver Centre Reservations Direct: 604-707-1939.

Please note that the pre-booking is held until February 20th, at which dates rooms not booked will be released. We won't be managing room booking, so make sure you have confirmed directly with the hotel before this date.

The hotel is a block away from the institute: map

Remote attendance
Will not be available. Sorry.

1. Monday 22nd
- New groups introductory presentations - OBI overview to date

9am to 12.15am


 * 9-9.15 am: Welcome. Ryan will go over few items such as network connection, catering etc...
 * 9.15 am: OBI overview to date. Bjoern will walk us through the OBI paper and mention some of the policies implemented during development of OBI (design patterns, metadata, deprecation...)

Bjoern presented the OBI overview available in the OBI repository


 * 10 am: Eagle-i presentation. (slides in svn)

Eagle-i presentations will be placed in the OBI repository


 * 10.30 am: break
 * 10.45 am - 12.15 am: Eagle-i use case

All slides are in docs/presentation/Obi workshop March 2010 Vancouver

Proposal (in obi.owl for draft + tracker items): "providing a service": a planned process executed by a service provider with the objective to enable a service consumer to achieve an objective. Realizes some (is_concretization of some 'plan_specification') and ('inheres_in' some has_role some role)) and achieves_planned_objective some 'objective specification

AI: Eagle-i to continue work on this in separate file, and present on OBI call Eagle-i to join developer call

1.15pm to 5.30pm


 * 1.10 - 1.15: ISMB 2010 Workshops Evidence Codes: Assay Tracking, ECO and OBI

http://www.iscb.org/ismb2010-program/workshops#w4

History: An evidence tracking Workshop has been approved at ISMB. OBO Foundry decision was substantial overlap with OBI and there should be coordination of efforts. Philippe has been working on this area and ECO should be invited to an OBI call where this work will be presented.

AI: Richard will send OBO Foundry review to ECO as a means of introduction and invite them to a meeting. AI: Richard to contact Philippe to present internally to obi pre-meeting.


 * 1.15 - 1.45: NIF presentation. Fahim will introduce the NIF project and how it relates to OBI.
 * 1.45 - 3.15: NIF use case

Went through Excel spreadsheet from NIF tracker item to identify where old OBI terms used in Birnlex would map to. Updated spreadsheet uploaded.

AI: Fahim will identify Data Transformation related terms and coordinate with James to get those into OBI. AI: Fahim will identify a NIF representative to add/edit the obi.owl file with data transformation terms. AI: Eagle-i/NIF will work with Helen over the next several days on how to edit obi.owl

Ongoing: Fahim to join conference call, add new terms that work well within the hierarchy into separate file to be first imported for verification and merged into OBI. After that tackle old terms to be modified.


 * 3.15 - 3.30: break
 * 3.30 - 4.00: BIRN presentation by Jessica.
 * 4.00 - 5.30: BIRN use case

2. Tuesday 23rd
During workshop some effort was spent on how to model scores within OBI

AI: Jessica - Report back with 5 examples developer of scales (e.g., Sledae score) and how to model in OBI based on initial model developed during workshop - April 26 developer call AI: Jessica - How to represent levels of scale into what data transformation are allowed coordinated with James/ Allan - Report back on April 26 developer call


 * 9 am to 9.30: BRO presentation (Trish/Dave)

AI: Trish will ensure BRO presentation will be put in OBI svn (March 28) AI: Melissa have identified instruments to be submitted to OBI on behalf of BRO (March 23) AI: Trish and Dave will coordinate with their groups to make OBI requests for terms (especially instruments) (Report back on OBI call April 30)


 * 9.30 to 10.30 am: Instruments efforts interoperability

Use case driven issues session ('We have issues'), ~1/2 day each

Format: 0) Premeeting: Prepare 1-4 1) present use case 2) summarize progress to date 3) introduce issue that needs work 4) hands on development, and commit to file

Several examples of processes were worked through on Google docs, and these were then modelled in OBI by Bjoern. The new methodology to classify instruments is through their over-arching function defined as a process combined with something else that defines instruments, which for now seems to be satisfied by added powered by electricity (e.g., chromotagraphy instruments and centrifuges have a separation function (and not contain/mechanical functions) and both plug into the wall)

AI: NIF to provide link to instrumentation doc (March 24) AI: NIF will move the example processes to a shareable document and will work through the remaining list of ~95 instruments based on the results of the modelling done by Bjoern during the meeting (April 28)


 * 11 to 12.30 and 1.30 to 3.30 pm: VO use case (Allen)

We added administration types added to OBI (e.g., oral, subcutaenous, subdermal) We worked on dose specification

AI: Allen will place VO presentation in OBI svn AI: Allan R will give an example of time measurement data that measures the interval between two events such as vaccination and challenge. (report back at developer call April 28)

- What is driving OBI post 1.0? - Taking on new groups + use cases vs. tackling difficult bits of existing ones - Should we revise coordinator structure? - External related efforts
 * 3.30 pm to 5 pm: Planning

3. Wednesday 24th - 9am to 12 am and 1pm to 5pm

 * 9 am to 12.30 : IEDB use case (Bjoern)

Study design, protocol, and assay were reviewed in detail. Concern about fuzzy boundaries between assays and studies in terms of being able to make a distinction for some tricky boundary cases, including Bjoern's "efficacy of treatment assays". See Bjoen's IEDB slides for more details on this subject.

To resolve in vitro/in vivo Added "in live organism assay" and "in live cell assay" and "in container assay". Communities will be able to combine these as required for their own use cases

AI: Discussion on how community tags will be used related to in vivo etc, AR favours OWL2/P4, JM worked on a way to model community tags in OWL1/P3: This second approach doesn't work so we need OWL2/P4 (AI for AR to test as that becomes available)

AI: Bjoern will put "Efficacy of treatment assay" and T-cell assay as a study design. This will done offline during the workshop AI: Bjoern will do Colony forming units for Allen and IEDB.


 * OBI paper

Based on the time and effort required to get NBT paper in the shape required by reviewers, the workshop proposal is to go back to NBT saying that it is crucial for us to get this published at this point and we are not going to address their killer use case due to production issues. They may agree to publish, if not Bioinformatics would be the selected alternative choice.

AI: Bjoern will contact NBT, and based on discussions make a wiki vote page for this proposal (March 28)


 * What is driving OBI

Implementations (what and how), adding lots of new terms, what are blockers to having people adopt so that we can fix these?

AI: Every community representative is to provide implementation details for next year to be provided by next coordinator call.


 * New groups

NIF, ECO have stepped up and have joined calls. The door is now open for others to join calls and there is no restriction any more as there have in the past due to time constraints on OBI's side


 * OBI Coord structure

AI: Bjoern will submit the following proposal for a vote & discussion on on the next coord call: Remove Coordinating group/developer distinction in OBI, only have "Contributors". These will self-identify to a community, and if they are able to speak for that community as to official policy. List of members will have "active flag" for current calendar year, as to if they are currently participating in OBI (e.g., we would track this no for 2010, then next year switch that to 2011) Votes will decided be by simple majority after 2 weeks.

AI: Clean up the website communities as part of this process, once a way forward has been decided


 * 1.30 pm to 5 pm: MGED use case (Jie)

AI: Jie will add some terms through MIEROT and has a pattern for doing so (report back on a call April 28)


 * 4pm OBI editing tutorial HP - see updated notes http://obi-ontology.org/page/Tutorials

4. Thursday 25th - 9am to 12.30 and 1.30 pm to 5pm
morning + afternoon: list of issues proposal

Use Case
- Integrate IDO terms into OBI - Qualitative positive / negative measurements - tying epitope 'conclusions' to assay outcomes
 * Use case: Immune Epitope Database export (Bjoern)

The E-TABM-34 files have been used to demo several software including annotation creation tool, eg. annotare, data and annotation management software, eg. CaArray, and data analysis platform, eg. GenePattern, MeV. - Integrate MO terms into OBI, and integrate terms used to annotate characteristics ie from other ontologies into OBI (mostly contained in EFO) - Annotate microarray experiments using OBI and further other kinds of experiments, such as Chip-seq and RNA-seq
 * Use case: Annotate the MAGE-TAB format files, E-TABM-34.idf.txt and E-TABM-34.sdrf.txt using OBI.

- Ontology modeling: This use case includes 18 parameters: (1) vaccine strain, (2) vaccine viability, (3) Addition of IL-12 as vaccine adjuvant, (4) Addition of SOD antigen, (5) gene deletion, (6) animal (host) species, (7) animal (host) strain, (8) animal (host) sex, (9) vaccination route, (10) vaccination dose, (11) animal age at vaccination, (12) pathogen strain for challenge, (13) challenge route, (14) challenge dose, (15) challenge time (e.g., interval after vaccination), (16) colony forming unit (CFU), (17) reduction of colony forming unit (CFU), and (18) Significance of vaccine protection (Three values: no protection, protection, enhanced protection). - Instance data: We have collected ~160 instance data from the literature, which investigated the protection levels of several Brucella vaccines at different conditions (with different values of these 18 parameters). - Hypothesis: Some parameters are more important than others in determining the result of the vaccine protection efficacy. - Method and Result: An ANOVA analysis was performed and indicated that 12 parameters significantly contribute to the protection (P value < 0.05). The other parameters do not (P value > 0.05). - Issues for discussion: (1) How to model these parameters using OBI, IAO, and VO; (2) How to model the hypothesis, ANOVA test, and the statistical results using OBI; (3) How to use OBI/IAO to help statistical data analysis of instance data? (4) Possible extension of this study to other ontology-based statistical data analysis?
 * Use case: Vaccine protection investigation This is an extension of the “vaccine protection investigation” use case introduced in the OBI JBMS paper. (Allen)

We need to coordinate about the future of BIRNLex-OBI proxy classes (the tracker link that you sent contains the list) within NIFSTD. The NIF-Investigation module included those proxy classes few years back when OBI was yet to be stable. Those proxy classes were intended to be replaced by OBI equivalents later. Now that we have OBI built off BFO 1.1, we need to align our progress. Now, OBI-Proxy classes were extended in NIF Investigation along with the addition of various MRI/DTI terms (coordination with Jessica Turner and Karl Helmer). Some portion of NIF-Investigation (extended from obi-proxy classes) would certainly be overlapping with current OBI. As the original hierarchies of our proxy classes have been changed in OBI along with other changes (some of the classes became non-existent, and some of the class IDs seems to have changed in OBI), we need to be careful during the process of adapting the updated OBI. Ideally I would think of importing OBI as a whole, given that the extended NIF classes are clearly separable with no overlaps (and OBI being comprised of only ‘universal’ bio-investigation terms with a generic hierarchy). Also, extracting a relevant portion of OBI using MIREOT approach can be an option. We need to reconcile this issue of BIRNlex-OBI proxy classes and need to come up with a good alignment approach between NIF-Investigation and the current version of OBI.
 * Use case: Coordinate future of BIRNLex-OBI proxy classes (Fahim)


 * Use case: Modeling relationships between experimental variables ('Knowledge Engineering from Experimental Design'): applications within BIRN projects. (Jessica)

The BIRN Knowledge Engineering Working Group is adopting an approach that can be thought of as a simplified projection of OBI's much larger scope (and we are seeking ways to interoperate with OBI as much as possible). We adopt a variable-centric view of modeling scientific experiments that is based on understanding the relationships between the independent, dependent and derived variables of a study. This model serves as the basis for several applications within BIRN-KEWG's overall activity, including tools for data integration across databases, the development of reasoning models within defined domains (such as neural connectivity) and tools for straightforward modeling of experimental design that can then serve as the basis for generic data repositories. We present two models formulated in this framework (which we would like to bring more closely into register with OBI): tract-tracing experiments involved in the study of neural connections and fMRI studies involving the Auditory Oddball Paradigm.

Tract tracing experiments involve injecting minute quantities of tracer chemicals into animals brains, and subsequently processing those brains to stain for the presence of tracer. These techniques reveal the presence of histological labeling within cells, axons and terminals. The location of the injection, the spread of the injection site and the location, type and density of labeling provide the underlying data to understand the existence of neural projections.

The Auditory Oddball Cognitive Paradigm is a behavioral paradigm involving the presentation of standard and oddball tones, in which subjects respond behaviorally to the oddball tones. The difference between the physiological response to the standard and oddball tones is usually the dependent variable of interest.


 * Use case: Modeling relationships between research resources: the eagle-i project (Melissa & Carlo)

The eagle-i consortium has the objective of developing a searchable network of research resources at research institutions nationwide. This project was funded in parallel and with the goal of interoperability with the Vivo project that will index people, their affiliations, publications, etc. We are developing an ontology for indexing and querying biomedical research entities, and this effort is being guided by discussions within the ontology community (http://RRontology.tk) aimed at promoting interoperability. We are utilizing a large set of use cases and queries to drive our ontology design.

There is a fair amount of overlap with OBI in that many of the “resources” that we are indexing play roles in biomedical investigation. However, one difference in usage is that we are not annotating data or experiments. We will be inventorying laboratories, services, instruments, reagents, organisms, persons, protocols, human studies (metadata), tissue/biological sample repositories and training opportunities. For discussion at the OBI meeting, we’d like to focus on three aspects, namely representation of organizations providing a service and service subtypes, the relationship between protocols, techniques and planned processes, and potential classification of instruments based on function or participation in planned processes.

Issues Proposals
Add any item for discussion here


 * Would be good to discuss OBI packaging options - different distributions of OBI for different purposes. Slims. Modules. etc.

Reasoner issues seem to indicate a need for packaging. A version without logical conditions would help here. A package without immunological terms for those working on cardiology. One without change tracking. One with inferred hierarchy. OBO version. What are the other types required? This also relates to release cycle. Allan has created a wiki page to outline proposal.

AI: James has student who will test slim and logical/slim and report back September 30


 * clean-up defined classes + follow/formulate policy


 * How to add terms: new files, main file?

AI: Eagle-i & NIF are going to add to a branched obi.owl and present their results at a appropriate devel call and then the changes will be merged


 * Handling convenience classes (e.g., specimen, material to be added): should they be marked, moved out of main file?

AI: need Allan, postponed
 * role hierarchy: for example we have role of being first subject treated, to be treated with active ingredient role, to be treated with placebo role but treated role obsolete.

AI: Articulate single inheritance hierarchy below convenience classes with initially trying to make all such children have necessary and sufficient branches. This will allow us to have Aristolean definitions in these single inheritance. BP will report back on BP's birthday May 18.

Helen led working through some tracker items, see tracker for details, some notes below. AI: Adding restriction to material_sampling (HP will try to resolve offline and report back April 28) AI: reference substance role will be fixed by HP according to tracker notes (April 28) AI: Reagent role is deferred will decision what a device/reagent is


 * release issue: regular release of OBI? monthly, bi-monthly?

Twice a year releases after workshop there will be an official release post-cleanup. There may be additional releases as needed. This is for outside people. We will continue to update svn as needed.

AI: Review tracker items for items to 9 for release, as fixed by HP during meeting to be fixed before releases to be reviewed during calls AI: Add level 9 items are required (All) AI: There will be a Vancouver2010 release by Jie once these items are fixed


 * instrument/device: We obsolete instrument and device for adding more specific classes such as measurement device. We need other kind of device/instrument to cover micro electrode, microarray wash station, syringe, etc.

Current status: We are asserting directly under device and we are using function to classify under device defined classes (HP/BP)


 * who would take care of instrument in general? e.g. https://sourceforge.net/tracker/?func=detail&aid=2887868&group_id=177891&atid=886178, or https://sourceforge.net/tracker/?func=detail&aid=2855265&group_id=177891&atid=886178
 * chemical solution https://sourceforge.net/tracker/index.php?func=detail&aid=2890158&group_id=177891&atid=886178 some issues regarding how chemicals in solutions should relate to parts, especially to exclude a cell in mixture not inferring as a child of this. Also issue about using roles without tying to process
 * Evidence Codes: Assay and other OBI spin offs (such as proposed organization ontology ORG) - there is interest from people not at workshop so discussion summary should go to mailing list or possibly discussed on a call
 * Discuss further relationship between organizations and the entities they control.
 * Sham treatment
 * Specified dose (left over, nice to get to)
 * labs in the sense of people and property
 * reagents function versus role

Participants

 * Ryan Brinkman (Mon-Thu)
 * Melanie Courtot (Mon-Thu)
 * James Malone (Mon-Thu)
 * Bjoern Peters (Mon-Thu)
 * Helen Parkinson (Mon-Thu)
 * Jessica Turner (Mon-Tues)
 * Jie Zheng (Mon-Thu)
 * Zuoshuang "Allen" Xiang (Mon-Tues)
 * Melissa Haendel (Mon-Thu)
 * Carlo Torniai (Mon-Thu)
 * Fahim Imam (Mon-Wed)
 * Alan Ruttenberg (Mon-Thu)
 * Trish Whetzel (Mon-Wed)
 * Dave Rubenson (Mon-Tue)
 * Richard Scheuermann (Mon-Thu)

Extracurricular Activities
Cypress does not look like it will be a viable option this year as it is only open till 7pm, though they do have tons of snow now.

A whole day trip to Whistler (for non skiers another) is planned on the Friday, and weekend for those that want to stay longer. They've had record snow this year. Please sign up below if you are interested in sharing a chalet or some other sort of accommodation over the weekend and we'll work something out. As for transportation, [Greyhound is the best way to go] You want to travel from Vancouver to Whistler village (or Creekside) You probably want the 6:30 am ride up to get there for when the mountain opens at 8:30 The mountain closes at 3:30, so the 4:30 gets you back downtown at 7. Ryan is happy to work out details with those interested. Please add your name to the appropriate section below if you are interested.


 * Day trip:


 * Weekend (indicate # of nights if you are interested in possibly getting a shared chalet (etc.)):
 * Ryan (2 nights, Fri/Sat)
 * Helen +1 (Fri 26-31 March)

Things to organize

 * Power bars
 * Whistler transportation
 * Dinner reservations (Banana Leaf Malaysian / Cactus Club upper scale pub/ Plaza 500 west coast/ Indian Buffet / All u can eat sushi on Broadway / New Milestones/ Memphis Blues BBQ)
 * Lunch catering (kitty? Tracy's food book & delivery)