Workshop OBI San Diego 2011

'Workshop OBI San Diego 2011'

The year 2011 Ontology for Biomedical Investigations (OBI) Workshop is scheduled for March 21-23 at the La Jolla Institute for Allergy and Immunology, La Jolla, California (﻿﻿﻿http://mapq.st/h5Ltcd).

Call Bjoern (858 366 3531) in case of problems

Schedule

Morning sessions will be 9-12, afternoon 1-5

Monday morning

Introductory session - Bjoern (OBI overview and IEDB) - Jie (EuPathDB) - Carlo - Marcos - Jessica - Philippe - Chris (manuscript + state of OBI)

Monday afternoon

- Services (Carlo) - Finalize the discussion we started in Vancouver last year. - Discuss design pattern and examples in OBI to discuss (is service a subclass of the related planned process offered as service?) - Result: Carlo and Matt to write up modeling and circulate

- Reagents (Carlo) - brief presentation of the work done since the Vancouver workshop - Result: Submit those material entities to OBI that are in scope (processed materials used as reagents)

- Shortcut Relations (Carlo) - Start with example from services (e.g. organization X 'offers service' Y)  - Participants should provide additional use cases / examples - Result: Go ahead with implementation of 'service provided by' as a shortcut; (similar to achieves_objective), Use domain / Range approach to have minimal inference already.

Tuesday morning - Genotype (Jie/Chris) - Discuss definition of genotype, allele, wildtype as needed for OBI '''- Result: Jie and Chris to move relevant classes and definitions from ExpDesign.owl into obi.owl. Produce a writeup and circulate. Further discussion required for 'genetic material.

Tuesday afternoon - Experimental Design for functional genomics (Chris/Jie) - complete to meet requirements by Jie '''- Result: Writeup produced, and circulated to Philippe for comment. Afterwards, circulate to all. Go ahead with implementation of study designs via MappingMaster."'''

- Epitope assay needs for IEDB (Bjoern) - presentation of assay solution - discuss impact on assay vs. study design '''- Result: Allow complex assays, meaning all IEDB needs are met. '''

Monday night (potential reschedule to Tuesday because of weather) - BBQ - Villa Peters (622 Colima Street, La Jolla) - Result: fat and happy with German and butter

Wednesday morning - Community views - FGED view (Chris / Jie) - IEDB view (Bjoern) - OBI slim for general use - Result: Email circulated

Wednesday afternoon - OBI business + coordination (Bjoern) - Manuscript completion '''Result:Email circulated. Input for new use cases by April 15.''' - discussion of challenges of software that uses OBI, how to develop it, examples? Result: Need to have higher frequency of releases.

- preparation for ICBO workshop Result is listed below - Advertisement for ICBO (complete by April 30 (paper acceptance date)) - make an attractive announcement on OBI webpage (BP to create; ask for content by April 15) - refine existing proposal - point out what specific problems this workshop will address - send to mailing list - direct contacts of projects that are (or should be) interested - consortium + all OBI mailing lists - who contacted OBI in the past 2 years - who mentioned OBI in paper - advertise on OBI website (new page) - add to ICBO website (check on easychair) - Prepare presentation content - Overview presentation of OBI (paper) - guiding design principles - what parts of OBI deal with what - Eagle-i+NIF+BRO: Using OBI to coordinate large scale knowledge base creation and management across communities - IEDB: Add semantic capabilities to your Database using OBI - EuPathDB: Use OBI to drive data collection from experimentalists - Philippe: Please add (?) - ECO: Coordinate development of existing ontologies with OBI - Prepare hands on session - give instructions what can be prepared in advance - allow for follow up with indivduals developers to address specific issues

- Release Process Result below - Technical problems (look like they are overcome): - Reasoning issues with LISP - OBI getting so big that stuff takes long - People: - some steps can only be performed by Alan; manual intervention by Alan - need to broaden number of people that can run the process --> Carlo will observe the next release done by Jie - Content problems: - Requirements that hold up: curation status, definition source --> integrate in QTT - need to review generated content to make it perfect OR adjust policies to be more lenient and allow frequent releases - Future frequency: - Start next release following QTT for study design etc. is in      - Goal was to do this monthly - Track for next release: what are the resources necessary to get it out (Carlo to give feedback)

- Approaches to obtain funding - U41 (NHGRI), http://grants.nih.gov/grants/guide/pa-files/PAR-11-095.html, submission dates September 25, 2011; January 25, 2012; - Chris to lead preparation until ICBO, where there will be a 1st night of ICBO get together to discuss plans - Teaming with NCBO for tool development - Anita: work with disease societies

Participants Hui Gong Jennifer Fostel Jason Greenbaum Bjoern Peters Philippe Rocca-Serra (remotely) Susanna Sansone (remotely) Chris Stoeckert Carlo Torniai Jessica Turner Randi Vita Jie Zheng (remotely) Marcus Chibucos Matthew Brush Anita Bandrowski