Workshop Bethesda 2007 July 9

Location: Natcher Conference Center

• The Workshop will be held at the Natcher Conference center.

      Delegate Room D 	   Monday, July 9
      Conference Room F1/F2   Tuesday, July 10 - Friday July 13

Workshop Bethesda 2007 July summary conclusions

Click here for a summary of all the notes from the Bathesda 2007 OBI workshop meeting

General Information

• The William H. Natcher Conference Center (45 Center Drive Bethesda, Maryland 20892) is part of the National Institutes of Health and is located on the NIH campus in Bethesda, MD. The Natcher Building is across the street and north from Building 38A and the National Library of Medicine. It is a 5-minute walk from the Medical Center Metro stop on the Red Line. The Medical Center Metro stop is the next station north from the Bethesda Metro stop located close to the Bethesda Court Hotel.
• Metrorail system map
• Bethesda Guide

Security

• The NIH has recently instituted new security measures. All visitors entering the NIH campus must show government-issued photo ID and be prepared to have their personal belongings inspected. Please visit the NIH Visitors and Security page for more information.

Parking

• Visitor parking is very limited but if you must drive, short-term metered parking may be available near the Natcher Conference Center in Lot B. Please visit the NIH Campus Parking Visitor Map to see the location of visitor parking areas.

Draft Agenda

Monday

AM

• Location: Natcher Delegate Room D
• Meeting with NIH Program Directors
• 10:00 AM - 10:10 AM - Welcome
  • Chris Stoeckert
  • Point of meeting
  • Topics to be covered Monday AM
  • presentation:
    • Image:InfoOnOBI.ppt: Informational meeting on OBI Welcome, MGED/FuGE, and discussion points.
• 10:10 AM - 10:40 AM - Overview of the Ontology of Biomedical Investigation (OBI)
  • Bill Bug
  • presentation:
    • What is OBI, who is involved, how is it being developed, etc.
• 10:40 AM - 11:00 AM - Discussion
  • Are there other communities efforts that should be involved in OBI?
• 11:00 - 11:40 AM - How does OBI relate to other standards efforts?
  • Chris Stoeckert
    • The Microarray Gene Expression Data (MGED) Society
    • Functional Genomics Expression (FuGE) Schema
  • Susanna-Assunta Sansone
    • presentation:
      • Image:InfoOnMIBBI.ppt: Information describing the MIBBI Project
    • Minimal Information for Biological and Biomedical Investigations (MIBBI)

PM

• to begin at roughly 1:00 PM, after lunch
• Summary of action items, & milestones from San Diego
• Update of status from development branches
• Discussion of agenda for the rest of the meeting, priorities, agreement on desired outcomes
• Maintenance of terminologies by participating communities or within the OBI ontology proper

Tuesday - Thursday Location: Natcher Conference Room F1/F2

• Vocabulary development; time allocated for other items (below)

Tuesday

AM

• Update of status from development branches (15-30 min ea)

PM

• Update on the ontology for clinical investigations, from the May workshop

Wednesday

PM

• Discussion on developing an application example

Thursday

PM

• Develop agenda for the data transformation workshop in Hinxton

Friday

• Discussion/appointment of editor-in-chief
• Discussion of items arising during workshop,
• Plan of action for the next development/workshop cycle & resetting milestones

Possible Issues To Discuss

• General Housekeeping

1. It would be useful if the major decsions and discussion points were recorded, with their justification, and published so those unable to attend the meeting can keep up to date.
2. Discussion of Trish's proposed SOP document, including the importance of running reasoners from an early stage
3. High-level discussion of how the various OBI owl file(s) will look once mature (Matt can provide a document on the wiki that I can go through at the meeting).

• Metadata

1. Change of annotation property 'example' from MUST to SHOULD be present (in Minimal Metadata)

   I have issue with the use of example being mandatory, it is my understanding that that a decsion of a "filler" should be added if they could not come up with an example". This makes no sense to me. It is either mandatory and required, or optional and not required. It is not good practice to bypass it with a null value.

   However the major issue is that very few, if any currently existing ontologies have examples. None of the PSI CVs do. You will not get anyone to systematically provide examples for 5000-odd terms in the PSI CVs. By making "example" mandatory you will exclude these resources and narrow your user base.

• Issues with Metadata Property Implementation Changes - due to changes for New SVN Branch set-up or Batch Term loading code

1. Change of annotation properties from type DatatypeAnnotationProperty to AnnotationProperty

   -this item is prompted by the change to the OWL files by Alan that subsequently broke the batch term loading code, tsk, tsk

2. Change of annotation property curation_status from no longer being an enumerated list

   -this item is prompted by a change made to the OWL files by Alan that appears to be contrary to the last discussion on the implementation of this as described on the MinimalMetadata wiki, tsk, tsk

3. Including property rdfs:label as well as preferred_term property

   -this is prompted by the unresolved discussion on this item and the fact that the batch term loading code is adding this as coded by Trish, tsk, tsk

• Modeling Issues

1. How to use the reasoner to generate multiple inheritance that is acceptable (Look at 'Normalisation' as proposed by Alan Rector)
2. Resolve how Company, Manufacturer names used as RU's will be represented

- Note: there are many ontologies which have tried to represent, companies and organisations. An example is sepCV , loosely based on SUMO

• Community Usage of OBI

• Branch development/Ontology QA

1. The curation_status flag, and using it in relations. I would like ask the relations branch to make use of the curation status flags on their relations, so we other branch users know when relations are stable or not.
2. A spell-checker should be used on the branch files, prior to SVN check-in
3. The definition_source values need to be checked to see if they are in the format requested on OBI Minimal metadata

-to me the word definition is confusing. An RU definition in the OWL world is the natural language definition the labels and the relations. My preference would be to use an annotation property called "description_source" to account for the Natural language description for a RU

List of Participants

Daniel Schober, EBI attends remotely using centra and skype.

Bethesda Court Hotel

• We have negotiated a special rate of $149.00/night with the Bethesda Court Hotel in downtown Bethesda. The rate includes continental breakfast and wireless internet, as described on their Accommodations web page.

• We will need to do a rooming list with the hotel, and to ensure availability of rooms the hotel needs an accurate number of participants by COB Friday May 11th. Please enter your name, e-mail, and check in/out dates here if you want to be included in the group reservation.

Interest in Bethesda Court Hotel