Meeting Notes

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Notes from Meeting at the EBI, Hinxton, Cambridge

Meeting Purpose: Compare development activities, discuss OBI interface

Participants: Joanne Luciano, MITRE James Malone, European Bioinformatics Institute

Dates: Tuesday June 17, 2008 3:00-4:30 Wednesday June 18, 2008 9:30-11:00

Background: Joanne was invited to EBI Industry Programme Workshop, Disease ontologies and information: its linkage to genes, gene ontologies and phenotypic information on 19th – 20th June 2008. The organizer, Dr. Dominic Clark invited her to visit the EBI before the workshop. James Malone works at the EBI and is active in the OBI Initiative ([Ontology for Biomedical Investigations]). I (Joanne) wanted to meet with him because he has extensive experience in the OBI development process. Since we are developing the ontology consistent with the OBO Foundry principles and since we need to link out to OBI, which is currently the most developed of the OBO ontologies, I wanted to hear what he had to say about interfacing to tools, linking to and/or extending OBI terms and about the ontology development process in general. Below is a summary of what we covered and what I learned.


  • James is involved in two projects:
    • OBI (Open Biomedical Investigations Ontology)
      • A community development effort and showcase for OBO Foundry Principles
    • ArrayExpress Experimental Factor Ontology (EFO)
      • An application ontology - being developed at EBI
    • Upon comparing notes, both James and I found that the development of the EFO and the I-IDO are very similar efforts. The differences were minor, basically the efforts parallel each other.
  • Reviewed I-IDO (Influenza) and what other ontologies it uses as well as the context within the Disease Ontology and the Infectious Disease Ontology development efforts
  • Reviewed/discussed OBO Foundry Principles (Richard Scheuermann very involved)
    • Application ontology
    • Link to other standards (OBI,etc.)
  • Review of the OBI ontology / development effort (Richard Scheuermann very involved)
    • OWL 1.0
      • Most using Protégé 3; Alan R using his own SW (lisp)
    • Some differences in our development effort are
      • EFO is using Protégé 3
      • EFO is developing in OWL
    • Development divided into several “branches” – developed independently
    • Example of a PATO quality: frozen state, radio active
    • Separate ontology for Digital Artifacts: Information Entity (IE) examples: serial number, algorithm
    • Curation Status (represented as individuals) – this a handy way to check the status and I plan on incorporating this into the I-IDO. e.g. “metadata complete”, “pending final vetting”
    • Uses Dublin core, but James is not sure of the status and if it will stay
    • Data transformations in Influenza – pass them through to be part of OBI, use the tracker on source forge to suggest the new terms (such as new data transformations) to be added to OBI (and then referenced by I-IDO)
    • The ontology – and especially things like the data transformations are intentionally flat (non-hierarchical) to avoid problems with multiple inheritance (multiple inheritance is considered bad practice in ontologies)
    • Many “objectives” – “directed towards plan” “not realizable” – clustering would be an objective that uses transformations, but an objective doesn’t have to be real, it can exist in a plan or a thought. You can plan to run down the hall, but something may prevent you from realizing it.
    • Feature describes characteristic or trait of a class – should just be called “property” to be consistent.
    • Role – a realizable entity
    • MIREOT- Minimum Information to Reference Existing Ontology Terms
    • Will evaluate using use cases and competency questions
    • Use/extend: Relation Ontology 2 (RO2)
    • The ontology contains “Bridging Classes” – it’s not clear what this is about.
    • Everything is subclassed from the BFO.
    • Look at one or two levels under EFO (and OBI) to see where they placed things; for example,– rather than independent continuant, sub class from hdevice, bio material
    • Tracker – under resources on sourceforge.
      • Submit to the tracker the bits in the I-IDO that should be in OBI (for example, data transformations)
      • Recommends using sorceforge tracker to keep track of issues/tasks and for assigning them.
    • On Windows – recommends Tortoise CVS
      • Google docs not good regarding versioning – and InfluenzO is getting to that stage where it’s getting cumbersome to manage manually.
    • OBI wiki website used for documentation, policy, decisions, meetings notes; OBI sourceforge site use for all development
    • The Ontology Look-up Service – there’s a link on right hand side that will link through though EFO (Experimental Factor Ontology) – OBI is not yet listed there.
    • OBI annotation properties: see annotation_properties.owl
      • Use these for I-IDO
    • Metadata Policy: See Minimal requirement for term annotations:
  • Mapping tool
    • Command line - suggests mapping between ontology terms – interactive;
    • Writes a tab delimited file (import to spreadsheet), is looking into getting it to us. The tools suggests prints the term, suggests match term(s) if found, provides the appropriate IDs and states whether it is a single, multiple or unmatched term. For example:
Example Output
Diagnosis Diagnosis obi:OBI_0000075 valid
Disease Severity disease_stage obi:OBI_0000278 single_match