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Protein Ontology 3rd Annual Meeting

The third annual meeting of the Protein Ontology project took place in University of Delaware on April 26-27, 2010. An annotation jamboree/workshop was conducted on April 28.

Location: Clayton Hall Conference Center [1] (Room 120), Laird Campus, University of Delaware, Newark. (Internal meeting).

The goals of this meeting were:

1. To survey work on the PRO thus far and to review next steps for the development of the ontology

2. To introduce the PRO to new groups of users with special reference to potential uses in areas such as drug discovery and disease biomarker research

3. To survey work on ontology and terminology artifacts in the chemistry and pharmacology areas and to assess possibilities for fruitful interaction

Agenda

Sunday, April 25

  • Arrival of Workshop Participants
  • 7pm Dinner


Day 1: Monday, April 26

  • 8:30am Registration and Continental Breakfast
  • 9:00am-11:00am Session 1: Protein Ontology - Chair: Barry Smith
    • Introduction to the Protein Ontology (Cathy Wu)  presentation
    • OBO Foundry update (Barry Smith) presentation
    • Protein Complex Ontology (Carol Bult)
  • 11:00am Break
  • 11:15am-12:15pm Session 2: PRO Use Cases - Chair: Cecilia Arighi
  • 12:15pm Lunch
  • 1:30pm-2:30pm Session 3: PRO Use Cases - Chair: Darren Natale
    • Reactome (Peter D’Eustachio) presentation
    • Mousecyc (Carol Bult)
  • 2:30pm-3:30pm Session 4: PRO Use Cases - Chair: Darren Natale
    • PRO and the Science Collaboration Framework (SCF) (Alan Ruttenberg) presentation
    • Semantic Resources (Paolo Ciccarese) presentation
  • 3:30pm Break
  • 3:45pm-5:15pm Session 5: Discussion - Chair: Judith Blake notes
  • 6:00pm Dinner


Day 2: Tuesday, April 27

  • 8:30am Continental Breakfast
  • 9:00am-10:00am Session 6: PRO, Structure and Disorder - Chair: Cathy Wu
  • 10:00am-10:15 Break
  • 10:15am-12:15pm Session 7: PRO, Chemistry and Drug Ontologies - Chair: Barry Smith
  • 12:15pm Lunch
  • 1:30pm-2:30pm Session 8: PRO, Drug Discovery and Biomarker Research - Chair: Barry Smith
  • 2:30pm-3:00pm Future Strategy (Cathy Wu)
  • 3:00pm-4:00pm Break
  • 4:00pm-5:30pm Orientation Session for Jamboree Participants - Chair: Cecilia Arighi
  • 6:00pm Dinner


Day 3: Wednesday, April 28 - Annotation Jamboree

  • 9:00am-10:15am PRO Annotation Tutorial (Cecilia Arighi/Harold Drabkin)
    • The RACE-PRO Annotation Interface (Cecilia Arighi)
    • Introduction to GO Annotation (Harold Drabkin) presentation
  • 10:15am-10:30am Break
  • 10:30am-11:30am Annotation and Discussion
    • Group Annotation Exercise
    • Discussion
  • 11:30am-12:30pm Lunch
  • 12:30pm-2:30pm Protein Complex Ontology (Peter D’Eustacchio/Carol Bult/Darren Natale)
    • Annotation in the Protein Complex Ontology: Challenges and Examples
    • Examples from Reactome (Peter D'Eustacchio) presentation
    • Examples from MouseCyc (Carol Bult) presentation
  • 2:30pm-3:00pm Wrap-up and Feedback

List of Confirmed Participants

  • Jiye Ai (UCLA)
  • Mauricio Almeida (UFMG, Brazil)
  • Cecilia Arighi (UD/PRO)
  • Judith Blake (Jax/PRO)
  • Carol Bult (Jax/mouseCyc/PRO)
  • Anastasia Christianson (AstraZeneca)
  • Paolo Ciccarese (Harvard/SWAN)
  • Peter D'Eustachio (NYU/Reactome/PRO)
  • Harold Drabkin (Jax/PRO)
  • Keith Dunker (Indiana University)
  • Xing Han (DuPont)
  • Janna Hastings (European Bioinformatics Institute, UK)
  • Robel Kahsay (DuPont)
  • Michael Keiser (UCSF)
  • Neocles Leontis (BGSU/RNA Ontology)
  • Peter Lyster (NIH/NIGMS)
  • Cythia G. Murphy (MDIBL/CTD)
  • Darren Natale (GU/PRO)
  • Connie Oshiro (PharmGKB)
  • Jaime Prilusky (Weizmann Institute of Science)
  • Karin Remington (NIH/NIGMS)
  • Phoebe Roberts (Pfizer)
  • Alan Ruttenberg (Science Commons)
  • Barry Smith (Buffalo/NCBO/PRO)
  • Jean-Francois Tomb (DuPont)
  • John Westbrook (PDB)
  • Robert Williams (Uniformed Services University)
  • Cathy Wu (UD/PRO)
  • Hui (Michael) Zhou (UCLA)

Protein Ontology

The Protein Ontology (PRO) project is funded by NIGMS / NIH Grant 1 R01 GM080646-01, PI: Cathy Wu.

The Aims of the project are:

Aim 1. Develop a Protein Evolution (ProEvo) ontology to describe proteins based on evolutionary relationships. In essence, ProEvo will reflect protein families (using sequence or structure similarities) in an ontology framework.

Aim 2. Develop a Protein Forms (ProForm) ontology to represent the multiple protein end-products from a gene. This will include "normal" and mutant forms, forms derived from different splice variants, and cleaved and post-translationally modified products.

Aim 3. Specify the relationships between the ProEvo, ProForm and other OBO Foundry ontologies. Several ontologies provide qualities that can be attributed to various forms of a protein or to an entire protein family. These qualities, in effect, can annotate the protein forms or families.

Aim 4. Disseminate PRO ontology, and demonstrate its usefulness in health-related research via scientific case studies.

More recently, PRO has been awarded a supplement to include a protein complex ontology. Within the scope of the parent grant, the primary goal of the proposed supplement is to further develop the PRO ontology to represent both proteins and protein complexes. This effort will address the gap in the current OBO ontologies and a fundamental need in the biomedical research community for accurate representation of protein biology.

The Aims of this supplement are:

Aim 1. Enhance the Protein Ontology framework to include an ontology for protein complexes.

Aim 2. Develop a curation system for protein complex curation in biological contexts.

Aim 3. Develop scientific cases for pathway/disease modeling and disseminate PRO complex ontology.

For more information:

PRO Wiki

PRO Website

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