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Protein Ontology 2nd Annual Meeting

The second annual meeting of the Protein Ontology project will take place in Georgetown University on November 18-19, 2008. This meeting will be co-located with a PRO annotation jamboree on November 20.

Location: Harris Building, Conference Room 1300. 3300 Whitehaven St, NW, Washington DC 20007. This is an internal meeting.

The goals of the meeting are:

  • to establish what we need to do in order to ensure that the ontology is maximally useful;
  • to establish plans for PRO's further development, dissemination and use.

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.

For more information:

PRO Website


Monday, November 17, 2008

  • Arrival of Workshop Participants
  • 6:30pm Dinner for Workshop Participants (Nathan's 3150 M Street. Meet in Hotel Lobby at 6:15pm)

Tuesday, November 18, 2008

  • 8:30am Registration and Continental Breakfast
  • 9:00am-10:00am Session 1: Protein Ontology (Chair Cathy Wu)
    • Introduction to the Protein Ontology (Cathy Wu) [1]
  • 10:00am Break
  • 10.15am-12:15pm Session 2: PRO and the OBO Foundry (Chair Barry Smith)
    • PRO within the OBO Foundry (Barry Smith) [2]
    • PRO, GO and Protein Complexes (Judy Blake) [3]
    • Protein Relations (Darren Natale) [4]
  • 12:15pm Lunch
  • 1:30pm-3:30pm Session 3: PRO Scientific Applications: Pathways/Networks A (Chair Gopal Gopinathrao)
    • BioCyc and PRO (Peter Karp) [5]
    • MouseCyc and PRO (Carol Bult) [6]
  • 3.30pm Break
  • 3:45pm-5:15pm Session 4: PRO Scientific Applications: Pathways/Networks B (Chair Gopal Gopinathrao)
    • Reactome and PRO (Gopal Gopinathrao) [7]
    • PID and PRO (Carl Schaefer) [8]
  • 6:30pm Dinner (Heritage India 2400 Wisconsin Ave NW. Meet in Hotel Lobby at 6:15pm)

Wednesday, November 19, 2008

  • 8:30am Continental Breakfast
  • 9:00am-10:00am Session 5: PRO Community Interactions (Chair Lindsay Cowell)
    • Cell Ontology (CL) and PRO (Lindsay Cowell) [9]
    • BIRN and PRO (Maryann Martone)
  • 10:00am Break
  • 10:15am-12:30pm Session 6: Representation of PRO classes A (Chair Darren Natale)
    • PRO-Evo Overview and PIRSF (Darren Natale) [10]
    • PANTHER and ProEvo (Paul Thomas) [11]
    • PRO-Form overview and UniProtKB (Cecilia Arighi) [12]
  • 12:30pm Lunch
  • 1:30pm-3:00pm Session 7: Representation of PRO classes B (Chair Darren Natale)
    • RefSeq (Kim Pruitt) [13]
    • SEED and PRO (Gary Olsen) [14]
  • 3:00pm-4:00pm Session 8: Next Step (Suzanna Lewis)

Thursday, November 20, 2008 Annotation Jamboree

  • 9.00am-11.00am PRO annotation tutorial (Cecilia Arighi/Harold Drabkin)
    • Introduction to PRO curation (Cecilia Arighi) [15]
    • GO annotation intro [16]
    • Introduction to PRO editing environment
    • Group annotation exercise
  • 11.00-11.15 Coffee Break
  • 11.15-12.30 First annotation session
  • 12.30-1.30pm Lunch
  • 1.30-3.00pm Second annotation session
  • 3.00-4.00pm Wrap-up and Feedback.
  • 4.00pm End

List of confirmed participants

  • Cecilia Arighi (GU/PRO)
  • Winona Barker (GU/PRO)
  • Judith Blake (Jax/PRO)
  • Carol Bult (Jax/mouseCyc)
  • Marc E.Colosimo (Mitre)
  • Lindsay Cowell (Duke)
  • Harold Drabkin (Jax/PRO)
  • John Garavelli (EBI/PSI-MOD)
  • Peter Good (NIH/NHGRI)
  • Gopal Gopinathrao (Cold Spring Harbor/Reactome)
  • Susan Gregurick (DOE, Program Manager, Computational Biology)
  • Michelle Gwinn Giglio (University of Maryland)
  • Lynette Hirschman (MITRE)
  • Fahim Imam (UCSD/BIRN/NIF)
  • Peter Karp (SRI/BioCyc)
  • Suzanna Lewis (Lawrence Berkeley National Labs)
  • Hongfang Liu (GU/PRO)
  • Maryann Martone (UCSD/BIRN/NIF)
  • Anna Maria Masci (Duke)
  • Folker Meyer (Argonne National Laboratory)
  • Darren Natale (GU/PRO)
  • Gary Olsen (University of Illinois)
  • Kim Pruitt (NCBI)
  • Karin Remington (NIH/NIGMS)
  • Alan Ruttenberg (Science Commons)
  • Carl Schaefer (NIH/NCI)
  • Barry Smith (Buffalo/NCBO/PRO)
  • Arlin Stoltzfus (NIST)
  • Paul D. Thomas (SRI)
  • Cathy Wu (GU/PRO)
  • Jasmine Young (Rutgers/PDB)


  • Latest publication [17]
  • PRO Curation Guideline Draft [18]
  • PRO Annotation Guidelines (PAF) [19]
  • Jamboree additional information [20]


Cecilia Arighi, Hongfang Liu, Darren Natale, Winona Barker, Harold Drabkin, Zhangzhi Hu, Judith Blake, Barry Smith and Cathy Wu, "TGF-beta Signaling Proteins and the Protein Ontology", Bio-Ontologies 2008, Special Interest Groups meeting at ISMB 2008, pg 25-29. [22]

Drabkin HJ., Arighi CN, Wu CH, Blake JA, "Functional Annotation of Protein Isoforms and Modified Forms", BioComp2008[23]

Darren A Natale, Cecilia N Arighi, Winona C Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith, and Cathy H Wu, "Framework for a Protein Ontology", BMC Bioinformatics 2007, 8(Suppl 9):S1. [24]

Darren A. Natale, Cecilia N. Arighi, Winona Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith, and Cathy H. Wu, "Framework for a Protein Ontology", Proceedings of the First International Workshop on Text Mining in Bioinformatics, 2006, p. 29-36.[25]

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