Child pages
  • Protein_Ontology_2ndAnnual_Meeting
Skip to end of metadata
Go to start of metadata

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

Agenda

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)

Documents

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

Literature

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]

  • No labels