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Protein Ontology 2nd Annual Meeting

Created by Meher Shruti S Yerramalla, last modified by Darren Natale on Feb 19, 2021

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]


PRO editor [16]


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]