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Protein Ontology 2nd Annual Meeting
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Created by Meher Shruti S Yerramalla, last modified by Darren Natale on Feb 19, 2021
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| 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:
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|  | 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. |
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Protein Ontology
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| 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
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Agenda
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Monday, November 17, 2008
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| | Arrival of Workshop Participants |
| | 6:30pm Dinner for Workshop Participants (Nathan's 3150 M Street. Meet in Hotel Lobby at 6:15pm) |
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Tuesday, November 18, 2008
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| | 8:30am Registration and Continental Breakfast |
| | 9:00am-10:00am Session 1: Protein Ontology (Chair Cathy Wu) |
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| | # | Introduction to the Protein Ontology (Cathy Wu) [1] |
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| | 10:00am Break |
| | 10.15am-12:15pm Session 2: PRO and the OBO Foundry (Chair Barry Smith) |
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| | # | PRO within the OBO Foundry (Barry Smith) [2] |
| | # | PRO, GO and Protein Complexes (Judy Blake) [3] |
| | # | Protein Relations (Darren Natale) [4] |
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| | 12:15pm Lunch |
| | 1:30pm-3:30pm Session 3: PRO Scientific Applications: Pathways/Networks A (Chair Gopal Gopinathrao) |
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| | # | BioCyc and PRO (Peter Karp) [5] |
| | # | MouseCyc and PRO (Carol Bult) [6] |
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| | 3.30pm Break |
| | 3:45pm-5:15pm Session 4: PRO Scientific Applications: Pathways/Networks B (Chair Gopal Gopinathrao) |
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| | # | Reactome and PRO (Gopal Gopinathrao) [7] |
| | # | PID and PRO (Carl Schaefer) [8] |
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| | 6:30pm Dinner (Heritage India 2400 Wisconsin Ave NW. Meet in Hotel Lobby at 6:15pm) |
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Wednesday, November 19, 2008
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| | 8:30am Continental Breakfast |
| | 9:00am-10:00am Session 5: PRO Community Interactions (Chair Lindsay Cowell) |
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| | # | Cell Ontology (CL) and PRO (Lindsay Cowell) [9] |
| | # | BIRN and PRO (Maryann Martone) |
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| | 10:00am Break |
| | 10:15am-12:30pm Session 6: Representation of PRO classes A (Chair Darren Natale) |
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| | # | PRO-Evo Overview and PIRSF (Darren Natale) [10] |
| | # | PANTHER and ProEvo (Paul Thomas) [11] |
| | # | PRO-Form overview and UniProtKB (Cecilia Arighi) [ [12] |
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| | 12:30pm Lunch |
| | 1:30pm-3:00pm Session 7: Representation of PRO classes B (Chair Darren Natale) |
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| | # | RefSeq (Kim Pruitt) [13] |
| | # | SEED and PRO (Gary Olsen) [ [14] |
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| | 3:00pm-4:00pm Session 8: Next Step (Suzanna Lewis) |
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Thursday, November 20, 2008 Annotation Jamboree
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| | 9.00am-11.00am PRO annotation tutorial (Cecilia Arighi/Harold Drabkin) |
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| | # | Introduction to PRO curation (Cecilia Arighi) [15] |
| | # | GO annotation intro [16] |
| | # | Introduction to PRO editing environment |
| | # | Group annotation exercise |
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| | 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
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List of confirmed participants
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| | 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) |
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Documents
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| | Latest publication [17]
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| | PRO Curation Guideline Draft [18]
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| | PRO Annotation Guidelines (PAF) [19]
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| | Jamboree additional information [20]
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Links
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| | PRO editor [16] |
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Literature
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| 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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