Protein Ontology Workshop: Difference between revisions
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''' | '''Date''': June 18-19, 2014 | ||
''' | '''Venue''': Georgetown University | ||
---- | ---- | ||
== '''Goals''' == | == '''Goals and outcomes''' == | ||
The goals of this meeting are: | The goals of this meeting are: | ||
*1. To contribute to the ontological understanding of phenotype and disease across organisms | *1. To contribute to the ontological understanding of phenotype and disease across organisms | ||
*2. To advance the treatment of protein-related clinical and translational data from the perspective of consistency, discoverability and support for diagnosis | *2. To advance the treatment of protein-related clinical and translational data from the perspective of consistency, discoverability and support for diagnosis | ||
*3. To advance coordination between the Protein Ontology and other protein-related resources | *3. To advance coordination between the Protein Ontology and other protein-related information resources | ||
Desired outcomes are of two sorts: | |||
*Relating to disease: | |||
: We will seek greater clarity as to | |||
: - how proteomic information in general and the PRO in particular can help us to understand the relationship between genotype and phenotype, for example in understanding disease etiology | |||
: - which [http://obofoundry.org/ontology/ro.html relations] we should use in linking the protein entities represented in the PRO to disease entities | |||
: - which are the important entities on the protein side that need to be linked | |||
*Relating to PRO's interactions with external resources: | |||
:'''UniProt''': Draft of policies/recommendations regarding accession/site tracking for UniProt and PRO | |||
:'''IntAct''': Identify points of agreement and discrepancy in curation pipelines and resolve as appropriate. Reach agreements for example on reciprocal links and accession issues | |||
=='''Schedule: Wednesday, June 18, 2014== | |||
<u>Chair: Barry Smith</u> | |||
8: | 8:45 Cathy Wu (Delaware/Georgetown): [http://ncor.buffalo.edu/2014/PRO/Wu.pdf Current Status and Future Goals of the Protein Ontology] | ||
9: | 9:45 Peter d'Eustachio (NYU): [http://ncor.buffalo.edu/2014/PRO/d'Eustachio.pptx PRO, Reactome and Disease Pathways] | ||
10:30 Break | 10:30 Break | ||
10:45 | 10:45 Olivier Bodenreider (NLM): [http://ncor.buffalo.edu/2014/PRO/Bodenreider.pdf Ontologies in the NLM] | ||
11:25 Sirarat Sarntivijai (FDA): [http://ncor.buffalo.edu/2014/PRO/Sarntivijai.ppt Using the Protein Ontology: The View from the Outside] | |||
11:55 Carol Bean (Stanford / NCBO): The Future of the [http://bioportal.bioontology.org/ Bioportal] | |||
12:15 Lunch | |||
14: | <u>Chair: Peter d'Eustachio</u> | ||
13:00 Sandra Orchard (EBI): [http://ncor.buffalo.edu/2014/PRO/Orchard.pptx PRO and IntAct] | |||
14:00 Evan Bolton (NCBI): [http://ncor.buffalo.edu/2014/PRO/Bolton.pdf PubChemRDF: Towards a Semantic Description of PubChem] | |||
14:40 Lynn Schriml (Baltimore): [http://ncor.buffalo.edu/2014/PRO/Schriml.pdf Collaboration of PRO and PubChem with the Disease Ontology] | |||
15:20 Break | |||
<u>Chair: Darren Natale</u> | |||
15:40 Veerasamy “Ravi” Ravichandran (NIGMS): [http://ncor.buffalo.edu/2014/PRO/Ravichandran.pptx NIGMS and the Protein Ontology] | |||
16:00 John Westbrook (PDB): [http://ncor.buffalo.edu/2014/PRO/Westbrook.pdf PRO Represention of Proteins Observed in 3D Experimental Structure Data] | |||
16:40 Alexander Diehl (Buffalo): [http://ncor.buffalo.edu/2014/PRO/Diehl.pptx PRO and the NIF / ImmPort Antibody Registries] | |||
17:20 Close | |||
18:00 Working Dinner: Cafe Divan, 1834 Wisconsin Ave | |||
=='''Schedule: Thursday, June 19th, 2014'''== | |||
Venue: Conference Room #1300, Harris Building, Georgetown University, [https://www.google.com/maps/place/3300+Whitehaven+St+NW/@38.917007,-77.06752,17z/data=!3m1!4b1!4m2!3m1!1s0x89b7b630848d084f:0x22bd0eb5dab5a2ff 3300 Whitehaven Street NW] | |||
8:00 Continental breakfast | 8:00 Continental breakfast | ||
9:00 | <u>Chair: Alexander Diehl</u> | ||
9:00 Donna Maglott (NIH): [http://ncor.buffalo.edu/2014/PRO/Maglott.pptx PRO and Medical Genetics resources at NCBI] | |||
9:40 Paul Martin Thomas (Northwestern): [http://ncor.buffalo.edu/2014/PRO/Thomas.pdf Descriptive and Quantitative Top Down Proteomics] | |||
10:20 John Garavelli (Delaware): [http://ncor.buffalo.edu/2014/PRO/Garavelli.ppt Use Cases for Modified Protein Interactions (for UniProt, PRO and proteomics)] | |||
10:30 Break | 10:30 Break | ||
10:45 | 10:45 Alexander Cox (Buffalo): [http://ncor.buffalo.edu/2014/PRO/Cox.pptx Neurofibrillary Tangles and Amyloid Plaques: The Treatment of Protein Aggregates in the Protein Ontology] | ||
11.15 Alan Ruttenberg and Jonathan Bona (Buffalo): [http://goo.gl/i1bMRo Issues surrounding coordination of UniProtKB and the Protein Ontology] | |||
12:30 Lunch | 12:30 Lunch | ||
<u>Chair: Cecilia Arrighi</u> | |||
14:15 | 13:30 Judith Blake (Jackson Lab): [http://ncor.buffalo.edu/2014/PRO/Blake.pptx Ontologies, Databases, Knowledgebases: How Should They Interoperate?] | ||
14:00 Barry Smith (Buffalo): [http://ncor.buffalo.edu/2014/PRO/Smith.ppt Introduction to the Relation Ontology] | |||
14:15 Darren Natale: [http://ncor.buffalo.edu/2014/PRO/Natale.pptx Relations linking Proteins to Diseases] | |||
14:30 Break | |||
14:45 Gilbert S. Omenn (Michigan): [http://ncor.buffalo.edu/2014/PRO/Omenn.pptx The Human Proteome Project] | |||
16:00 Close | 16:00 Close | ||
Line 73: | Line 105: | ||
== '''Participants''' == | == '''Participants''' == | ||
:Cecilia Arighi ( | :Cecilia Arighi (Delaware / PRO) | ||
:Carol Bean (NCBO / Stanford) | :Carol Bean (NCBO / Stanford) | ||
:Judith Blake (JAX) | :Judith Blake (JAX) | ||
:Evan Bolton (NCBI | :Olivier Bodenreider (NIH / NLM / LHC) | ||
:Evan Bolton (NIH / NCBI) | |||
:Jonathan Bona (Buffalo) | :Jonathan Bona (Buffalo) | ||
:Karen Christie (JAX) | :Karen Christie (JAX) | ||
:Alexander Cox (Buffalo) | |||
:Peter d'Eustachio (NYU / Reactome) | :Peter d'Eustachio (NYU / Reactome) | ||
:Alex Diehl (Buffalo) | :Alex Diehl (Buffalo) | ||
:Harold Drabkin (JAX) | :Harold Drabkin (JAX) | ||
:Gang Fu (NCBI / NIH) | :Gang Fu (NCBI / NIH) | ||
:John S. Garavelli (Delaware) | |||
:Donna Maglott (NIH / NLM / NCBI) | |||
:John Mattison (Global Alliance for Genomics and Health) | |||
:Darren Natale (Georgetown) | :Darren Natale (Georgetown) | ||
:Claire O'Donovan (EBI / UniProt) | :Claire O'Donovan (EBI / UniProt) | ||
:Gilbert S. Omenn (Michigan) | |||
:Sandra Orchard (EBI / IntAct) | |||
:Veerasamy “Ravi” Ravichandran (NIH / NIGMS) | |||
:Karen Ross (Delaware) | |||
:Alan Ruttenberg (Buffalo) | :Alan Ruttenberg (Buffalo) | ||
:Sirarat Sarntivijai (FDA) | :Sirarat Sarntivijai (FDA) | ||
:Selja Seppälä (Buffalo) | |||
:Lynn Schriml (Baltimore) | :Lynn Schriml (Baltimore) | ||
:Barry Smith (Buffalo) | :Barry Smith (Buffalo) | ||
:Paul Martin Thomas ([http://www.kelleher.northwestern.edu/research/top-down-proteomics Top Down Proteomics] / Northwestern) | |||
:John Westbrook (PDB / Rutgers) | :John Westbrook (PDB / Rutgers) | ||
:Cathy Wu (Delaware | :Cathy Wu (Delaware / PRO) | ||
Please contact [mailto:phismith@buffalo.edu Barry Smith] for further information. | Please contact [mailto:phismith@buffalo.edu Barry Smith] for further information. | ||
Line 98: | Line 140: | ||
:[http://pir.georgetown.edu/pro/ The Protein Ontology Consortium] | :[http://pir.georgetown.edu/pro/ The Protein Ontology Consortium] | ||
:[http://bioontologies.org National Center for Biomedical Ontology] | :[http://bioontologies.org National Center for Biomedical Ontology] | ||
:[http://ncor.buffalo.edu National Center for Ontological Research] | :[http://ncor.buffalo.edu National Center for Ontological Research] |
Latest revision as of 18:58, 5 September 2017
Date: June 18-19, 2014
Venue: Georgetown University
Goals and outcomes
The goals of this meeting are:
- 1. To contribute to the ontological understanding of phenotype and disease across organisms
- 2. To advance the treatment of protein-related clinical and translational data from the perspective of consistency, discoverability and support for diagnosis
- 3. To advance coordination between the Protein Ontology and other protein-related information resources
Desired outcomes are of two sorts:
- Relating to disease:
- We will seek greater clarity as to
- - how proteomic information in general and the PRO in particular can help us to understand the relationship between genotype and phenotype, for example in understanding disease etiology
- - which relations we should use in linking the protein entities represented in the PRO to disease entities
- - which are the important entities on the protein side that need to be linked
- Relating to PRO's interactions with external resources:
- UniProt: Draft of policies/recommendations regarding accession/site tracking for UniProt and PRO
- IntAct: Identify points of agreement and discrepancy in curation pipelines and resolve as appropriate. Reach agreements for example on reciprocal links and accession issues
Schedule: Wednesday, June 18, 2014
Chair: Barry Smith
8:45 Cathy Wu (Delaware/Georgetown): Current Status and Future Goals of the Protein Ontology
9:45 Peter d'Eustachio (NYU): PRO, Reactome and Disease Pathways
10:30 Break
10:45 Olivier Bodenreider (NLM): Ontologies in the NLM
11:25 Sirarat Sarntivijai (FDA): Using the Protein Ontology: The View from the Outside
11:55 Carol Bean (Stanford / NCBO): The Future of the Bioportal
12:15 Lunch
Chair: Peter d'Eustachio
13:00 Sandra Orchard (EBI): PRO and IntAct
14:00 Evan Bolton (NCBI): PubChemRDF: Towards a Semantic Description of PubChem
14:40 Lynn Schriml (Baltimore): Collaboration of PRO and PubChem with the Disease Ontology
15:20 Break
Chair: Darren Natale
15:40 Veerasamy “Ravi” Ravichandran (NIGMS): NIGMS and the Protein Ontology
16:00 John Westbrook (PDB): PRO Represention of Proteins Observed in 3D Experimental Structure Data
16:40 Alexander Diehl (Buffalo): PRO and the NIF / ImmPort Antibody Registries
17:20 Close
18:00 Working Dinner: Cafe Divan, 1834 Wisconsin Ave
Schedule: Thursday, June 19th, 2014
Venue: Conference Room #1300, Harris Building, Georgetown University, 3300 Whitehaven Street NW
8:00 Continental breakfast
Chair: Alexander Diehl
9:00 Donna Maglott (NIH): PRO and Medical Genetics resources at NCBI
9:40 Paul Martin Thomas (Northwestern): Descriptive and Quantitative Top Down Proteomics
10:20 John Garavelli (Delaware): Use Cases for Modified Protein Interactions (for UniProt, PRO and proteomics)
10:30 Break
10:45 Alexander Cox (Buffalo): Neurofibrillary Tangles and Amyloid Plaques: The Treatment of Protein Aggregates in the Protein Ontology
11.15 Alan Ruttenberg and Jonathan Bona (Buffalo): Issues surrounding coordination of UniProtKB and the Protein Ontology
12:30 Lunch
Chair: Cecilia Arrighi
13:30 Judith Blake (Jackson Lab): Ontologies, Databases, Knowledgebases: How Should They Interoperate?
14:00 Barry Smith (Buffalo): Introduction to the Relation Ontology
14:15 Darren Natale: Relations linking Proteins to Diseases
14:30 Break
14:45 Gilbert S. Omenn (Michigan): The Human Proteome Project
16:00 Close
Participants
- Cecilia Arighi (Delaware / PRO)
- Carol Bean (NCBO / Stanford)
- Judith Blake (JAX)
- Olivier Bodenreider (NIH / NLM / LHC)
- Evan Bolton (NIH / NCBI)
- Jonathan Bona (Buffalo)
- Karen Christie (JAX)
- Alexander Cox (Buffalo)
- Peter d'Eustachio (NYU / Reactome)
- Alex Diehl (Buffalo)
- Harold Drabkin (JAX)
- Gang Fu (NCBI / NIH)
- John S. Garavelli (Delaware)
- Donna Maglott (NIH / NLM / NCBI)
- John Mattison (Global Alliance for Genomics and Health)
- Darren Natale (Georgetown)
- Claire O'Donovan (EBI / UniProt)
- Gilbert S. Omenn (Michigan)
- Sandra Orchard (EBI / IntAct)
- Veerasamy “Ravi” Ravichandran (NIH / NIGMS)
- Karen Ross (Delaware)
- Alan Ruttenberg (Buffalo)
- Sirarat Sarntivijai (FDA)
- Selja Seppälä (Buffalo)
- Lynn Schriml (Baltimore)
- Barry Smith (Buffalo)
- Paul Martin Thomas (Top Down Proteomics / Northwestern)
- John Westbrook (PDB / Rutgers)
- Cathy Wu (Delaware / PRO)
Please contact Barry Smith for further information.