Protein Ontology Workshop: Difference between revisions

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'''Date''': June (17)-18-19, 2014. The meeting will begin with an informal reception in the [http://www.ihg.com/holidayinn/hotels/us/en/washington/wasgt/hoteldetail Holiday Inn, Georgetown], on Tuesday, June 17 and conclude at 4pm on June 19.
'''Date''': June 18-19, 2014


'''Venue''': Georgetown University's [https://www.google.com/maps/place/3300+Whitehaven+St+NW/@38.917007,-77.06752,17z/data=!3m1!4b1!4m2!3m1!1s0x89b7b630848d084f:0x22bd0eb5dab5a2ff Harris Building] is about 3 miles from Union Station, and 1.5 miles from the Woodley Park subway station. The [http://www.dccirculator.com/Home/BusRoutesandSchedules.aspx DC Circulator Georgetown Line] services the Holiday Inn Georgetown the Union Station train station. If you arrive via the Woodley Park subway station, the hotel provides free shuttle service.
'''Venue''': Georgetown University
The cost is just $1. Parking is available at the Holiday Inn, which is half a block from Georgetown University's Harris Building.


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: We will seek greater clarity as to   
: 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
: - 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/ro/ relations] we should use in linking the protein entities represented in the PRO to disease entities
: - 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
: - which are the important entities on the protein side that need to be linked


Line 28: Line 27:
=='''Schedule: Wednesday, June 18, 2014==
=='''Schedule: Wednesday, June 18, 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]
<u>Chair: Barry Smith</u>


8:00 Continental Breakfast
8:45 Cathy Wu (Delaware/Georgetown): [http://ncor.buffalo.edu/2014/PRO/Wu.pdf ​Current Status and Future Goals of the Protein Ontology]


8:45 Cathy Wu (Delaware/Georgetown): ​Current Status and Future Goals of the Protein Ontology
9:45 Peter d'Eustachio (NYU): [http://ncor.buffalo.edu/2014/PRO/d'Eustachio.pptx PRO, Reactome and Disease Pathways]


9:45 Peter d'Eustachio (NYU): PRO, Reactome and Disease Pathways
10:30 Break


10:30 Break
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]


10:45 Olivier Bodenreider (NLM): Ontologies in the NLM
11:55 Carol Bean (Stanford / NCBO): The Future of the [http://bioportal.bioontology.org/ Bioportal]


11:25 Sirarat Sarntivijai (FDA): Using the Protein Ontology: The View from the Outside
12:15 Lunch


12:00 Lunch
<u>Chair: Peter d'Eustachio</u>


13:00 Sandra Orchard (EBI): PRO and IntAct
13:00 Sandra Orchard (EBI): [http://ncor.buffalo.edu/2014/PRO/Orchard.pptx PRO and IntAct]


14:00 Evan Bolton (NCBI): [https://pubchem.ncbi.nlm.nih.gov/rdf/ PubChemRDF]: Towards a Semantic Description of PubChem
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): Collaboration of PRO and PubChem with the [http://nar.oxfordjournals.org/content/40/D1/D940.full Disease Ontology]
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
15:20 Break


15:40 Veerasamy “Ravi” Ravichandran (NIGMS): NIGMS and the Protein Ontology
<u>Chair: Darren Natale</u>


16:00 John Westbrook (PDB): PRO Represention of Proteins Observed in 3D Experimental Structure Data
15:40 Veerasamy “Ravi” Ravichandran (NIGMS): [http://ncor.buffalo.edu/2014/PRO/Ravichandran.pptx NIGMS and the Protein Ontology]


16:40 Alexander Diehl (Buffalo): PRO and the NIF / ImmPort Antibody Registries
16:00 John Westbrook (PDB): [http://ncor.buffalo.edu/2014/PRO/Westbrook.pdf PRO Represention of Proteins Observed in 3D Experimental Structure Data]


17:05 Alexander Cox (Buffalo): Neurofibrillary Tangles and Amyloid Plaques: The Treatment of Protein Aggregates in the Protein Ontology
16:40 Alexander Diehl (Buffalo): [http://ncor.buffalo.edu/2014/PRO/Diehl.pptx PRO and the NIF / ImmPort Antibody Registries]


17:30 Close  
17:20 Close  


18:00 Working Dinner
18:00 Working Dinner: Cafe Divan, 1834 Wisconsin Ave


=='''Schedule: Thursday, June 19th, 2014'''==
=='''Schedule: Thursday, June 19th, 2014'''==
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8:00 Continental breakfast
8:00 Continental breakfast


9:00 Donna Maglott (NIH): PRO and Medical Genetics resources at NCBI
<u>Chair: Alexander Diehl</u>


9:45 Claire Donovan (EBI): Ontologies at the EBI
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 Paul Martin Thomas (Northwestern): Descriptive and Quantitative Top Down Proteomics
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]


11:30 Jonathan Bona and Alan Ruttenberg (Buffalo): UniProt Accessions - Issues of Tracking and Stability
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


13:30 Judith Blake (Jackson Lab) and Barry Smith (Buffalo):  
<u>Chair: Cecilia Arrighi</u>
*1. Ontologies, Databases, Knowledgebases: How Should They Interoperate?
 
*2. Relations linking Proteins to Diseases
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
14:30 Break


14:45 Gilbert S. Omenn (Michigan): The Human Proteome Project
14:45 Gilbert S. Omenn (Michigan): [http://ncor.buffalo.edu/2014/PRO/Omenn.pptx The Human Proteome Project]


16:00 Close
16:00 Close
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== '''Participants''' ==
== '''Participants''' ==


:Cecilia Arighi (Georgetown)
:Cecilia Arighi (Delaware / PRO)
:Carol Bean (NCBO / Stanford)
:Carol Bean (NCBO / Stanford)
:Judith Blake (JAX)
:Judith Blake (JAX)
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:Paul Martin Thomas ([http://www.kelleher.northwestern.edu/research/top-down-proteomics Top Down Proteomics] / Northwestern)
: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.

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.

Sponsors

The Protein Ontology Consortium
National Center for Biomedical Ontology
National Center for Ontological Research