The HUPO Proteomics Standards Initiative Ontologies development for Proteomics Kai Runte Bielefeld U

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The HUPO Proteomics Standards Initiative -
Ontologies development for ProteomicsKai Runte
(Bielefeld University)Randall K. Julian (Eli
Lilly Corp.)Chris Taylor, Henning Hermjakob,
Weimin Zhu, Rolf Apweiler (European
Bioinformatics Institute)The Proteomics
Standards Initiativehttp//www.hupo.org/
http//psidev.sourceforge.net/
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Overview

• Introduction of HUPO/Proteomics Standards
  Initiative
• The why and how of general proteomics standards
  (GPS)
• Status of GPS
• Ontologies in GPS
• Conclusions

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HUPO - Background

• Human proteome organisation
• Founded in 2001 with several objectives
• Consolidate national and regional proteome
  organisations
• Assist in the coordination of public proteome
  initiatives
• Engage in scientific and educational activities
• Tissue proteome projects and other initiatives
• Plasma, Liver, Brain, Glyco Antibody and
  Proteomics Standards Initiative (PSI)
• http//www.hupo.org/

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HUPO PSI - Background

• The Proteomics Standards Initiative (PSI)
• Develops standards for
• Data representation and annotation
• Data formats
• Not for methods!
• Involved in two key areas in proteomics
• Protein-protein interactions (stable)
• Mass spectrometry (in development)
• Creates and establishes general proteomics
  standards (GPS)
• http//psidev.sourceforge.net/

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General Proteomics Standards
The Lab
The Public
Publication
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General Proteomics Standards

• Publicly available proteomics data is rather
  limited
• Sample extraction and preparation usually
  undocumented
• Analytical methods employed in deriving
  conclusions absent
• No widely used databases of (for example) mass
  spectral data

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General Proteomics Standards

• But the generation and analysis of proteome data
  are widespread
• High-throughput approaches are commonplace
• Techniques continue to increase in complexity

Gel
DIGE Gel
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General Proteomics Standards

• Imagine using Blast without having GenBank
• Standards
• Help synchronising data (cf. GenBank)
• Make research results comparable
• Make it possible to re-evaluate data with new
  technologies
• A robust, future proofed, standard representation
  of both methods and data from proteomics
  experiments is required

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General Proteomics Standards
The Lab
The Public
Minimal Data Set Required by Publisher
2) Publication
1) Public Repositories
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GPS - Scope

• Sample generation
• Origin of sample
• Sample processing
• Gels (1D/2D), columns, other methods
• Mass Spectrometry
• Spectra, machine and componentry types,
  parameter, processing methods
• In Silico analysis
• Database name version, partial sequence, search
  parameters, search hits, accession numbers

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GPS - Background

• The PEDRo Model
• Developed at Manchester University in
  collaboration with the PSI and the EBI
• A proof of concept model
• Intended to stimulate discussion

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GPS - Technical Scope
GPS
MIAPE
Data Model
Ontology
Exchange Formats
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GPS - Whats in it?

• Minimum Information About a Proteomics Experiment
  (MIAPE)
• Requirement to be enforced by journals,
  repositories, funders (cf. MIAME)
• Technology-specific modules associated with a
  parent document
• Data Models, and XML formats for Data Exchange
• Markup language (PSI-ML) designed for data
  exchange, and submission
• All based on the GPS proteomics workflow/data
  object model, PSI-OM
• mzData now in a mature state implementations
  and the ontology next

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GPS - Whats in it?

• Ontologies
• Crucial for the construction of unambiguously
  worded data files
• GPS will contribute terms to the MGED ontology
  (extended)
• The Mass Spec (and Search Engines) working
  groups ontology terms will likely be owned by
  the American Society for Mass Spectrometry (ASMS)
• Other activities
• Study on what constitutes a good
  peptide/protein identification
• Document examining the comparability of search
  engine metrics

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GPS - Ontologies
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The ASTM Glossary
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GPS - Ontology extensions
Vendor ontology
Vendor ontology
Vendor ontology
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GPS - Ontologies Conclusions

• We need your help (as ontology developer and
  domain expert)
• Please contact us via (and subscribe to)
• psidev-gps-dev_at_sourceforge.net
• or simply have a chat with me after the talk!

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Acknowledgements

• Chris Taylor, Weimin Zhu, Henning Hermjakob, Rolf
  Apweiler(EBI,UK)Andy Brass, Steve Oliver, Norman
  Paton (Manchester, UK)Randall Julian
  (ASTM/ASMS)Simon Hubbard and group, Simon
  Gaskell and group (UMIST, UK)Kathryn Lilley and
  group (Cambridge, UK)Ruedi Aebersold and group,
  esp. Eric Deutsch (ISB Seattle, USA)Al Brown and
  group (Aberdeen, UK) and many more at the various
  HUPO/PSI meetings 2002-2004
• Thank you!