HUPO

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HUPO Proteomics Standards Initiative
(PSI) Controlled Terminologies Luisa
Montecchi PSI Ontology Chair (The European
Bioinformatics Institutes EBI) On behalf of
the PSI Ontology Working Groups http//psidev.info
/
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HUPO PSI Since 2001

• Provides minimum reporting requirements
• - Also contributing to the MIBBI project
• Develops data format and annotation standards
• - Also contributing to FuGE and OBI projects
• Develops tools to spread the standards
• Includes several stakeholders (commercial and
  academic)
• Data producers
• Database developers/providers
• Software producers
• Publishers

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Management Structure
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Working Group Status
Announcement The PSI Minimum Requirement papers
are on Nature Biotechnology community
consultation web site http//www.nature.com/nbt
/consult/index.html Thanks for your feedback!
Not yet public
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Controlled Vocabularies (CVs)

• CVs are in OBO format
• Have a registered namespace on the OBO web site
• Can be used in one or more PSI data exchange
  format
• Common guidelines for CV development (in
  progress)
• - Design principles and naming conventions
• - Collaboration with MSI Ontology WG
• Common mapping mechanisms (in progress)
• - XML elements and terms in the CVs via a mapping
  file

PSI CVs information http//www.psidev.info/index.
php?qnode/159
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CVs Status by Working Group

• PSI-MI 2.5 (molecular interaction)
• - 715 terms (100 definitions)
• PSI-MS (mass spectrometry)
• - 466 terms (95 definitions)
• PSI-MOD (protein modification)
• - 1147 terms (60 definition).
• PSI-SEP (sample processing for gel)
• 190 terms (100 definitions)
• ? Common experimental and sample descriptors
• - Provide terms to OBI