EBI is an Outstation of the European Molecular Biology Laboratory.
Bird‘s Eye View of ...
Molecular Interaction Standards: PSI-MI XML
PSI-MI Tool support (APIs, Validator)
ChEBI
APO-SYS workshop20 – 21st January 2009Berlin
PROTEOMICS STANDARD INITIATIVE
A gentle introduction to the
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Engineering 1850Engineering 1850
• Nuts and bolts fit perfectly together, but only if they originate from the same factory
• Standardisation proposal in 1864 by William Sellers
• It took until after WWII until it was generally accepted, though …
Proteomics 2003Proteomics 2003
• Proteomics data are perfectly compatible, but only if they are from the same lab / database / software
• “Publish and vanish” by data producers
• Collecting all publicly available data requires huge effort
• Urgent need for standardisation
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• Community standard for Molecular Interactions
• XML schema and detailed controlled vocabularies
• Jointly developed by major data providers: BIND, CellZome, DIP, GSK, HPRD, Hybrigenics, IntAct, MINT, MIPS, Serono, U. Bielefeld, U. Bordeaux, U. Cambridge, and others
• Version 1.0 published in February 2004The HUPO PSI Molecular Interaction Format - A community standard for the representation of protein interaction data.Henning Hermjakob et al, Nature Biotechnology 2004, 22, 176-183.
• Version 2.5 published in October 2007Broadening the Horizon – Level 2.5 of the HUPO-PSI Format for Molecular Interactions;
Samuel Kerrien et al. BioMed Central. 2007.
PSI-MI XML format
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• Collecting and combining data from different sources has become easier
• Standardized annotation through PSI-MI ontologies
• Tools from different organizations can be chained, e.g. analysis of IntAct data in Cytoscape.
PSI-MI XML benefits
http://www.psidev.info/MIHome page
PSI-MI CONTROLLED VOCABULARIES
An overview of the
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Ontology Lookup Service• Makes available OBO controlled vocabularies• Web site allows for searching and browsing their
hierarchy
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Ontology Lookup Service
• Each term has a definition as well as literature reference
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PSI-MI XML 2.5 DATA MODELAn overview of the
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PSI-MI 2.5 Standards
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• Top level structure unchangedcompared to PSI-MI 1.0
• Use of Id/Ref on main objects
Bird’s eye view of PSI-MI XML 2.5
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Main objects - Experiment
Controlled by Ontologies
Literature references
Confidence measures
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Main objects - Interactor
Generic interactor
Reference to a public database
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Main objects - Interaction
Controlled by Ontology
Copyright
Experiment
Kinetics parameters
Confidence value
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Basics – Controlled Vocabularies• Why ?
• Ensure data consistency
• Provide reliable mean for searching & filtering data
• How ?
• By providing a reference to an ontology term
Using
Xref !
!
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Main objects - Participant
e.g. enzyme target
Interactor
e.g. bait, prey
Delivery methodexpression level…
Interactor used experimentally
Building of Complex
PSI-MI TAB DATA MODELAn overview of the
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Standard columns (15):• ID(s) interactor A & B• Alt. ID(s) interactor A & B • Alias(es) interactor A & B• Interaction detection method(s)• Publication 1st author(s)• Publication Identifier(s)• Taxid interactor A & B• Interaction type(s)• Source database(s)• Interaction identifier(s)• Confidence value(s)
PSIMITAB Standard Columns
INTACT EXTENDED MITABA quick look into
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IntAct specific columns (+11):• Experimental role(s) of interactors• Biological role(s) of interactors• Properties (CrossReference) of interactors• Type(s) of interactors• HostOrganism(s)• Expansion method(s)• Dataset name(s)
Standard columns (15):• ID(s) interactor A & B• Alt. ID(s) interactor A & B • Alias(es) interactor A & B• Interaction detection method(s)• Publication 1st author(s)• Publication Identifier(s)• Taxid interactor A & B• Interaction type(s)• Source database(s)• Interaction identifier(s)• Confidence value(s)
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PSIMITAB Extended Columns
PSI-MI XML 2.5 JAVA APIA hands on introduction to
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PSI-MI XML Java API
• Uses Java 5• Provides binding between XML and Java object model• Tools to read/write XML from/to file• Read can be done in 2 fashions:
• Load a whole file in an EntrySet• Only allows to load large files if you have enough memory• Easy to update content and write back to file
• Index XML data and give access though an IndexedEntry• Memory efficient with large files• Allows to browse through interactions, experiments…• Trickier to write updated content (yet, feasible)
PSI-MI TAB 2.5 JAVA APIA hands on introduction to
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PSI-MI TAB Java API
• Uses Java 5• Provides binding between TAB and a Java object model• Tools to read/write TAB from/to file• You can read in 2 fashions:
• Load a whole file in a Collection<BinaryInteraction>• Only allows to load large files if you have enough memory
• Load interaction one at a time using Iterator<BinaryInteraction>• Memory efficient with large files
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• PSI-MI XML is the de facto standard for molecular interactions
• We have code samples & exercises for both APIs ! Let me know if you want access to it …
• The Java API makes it easy to handle
Summary
http://psidev.info/MIPSI-MI Home page
http://www.psidev.info/index.php?q=node/60#toolsAPI Download
ftp://ftp.ebi.ac.uk/pub/databases/intact/current/psi25Data
R packages for PSI-MIQuick introduction to
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Rintact & RpsiXML
• Initiative from the Wolfgang Huber’s group at the EBI
• Allows to read PSI-MI XML data into R data structure
• Enables data analysis using existing packages such as: RBGL, ppiStats, apComplex, …
• Currently supports: IntAct, MINT, HPRD, DIP, BioGRID, MIPS/CORUM, MatriDB, MPACT.
http://www.bioconductor.org/packages/2.1/bioc/html/Rintact.html
API Download
http://www.bioconductor.org/packages/2.3/bioc/vignettes/RpsiXML/inst/doc/RpsiXML.pdf
Documentation
PSI SEMANTIC VALIDATORQuick introduction to
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The PSI validator framework automatically checks that experimental data reported using a specific XML format and various CVs are compliant with the overall MIAPE recommendations.
The semantic validator checks :
- the XML syntax
- the appropriate CV terms are used in specific locations of a document
- misc. consistency check
The Framework (in the context of PSI)
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OntologyManager
Ontology Mapping Rule Object Rule
Semantic ValidatorMessagesData Model
Config Config Config
OBO
OLS
DataFile
Components of the Validator
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The Ontology Manager
Declaration of ontologies or Controlled Vocabularies:
• location,
• format,
• retrieval method (local file or via web services)
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Ontology Lookup Service
Currrently 61 Ontologies available
Web Service for easy access
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CV Mapping Rules
Is an explicit specification of which CV terms may/should/must be used in a given location.
•crucial to bind a data model to a set of CVs
•necessary to enforce MIAPE guidelines
•allows to develop CVs independently from a schema (necessary to comply to CV guidelines)
•this mapping is specified in an XML file
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Exchange Format
Referenced ontologies and CVs
Resulting mapping file <CvMappingRule scopePath="/mzML/sampleList/sample” cvTermsCombinationLogic="OR" requirementLevel="MAY">
<CvTerm termAccession="GO:0005575" useTerm="false" termName="cellular_component" allowChildren="true" isRepeatable="true" cvIdentifierRef="GO"></CvTerm> <CvTerm termAccession="BTO:0000000" useTerm="false" termName="brenda source tissue ontology" allowChildren="true" isRepeatable="true" cvIdentifierRef="BTO"/> </CvMappingRule>
<CvMappingRule scopePath="/mzML/instrumentList/instrument/componentList/analyzer” cvTermsCombinationLogic=“AND" requirementLevel="MUST"> <CvTerm termAccession="MS:1000443" useTerm="false" termName="data file checksum type" allowChildren="true" isRepeatable="true" cvIdentifierRef="MS"></CvTerm> <CvTerm termAccession="MS:1000480" useTerm="false" termName=“Mass Analyzer" allowChildren="true" isRepeatable="true" cvIdentifierRef="MS"></CvTerm></CvMappingRule>
<CvMappingRule scopePath="/mzML/instrumentList/instrument/componentList/detector" cvTermsCombinationLogic=“AND" requirementLevel="MUST"> <CvTerm termAccession="MS:1000026" useTerm="false" termName=“Detector Type" allowChildren="true" isRepeatable="false" cvIdentifierRef="MS"/> <CvTerm termAccession="MS:1000027" useTerm="false" termName="detector acquisition mode" allowChildren="false" isRepeatable="true" cvIdentifierRef="MS"/></CvMappingRule>
CV Mapping Rules – example with MzML
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•A data model is not bound to a single mapping
•PSI MI and MS workgroup provide a mapping corresponding to their respective minimum reporting guidelines (MIAPE)
•Mapping can be customized by any end user of a standard to be more or less granular
CV Mapping Rules – final thoughts
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List of consistency check tailored to specific data type
Examples:- taxid is an existing entry at NCBI- PubMed ID is an existing publication- protein and DNA sequence defined using
appropriate alphabet- CV dependency rules
Note: These rules are to be programmed in Java
The Object Rules
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Fancy Building Your Own ?
We are currently finalizing a tutorial to guide users in writing a validator based on their own data model. It provides:
• Additional explanation on the Validator’s modules
• Example of configuration files
• A working prototype based on a made up data model
• Source code available to get you quick-started.http://psidev.info/validator
EBI is an Outstation of the European Molecular Biology Laboratory.
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EBI is an Outstation of the European Molecular Biology Laboratory.
• Luisa Montecchi-Palazzi• Florian Reisinger• Lennart Martens• Andy Jones• Mathias Oesterheld• Bruno Aranda• Prem Achuthan • Henning Hermjakob
PSI participants(direct contributors to the validator)
• Juan A Vizcaino• Chris Taylor• Eric Deutsch• Pierre Alain Binz• Susanna Sansone• Frank Gibson• Zsuzsanna Bencsath• Daniel Schober• Trish Wetzel• Pete Souda
Other PSI participants
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