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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