ebi is an outstation of the european molecular biology laboratory. bird‘s eye view of... molecular...

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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