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BioModels Database, MIRIAM Registry, and Identifiers.org Lukas - - PowerPoint PPT Presentation

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BioModels Database, MIRIAM Registry, and Identifiers.org Lukas Endler Lukas Endler Waiheke, March 13 th 2012 <lukas.endler@gmx.at> EBI is an Outstation of the European Molecular Biology Laboratory. Outline BioModels Database

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EBI is an Outstation of the European Molecular Biology Laboratory.

BioModels Database, MIRIAM Registry, and Identifiers.org

Lukas Endler

Waiheke, March 13th 2012 Lukas Endler <lukas.endler@gmx.at>

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Lukas Endler <lukas@ebi.ac.uk> 13.03.12 2

Outline

  • BioModels Database
  • MIRIAM annotations
  • MIRIAM registry
  • Identifiers.org
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http://biomodels.net

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Lukas Endler <lukas@ebi.ac.uk> 13.03.12 4

Biomodels.net

Standards and Guidelines:

  • MIRIAM (Minimal Information Required In the Annotation of Models)
  • MIRIAM Registry
  • BioModels.net Qualifiers
  • MIASE (Minimal Information About a Simulation Experiment)

Ontologies:

  • KiSAO (Kinetic Simulation Algorithm Ontology)
  • TEDDY (TErminology for the Description of DYnamics)
  • SBO (Systems Biology Ontology)

BioModels Database

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BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models.

Li C. et al., BMC Systems Biology (2010), 4:92 BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems. Le Novère N. et al., Nucleic Acids Research, (2006), 34: D689-D691

http://www.ebi.ac.uk/biomodels/

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Lukas Endler <lukas@ebi.ac.uk> 13.03.12 6

BioModels Database

  • contains only models from the peer reviewed literature
  • models are manually curated and checked to ensure reliability

(MIRIAM* compliance)

  • the model faithfully reflects the description in its reference publication
  • it can reproduce the results given in the reference publication
  • unique identifiers for models
  • can be referenced, eg. in publications
  • models freely accessible and reusable
  • stored in SBML and exported in many other formats
  • models and model elements cross-linked to and annotated with

controlled vocabularies and databases

  • allows for complex queries and detailed searching
  • adds information and eases identification of model elements

* MIRIAM: Minimal Information Required In the Annotation of Biochemical Models Nicolas Le Novère et al., Nature Biotechnology, 23(12), 2005

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Lukas Endler <lukas@ebi.ac.uk> 13.03.12 7

Database Growth

11/04/05 01/06/05 28/07/05 31/01/06 05/06/06 03/10/06 05/01/07 05/06/07 25/09/07 28/03/08 21/08/08 03/12/08 25/03/09 16/06/09 02/09/09 26/01/10 27/04/10 28/09/10 13/04/11 01/10/11 08/02/12

20000 40000 60000 80000 100000 120000 140000 160000 100 200 300 400 500 600 700 800 900

Models Reactions

Releases R e a c t i

  • n

s M

  • d

e l s

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Types of Models

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Lukas Endler <lukas@ebi.ac.uk> 13.03.12 9

Model Formats

BioPAX

Level 1 Version 1 Level 1 Version 2 Level 2 Version 1 Level 2 Version 3 Level 2 Version 4 Level 2 Version 1 Level 2 Version 2 Level 2 Version 3 Level 2 Version 4 Version 1.0 Version 1.1 Version 1.1

XPP-Aut VCell

Temporarily unavailable

Octave

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Lukas Endler <lukas@ebi.ac.uk> 13.03.12 10

Model Submission

Where do models come from?

  • submitted by curators
  • from other repositories (JWS online, DOQCS, VCell and CellML

repositories, ...)

  • reimplemented from literature
  • from journals webpages
  • from authors before publication

some journals advocate submission to BioModels DB:

  • Molecular Systems Biology
  • PLoS journals
  • BioMedCentral journals
  • various people working on a model
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model accession ID is unique and perennial and can be used as a reference in publications and for searching and retrieving the model

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Lukas Endler <lukas@ebi.ac.uk> 13.03.12 14

Curated and Non-curated Branch

Curated models

  • models reproduce results, fully annotated, MIRIAM compliant

Non-Curated models

  • valid SBML, not curated or annotated by the curators.
  • not MIRIAM compliant
  • can not reproduce results published in the paper.
  • non kinetic models (eg. FBA, stoichiometric maps).
  • MIRIAM compliant
  • models contain kinetics that we cannot curate up to now.
  • back lag in curation, the curators just did not have the time → these

models will be moved into the curated branch as soon as possible.

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MIRIAM Annotations

Each model element is linked to external data resources. This

  • enhances model semantics
  • is essential for searching.

MIRIAM Annotations are represented as a triplet which consists of:

  • data collection (eg. Enzyme Nomenclature)
  • identifier (eg. EC 3.1.3.16 = phosphoprotein phosphatase)
  • qualifier (eg. is Version of)

Data collection and identifier together, are in the form of URI (Uniform Resource Identifier): urn:miriam:ec-code:3.1.3.16 these are resolved to a URL using the MIRIAM Registry (http://www.ebi.ac.uk/miriam/)

Taxonamy, Gene Ontology, ChEBI, UniPROT, KEGG, Reactome, Enzyme Nomenclature, etc.

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Lukas Endler <lukas@ebi.ac.uk> 13.03.12 18

MIRIAM Annotation in SBML

  • included as RDF
  • linked via MetaID of model element
  • URIs can be combined in a bag

Hemoglobin subunit beta Hemoglobin subunit alpha ferroheme b

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Lukas Endler <lukas@ebi.ac.uk> 13.03.12

MIRIAM Annotations

Namespace (required) URN/URL Identifier (required) text string Identifier (required) text string Identifies data collection eg. pubmed, uniprot Format depends

  • n the collection

identified by the namespace the namespace and the identifier are combined into a single URN urn:miriam:datatype:identifier urn:miriam:pubmed:16333295 MIRIAM publication urn:miriam:uniprot:P69905 Alpha-globin (human) urn:miriam:taxonomy:9606 Homo sapiens

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http://identifiers.org

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Lukas Endler <lukas@ebi.ac.uk> 13.03.12

MIRIAM Annotations

Namespace (required) URN/URL Identifier (required) text string Identifier (required) text string Identifies data collection eg. pubmed, uniprot Format depends

  • n the resource

identified by the data-type alternatively an equivalent, directly resolvable URL version exists: urn:miriam:namespace:identifier http://identifiers.org/namespace/identifier urn:miriam:pubmed:16333295 http://identifiers.org/pubmed/16333295 urn:miriam:uniprot:P69905 http://identifiers.org/uniprot/P69905 urn:miriam:taxonomy:9606 http://identifiers.org/taxonomy/9606

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http://www.ebi.ac.uk/miriam

MIRIAM Registry

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Data Collections

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Collection Entry

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Resource Information

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Lukas Endler <lukas@ebi.ac.uk> 13.03.12

What resources are suitable to become data types?

  • resource must be freely accessible to academic users and

commercial users without restrictions

  • access should not require registration
  • must be actively maintained and accepted by the community
  • identifiers must be stable, perennial and unique for the data type and

point to a single piece of information

  • atomicity of information should be on the same level (not proteins,

reactions, and pathways in same data type)

  • eg. KEGG – split into compounds, reactions, genes, pathways
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Lukas Endler <lukas@ebi.ac.uk> 13.03.12

Basic Access:

Collections: http://identifiers.org/pubmed Record (location independent): http://identifiers.org/pubmed/16333295 Custom queries + format: Specific resource: http://identifiers.org/pubmed/16333295?resource=MIR:00100028 Format (html/rdfxml): http://identifiers.org/pubmed/16333295?format=rdfxml Profiles (list of settings for collections, user-interface not yet implemented): http://identifiers.org/pubmed/16333295?profile=most_reliable

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http://identifiers.org/pubmed/16333295

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http://identifiers.org/pubmed/16333295?resource=MIR:00100028

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http://identifiers.org/pubmed/16333295?profile=most_reliable

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Lukas Endler <lukas@ebi.ac.uk> 13.03.12

Nicolas Le Novère Nick Juty Camille Laibe Nicolas Rodriguez Michael Hucka Vijayalakshmi Chelliah

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Lukas Endler <lukas@ebi.ac.uk> 13.03.12 32

fungi/ metazoa mammalia pisces vertebrata metazoa fungi arthropoda

Taxonomic Searches

linking to hierarchical controlled vocabularies allows for more elaborate searching: e.g.: searching BioModels DataBase for all models fitting mammals rodentia homo drosophilidae

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metazoa/fungi amniota rattus mammalia homo sapiens hamster

http://www.ebi.ac.uk/biomodels

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Lukas Endler <lukas@ebi.ac.uk> 13.03.12 34

Ranking and retrieval

Henkel et al (2010) BMC Bioinformatics, 11:423

improved searching

  • search query expansion
  • uses ontologies
  • uses resolved identifier information
  • returns ranked list of models
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Lukas Endler <lukas@ebi.ac.uk> 13.03.12 35

Semantic SBML

http://www.semanticsbml.org/

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Lukas Endler <lukas@ebi.ac.uk> 13.03.12 36

gene list

modeling workflow

qualitative model MIRIAM identifiers

parameterisation workflow

kinetic data kinetic model

c a l i b r a t i

  • n

w

  • r

k f l

  • w

calibrate d model experimental data

simulation workflow

sets of simulations simulation data Taverna workflow

Li et al. BMC Bioinformatics, 11:582

MODEL1012110001

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Lukas Endler <lukas@ebi.ac.uk> 13.03.12 37

Some Software supporting MIRIAM annotations

  • SBMLharvester (http://code.google.com/p/sbmlharvester/ )

Robert Hoehndorf et al., Department of Genetics, Cambridge Univ.

  • creates an OWL representation of model and annotations
  • allows reasoning on and checking of annotation
  • RICORDO toolset (http://bioonto.gen.cam.ac.uk:8080/ricordo/)

Sarala M. Wimalaratne et. al, EBI

  • creates a smartly indexed RDF triple storage of annotated models and

allows complex queries

  • SemanticSBML (Krause et al., Bioinformatics (2010), 26: 421)
  • model merging, SBO term prediction, checking annotations, model

comparison and clustering via metadata

  • SAINT (Lister et al., Bioinformatics (2009) 25(22): 3026-3027 )
  • libAnnotationSBML (Swainston and Mendes, Bioinformatics (2009), 25: 2292)
  • access some resources over webservices, finds potential annotations, checks

balancing of chemical formulas in reactions

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Lukas Endler <lukas@ebi.ac.uk> 13.03.12 38

Modelling efforts using MIRIAM annotations

  • Herrgård et al (2008) A consensus yeast metabolic network

reconstruction obtained from a community approach to systems

  • biology. Nature Biotechnology, 26: 1155-1160
  • MODEL0072364382: 2152 species, 1857 reactions
  • stoichiometric map, no concentrations, no kinetics
  • Smallbone et al (2010) Towards a genome-scale kinetic model of

cellular metabolism. BMC Systems Biology, 4:6

  • MODEL1001200000: 1748 species, 1059 reactions
  • Concentrations and flux added from BioModels Database
  • Constraint-based model and simplified linlog kinetics
  • Dobson et al (2010) Further developments towards a genome-scale

metabolic model of yeast. BMC Systems Biology, 4:145

  • MODEL1012110000: 2657 species, 1865 reactions