BioModels Database, a curated resource of annotated published models

Nicolas Le Novère, EMBL-EBI http://www.ebi.ac.uk/biomodels/ What is BioModels Database?

Store and serve quantitative models of biomedical interest

Only models described in the peer-reviewed scientific literature.

Models are curated: computer software check the syntax, while human curators check the semantics.

Models are simulated to check the reference correspondence

Model components are annotated, to improve identification and retrieval.

BioModels DB native format is SBML but models are accepted in several formats, and served in several others. Where are the models coming from

I) Individuals Authors (prior to grant application, before publication etc.) Members of the SBML community (developers+modellers)

II) Existing model repositories SBML repository, JWS Online, The , Database Of Quantitative Cell Signalling, CellML repository

III) Journals (> 200 journals advise deposition, including all PloS journals, all BMC journals, Nature Molecular )

IV) BioModels DB curators encode new models from literature Increase of content

models reactions

800

700 35000

models 600 reactions (x50) 30000

500 25000

400 20000

300 15000

200 10000

100 5000

0

Apr2005 March2009 Production pipeline

Submission Curation Annotation Public

Non-curated Non-curated Models Models

Consistency Check distribution

MIRIAM Curated Curated Curation Models Models Perfect pipeline: model unchanged

SBML compare model submission consistency with original check publication

non curated branch

curated branch compare annotation gets BIOMD ID simulation results still not public with publication

curated branch public

7 Model manually correct changed SBML Re: Submission SBML compare model submission consistency with original check publication

beautify and correct non curated SBML, enter units branch change IDs and names

curated branch compare annotation gets BIOMD ID simulation results still not public with publication

curated branch public

8 contact: Model manually correct submitter, creator changed SBML or finally authors add notes of Re: Publications changes SBML compare model submission consistency with original check publication

beautify and correct non curated SBML, enter units branch change IDs and names

curated branch compare annotation gets BIOMD ID simulation results still not public with publication

add notes of changes contact: curated branch submitter, creator public or finally authors

9 BioModels DB supported format

Level 2 Version 1 Level 2 Version 3 all Levels and Versions Version 1.1

XPP-Aut

NeuroML VCML VCML

BioPAX Version 1.0 PDF Version 1.1

BioModels DB Infrastructure (1)

Users . . .

Application Servers Cluster .caltech.edu

Node 1 Node 2

computing-intensive tasks, external formats' conversions and some user-driven tasks will be running on clusters www.ebi.ac.uk/biomodels ... BioModels DB Infrastructure (2)

external resources

MIRIAM annotations

models in SBML export (all versions) text indices files direct search in BioModels DB retrieval of IDs from 3rd party eg. in notes, SBML elements, resources by search terms → specific annotations by ID then search specific annotations

15

Explore for relevant models

fungi Homo sapiens fungi/metazoa mammalia

Rattus norvegicus metazoa

arthropoda fungi/metazoa Homo sapiens

Rattus norvegicus

Different views of a model http://www.ebi.ac.uk/biomodels/webservices.html

Model of Month (RSS) Usage increase hitsper day (averagedper month) Funding structure

Nicolas Le Novère PI Camille Laibe developer Chen Li Lukas Endler (MIRIAM, developer curator SBO) Nick Juty curator (MIRIAM, SBO)

Melanie Stefan (model of the month) Nicolas Vijayalakshmi Rodriguez Chelliah Michael Hucka developer curator PI (50%)