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 Virtual Cell, Database Of Quantitative Cell Signalling, CellML repository

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

IV) BioModels DB curators encode new models from literature

Increase of content

0

100

200

300

400

500

600

700

800

modelsreactions (x50)

Apr2005 March2009

5000

10000

15000

20000

25000

30000

models reactions

35000

Curation Annotation Public

ConsistencyCheck

MIRIAMCuration

Non-curated Models

Curated Models

Non-curatedModels

CuratedModels

Production pipeline

distribution

Submission

7

SBML consistency

check

compare model with original publication

non curatedbranch

compare simulation results with publication

curated branch gets BIOMD IDstill not public

annotation

curated branchpublic

submission

Perfect pipeline: model unchanged

8

SBML consistency

check

compare model with original publication

non curatedbranch

compare simulation results with publication

curated branch gets BIOMD IDstill not public

annotation

curated branchpublic

submission

manually correct SBML

beautify and correct SBML, enter units

change IDs and names

Model changedRe: Submission

9

SBML consistency

check

compare model with original publication

non curatedbranch

compare simulation results with publication

contact: submitter, creator or finally authors

curated branch gets BIOMD IDstill not public

annotation

curated branchpublic

submission

manually correct SBML

beautify and correct SBML, enter units

change IDs and names

add notes of changes

contact: submitter, creator or finally authors add notes of

changes

Model changedRe: Publications

BioPAX

all Levels and Versions

Level 2 Version 1Level 2 Version 3

Version 1.0Version 1.1

Version 1.1

XPP-Aut

VCML

BioModels DB supported format

PDF

VCML

NeuroML

BioModels DB Infrastructure (1)

Application Servers Cluster

Node 1

computing-intensive tasks,external formats' conversions and some user-driven tasks

will be running on

clusters...

Users . . .

biomodels.caltech.edu

Node 2

www.ebi.ac.uk/biomodels

BioModels DB Infrastructure (2)

models in SBML

(all versions)

externalresources

text indicesexportfiles

MIRIAM annotations

15

direct search in BioModels DBeg. in notes, SBML elements, specific annotations by ID

retrieval of IDs from 3rd party resources by search terms →then search specific annotations

Explore taxonomy for relevant models

fungi/metazoa

Homo sapiens

Rattus norvegicus

mammalia

metazoa

fungi

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

hit

s p

er

day (

avera

ged

per

mon

th)

Funding structure

Nicolas Le NovèrePI

Chen Lideveloper

NicolasRodriguezdeveloper

(50%)

Lukas Endlercurator

Vijayalakshmi Chelliahcurator

Camille Laibedeveloper(MIRIAM,

SBO) Nick Jutycurator

(MIRIAM,SBO)

Melanie Stefan(model of the month)

Michael HuckaPI