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
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 biomodels.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 taxonomy 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%)