biomodels database, a curated resource of annotated ...€¦ · non curated branch compare...
TRANSCRIPT
![Page 1: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/1.jpg)
BioModels Database, a curated resource of annotated published models
Nicolas Le Novère, EMBL-EBI
![Page 2: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/2.jpg)
http://www.ebi.ac.uk/biomodels/
![Page 3: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/3.jpg)
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.
![Page 4: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/4.jpg)
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
![Page 5: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/5.jpg)
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
![Page 6: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/6.jpg)
Curation Annotation Public
ConsistencyCheck
MIRIAMCuration
Non-curated Models
Curated Models
Non-curatedModels
CuratedModels
Production pipeline
distribution
Submission
![Page 7: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/7.jpg)
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
![Page 8: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/8.jpg)
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
![Page 9: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/9.jpg)
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
![Page 10: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/10.jpg)
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
VCML
NeuroML
![Page 11: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/11.jpg)
![Page 12: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/12.jpg)
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
![Page 13: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/13.jpg)
BioModels DB Infrastructure (2)
models in SBML
(all versions)
externalresources
text indicesexportfiles
MIRIAM annotations
![Page 14: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/14.jpg)
![Page 15: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/15.jpg)
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
![Page 16: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/16.jpg)
![Page 17: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/17.jpg)
![Page 18: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/18.jpg)
![Page 19: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/19.jpg)
![Page 20: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/20.jpg)
Explore taxonomy for relevant models
fungi/metazoa
Homo sapiens
Rattus norvegicus
mammalia
metazoa
fungi
arthropoda
![Page 21: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/21.jpg)
fungi/metazoa
Homo sapiens
Rattus norvegicus
![Page 22: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/22.jpg)
![Page 23: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/23.jpg)
![Page 24: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/24.jpg)
![Page 25: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/25.jpg)
![Page 26: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/26.jpg)
![Page 27: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/27.jpg)
![Page 28: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/28.jpg)
![Page 29: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/29.jpg)
![Page 30: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/30.jpg)
![Page 31: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/31.jpg)
Different views of a model
![Page 32: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/32.jpg)
![Page 33: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/33.jpg)
http://www.ebi.ac.uk/biomodels/webservices.html
![Page 34: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/34.jpg)
![Page 35: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/35.jpg)
![Page 36: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/36.jpg)
Model of Month (RSS)
![Page 37: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/37.jpg)
Usage increase
hit
s p
er
day (
avera
ged
per
mon
th)
![Page 38: BioModels Database, a curated resource of annotated ...€¦ · non curated branch compare simulation results with publication contact: submitter, creator or finally authors curated](https://reader030.vdocuments.us/reader030/viewer/2022040609/5ecc2599aa8f89389a23172a/html5/thumbnails/38.jpg)
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