1. MIRIAM Resources:
Cross­referencing framework
Camille Laibe
Nick Juty
BioDBCore, 10 December 2010, 2nd conference call EBI is an Outstation of the European Molecular Biology Laboratory.

2. BioModels.net
Community aiming to improve model annotation, interpretation, exchange
and re­use. Not restricted to any format (eg. SBML, CellML, …)
Current projects:
A checklist for model annotation: MIRIAM and its supporting
infrastructure: MIRIAM Resources
A set of relationships (qualifiers) to link model and data:
BioModels.net qualifiers
An ontology to precise the semantics of models: SBO
A public database of published models of biological interest:
BioModels Database
Several ongoing efforts: MIASE, KiSAO, SED­ML, TEDDY, ...
http://biomodels.net/ 2

3. MIRIAM STANDARD
MIRIAM
proposed guidelines for curation
and annotation of quantitative
models
about encoding and annotation
applicable to any structured
model format
cf. Nicolas Le Novère et al. Minimum
Information Requested in the Annotation
of biochemical Models (MIRIAM). Nature
Biotechnology, 2005
http://biomodels.net/miriam/

4. MIRIAM Compliance
Models must:
be encoded in a public machine­readable format
be clearly linked to a single publication
reflect the structure of the biological processes described in the
reference paper (list of reactions, ...)
be instantiable in a simulation (possess initial conditions, ...)
be able to reproduce the results given in the reference paper
contain creator’s contact details
annotated: must unambiguously identify each model constituent

5. MIRIAM Compliance
Models must:
be encoded in a public machine­readable format
be clearly linked to a single publication
reflect the structure of the biological processes described in the
reference paper (list of reactions, ...)
be instantiable in a simulation (possess initial conditions, ...)
be able to reproduce the results given in the reference paper
contain creator’s contact details
annotated: must unambiguously identify each model constituent

6. Annotations
Essential for data identification and semantics:
Understanding
Search
Reuse
Comparison
Integration
…

7. Annotations
Essential for data identification and semantics:
Understanding
Search
Reuse
Comparison
Integration
…
→ True for any kind of data, not only models!

8. Identifiers for annotations
Unique and unambiguous
an identifier must never be assigned to two different objects
Perennial
the identifier is constant and its lifetime is permanent
Standards compliant
must conform on existing standards, such as URI
Resolvable
identifiers must be able to be transformed into locations of online
resources storing the object or information about the object
Free for use
everybody should be able to use and create identifiers, freely and at no
cost

9. MIRIAM URNs
Dataset
Data type
Identifier
Format depends
Not a URL,
on the resource
not a “Web­
identified by
address”!
the data type
Human calmodulin: P62158 in UniProt urn:miriam:uniprot:P62158
Alcohol dehydrogenase: 1.1.1.1 in EC code urn:miriam:ec-code:1.1.1.1
Activation of MAPKK activity: GO:0000186 in Gene Ontology
urn:miriam:obo.go:GO%3A0000186 9

10. MIRIAM Resources: data type compliance
Open access
Anybody can access any public data without restriction (no commercial
licence, no login page, …)
Atomicity
The granularity of the data distributed has to be appropriately selected (a
database of “reactions” distributes reactions and not pathways) and
consistent (e.g. classes or instances but not classes and instances)
Identifier
An atomic data is associated to a unique and perennial identifier
Community recognition
The resource has to be “recognised” by the corresponding experimental
community, be reasonably supported, ...

11. MIRIAM Resources
Generation and resolving of MIRIAM URNs
Camille Laibe and Nicolas Le Novère.
MIRIAM Resources: tools to generate and resolve robust cross­references in Systems Biology.
BMC Systems Biology, 2007
http://www.ebi.ac.uk/miriam/

12. MIRIAM data types

13. MIRIAM data type

14. MIRIAM data type
Resources

15. MIRIAM tags

16. MIRIAM usage examples

17. MIRIAM web services

18. MIRIAM resources reliability

19. MIRIAM resources reliability

20. MIRIAM submission

21. MIRIAM generate URI

22. MIRIAM resolve URI

23. Tools developing support for MIRIAM URNs
Data resources Application software
BioModels Database (kinetic models) ARCADIA (graph editor)
Pathway Commons (BioPAX) BIOUML (modelling and simulation)
Proteomics Standards Initiative (PSI) COPASI (Simulation)
Physiome Model Repository (CellML) LibAnnotationSBML
SABIO­RK (reaction kinetics) LibSBML
Yeast consensus model database SAINT (semantic annotation)
Human consensus model database SBML2BioPAX
Systems Biology Ontology Browser SBML2LaTeX
E­MeP (structural genomics) SBMLeditor (model editor)
SemanticSBML (annotation,
merging, comparison, ...)
Snazer (network analysis, simulations)
Systems Biology Workbench
(model design and simulation)
The Virtual Cell (simulation)

24. Acknowledgements
The community of computational systems biology
for the development of MIRIAM and the implementation of MIRIAM support
Data providers
who replied, discussed and even complied with MIRIAM rules
Nicolas Le Novère
Nick Juty
Camille Laibe
24
laibe@ebi.ac.uk - juty@ebi.ac.uk