1. Model Curation Edmund J. Crampin Auckland Bioengineering Institute
CellML Curation
MIRIAM
Automated Curation
What is a valid ‘reference description’?
Going Further
models and data
community forum

2. Curation of CellML Models
Level 0
not curated
Level 1
encoded model represents published model
Level 2
encoded model reproduces published results
Level 3
encoded model satisfies domain-specific requirements
Levels are not a hierarchy – Level 2 compliance may break Level 1 compliance

3. Level 2: Validity Checking
Validation
Simulates reference set of results
Simulation / Graphing Metadata (Andrew and Andre)
Reference Description
Script process of running model, generating plots, validating against published results

4. Domain-Specific Requirements
Units
Biophysics
Mass balance
Charge balance
Osmotic balance
Thermodynamic consistency
Mathematics
ICs
BCs
well-posed

5. MIRIAM
Minimum Information Requested In the Annotation of (Biochemical) Models
Le Novère et al., Nature Biotechnology , 2005
Arose from ICSB 2004 Heidelberg
Proposal in 2 parts:
Correspondence to a Reference Description
Set of rules for dealing with encoding, structure and results when simulated
Annotation scheme
documentation of model
Ensure that model is properly associated with and reference description and that it is consistent with reference description.
Reference description – a scientific article.

6. MIRIAM Reference Correspondence
Encoding in public, machine-readible format
Compliance with standard in which encoded
Explicit relationship to a set of results
Model structure should reflect biological processes
Instantiation in a simulation (all quantitative attributes defined – ICs, parameters etc)
Instantiation of simulation reproduces set of results listed in 3.

7. MIRIAM Annotation Scheme
Attribution Annotation:
association of the model with reference description and encoding process
External Data Resources Annotation:
link model components to corresponding databases, ontologies (etc.)
allows models to be queried

8. MIRIAM Attribution Annotation
Name of model
Citation (of Reference Description)
Name(s) of creator(s) of encoding
Time and date of encoding and modifications
Statement of terms of distribution

9. MIRIAM Resources External data resources annotation
Database and web services to map Unique Resource Identifiers (URIs) to worldwide open access bioinformatics resources
Implemented in biomodels.net

10. Automating Curation What can be automated?
What must be manually curated?
Units (Jsim, Jonathan Cooper – Oxford)
Checking of biophysical properties? (mass, charge, osmotic balance?)

11. What is a valid reference description?
MIRIAM:
Scientific article
Any other unique publication, print or online, which describes precisely the structure of the model, parameters, and expected output
Encoded model must correspond to a single RD.
Better (?)
Can an annotated CellML model be its own reference description?
ModelML?

12. Going Further Relationship between model and data Community commentary
Databasing of data used to fit models
Automated validation of model results against newly added data sets
Community commentary
Comments from authors
Critiques from community
‘Expert’ information
Moderated forum?