Model Curation Edmund J Crampin Auckland Bioengineering Institute

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

Curation of Cell. ML Models http: //www. cellml. org/notes/curation-document/ • 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

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

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

MIRIAM • Minimum Information Requested In the Annotation of (Biochemical) Models Le Novère et al. , Nature Biotechnology 23 1509 -1515, 2005 http: //www. ebi. ac. uk/compneur-srv/miriam/ • • 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

MIRIAM Reference Correspondence 1. 2. 3. 4. 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 5. Instantiation in a simulation (all quantitative attributes defined – ICs, parameters etc) 6. Instantiation of simulation reproduces set of results listed in 3.

MIRIAM Annotation Scheme 1. Attribution Annotation: – association of the model with reference description and encoding process 2. External Data Resources Annotation: – link model components to corresponding databases, ontologies (etc. ) – allows models to be queried

MIRIAM Attribution Annotation 1. 2. 3. 4. Name of model Citation (of Reference Description) Name(s) of creator(s) of encoding Time and date of encoding and modifications 5. Statement of terms of distribution

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

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

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 Cell. ML model be its own reference description? – Model. ML?

Going Further • Relationship between model and data – 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?