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Just been thinking about how we could test/specify that models in the
CellML model repository are MIRIAM-compliant. For a model to be
"MIRIAM-compliant" it must pass all the tests (box 3) and contain all
required annotations (box 4) specified in the MIRIAM article
(http://www.nature.com/nbt/journal/v23/n12/abs/nbt1156.html).

The six tests can be summarised as:

1. The model must be encoded in a public, machine readable format.
2. The encoded model must comply with the standard in which it is encoded.
3. The model must be clearly related to a single reference description
that describes or references a set of results that one can expect to
reproduce using the model.
4. The encoded model must reflect the biological processes listed in the
reference description.
5. The encoded model must be instantiated in a simulation (including:
the values of quantitative variables and their units must be equivalent
to the values listed in the reference description).
6. The model, when instantiated within a suitable simulation
environment, must be able to reproduce all relevant results given in the
reference description.

Test 1 is easy since all models in the repository are in CellML and test
2 can be automated using a CellML validator.

Test 3 can be satisfied if we could somehow indicate the reference
description for a given model - currently these are generally specified
using a <bqs:reference> to the journal publication so we just need to
tag or reference the approriate piece of metadata as the reference
description for the model. This gets more complicated for CellML 1.1
models that split a single journal publication into multiple models or
combine multiple journal articles into one model.

I can't think of a way to automatically perform test 4, so it probably
requires new metadata in a model that specifies the result of this test,
added either by the model author (preferably) or model curator.

Tests 5 and 6 could be peformed automatically if simulation results have
been included with a model in the repository but we probably still need
to manually specify that the model parameter values and initial
conditions etc. match those given in the reference description (at least
until the CellML models start becoming the reference description). We
also want to start including metadata specifing what simulation
environments have been used with each model and what kind of success has
been had, so checks for tests 5 and 6 could be implied from this data.

Model annotation required for MIRIAM-compliance:

1. The preferred name of the model.
2. A citation of the reference description with which the model is
associated.
3. Name and contact information for the model creators, that is, the
people who actually contributed to the encoding of the model in its
present form.
4. The date and time of creation, and the date and time of last
modification.
5. A precise statement about the terms of distribution.

The preferred name of a model is given by the model element's name
attribute, right? Which will be appropriately generated/set on model
upload to the repository.

As with test 3, requirement 2 can be satisfied once we can indicate the
reference description for a model.

Requirement 3 is satisfied if a model contains the model creator
metadata from the section 4.1 of the CellML Metadata specification and
modification's can be included through the modification history metadata
(section 4.6).

Even the example in the MIRIAM paper doesn't include the actual time of
creation/modifcation, but requirement 4 is satisfied through the use of
the creation date metadata (section 4.5) and modification history
metadata includes the date of modifications.

The CellML metadata specification provides for specification of
copyright notices (section 4.4) but we probably need to extend this to
cover the range required by the 5th annotation requirement, especially
to enable the specification that a model is public vs confidental.

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• [cellml-discussion] MIRIAM compliance for the CellML model repository, David Nickerson, 02/01/2006
  • [cellml-discussion] MIRIAM compliance for the CellML model repository, Andrew Miller, 02/01/2006
    • [cellml-discussion] freezing, Peter Villiger, 02/03/2006

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