3.1.13. The Physiome Model Repository and the link to bioinformatics¶
The Physiome Model Repository (PMR) [LCPF08] is the main online repository for the IUPS Physiome Project, providing version and access controlled repositories, called workspaces, for users to store their data. Currently there are approximately 640 public workspaces and another 200 private workspaces in the repository. PMR also provides a mechanism to create persistent access to specific revisions of a workspace, termed exposures. Exposure plugins are available for specific types of data (e.g. CellML or FieldML documents) which enable customizable views of the data when browsing the repository via a web browser, or an application accessing the repository’s content via web services.
The CellML project website and the CellML Physiome Model Repository are shown in Fig. 3.39 and Fig. 3.40.
The CellML models on models.physiomeproject.org are listed under 20 categories, shown below: (numbers of exposures in each category are given besides the bar graph)
Browse by category
Note that searching of models can be done anywhere on the site using the search box on the upper right hand corner. An important benefit of ensuring that the models on the PMR are annotated is that models can then be retrieved by a web-search using any of the annotated terms in the models.
To illustrate the features of PMR, click on the Hund, Rudy 2004 (Basic) model in the alphabetic listing of models under Electrophysiology. This opens a web page (Fig. 3.41) using a 32 character string that has been randomly generated as the ID for the exposure page for that model.
Note that the string is still unique even with only 5 characters:
e.g. https://models.physiomeproject.org/exposure/f4b71/hund_rudy_2004_a.cellml/view
The section labelled ‘Model Structure’ contains the journal paper abstract and often a diagram of the model[1]. This is shown for the Hund-Rudy 2004 model in Fig. 3.42. This model, with over 22 separate protein model components, is also a good example of why it is important to build models from modular components [CMEJ08], and in particular the individual ion channels for electrophysiology models.
There is a list of ‘Views Available’ for the CellMLmodel on the lower right hand side of the exposure page. The function of each of these views is as follows:
Views Available
Documentation - Takes you to the main exposure page.
Model Metadata - Lists metadata including authors, title, journal, Pubmed ID and model annotations.
Model Curation - Provides the curation status of the model. Note: this is soon to be updated.
Mathematics - Displays all the mathematical equations contained in the model.
Generated Code - Creates code (C, C-IDA, F77, MATLAB or Python) for the model.
Cite this model - Provides details on how to cite use of the CellML model.
Source view - Gives a full listing of the XML code for the model.
Simulate using OpenCell - This will be OpenCOR once the SED-ML API is included in OpenCOR.
Note that CellML models are available under a Creative Commons Attribution 3.0 Unported License[2]. This means that you are free to:
- Share — copy and redistribute the material in any medium or format
- Adapt — remix, transform, and build upon the material
for any purpose, including commercial use.
The next stage of content development for PMR is to provide a list of the modular components of these models each with their own exposure. For example, models for each of the individual ion channels used in the publication-based electrophysiological models will be available as standalone models that can then be imported as appropriate into a new composite model. Similarly for enzymes in metabolic pathways and signalling complexes in signalling pathways, etc. Some examples of these protein modules are:
Sodium/hydrogen exchanger 3 https://models.physiomeproject.org/e/236/
Thiazide-sensitive Na-Cl cotransporter https://models.physiomeproject.org/e/231/
Sodium/glucose cotransporter 1 https://models.physiomeproject.org/e/232/
Sodium/glucose cotransporter 2 https://models.physiomeproject.org/e/233/
Note that in each case, as well as the CellML-encoded mathematical model, links are provided (see Fig. 3.43) to the UniProt Knowledgebase for that protein, and to the Foundational Model of Anatomy (FMA) ontology (via the EMBLE-EBI Ontology Lookup Service) for information about tissue regions relevant to the expression of that protein (e.g. Proximal convoluted tubule, Apical plasma membrane; Epithelial cell of proximal tubule; Proximal straight tubule). Similar facilities are available for SMBL-encoded biochemical reaction models through the Biomodels database [AYY].
Footnotes
[1] | These are currently hand drawn SVG diagrams but the plan is to automatically generate them from the model annotation and also (at some stage!) to animate them as the model is executed. |
[2] | https://creativecommons.org/licenses/by/3.0/ |