1. Welcome to the NSR Physiome Project!
  2. Physiome JSim
  3. (Beta) JSim Consolidated Model Database
  4. (Beta) JSim Consolidated Model Database: About This Database

(Beta) JSim Consolidated Model Database: About This Database

Contents:

Source Archives

This database indexes 73775 models across 5 archives:

Model IDs

Each model within this database is assigned a unique model ID . Model IDs are assigned as follows:

  • NSR Webmodels: the letters NSR followed by a 4-digit ascension number drawn from the original archive
    (e.g. NSR0001 for the first NSR Webmodel);
  • Biomodels: the letters BIO followed by a 4-digit ascension number drawn from the original archive
    (e.g. BIO0001 for the first Biomodel);
  • JWS: the original JWS model name - 3-15 characters, based upon the lead author name
    (e.g. assmus for the first JWS model);
  • CellML: the letters CML followed by a 4-digit ascension number assigned by this database
    (e.g. CML0001 for the first CellML model);
  • Kegg: a 3-4 letter alphabetic genome identified, followed by a 5-digit pathway
    (e.g. aae00010 for the first Kegg model);

Currently Available Annotations

The goal of this database is to allow keyword and ontological searches across the 5 archives above. Since each constituent archive has different standards for model indexing, this approach will be, at present, fairly imperfect. The hope is by providing a common search mechanism, the archives will evolve toward common standards for model indexing. Below is a short summary of indexing information currently available:

  • NSR Webmodels: models are annotated by name, description, reference, author, and keyword.
  • Biomodels: models are annotated by name, description, and by ontological term.
  • JWS: models are annotated by name only.
  • CellML: models are annotated by name (which consists of author last names and year of publication) and description. Some models have ontological terms.
  • Kegg: models are annotated by name (which combines the names of the relevant genome and pathway) and by the kegg.genome and kegg.pathway ontologies.

Search Mechanisms

The "Model Search" portion of the main page currently allows searching for a single term across any combination of the ModelID, Name, Description, Reference, Author and Keyword fields. Three search buttons are available: [Search All Fields], [Search Selected Fields] (determined by user checkboxes) and [Search ID Field] (only). Any of these searches result in a list of relevant models. Clicking on the model ID in this list displays a page with all the information this database has about the model.

The "Ontology Search" portion of the main page enables searching via ontological term. Models are currently annotated via 37 distince ontologies, which may be viewed via the "List all ontologies" button. Each ontology contains a large set of terms. Those that have been used to tag models within this database may be viewed by clicking on the number in the "# tags" column. The resulting display shows the tags IDs and descriptions for the ontology. Unfortunately, at present, only a small number of ontologies (kegg.genome, kegg.pathway, [others in progress]) have descriptions available. With more work, the number of available descriptions will be improved in the future. Clicking on any tag ID will carry you (via the Web services at identifiers.org) to a page fully describing the tag (in some cases, there are several relevant pages, and you'll be asked to make a choice of which.) Tag IDs and descriptions can also be searched for relevant terms using the [Search Tag Descriptions] and [Search Tag IDs] buttons.

Ontology Search Example

Type "ATP" into the Ontology search box and click "Search Tag Descriptions". A list of ontological terms containing "ATP" will appear, including the following:

 CHEBI:15422   ATP                                          
 GO:0016887    ATPase activity                              
 GO:0006754    ATP biosynthetic process                     
 GO:0005388    calcium-transporting ATPase activity         
 GO:0005391    sodium:potassium-exchanging ATPase activity  
 GO:0006200    ATP catabolic process                        
 GO:0030899    calcium-dependent ATPase activity            
 GO:0005471    ATP:ADP antiporter activity

From this list, select the most appropriate ontological tag. For more details about the meaning of the tag, click in the "Tag" column. For a list of tagged models, click the "# models" column.

Future Plans

Work still needed and plans for the future:

  • Make database dynamic, currently it is rebuilt with each update.
  • Obtain descriptions for all ontology tags;
  • Refined search mechanism (boolean and & or) and user interface for search results ;
  • Add additional model databases as users require.
  • Continued evolution of the database based on user feedback.

Model development and archiving support at https://www.imagwiki.nibib.nih.gov/physiome provided by the following grants: NIH U01HL122199 Analyzing the Cardiac Power Grid, 09/15/2015 - 05/31/2020, NIH/NIBIB BE08407 Software Integration, JSim and SBW 6/1/09-5/31/13; NIH/NHLBI T15 HL88516-01 Modeling for Heart, Lung and Blood: From Cell to Organ, 4/1/07-3/31/11; NSF BES-0506477 Adaptive Multi-Scale Model Simulation, 8/15/05-7/31/08; NIH/NHLBI R01 HL073598 Core 3: 3D Imaging and Computer Modeling of the Respiratory Tract, 9/1/04-8/31/09; as well as prior support from NIH/NCRR P41 RR01243 Simulation Resource in Circulatory Mass Transport and Exchange, 12/1/1980-11/30/01 and NIH/NIBIB R01 EB001973 JSim: A Simulation Analysis Platform, 3/1/02-2/28/07.