Journal: BMC Systems Biology

Article Title: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

doi: 10.1186/1752-0509-4-92

Figure Lengend Snippet: Database structure . Shown here is a schematic of the relational database structure used by BioModels Database. It depicts the different database tables and their relationships. The three main steps of the pipeline (curation, annotation and publication) are organized by the three main tables, cura, anno and publ , respectively. The two branches can be distinguished by the fact that the tables related to the non-curated branch are prefixed with uncura .

Article Snippet: The BioModels Database server software uses a typical three-tier architecture, in which the data storage, processing and presentation are logically separated.

Techniques:

Journal: BMC Systems Biology

Article Title: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

doi: 10.1186/1752-0509-4-92

Figure Lengend Snippet: BioModels Database pipeline . The BioModels Database pipeline encompasses all the steps undergone by each model, from its submission to its publication. This figure illustrates the sequence of steps. It encompasses both public branches of the database (curated and non-curated) as well as the possibility of curating and annotating models already published in the non-curated branch.

Article Snippet: The BioModels Database server software uses a typical three-tier architecture, in which the data storage, processing and presentation are logically separated.

Techniques: Sequencing

Journal: BMC Systems Biology

Article Title: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

doi: 10.1186/1752-0509-4-92

Figure Lengend Snippet: Models tree based on Gene Ontology . BioModels Database provides users with three primary facilities for finding and discovering models: the system's search interface, the browsable list of all models, and an alternative list based on Gene Ontology (GO) terms. A screen image of the last alternative is shown here. The GO-based view is derived from the annotations of models in the database; the annotations of all models are collected and used to generate a pruned GO tree, and this tree can be browsed in order to find models annotated with a specific GO term.

Article Snippet: The BioModels Database server software uses a typical three-tier architecture, in which the data storage, processing and presentation are logically separated.

Techniques: Derivative Assay

Journal: BMC Systems Biology

Article Title: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

doi: 10.1186/1752-0509-4-92

Figure Lengend Snippet: Thematic content of models . Categorisation of models in BioModels Database using the Gene Ontology (GO) terms present in each model's annotations. This chart was generated by enumerating models in the database whose annotations refer to children of the GO terms listed here, after first removing certain GO terms ( translation , GO:0006350; transcription , GO:0006412; and cellular metabolic process , GO:0044237) that appear across different categories, and hence would have biased the analysis.

Article Snippet: The BioModels Database server software uses a typical three-tier architecture, in which the data storage, processing and presentation are logically separated.

Techniques: Generated

Journal: BMC Systems Biology

Article Title: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

doi: 10.1186/1752-0509-4-92

Figure Lengend Snippet: Search engine . The BioModels Database search engine processes three different types of data in order to provide an accurate result. First, it searches the annotations (by querying the internal database), then the models (using Lucene), and finally, data linked from external resources. Searching for the last is accomplished via direct connection to remote databases and by using remote web services. Ultimately, all the results are collected, processed to remove duplicates, then classified based on which branch the models come from, ordered, and finally, returned to the user.

Article Snippet: The BioModels Database server software uses a typical three-tier architecture, in which the data storage, processing and presentation are logically separated.

Techniques:

Journal: BMC Systems Biology

Article Title: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

doi: 10.1186/1752-0509-4-92

Figure Lengend Snippet: Taxonomic search . When a user's search is based on a taxonomic term, the BioModels Database search algorithm considers the entire taxonomic hierarchy. For example, searching for the term "mammalia" will catch not only models annotated with the term Mammalia , but also models annotated with terms related to it, such as Metazoa , Homo sapiens or Rattus norvegicus (represented in red in this figure).

Article Snippet: The BioModels Database server software uses a typical three-tier architecture, in which the data storage, processing and presentation are logically separated.

Techniques:

Journal: BMC Systems Biology

Article Title: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

doi: 10.1186/1752-0509-4-92

Figure Lengend Snippet: View of a model page . This screen image shows the interface of BioModels Database as it displays the model Kholodenko1999 EGFRsignaling (BIOMD0000000048). As illustrated here, the display of a model in the system is divided into several areas. The areas have been highlighted and numbered here for discussion purposes. The first area, across the top, contains general links for accessing the various features of BioModels Database. The second allows the user to perform actions specific to the model currently displayed (for example, to download the model in various formats or simulate it online). The third area contains all the different views of the model in separate tabbed window panes; each tabbed area is dedicated to a given aspect of the model (e.g., overview, mathematics, model entities, parameters, curation information, etc.). The fourth area is used to display content specific to the currently selected view of the model.

Article Snippet: The BioModels Database server software uses a typical three-tier architecture, in which the data storage, processing and presentation are logically separated.

Techniques:

Journal: BMC Systems Biology

Article Title: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

doi: 10.1186/1752-0509-4-92

Figure Lengend Snippet: Growth of BioModels Database . Graph depicting the number of models (green) and the number of reactions (yellow) stored in BioModels Database at each release of the database made so far. The number of reactions includes SBML "rate rules", since some models only use rate rules. The graph illustrates that not only has the number of models increased approximately ten-fold since 2005, but the average complexity of those models has nearly tripled in the same period.

Article Snippet: The BioModels Database server software uses a typical three-tier architecture, in which the data storage, processing and presentation are logically separated.

Techniques: