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BioModels: ten-year anniversary.

Chelliah V, Juty N, Ajmera I, Ali R, Dumousseau M, Glont M, Hucka M, Jalowicki G, Keating S, Knight-Schrijver V, Lloret-Villas A, Natarajan KN, Pettit JB, Rodriguez N, Schubert M, Wimalaratne SM, Zhao Y, Hermjakob H, Le Novère N, Laibe C - Nucleic Acids Res. (2014)

Bottom Line: BioModels currently hosts over 1200 models derived directly from the literature, as well as in excess of 140,000 models automatically generated from pathway resources.This article describes updates to the resource over this period, which include changes to the user interface, the annotation profiles of models in the curation pipeline, major infrastructure changes, ability to perform online simulations and the availability of model content in Linked Data form.We also outline planned improvements to cope with a diverse array of new challenges.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK viji@ebi.ac.uk.

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BioModels homepage. Due to the growing complexity and number of models, BioModels provides an improved interface to assist users in locating their target model(s). Models can be browsed through a simple listing, viewed through a GO categorization chart, or listed using an expandable GO tree view. Models generated from pathway resources (Path2Models) are listed by category, or alternatively may be viewed thought a taxonomic listing. Search mechanisms are available for both types of models.
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Figure 2: BioModels homepage. Due to the growing complexity and number of models, BioModels provides an improved interface to assist users in locating their target model(s). Models can be browsed through a simple listing, viewed through a GO categorization chart, or listed using an expandable GO tree view. Models generated from pathway resources (Path2Models) are listed by category, or alternatively may be viewed thought a taxonomic listing. Search mechanisms are available for both types of models.

Mentions: Over the years, the web interface to BioModels has seen a number of rounds of improvement culminating in the current version (Figure 2). With the growing number of models and their components, it has become increasingly difficult for a user to efficiently retrieve their target models. This issue will be exacerbated by the growing number of models generated by automated processing of genomic information. BioModels now provides a number of ways to browse models, a much improved search interface, and also permits the programmatic search and download of models through Web Services (15).


BioModels: ten-year anniversary.

Chelliah V, Juty N, Ajmera I, Ali R, Dumousseau M, Glont M, Hucka M, Jalowicki G, Keating S, Knight-Schrijver V, Lloret-Villas A, Natarajan KN, Pettit JB, Rodriguez N, Schubert M, Wimalaratne SM, Zhao Y, Hermjakob H, Le Novère N, Laibe C - Nucleic Acids Res. (2014)

BioModels homepage. Due to the growing complexity and number of models, BioModels provides an improved interface to assist users in locating their target model(s). Models can be browsed through a simple listing, viewed through a GO categorization chart, or listed using an expandable GO tree view. Models generated from pathway resources (Path2Models) are listed by category, or alternatively may be viewed thought a taxonomic listing. Search mechanisms are available for both types of models.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383975&req=5

Figure 2: BioModels homepage. Due to the growing complexity and number of models, BioModels provides an improved interface to assist users in locating their target model(s). Models can be browsed through a simple listing, viewed through a GO categorization chart, or listed using an expandable GO tree view. Models generated from pathway resources (Path2Models) are listed by category, or alternatively may be viewed thought a taxonomic listing. Search mechanisms are available for both types of models.
Mentions: Over the years, the web interface to BioModels has seen a number of rounds of improvement culminating in the current version (Figure 2). With the growing number of models and their components, it has become increasingly difficult for a user to efficiently retrieve their target models. This issue will be exacerbated by the growing number of models generated by automated processing of genomic information. BioModels now provides a number of ways to browse models, a much improved search interface, and also permits the programmatic search and download of models through Web Services (15).

Bottom Line: BioModels currently hosts over 1200 models derived directly from the literature, as well as in excess of 140,000 models automatically generated from pathway resources.This article describes updates to the resource over this period, which include changes to the user interface, the annotation profiles of models in the curation pipeline, major infrastructure changes, ability to perform online simulations and the availability of model content in Linked Data form.We also outline planned improvements to cope with a diverse array of new challenges.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK viji@ebi.ac.uk.

Show MeSH