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BioModels: ten-year anniversary
BioModels (http://www.ebi.ac.uk/biomodels/) is a repository of mathematical models of biological processes. A large set of models is curated to verify both correspondence to the biological process that the model seeks to represent, and reproducibility of the simulation results as described in the co...
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Published in: | Nucleic acids research 2015-01, Vol.43 (Database issue), p.D542-D548 |
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container_issue | Database issue |
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container_title | Nucleic acids research |
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creator | Chelliah, Vijayalakshmi Juty, Nick Ajmera, Ishan Ali, Raza Dumousseau, Marine Glont, Mihai Hucka, Michael Jalowicki, Gaël Keating, Sarah Knight-Schrijver, Vincent Lloret-Villas, Audald Natarajan, Kedar Nath Pettit, Jean-Baptiste Rodriguez, Nicolas Schubert, Michael Wimalaratne, Sarala M Zhao, Yangyang Hermjakob, Henning Le Novère, Nicolas Laibe, Camille |
description | BioModels (http://www.ebi.ac.uk/biomodels/) is a repository of mathematical models of biological processes. A large set of models is curated to verify both correspondence to the biological process that the model seeks to represent, and reproducibility of the simulation results as described in the corresponding peer-reviewed publication. Many models submitted to the database are annotated, cross-referencing its components to external resources such as database records, and terms from controlled vocabularies and ontologies. BioModels comprises two main branches: one is composed of models derived from literature, while the second is generated through automated processes. 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 represents an approximate 60-fold growth for literature-based model numbers alone, since BioModels' first release a decade ago. 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. |
doi_str_mv | 10.1093/nar/gku1181 |
format | article |
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A large set of models is curated to verify both correspondence to the biological process that the model seeks to represent, and reproducibility of the simulation results as described in the corresponding peer-reviewed publication. Many models submitted to the database are annotated, cross-referencing its components to external resources such as database records, and terms from controlled vocabularies and ontologies. BioModels comprises two main branches: one is composed of models derived from literature, while the second is generated through automated processes. 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 represents an approximate 60-fold growth for literature-based model numbers alone, since BioModels' first release a decade ago. 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.</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gku1181</identifier><identifier>PMID: 25414348</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Computer Simulation ; Database Issue ; Databases, Factual ; Internet ; Models, Biological</subject><ispartof>Nucleic acids research, 2015-01, Vol.43 (Database issue), p.D542-D548</ispartof><rights>The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.</rights><rights>The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. 2015</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c451t-4eddadd0adb45cdae1dda02920ce854c6dc9499b165ab284657266d7cdc316433</citedby><cites>FETCH-LOGICAL-c451t-4eddadd0adb45cdae1dda02920ce854c6dc9499b165ab284657266d7cdc316433</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383975/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383975/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25414348$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Chelliah, Vijayalakshmi</creatorcontrib><creatorcontrib>Juty, Nick</creatorcontrib><creatorcontrib>Ajmera, Ishan</creatorcontrib><creatorcontrib>Ali, Raza</creatorcontrib><creatorcontrib>Dumousseau, Marine</creatorcontrib><creatorcontrib>Glont, Mihai</creatorcontrib><creatorcontrib>Hucka, Michael</creatorcontrib><creatorcontrib>Jalowicki, Gaël</creatorcontrib><creatorcontrib>Keating, Sarah</creatorcontrib><creatorcontrib>Knight-Schrijver, Vincent</creatorcontrib><creatorcontrib>Lloret-Villas, Audald</creatorcontrib><creatorcontrib>Natarajan, Kedar Nath</creatorcontrib><creatorcontrib>Pettit, Jean-Baptiste</creatorcontrib><creatorcontrib>Rodriguez, Nicolas</creatorcontrib><creatorcontrib>Schubert, Michael</creatorcontrib><creatorcontrib>Wimalaratne, Sarala M</creatorcontrib><creatorcontrib>Zhao, Yangyang</creatorcontrib><creatorcontrib>Hermjakob, Henning</creatorcontrib><creatorcontrib>Le Novère, Nicolas</creatorcontrib><creatorcontrib>Laibe, Camille</creatorcontrib><title>BioModels: ten-year anniversary</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>BioModels (http://www.ebi.ac.uk/biomodels/) is a repository of mathematical models of biological processes. 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language | eng |
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source | Oxford Open (Open Access); PubMed Central |
subjects | Computer Simulation Database Issue Databases, Factual Internet Models, Biological |
title | BioModels: ten-year anniversary |
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