{"id":141879,"date":"2011-10-24T01:45:42","date_gmt":"2011-10-24T01:45:42","guid":{"rendered":"https:\/\/staging2.simonw59.sg-host.com\/sustainable-model-building-the-role-of-standards-and-biological-semantics\/"},"modified":"2022-05-26T13:43:14","modified_gmt":"2022-05-26T13:43:14","slug":"sustainable-model-building-the-role-of-standards-and-biological-semantics","status":"publish","type":"post","link":"https:\/\/force11.org\/post\/sustainable-model-building-the-role-of-standards-and-biological-semantics\/","title":{"rendered":"Sustainable Model Building the Role of Standards and Biological Semantics"},"content":{"rendered":"<div class=\"ct_body\">\n<p>Authors: Krause, Falko<\/p>\n<p>Schulz, Marvin<\/p>\n<p>Swainston, Neil<\/p>\n<p>Liebermeister, Wolfram<\/p>\n<p>Systems biology models can be reused within new simulation scenarios, as parts of more complex models or as sources of biochemical knowledge. Reusability does not come by itself but has to be ensured while creating a model. Most important, models should be designed to remain valid in different contexts-for example, for different experimental conditions-and be published in a standardized and well-documented form. Creating reusable models is worthwhile, but it requires some efforts when a model is developed, implemented, documented, and published. Minimum requirements for published systems biology models have been formulated by the MIRIAM initiative. Main criteria are completeness of information and documentation, availability of machine-readable models in standard formats, and semantic annotations connecting the model elements with entries in biological Web resources. In this chapter, we discuss the assumptions behind bottom-up modeling; present important standards like MIRIAM, the Systems Biology Markup Language (SBML), and the Systems Biology Graphical Notation (SBGN); and describe software tools and services for handling semantic annotations. Finally, we show how standards can facilitate the construction of large metabolic network models.<\/p>\n<p>Journal: Methods in Enzymology 2011 vol 500 pagination 371-95<\/p>\n<p>PMID: 21943907<\/p>\n<p>PMCID: 0<\/p>\n<p>ISSN: 1557-7988<\/p>\n<\/div>\n<p class=\"ct_meta\"><span class=\"ct_label\">Archive:<\/span>&nbsp;<a class=\"ct_archive\" target=\"_blank\" href=\"https:\/\/archive.force11.net\/node\/6356\" rel=\"noopener\">https:\/\/archive.force11.net\/node\/6356<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Authors: Krause, Falko Schulz, Marvin Swainston, Neil Liebermeister, Wolfram Systems biology models can be reused within new simulation scenarios, as parts of more complex models or as sources of biochemical knowledge. Reusability does not come by itself but has to be ensured while creating a model. Most important, models should be designed to remain valid &#8230; <a title=\"Sustainable Model Building the Role of Standards and Biological Semantics\" class=\"read-more\" href=\"https:\/\/force11.org\/post\/sustainable-model-building-the-role-of-standards-and-biological-semantics\/\" aria-label=\"More on Sustainable Model Building the Role of Standards and Biological Semantics\">Read more<\/a><\/p>\n","protected":false},"author":205903,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"advgb_blocks_editor_width":"","advgb_blocks_columns_visual_guide":"","footnotes":""},"categories":[151],"tags":[],"force11":[],"blog_series":[],"working_group":[],"class_list":["post-141879","post","type-post","status-publish","format-standard","hentry","category-news"],"acf":[],"author_meta":{"display_name":"FORCE11 Admin","author_link":"\/members\/admin"},"featured_img":null,"coauthors":[],"tax_additional":{"categories":{"linked":["<a href=\"https:\/\/force11.org\/category\/news\/\" class=\"advgb-post-tax-term\">News<\/a>"],"unlinked":["<span class=\"advgb-post-tax-term\">News<\/span>"]}},"comment_count":"0","relative_dates":{"created":"Posted 14 years ago","modified":"Updated 4 years ago"},"absolute_dates":{"created":"Posted on 24 Oct 2011","modified":"Updated on 26 May 2022"},"absolute_dates_time":{"created":"Posted on 24 Oct 2011 01:45","modified":"Updated on 26 May 2022 13:43"},"featured_img_caption":"","series_order":"","_links":{"self":[{"href":"https:\/\/force11.org\/wp-json\/wp\/v2\/posts\/141879","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/force11.org\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/force11.org\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/force11.org\/wp-json\/wp\/v2\/users\/205903"}],"replies":[{"embeddable":true,"href":"https:\/\/force11.org\/wp-json\/wp\/v2\/comments?post=141879"}],"version-history":[{"count":0,"href":"https:\/\/force11.org\/wp-json\/wp\/v2\/posts\/141879\/revisions"}],"wp:attachment":[{"href":"https:\/\/force11.org\/wp-json\/wp\/v2\/media?parent=141879"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/force11.org\/wp-json\/wp\/v2\/categories?post=141879"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/force11.org\/wp-json\/wp\/v2\/tags?post=141879"},{"taxonomy":"force11","embeddable":true,"href":"https:\/\/force11.org\/wp-json\/wp\/v2\/force11?post=141879"},{"taxonomy":"blog_series","embeddable":true,"href":"https:\/\/force11.org\/wp-json\/wp\/v2\/blog_series?post=141879"},{"taxonomy":"working_group","embeddable":true,"href":"https:\/\/force11.org\/wp-json\/wp\/v2\/working_group?post=141879"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}