{"id":10,"date":"2012-10-02T13:32:20","date_gmt":"2012-10-02T10:32:20","guid":{"rendered":"http:\/\/mednis.info\/wp\/?p=10"},"modified":"2012-10-02T13:42:24","modified_gmt":"2012-10-02T10:42:24","slug":"sbml-does-not-support-species-chemical-formulas","status":"publish","type":"post","link":"http:\/\/mednis.info\/wp\/?p=10","title":{"rendered":"LibSBML does not support chemical formulas for species"},"content":{"rendered":"<p>Yes, this is true. You can not store metabolites chemical formulas directly in SBML. I have seen various approaches, like, adding chemical formula to the name of the metabolite or storing formula in the <code>htmlNotes<\/code> tags.<br \/>\nI have been struggling to find an appropriate way to read&#038;write chemical formulas in SBML files until my recent correspondance with authors of libSBML.<\/p>\n<p>Quoting Sarah Keating:<\/p>\n<blockquote><p>The most robust way to currently store this information is to use a miriam compliant annotation to point to a database\/resource that specifies the formula. Section 6 of the SBML Level 3 Version 1 Core specification details of this type of annotation and libSBML provides an API that allows users to interact with the annotation via a class CVTerms (see the addCVTerms example).<br \/>\nDirectly adding chemicalFormula to the Species element is being facilitated by the SBML L3 Flux Balance Constraints package (<a href=\"http:\/\/sbml.org\/Documents\/Specifications\/SBML_Level_3\/Packages\/Flux_Balance_Constraints_%28flux%29\">http:\/\/sbml.org\/Documents\/Specifications\/SBML_Level_3\/Packages\/Flux_Balance_Constraints_%28flux%29<\/a>). LibSBML does provide &#8220;experimental&#8221; support for this package.\n<\/p><\/blockquote>\n","protected":false},"excerpt":{"rendered":"<p>Yes, this is true. You can not store metabolites chemical formulas directly in SBML. I have seen various approaches, like, adding chemical formula to the name of the metabolite or storing formula in the htmlNotes tags. I have been struggling to find an appropriate way to read&#038;write chemical formulas in SBML files until my recent &hellip; <a href=\"http:\/\/mednis.info\/wp\/?p=10\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">LibSBML does not support chemical formulas for species<\/span><\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[4],"tags":[],"_links":{"self":[{"href":"http:\/\/mednis.info\/wp\/index.php?rest_route=\/wp\/v2\/posts\/10"}],"collection":[{"href":"http:\/\/mednis.info\/wp\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/mednis.info\/wp\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/mednis.info\/wp\/index.php?rest_route=\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"http:\/\/mednis.info\/wp\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=10"}],"version-history":[{"count":7,"href":"http:\/\/mednis.info\/wp\/index.php?rest_route=\/wp\/v2\/posts\/10\/revisions"}],"predecessor-version":[{"id":41,"href":"http:\/\/mednis.info\/wp\/index.php?rest_route=\/wp\/v2\/posts\/10\/revisions\/41"}],"wp:attachment":[{"href":"http:\/\/mednis.info\/wp\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=10"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/mednis.info\/wp\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=10"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/mednis.info\/wp\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=10"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}