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type="application/ld+json">{"@context":"https://schema.org/","@type":"DataSet","@id":"https://www.expasy.org/","http://purl.org/dc/terms/conformsTo":{"@id":"https://bioschemas.org/profiles/Dataset/1.0-RELEASE","@type":"CreativeWork"},"name":"Expasy","description":"Expasy is the bioinformatics resource portal of the SIB Swiss Institute of Bioinformatics.","url":"https://www.expasy.org/","identifier":"https://doi.org/10.25504/FAIRsharing.ceeffa","thumbnailUrl":"https://www.expasy.org/images/expasy-homepage.png","keywords":"bioinformatics, registry, resource, database, tool, SIB, Swiss, Swiss Institute of Bioinformatics","isAccessibleForFree":true,"potentialAction":{"@type":"SearchAction","target":"https://www.expasy.org/search/{search_term_string}?type=keyword","query-input":"required name=search_term_string"},"citation":{"@type":"ScholarlyArticle","name":"Expasy, the Swiss Bioinformatics Resource Portal, as designed by its users.","author":[{"@type":"Person","givenName":"Severine","familyName":"Duvaud","identifier":"http://orcid.org/0000-0001-7892-9678"},{"@type":"Person","givenName":"Chiara","familyName":"Gabella","identifier":"http://orcid.org/0000-0002-7104-5025"},{"@type":"Person","givenName":"Frederique","familyName":"Lisacek","identifier":"https://orcid.org/0000-0002-0948-4537"},{"@type":"Person","givenName":"Heinz","familyName":"Stockinger","identifier":"https://orcid.org/0000-0003-4666-7719"},{"@type":"Person","givenName":"Vassilios","familyName":"Ioannidis","identifier":"https://orcid.org/0000-0002-4209-2578"},{"@type":"Person","givenName":"Christine","familyName":"Durinx","identifier":"https://orcid.org/0000-0003-4237-8899"}],"identifier":"http://dx.doi.org/10.1093/nar/gkab225","sameas":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8265094/"},"provider":{"@type":"Organization","sameAs":"https://ror.org/002n09z45","name":"SIB Swiss Institute of 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high-quality biological data resources </label> <input id="search" name="search" type="search" required="required" class="field search__input"> <button type="submit" class="btn search__submit"><svg aria-hidden="true" focusable="false" role="img" class="icon icon--search icon--150"> <use xlink:href="/_nuxt/img/icons.2l2yMrcx.svg#search"></use></svg></button></div> <div class="text-sm"> e.g. <a href="/search/blast">BLAST</a>, <a href="/search/uniprot">UniProt</a>, <a href="/search/msh6">MSH6</a>, <a href="/search/albumin">Albumin</a>... </div> </form></div> <div class="container"><div class="resource-page"><div class="flex-grid flex-grid--md flex-grid--even"><div class="lg:w-2/3 xl:w-3/4 flex-grid__item w-full"><section class="flex flex-col pt-5 max-md:pb-5 border-neutral-200 border-t"><div class="flex-auto"><div class="mb-3 md:flex md:items-center"><div class="md:flex-1"><h1 class="mb-5"> EnzChemRED </h1></div> <ul aria-label="Resource categories and types" class="resource-page__filters"><li class="resource-page__filter"><svg aria-hidden="true" focusable="false" role="img" class="text-primary-500 icon icon--protein icon--150"> <use xlink:href="/_nuxt/img/icons.2l2yMrcx.svg#protein"></use></svg> <div class="flex-1"> Proteins & Proteomes </div></li> <li class="resource-page__filter"><svg aria-hidden="true" focusable="false" role="img" class="icon icon--db icon--150"> <use xlink:href="/_nuxt/img/icons.2l2yMrcx.svg#db"></use></svg> <div class="flex-1"> Database </div></li></ul></div> <div class="mb-8">EnzChemRED is a training and benchmarking dataset to support the development of Natural Language Processing (NLP) methods such as (large) language models that can assist enzyme curation. EnzChemRED consists of 1,210 expert curated PubMed abstracts in which enzymes and the chemical reactions they catalyze are annotated using identifiers from the UniProt Knowledgebase (UniProtKB) and the ontology of Chemical Entities of Biological Interest (ChEBI).</div> <div class="flex flex-col items-start gap-8 lg:items-center lg:gap-12 lg:flex-row"><div class="flex items-start justify-center lg:justify-start"><a href="https://ftp.expasy.org/databases/rhea/nlp/" target="_blank" rel="noopener noreferer" class="btn btn--primary"> Browse the resource website </a></div> <div class="flex flex-col items-start gap-3"> <div><a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC11384730/" target="_blank" rel="noopener noreferer" class="flex items-center gap-2 no-underline"><svg aria-hidden="true" focusable="false" role="img" class="icon icon--book icon--150"> <use xlink:href="/_nuxt/img/icons.2l2yMrcx.svg#book"></use></svg> <span>Read the documentation</span></a></div> </div></div></div> <footer class="p-5 resource-page__info bg-neutral-100 border-neutral-200 border-t border-b"><div><p>Developed by the <a target="_blank" rel="noopener noreferrer nofollow" href="https://www.sib.swiss/alan-bridge-group" tt-mode="url">Swiss-Prot group</a> and partners at National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), and Dalian University of Technology; supported by the <a target="_blank" rel="noopener noreferrer nofollow" href="https://www.sib.swiss/database-software-tools/sib-resources" tt-mode="url">SIB Swiss Institute of Bioinformatics</a>.</p></div> This resource is released under a Creative Commons Attribution International license <a href="https://creativecommons.org/licenses/by/4.0/" target="_blank" rel="noopener noreferer" class="btn"> CC BY 4.0</a>. </footer></section></div> <aside class="lg:w-1/3 xl:w-1/4 flex-grid__item w-full"><div class="resource-page__ontologie"><section class="p-5 bg-neutral-100 border-neutral-200 border-t border-b"><h2 class="mb-5 h4"> What you can do with this resource </h2> <ul><li class="inline-block"><a href="/search/Information%20extraction?type=keyword"> Information extraction </a></li></ul></section> <section class="p-5 bg-neutral-100 border-neutral-200 border-t border-b"><h2 class="mb-5 h4"> Browse these keywords in Expasy </h2> <ul><li class="inline-block"><a href="/search/Data%20reference?type=keyword"> Data reference </a><span>,聽</span></li><li class="inline-block"><a href="/search/Reaction%20data?type=keyword"> Reaction data </a><span>,聽</span></li><li class="inline-block"><a href="/search/Abstract?type=keyword"> Abstract </a><span>,聽</span></li><li class="inline-block"><a href="/search/Natural%20language%20processing?type=keyword"> Natural language processing </a><span>,聽</span></li><li class="inline-block"><a href="/search/ChEBI%20ID?type=keyword"> ChEBI ID </a><span>,聽</span></li><li class="inline-block"><a href="/search/PubMed%20ID?type=keyword"> PubMed ID </a><span>,聽</span></li><li class="inline-block"><a href="/search/TSV?type=keyword"> TSV </a><span>,聽</span></li><li class="inline-block"><a href="/search/BioC?type=keyword"> BioC </a><span>,聽</span></li><li class="inline-block"><a href="/search/Enzymes?type=keyword"> Enzymes </a><span>,聽</span></li><li class="inline-block"><a href="/search/Enzyme%20name?type=keyword"> Enzyme name </a></li></ul></section></div></aside></div></div> <section class="py-5 mt-10 border-neutral-200 border-t"><h2 class="mb-5 h3"> You might also be interested in </h2> <ul class="flex-grid flex-grid--multiline flex-grid--even"><li class="sm:w-1/2 md:w-1/2 lg:w-1/3 xl:w-1/4 flex-grid__item w-full"><article class="resource"><div class="flex items-center mb-3"><div class="flex-1 text-primary-500"><ul><li class="inline-block mr-2 last:mr-0"><svg aria-hidden="true" focusable="false" role="img" class="icon icon--text-mining icon--125"> <use 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class="resource__link"><h3 class="h5"> SwissLipids </h3></a> <div class="text-sm leading-snug mt-1"> Knowledge resource for lipids </div></article></li><li class="sm:w-1/2 md:w-1/2 lg:w-1/3 xl:w-1/4 flex-grid__item w-full"><article class="resource"><div class="flex items-center mb-3"><div class="flex-1 text-primary-500"><ul><li class="inline-block mr-2 last:mr-0"><svg aria-hidden="true" focusable="false" role="img" class="icon icon--protein icon--125"> <use xlink:href="/_nuxt/img/icons.2l2yMrcx.svg#protein"></use></svg> <ul aria-label="Resource Categories"><li class="inline-block sr-only"> Proteins & Proteomes </li></ul></li><li class="inline-block mr-2 last:mr-0"><svg aria-hidden="true" focusable="false" role="img" class="icon icon--sys-biology icon--125"> <use xlink:href="/_nuxt/img/icons.2l2yMrcx.svg#sys-biology"></use></svg> <ul aria-label="Resource Categories"><li class="inline-block sr-only"> Systems Biology </li><li class="inline-block sr-only"><span>, </span> Metabolomics 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Proteins & Proteomes </li></ul></li></ul></div> <div class="text-neutral-500"><ul><li class="inline-block mr-2 last:mr-0"><svg aria-hidden="true" focusable="false" role="img" class="icon icon--tool icon--125"> <use xlink:href="/_nuxt/img/icons.2l2yMrcx.svg#tool"></use></svg> <ul aria-label="Resource Types"><li class="inline-block sr-only"> Software tool </li></ul></li></ul></div></div> <a href="/resources/peptidecutter" class="resource__link"><h3 class="h5"> PeptideCutter </h3></a> <div class="text-sm leading-snug mt-1"> Potential cleavage sites in a protein </div></article></li><li class="sm:w-1/2 md:w-1/2 lg:w-1/3 xl:w-1/4 flex-grid__item w-full"><article class="resource"><div class="flex items-center mb-3"><div class="flex-1 text-primary-500"><ul><li class="inline-block mr-2 last:mr-0"><svg aria-hidden="true" focusable="false" role="img" class="icon icon--protein icon--125"> <use xlink:href="/_nuxt/img/icons.2l2yMrcx.svg#protein"></use></svg> <ul aria-label="Resource Categories"><li 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Categories"><li class="inline-block sr-only"> Systems Biology </li><li class="inline-block sr-only"><span>, </span> Metabolomics </li></ul></li><li class="inline-block mr-2 last:mr-0"><svg aria-hidden="true" focusable="false" role="img" class="icon icon--protein icon--125"> <use xlink:href="/_nuxt/img/icons.2l2yMrcx.svg#protein"></use></svg> <ul aria-label="Resource Categories"><li class="inline-block sr-only"> Proteins & Proteomes </li></ul></li></ul></div> <div class="text-neutral-500"><ul><li class="inline-block mr-2 last:mr-0"><svg aria-hidden="true" focusable="false" role="img" class="icon icon--db icon--125"> <use xlink:href="/_nuxt/img/icons.2l2yMrcx.svg#db"></use></svg> <ul aria-label="Resource Types"><li class="inline-block sr-only"> Database </li></ul></li></ul></div></div> <a href="/resources/sparql-rhea-db-org" class="resource__link"><h3 class="h5"> Rhea SPARQL endpoint </h3></a> <div class="text-sm leading-snug mt-1"> SPARQL access to the Rhea knowledgebase </div></article></li><li class="sm:w-1/2 md:w-1/2 lg:w-1/3 xl:w-1/4 flex-grid__item w-full"><article class="resource"><div class="flex items-center mb-3"><div class="flex-1 text-primary-500"><ul><li class="inline-block mr-2 last:mr-0"><svg aria-hidden="true" focusable="false" role="img" class="icon icon--sys-biology icon--125"> <use xlink:href="/_nuxt/img/icons.2l2yMrcx.svg#sys-biology"></use></svg> <ul aria-label="Resource Categories"><li class="inline-block sr-only"> Glycomics </li><li class="inline-block sr-only"><span>, </span> Systems Biology </li></ul></li></ul></div> <div class="text-neutral-500"><ul><li class="inline-block mr-2 last:mr-0"><svg aria-hidden="true" focusable="false" role="img" class="icon icon--tool icon--125"> <use xlink:href="/_nuxt/img/icons.2l2yMrcx.svg#tool"></use></svg> <ul aria-label="Resource Types"><li class="inline-block sr-only"> Software tool </li></ul></li></ul></div></div> <a href="/resources/hmo-glycologue" class="resource__link"><h3 class="h5"> 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genomes",license_type:{id:g,title:t,link_url:u,link_label:v,created_at:b,updated_at:w},categories:[{id:s,title:Z,icon:J,children:[{id:B,title:O,parent_id:s,icon:a,created_at:b,updated_at:b},{id:F,title:R,parent_id:s,icon:a,created_at:b,updated_at:b}]}],created_at:V,updated_at:"2024-10-16T12:08:05.000000Z",typesAndCategories:[s,d,c]},{id:588,title:"PACMAN",slug:"pacman",pinned:e,types:[{id:c,icon:c,title:i}],url:"https:\u002F\u002Fbugfri.unibe.ch\u002Fpacman\u002F",documentation_url:a,tutorial_url:a,short_description:"Publication quality images of DNA locations",license_type:a,categories:[{id:g,title:r,icon:m,children:[]}],created_at:"2020-06-24T11:29:27.000000Z",updated_at:"2024-07-16T15:35:14.000000Z",typesAndCategories:[g,c]},{id:736,title:"OMArk",slug:"omark",pinned:e,types:[{id:c,icon:c,title:i}],url:"https:\u002F\u002Fomark.omabrowser.org\u002F",documentation_url:a,tutorial_url:a,short_description:"OMArk determines the quality and completeness of gene 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4.0","2022-04-14T10:32:25.000000Z","Glycomics",9,16,"Metabolomics",7,15,"Transcriptomics","Lipidomics",8,"Systems Biology","2020-06-10T11:03:54.000000Z",3,"evolution","stru-biology",11,12,17,"Evolution biology",true,10,"Population genetics","Medicinal chemistry","Structural analysis","Metagenomics","2020-06-18T13:59:48.000000Z","Text mining & Machine learning","text-mining","Genes & Genomes","Evolution & Phylogeny","Drug design","Structural Biology","the","the GNU General Public License","https:\u002F\u002Fwww.gnu.org\u002Flicenses\u002Fgpl-3.0.en.html","GPL 3","2020-07-16T10:56:27.000000Z","2020-06-18T13:59:49.000000Z","a Creative Commons Attribution-ShareAlike International license","https:\u002F\u002Fcreativecommons.org\u002Flicenses\u002Fby-sa\u002F4.0\u002F","CC BY-SA 4.0","2022-04-14T10:32:09.000000Z","https:\u002F\u002Fopensource.org\u002Flicenses\u002FMIT","MIT License","2020-06-23T16:41:42.000000Z","a Creative Commons Universal license","https:\u002F\u002Fcreativecommons.org\u002Fpublicdomain\u002Fzero\u002F1.0\u002F","CC0","2022-04-14T10:32:34.000000Z",20,"2023-03-23T09:28:20.000000Z","https:\u002F\u002Fwww.youtube.com\u002Fwatch?v=9S-A4gBz8Cg","a free license for academic use. A licence is required for private companies.","http:\u002F\u002Fwww.swisstargetprediction.ch\u002Fcontact.php","Contact the team","2020-07-16T11:12:03.000000Z","2025-02-05T09:02:28.000000Z",21,740,"EnzChemRED","enzchemred","https:\u002F\u002Fftp.expasy.org\u002Fdatabases\u002Frhea\u002Fnlp\u002F","https:\u002F\u002Fpmc.ncbi.nlm.nih.gov\u002Farticles\u002FPMC11384730\u002F","Enzyme Chemistry Relation Extraction Dataset","2024-11-18T08:54:45.000000Z","2024-11-18T12:00:56.000000Z",559,0,700,"SIBiLS","sibils","https:\u002F\u002Fsibils.org\u002F","Personalized information retrieval from the literature","2020-12-01T16:16:51.000000Z","2024-11-04T14:25:53.000000Z","\u003Cp\u003EDeveloped by the \u003Ca href=\"https:\u002F\u002Fwww.sib.swiss\u002Fpatrick-ruch-group\" rel=\"noopener noreferrer nofollow\"\u003EText Mining 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Biology\u003C\u002Fspan\u003E group\u003C\u002Fa\u003E.\u003C\u002Fp\u003E",611,"GlycoDigest","glycodigest","https:\u002F\u002Fglycoproteome.expasy.org\u002Fglycodigest\u002F","In silico digestion of glycans by exoglycosidases","2020-06-26T17:54:21.000000Z","2020-07-16T12:08:34.000000Z","\u003Cp\u003EDeveloped by the \u003Ca href=\"https:\u002F\u002Fwww.sib.swiss\u002Ffrederique-lisacek-group\" rel=\"noopener noreferrer nofollow\"\u003EProteome Informatics group\u003C\u002Fa\u003E.\u003C\u002Fp\u003E",18,"SwissLipids","swisslipids","https:\u002F\u002Fwww.swisslipids.org\u002F#\u002F","Knowledge resource for lipids","2024-11-08T13:34:17.000000Z",630,"Rhea","rhea","https:\u002F\u002Fwww.rhea-db.org\u002F","https:\u002F\u002Fwww.rhea-db.org\u002Fhelp","https:\u002F\u002Fwww.rhea-db.org\u002Fhelp\u002Fsearching-rhea","Expert-curated database of biochemical reactions","2020-06-30T16:31:34.000000Z","2024-11-08T08:39:50.000000Z",639,"PeptideCutter","peptidecutter","https:\u002F\u002Fweb.expasy.org\u002Fpeptide_cutter\u002F","https:\u002F\u002Fweb.expasy.org\u002Fpeptide_cutter\u002Fpeptidecutter_instructions.html","Potential cleavage sites in a protein","2020-06-30T17:51:00.000000Z","2025-02-20T11:03:40.000000Z","ENZYME","enzyme","https:\u002F\u002Fenzyme.expasy.org\u002F","https:\u002F\u002Fftp.expasy.org\u002Fdatabases\u002Fenzyme\u002Fenzuser.txt","Enzyme nomenclature database","2025-02-11T12:46:37.000000Z",698,"Rhea SPARQL endpoint","sparql-rhea-db-org","https:\u002F\u002Fsparql.rhea-db.org","https:\u002F\u002Fftp.expasy.org\u002Fdatabases\u002Frhea\u002Frdf\u002Frhea_rdf_documentation.pdf","https:\u002F\u002Fgithub.com\u002Fsib-swiss\u002Fsparql-training\u002Ftree\u002Fmaster\u002Frhea","SPARQL access to the Rhea knowledgebase","2020-11-25T10:00:22.000000Z","2024-11-11T10:42:44.000000Z","\u003Cp\u003EDeveloped by the \u003Ca href=\"https:\u002F\u002Fwww.sib.swiss\u002Falan-bridge-group\" rel=\"noopener noreferrer nofollow\"\u003ESwiss-Prot group\u003C\u002Fa\u003E and supported by the \u003Ca href=\"https:\u002F\u002Fwww.sib.swiss\" rel=\"noopener noreferrer nofollow\"\u003E\u003Cu\u003ESIB Swiss Institute of Bioinformatics\u003C\u002Fu\u003E\u003C\u002Fa\u003E.\u003C\u002Fp\u003E",705,"HMO-Glycologue","hmo-glycologue","https:\u002F\u002Fglycologue.org\u002Fm\u002F","Simulator of Human Milk Oligosaccharide synthesis","2021-01-21T19:03:24.000000Z","2024-08-21T13:51:01.000000Z",719,"SwissLipids SPARQL endpoint","swisslipids-sparql-endpoint","https:\u002F\u002Fbeta.sparql.swisslipids.org\u002F","SPARQL access to the SwissLipids knowledgebase","2022-09-16T09:38:49.000000Z","2024-11-11T10:43:50.000000Z",720,"MetaNetX SPARQL endpoint","metanetx-sparql-endpoint","https:\u002F\u002Frdf.metanetx.org\u002F","SPARQL access to MetaNetX","2022-09-16T09:47:08.000000Z","2025-01-09T15:40:17.000000Z","https:\u002F\u002Fmyhits.sib.swiss\u002Fcgi-bin\u002Fhelp","https:\u002F\u002Fwww.apache.org\u002Flicenses\u002FLICENSE-2.0","Apache License","2020-06-23T16:41:00.000000Z","MHC Motif Atlas","fastsimcoal","pftools","a Creative Commons Attribution-NonCommercial-NoDerivatives International license","https:\u002F\u002Fcreativecommons.org\u002Flicenses\u002Fby-nc-nd\u002F4.0\u002F","CC BY-NC-ND 4.0","2022-04-14T10:31:12.000000Z","2025-01-09T15:16:33.000000Z","https:\u002F\u002Fwww.uniprot.org\u002Fhelp","2025-01-23T12:45:44.000000Z","rawrr",25,"the GNU Affero General Public License","https:\u002F\u002Fwww.gnu.org\u002Flicenses\u002Fagpl-3.0.en.html","GNU AGPL","https:\u002F\u002Fswissmodel.expasy.org\u002F","https:\u002F\u002Fswissmodel.expasy.org\u002Fdocs\u002Fhelp","https:\u002F\u002Fswissmodel.expasy.org\u002Fdocs\u002Ftutorial","https:\u002F\u002Fprosite.expasy.org\u002Fprosite_license.html","PROSITE license","2020-07-16T11:36:48.000000Z","2022-04-14T10:30:04.000000Z","https:\u002F\u002Fwww.bgee.org\u002Fsupport\u002Ftutorials","2025-01-30T13:15:05.000000Z","2024-03-01T14:11:56.000000Z"));</script><script src="/_nuxt/ab75555.js" defer></script><script src="/_nuxt/40c1276.js" defer></script><script src="/_nuxt/7a4419e.js" defer></script><script src="/_nuxt/f177c5f.js" defer></script><script src="/_nuxt/b680205.js" defer></script> </body> </html>