The BioCyc collection of microbial genomes and metabolic pathways
Abstract BioCyc.org is a microbial genome Web portal that combines thousands of genomes with additional information inferred by computer programs, imported from other databases and curated from the biomedical literature by biologist curators. BioCyc also provides an extensive range of query tools, v...
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| Veröffentlicht in: | Briefings in bioinformatics 2019-07, Vol.20 (4), p.1085-1093 |
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| container_title | Briefings in bioinformatics |
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| creator | Karp, Peter D Billington, Richard Caspi, Ron Fulcher, Carol A Latendresse, Mario Kothari, Anamika Keseler, Ingrid M Krummenacker, Markus Midford, Peter E Ong, Quang Ong, Wai Kit Paley, Suzanne M Subhraveti, Pallavi |
| description | Abstract
BioCyc.org is a microbial genome Web portal that combines thousands of genomes with additional information inferred by computer programs, imported from other databases and curated from the biomedical literature by biologist curators. BioCyc also provides an extensive range of query tools, visualization services and analysis software. Recent advances in BioCyc include an expansion in the content of BioCyc in terms of both the number of genomes and the types of information available for each genome; an expansion in the amount of curated content within BioCyc; and new developments in the BioCyc software tools including redesigned gene/protein pages and metabolite pages; new search tools; a new sequence-alignment tool; a new tool for visualizing groups of related metabolic pathways; and a facility called SmartTables, which enables biologists to perform analyses that previously would have required a programmer’s assistance. |
| doi_str_mv | 10.1093/bib/bbx085 |
| format | Article |
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BioCyc.org is a microbial genome Web portal that combines thousands of genomes with additional information inferred by computer programs, imported from other databases and curated from the biomedical literature by biologist curators. BioCyc also provides an extensive range of query tools, visualization services and analysis software. Recent advances in BioCyc include an expansion in the content of BioCyc in terms of both the number of genomes and the types of information available for each genome; an expansion in the amount of curated content within BioCyc; and new developments in the BioCyc software tools including redesigned gene/protein pages and metabolite pages; new search tools; a new sequence-alignment tool; a new tool for visualizing groups of related metabolic pathways; and a facility called SmartTables, which enables biologists to perform analyses that previously would have required a programmer’s assistance.</description><identifier>ISSN: 1467-5463</identifier><identifier>ISSN: 1477-4054</identifier><identifier>EISSN: 1477-4054</identifier><identifier>DOI: 10.1093/bib/bbx085</identifier><identifier>PMID: 29447345</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Biologists ; Computational Biology ; Computer programs ; Databases, Genetic ; Escherichia coli - genetics ; Escherichia coli - metabolism ; Genome, Microbial ; Genomes ; Genomics ; Internet ; Metabolic Networks and Pathways ; Metabolic pathways ; Metabolites ; Microorganisms ; Models, Biological ; Search Engine ; Software</subject><ispartof>Briefings in bioinformatics, 2019-07, Vol.20 (4), p.1085-1093</ispartof><rights>The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com 2017</rights><rights>The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.</rights><rights>The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c432t-3c409cd992ec1c4dfb0ab4a92d7d5f9a5ddad63b428034fd68b00bd7378d9e403</citedby><cites>FETCH-LOGICAL-c432t-3c409cd992ec1c4dfb0ab4a92d7d5f9a5ddad63b428034fd68b00bd7378d9e403</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/PMC6781571/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6781571/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,315,728,781,785,886,1605,27929,27930,53796,53798</link.rule.ids><linktorsrc>$$Uhttps://dx.doi.org/10.1093/bib/bbx085$$EView_record_in_Oxford_University_Press$$FView_record_in_$$GOxford_University_Press</linktorsrc><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29447345$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Karp, Peter D</creatorcontrib><creatorcontrib>Billington, Richard</creatorcontrib><creatorcontrib>Caspi, Ron</creatorcontrib><creatorcontrib>Fulcher, Carol A</creatorcontrib><creatorcontrib>Latendresse, Mario</creatorcontrib><creatorcontrib>Kothari, Anamika</creatorcontrib><creatorcontrib>Keseler, Ingrid M</creatorcontrib><creatorcontrib>Krummenacker, Markus</creatorcontrib><creatorcontrib>Midford, Peter E</creatorcontrib><creatorcontrib>Ong, Quang</creatorcontrib><creatorcontrib>Ong, Wai Kit</creatorcontrib><creatorcontrib>Paley, Suzanne M</creatorcontrib><creatorcontrib>Subhraveti, Pallavi</creatorcontrib><title>The BioCyc collection of microbial genomes and metabolic pathways</title><title>Briefings in bioinformatics</title><addtitle>Brief Bioinform</addtitle><description>Abstract
BioCyc.org is a microbial genome Web portal that combines thousands of genomes with additional information inferred by computer programs, imported from other databases and curated from the biomedical literature by biologist curators. BioCyc also provides an extensive range of query tools, visualization services and analysis software. Recent advances in BioCyc include an expansion in the content of BioCyc in terms of both the number of genomes and the types of information available for each genome; an expansion in the amount of curated content within BioCyc; and new developments in the BioCyc software tools including redesigned gene/protein pages and metabolite pages; new search tools; a new sequence-alignment tool; a new tool for visualizing groups of related metabolic pathways; and a facility called SmartTables, which enables biologists to perform analyses that previously would have required a programmer’s assistance.</description><subject>Biologists</subject><subject>Computational Biology</subject><subject>Computer programs</subject><subject>Databases, Genetic</subject><subject>Escherichia coli - genetics</subject><subject>Escherichia coli - metabolism</subject><subject>Genome, Microbial</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Internet</subject><subject>Metabolic Networks and Pathways</subject><subject>Metabolic pathways</subject><subject>Metabolites</subject><subject>Microorganisms</subject><subject>Models, Biological</subject><subject>Search Engine</subject><subject>Software</subject><issn>1467-5463</issn><issn>1477-4054</issn><issn>1477-4054</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kUtLw0AUhQdRbH1s_AESEEGE6M08MpmNoMUXCG50Pcwr7ZQkUzOJ2n9vSlXUhat74X4czrkHoYMMzjIQ5Fx7fa71OxRsA40zynlKgdHN1Z7zlNGcjNBOjHMADLzIttEIC0o5oWyMLp9mLrnyYbI0iQlV5UznQ5OEMqm9aYP2qkqmrgm1i4lqbFK7TulQeZMsVDd7U8u4h7ZKVUW3_zl30fPN9dPkLn14vL2fXD6khhLcpcRQEMYKgZ3JDLWlBqWpEthyy0qhmLXK5kRTXAChpc0LDaAtJ7ywwlEgu-hirbvode2scU3XqkouWl-rdimD8vL3pfEzOQ2vMh8yM54NAiefAm146V3sZO2jcVWlGhf6KDEAAcIwXaFHf9B56NtmiCexYAxjgTM2UKdranhUjK0rv81kIFfNyKEZuW5mgA9_2v9Gv6oYgOM1EPrFf0If93qXYg</recordid><startdate>20190719</startdate><enddate>20190719</enddate><creator>Karp, Peter D</creator><creator>Billington, Richard</creator><creator>Caspi, Ron</creator><creator>Fulcher, Carol A</creator><creator>Latendresse, Mario</creator><creator>Kothari, Anamika</creator><creator>Keseler, Ingrid M</creator><creator>Krummenacker, Markus</creator><creator>Midford, Peter E</creator><creator>Ong, Quang</creator><creator>Ong, Wai Kit</creator><creator>Paley, Suzanne M</creator><creator>Subhraveti, Pallavi</creator><general>Oxford University Press</general><general>Oxford Publishing Limited (England)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>7SC</scope><scope>8FD</scope><scope>FR3</scope><scope>JQ2</scope><scope>K9.</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20190719</creationdate><title>The BioCyc collection of microbial genomes and metabolic pathways</title><author>Karp, Peter D ; Billington, Richard ; Caspi, Ron ; Fulcher, Carol A ; Latendresse, Mario ; Kothari, Anamika ; Keseler, Ingrid M ; Krummenacker, Markus ; Midford, Peter E ; Ong, Quang ; Ong, Wai Kit ; Paley, Suzanne M ; Subhraveti, Pallavi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c432t-3c409cd992ec1c4dfb0ab4a92d7d5f9a5ddad63b428034fd68b00bd7378d9e403</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Biologists</topic><topic>Computational Biology</topic><topic>Computer programs</topic><topic>Databases, Genetic</topic><topic>Escherichia coli - genetics</topic><topic>Escherichia coli - metabolism</topic><topic>Genome, Microbial</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Internet</topic><topic>Metabolic Networks and Pathways</topic><topic>Metabolic pathways</topic><topic>Metabolites</topic><topic>Microorganisms</topic><topic>Models, Biological</topic><topic>Search Engine</topic><topic>Software</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Karp, Peter D</creatorcontrib><creatorcontrib>Billington, Richard</creatorcontrib><creatorcontrib>Caspi, Ron</creatorcontrib><creatorcontrib>Fulcher, Carol A</creatorcontrib><creatorcontrib>Latendresse, Mario</creatorcontrib><creatorcontrib>Kothari, Anamika</creatorcontrib><creatorcontrib>Keseler, Ingrid M</creatorcontrib><creatorcontrib>Krummenacker, Markus</creatorcontrib><creatorcontrib>Midford, Peter E</creatorcontrib><creatorcontrib>Ong, Quang</creatorcontrib><creatorcontrib>Ong, Wai Kit</creatorcontrib><creatorcontrib>Paley, Suzanne M</creatorcontrib><creatorcontrib>Subhraveti, Pallavi</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Computer and Information Systems Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>ProQuest Computer Science Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Computer and Information Systems Abstracts Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Briefings in bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext_linktorsrc</fulltext></delivery><addata><au>Karp, Peter D</au><au>Billington, Richard</au><au>Caspi, Ron</au><au>Fulcher, Carol A</au><au>Latendresse, Mario</au><au>Kothari, Anamika</au><au>Keseler, Ingrid M</au><au>Krummenacker, Markus</au><au>Midford, Peter E</au><au>Ong, Quang</au><au>Ong, Wai Kit</au><au>Paley, Suzanne M</au><au>Subhraveti, Pallavi</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The BioCyc collection of microbial genomes and metabolic pathways</atitle><jtitle>Briefings in bioinformatics</jtitle><addtitle>Brief Bioinform</addtitle><date>2019-07-19</date><risdate>2019</risdate><volume>20</volume><issue>4</issue><spage>1085</spage><epage>1093</epage><pages>1085-1093</pages><issn>1467-5463</issn><issn>1477-4054</issn><eissn>1477-4054</eissn><abstract>Abstract
BioCyc.org is a microbial genome Web portal that combines thousands of genomes with additional information inferred by computer programs, imported from other databases and curated from the biomedical literature by biologist curators. BioCyc also provides an extensive range of query tools, visualization services and analysis software. Recent advances in BioCyc include an expansion in the content of BioCyc in terms of both the number of genomes and the types of information available for each genome; an expansion in the amount of curated content within BioCyc; and new developments in the BioCyc software tools including redesigned gene/protein pages and metabolite pages; new search tools; a new sequence-alignment tool; a new tool for visualizing groups of related metabolic pathways; and a facility called SmartTables, which enables biologists to perform analyses that previously would have required a programmer’s assistance.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>29447345</pmid><doi>10.1093/bib/bbx085</doi><tpages>9</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Biologists Computational Biology Computer programs Databases, Genetic Escherichia coli - genetics Escherichia coli - metabolism Genome, Microbial Genomes Genomics Internet Metabolic Networks and Pathways Metabolic pathways Metabolites Microorganisms Models, Biological Search Engine Software |
| title | The BioCyc collection of microbial genomes and metabolic pathways |
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