The Natural Products Atlas 2.0: a database of microbially-derived natural products
Abstract Within the natural products field there is an increasing emphasis on the study of compounds from microbial sources. This has been fuelled by interest in the central role that microorganisms play in mediating both interspecies interactions and host-microbe relationships. To support the study...
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| Veröffentlicht in: | Nucleic acids research 2022-01, Vol.50 (D1), p.D1317-D1323 |
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| creator | van Santen, Jeffrey A Poynton, Ella F Iskakova, Dasha McMann, Emily Alsup, Tyler A Clark, Trevor N Fergusson, Claire H Fewer, David P Hughes, Alison H McCadden, Caitlin A Parra, Jonathan Soldatou, Sylvia Rudolf, Jeffrey D Janssen, Elisabeth M-L Duncan, Katherine R Linington, Roger G |
| description | Abstract
Within the natural products field there is an increasing emphasis on the study of compounds from microbial sources. This has been fuelled by interest in the central role that microorganisms play in mediating both interspecies interactions and host-microbe relationships. To support the study of natural products chemistry produced by microorganisms we released the Natural Products Atlas, a database of known microbial natural products structures, in 2019. This paper reports the release of a new version of the database which includes a full RESTful application programming interface (API), a new website framework, and an expanded database that includes 8128 new compounds, bringing the total to 32 552. In addition to these structural and content changes we have added full taxonomic descriptions for all microbial taxa and have added chemical ontology terms from both NP Classifier and ClassyFire. We have also performed manual curation to review all entries with incomplete configurational assignments and have integrated data from external resources, including CyanoMetDB. Finally, we have improved the user experience by updating the Overview dashboard and creating a dashboard for taxonomic origin. The database can be accessed via the new interactive website at https://www.npatlas.org. |
| doi_str_mv | 10.1093/nar/gkab941 |
| format | Article |
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Within the natural products field there is an increasing emphasis on the study of compounds from microbial sources. This has been fuelled by interest in the central role that microorganisms play in mediating both interspecies interactions and host-microbe relationships. To support the study of natural products chemistry produced by microorganisms we released the Natural Products Atlas, a database of known microbial natural products structures, in 2019. This paper reports the release of a new version of the database which includes a full RESTful application programming interface (API), a new website framework, and an expanded database that includes 8128 new compounds, bringing the total to 32 552. In addition to these structural and content changes we have added full taxonomic descriptions for all microbial taxa and have added chemical ontology terms from both NP Classifier and ClassyFire. We have also performed manual curation to review all entries with incomplete configurational assignments and have integrated data from external resources, including CyanoMetDB. Finally, we have improved the user experience by updating the Overview dashboard and creating a dashboard for taxonomic origin. The database can be accessed via the new interactive website at https://www.npatlas.org.</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkab941</identifier><identifier>PMID: 34718710</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Bacteria - classification ; Biological Products - classification ; Classification ; Database Issue ; Databases, Factual ; Fungi - classification ; Host Microbial Interactions - genetics ; Humans ; Software ; User-Computer Interface</subject><ispartof>Nucleic acids research, 2022-01, Vol.50 (D1), p.D1317-D1323</ispartof><rights>The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. 2022</rights><rights>The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c454t-ef11bc5a33641ed4a10883e090439300346ac32da3ae702f9e7b0fd2fb9977973</citedby><cites>FETCH-LOGICAL-c454t-ef11bc5a33641ed4a10883e090439300346ac32da3ae702f9e7b0fd2fb9977973</cites><orcidid>0000-0003-1818-4971 ; 0000-0002-5424-804X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8728154/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8728154/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,1598,27903,27904,53770,53772</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/34718710$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>van Santen, Jeffrey A</creatorcontrib><creatorcontrib>Poynton, Ella F</creatorcontrib><creatorcontrib>Iskakova, Dasha</creatorcontrib><creatorcontrib>McMann, Emily</creatorcontrib><creatorcontrib>Alsup, Tyler A</creatorcontrib><creatorcontrib>Clark, Trevor N</creatorcontrib><creatorcontrib>Fergusson, Claire H</creatorcontrib><creatorcontrib>Fewer, David P</creatorcontrib><creatorcontrib>Hughes, Alison H</creatorcontrib><creatorcontrib>McCadden, Caitlin A</creatorcontrib><creatorcontrib>Parra, Jonathan</creatorcontrib><creatorcontrib>Soldatou, Sylvia</creatorcontrib><creatorcontrib>Rudolf, Jeffrey D</creatorcontrib><creatorcontrib>Janssen, Elisabeth M-L</creatorcontrib><creatorcontrib>Duncan, Katherine R</creatorcontrib><creatorcontrib>Linington, Roger G</creatorcontrib><title>The Natural Products Atlas 2.0: a database of microbially-derived natural products</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>Abstract
Within the natural products field there is an increasing emphasis on the study of compounds from microbial sources. This has been fuelled by interest in the central role that microorganisms play in mediating both interspecies interactions and host-microbe relationships. To support the study of natural products chemistry produced by microorganisms we released the Natural Products Atlas, a database of known microbial natural products structures, in 2019. This paper reports the release of a new version of the database which includes a full RESTful application programming interface (API), a new website framework, and an expanded database that includes 8128 new compounds, bringing the total to 32 552. In addition to these structural and content changes we have added full taxonomic descriptions for all microbial taxa and have added chemical ontology terms from both NP Classifier and ClassyFire. We have also performed manual curation to review all entries with incomplete configurational assignments and have integrated data from external resources, including CyanoMetDB. Finally, we have improved the user experience by updating the Overview dashboard and creating a dashboard for taxonomic origin. The database can be accessed via the new interactive website at https://www.npatlas.org.</description><subject>Bacteria - classification</subject><subject>Biological Products - classification</subject><subject>Classification</subject><subject>Database Issue</subject><subject>Databases, Factual</subject><subject>Fungi - classification</subject><subject>Host Microbial Interactions - genetics</subject><subject>Humans</subject><subject>Software</subject><subject>User-Computer Interface</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNp9kc1Lw0AQxRdRbK2evMueRJDY2Y80WQ9CKX5BUZF6XibJpo2mSd1NCv3vXWksevE0h_nNm5n3CDllcMVAiWGFdjj_wERJtkf6TIx4INWI75M-CAgDBjLukSPn3gGYZKE8JD0hIxZHDPrkdbYw9Amb1mJJX2ydtWnj6Lgp0VF-BdcUaYYNJugMrXO6LFJbJwWW5SbIjC3WJqNVN73qpo_JQY6lMyddHZC3u9vZ5CGYPt8_TsbTIJWhbAKTM5akIQoxksxkEhnEsTCgQAolAIQcYSp4hgJNBDxXJkogz3ieKBVFKhIDcrPVXbXJ0mSpqRp_hl7ZYol2o2ss9N9OVSz0vF7rOOKx98ELXHQCtv5sjWv0snCpKUusTN06zUPFuPcJuEcvt6h_3zlr8t0aBvo7Be1T0F0Knj77fdmO_bHdA-dboG5X_yp9AbHCkVY</recordid><startdate>20220107</startdate><enddate>20220107</enddate><creator>van Santen, Jeffrey A</creator><creator>Poynton, Ella F</creator><creator>Iskakova, Dasha</creator><creator>McMann, Emily</creator><creator>Alsup, Tyler A</creator><creator>Clark, Trevor N</creator><creator>Fergusson, Claire H</creator><creator>Fewer, David P</creator><creator>Hughes, Alison H</creator><creator>McCadden, Caitlin A</creator><creator>Parra, Jonathan</creator><creator>Soldatou, Sylvia</creator><creator>Rudolf, Jeffrey D</creator><creator>Janssen, Elisabeth M-L</creator><creator>Duncan, Katherine R</creator><creator>Linington, Roger G</creator><general>Oxford University Press</general><scope>TOX</scope><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>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-1818-4971</orcidid><orcidid>https://orcid.org/0000-0002-5424-804X</orcidid></search><sort><creationdate>20220107</creationdate><title>The Natural Products Atlas 2.0: a database of microbially-derived natural products</title><author>van Santen, Jeffrey A ; Poynton, Ella F ; Iskakova, Dasha ; McMann, Emily ; Alsup, Tyler A ; Clark, Trevor N ; Fergusson, Claire H ; Fewer, David P ; Hughes, Alison H ; McCadden, Caitlin A ; Parra, Jonathan ; Soldatou, Sylvia ; Rudolf, Jeffrey D ; Janssen, Elisabeth M-L ; Duncan, Katherine R ; Linington, Roger G</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c454t-ef11bc5a33641ed4a10883e090439300346ac32da3ae702f9e7b0fd2fb9977973</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Bacteria - classification</topic><topic>Biological Products - classification</topic><topic>Classification</topic><topic>Database Issue</topic><topic>Databases, Factual</topic><topic>Fungi - classification</topic><topic>Host Microbial Interactions - genetics</topic><topic>Humans</topic><topic>Software</topic><topic>User-Computer Interface</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>van Santen, Jeffrey A</creatorcontrib><creatorcontrib>Poynton, Ella F</creatorcontrib><creatorcontrib>Iskakova, Dasha</creatorcontrib><creatorcontrib>McMann, Emily</creatorcontrib><creatorcontrib>Alsup, Tyler A</creatorcontrib><creatorcontrib>Clark, Trevor N</creatorcontrib><creatorcontrib>Fergusson, Claire H</creatorcontrib><creatorcontrib>Fewer, David P</creatorcontrib><creatorcontrib>Hughes, Alison H</creatorcontrib><creatorcontrib>McCadden, Caitlin A</creatorcontrib><creatorcontrib>Parra, Jonathan</creatorcontrib><creatorcontrib>Soldatou, Sylvia</creatorcontrib><creatorcontrib>Rudolf, Jeffrey D</creatorcontrib><creatorcontrib>Janssen, Elisabeth M-L</creatorcontrib><creatorcontrib>Duncan, Katherine R</creatorcontrib><creatorcontrib>Linington, Roger G</creatorcontrib><collection>Oxford Journals Open Access Collection</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nucleic acids research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>van Santen, Jeffrey A</au><au>Poynton, Ella F</au><au>Iskakova, Dasha</au><au>McMann, Emily</au><au>Alsup, Tyler A</au><au>Clark, Trevor N</au><au>Fergusson, Claire H</au><au>Fewer, David P</au><au>Hughes, Alison H</au><au>McCadden, Caitlin A</au><au>Parra, Jonathan</au><au>Soldatou, Sylvia</au><au>Rudolf, Jeffrey D</au><au>Janssen, Elisabeth M-L</au><au>Duncan, Katherine R</au><au>Linington, Roger G</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The Natural Products Atlas 2.0: a database of microbially-derived natural products</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2022-01-07</date><risdate>2022</risdate><volume>50</volume><issue>D1</issue><spage>D1317</spage><epage>D1323</epage><pages>D1317-D1323</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><abstract>Abstract
Within the natural products field there is an increasing emphasis on the study of compounds from microbial sources. This has been fuelled by interest in the central role that microorganisms play in mediating both interspecies interactions and host-microbe relationships. To support the study of natural products chemistry produced by microorganisms we released the Natural Products Atlas, a database of known microbial natural products structures, in 2019. This paper reports the release of a new version of the database which includes a full RESTful application programming interface (API), a new website framework, and an expanded database that includes 8128 new compounds, bringing the total to 32 552. In addition to these structural and content changes we have added full taxonomic descriptions for all microbial taxa and have added chemical ontology terms from both NP Classifier and ClassyFire. We have also performed manual curation to review all entries with incomplete configurational assignments and have integrated data from external resources, including CyanoMetDB. Finally, we have improved the user experience by updating the Overview dashboard and creating a dashboard for taxonomic origin. The database can be accessed via the new interactive website at https://www.npatlas.org.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>34718710</pmid><doi>10.1093/nar/gkab941</doi><orcidid>https://orcid.org/0000-0003-1818-4971</orcidid><orcidid>https://orcid.org/0000-0002-5424-804X</orcidid><oa>free_for_read</oa></addata></record> |
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| identifier | ISSN: 0305-1048 |
| ispartof | Nucleic acids research, 2022-01, Vol.50 (D1), p.D1317-D1323 |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Oxford Journals Open Access Collection; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Bacteria - classification Biological Products - classification Classification Database Issue Databases, Factual Fungi - classification Host Microbial Interactions - genetics Humans Software User-Computer Interface |
| title | The Natural Products Atlas 2.0: a database of microbially-derived natural products |
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