Lotus Base: An integrated information portal for the model legume Lotus japonicus
Lotus japonicus is a well-characterized model legume widely used in the study of plant-microbe interactions. However, datasets from various Lotus studies are poorly integrated and lack interoperability. We recognize the need for a comprehensive repository that allows comprehensive and dynamic explor...
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| Veröffentlicht in: | Scientific reports 2016-12, Vol.6 (1), p.39447-39447, Article 39447 |
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| creator | Mun, Terry Bachmann, Asger Gupta, Vikas Stougaard, Jens Andersen, Stig U. |
| description | Lotus japonicus
is a well-characterized model legume widely used in the study of plant-microbe interactions. However, datasets from various
Lotus
studies are poorly integrated and lack interoperability. We recognize the need for a comprehensive repository that allows comprehensive and dynamic exploration of
Lotus
genomic and transcriptomic data. Equally important are user-friendly in-browser tools designed for data visualization and interpretation. Here, we present
Lotus
Base, which opens to the research community a large, established
LORE1
insertion mutant population containing an excess of 120,000 lines, and serves the end-user tightly integrated data from
Lotus
, such as the reference genome, annotated proteins, and expression profiling data. We report the integration of expression data from the
L. japonicus
gene expression atlas project, and the development of tools to cluster and export such data, allowing users to construct, visualize, and annotate co-expression gene networks.
Lotus
Base takes advantage of modern advances in browser technology to deliver powerful data interpretation for biologists. Its modular construction and publicly available application programming interface enable developers to tap into the wealth of integrated
Lotus
data.
Lotus
Base is freely accessible at:
https://lotus.au.dk
. |
| doi_str_mv | 10.1038/srep39447 |
| format | Article |
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is a well-characterized model legume widely used in the study of plant-microbe interactions. However, datasets from various
Lotus
studies are poorly integrated and lack interoperability. We recognize the need for a comprehensive repository that allows comprehensive and dynamic exploration of
Lotus
genomic and transcriptomic data. Equally important are user-friendly in-browser tools designed for data visualization and interpretation. Here, we present
Lotus
Base, which opens to the research community a large, established
LORE1
insertion mutant population containing an excess of 120,000 lines, and serves the end-user tightly integrated data from
Lotus
, such as the reference genome, annotated proteins, and expression profiling data. We report the integration of expression data from the
L. japonicus
gene expression atlas project, and the development of tools to cluster and export such data, allowing users to construct, visualize, and annotate co-expression gene networks.
Lotus
Base takes advantage of modern advances in browser technology to deliver powerful data interpretation for biologists. Its modular construction and publicly available application programming interface enable developers to tap into the wealth of integrated
Lotus
data.
Lotus
Base is freely accessible at:
https://lotus.au.dk
.</description><identifier>ISSN: 2045-2322</identifier><identifier>EISSN: 2045-2322</identifier><identifier>DOI: 10.1038/srep39447</identifier><identifier>PMID: 28008948</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>38/70 ; 45/91 ; 631/114/129 ; 631/114/2401 ; 631/449/2491 ; Data interpretation ; Data processing ; Gene expression ; Gene Expression - genetics ; Genome, Plant - genetics ; Genomes ; Genomics - methods ; Humanities and Social Sciences ; Integration ; Legumes ; Lotus - genetics ; multidisciplinary ; Mutagenesis, Insertional - genetics ; Mutation - genetics ; Science ; Web portals</subject><ispartof>Scientific reports, 2016-12, Vol.6 (1), p.39447-39447, Article 39447</ispartof><rights>The Author(s) 2016</rights><rights>Copyright Nature Publishing Group Dec 2016</rights><rights>Copyright © 2016, The Author(s) 2016 The Author(s)</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c504t-ba7a483735e4d7d87b7680f2b2755694d5bd35c1469277dd14e02b73e11892283</citedby><cites>FETCH-LOGICAL-c504t-ba7a483735e4d7d87b7680f2b2755694d5bd35c1469277dd14e02b73e11892283</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/PMC5180183/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5180183/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,27901,27902,41096,42165,51551,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28008948$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Mun, Terry</creatorcontrib><creatorcontrib>Bachmann, Asger</creatorcontrib><creatorcontrib>Gupta, Vikas</creatorcontrib><creatorcontrib>Stougaard, Jens</creatorcontrib><creatorcontrib>Andersen, Stig U.</creatorcontrib><title>Lotus Base: An integrated information portal for the model legume Lotus japonicus</title><title>Scientific reports</title><addtitle>Sci Rep</addtitle><addtitle>Sci Rep</addtitle><description>Lotus japonicus
is a well-characterized model legume widely used in the study of plant-microbe interactions. However, datasets from various
Lotus
studies are poorly integrated and lack interoperability. We recognize the need for a comprehensive repository that allows comprehensive and dynamic exploration of
Lotus
genomic and transcriptomic data. Equally important are user-friendly in-browser tools designed for data visualization and interpretation. Here, we present
Lotus
Base, which opens to the research community a large, established
LORE1
insertion mutant population containing an excess of 120,000 lines, and serves the end-user tightly integrated data from
Lotus
, such as the reference genome, annotated proteins, and expression profiling data. We report the integration of expression data from the
L. japonicus
gene expression atlas project, and the development of tools to cluster and export such data, allowing users to construct, visualize, and annotate co-expression gene networks.
Lotus
Base takes advantage of modern advances in browser technology to deliver powerful data interpretation for biologists. Its modular construction and publicly available application programming interface enable developers to tap into the wealth of integrated
Lotus
data.
Lotus
Base is freely accessible at:
https://lotus.au.dk
.</description><subject>38/70</subject><subject>45/91</subject><subject>631/114/129</subject><subject>631/114/2401</subject><subject>631/449/2491</subject><subject>Data interpretation</subject><subject>Data processing</subject><subject>Gene expression</subject><subject>Gene Expression - genetics</subject><subject>Genome, Plant - genetics</subject><subject>Genomes</subject><subject>Genomics - methods</subject><subject>Humanities and Social Sciences</subject><subject>Integration</subject><subject>Legumes</subject><subject>Lotus - genetics</subject><subject>multidisciplinary</subject><subject>Mutagenesis, Insertional - genetics</subject><subject>Mutation - genetics</subject><subject>Science</subject><subject>Web portals</subject><issn>2045-2322</issn><issn>2045-2322</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNplkV9LHDEUxUOpVFEf-gVKwJdWWM3fTeKDoKJVWCiF9jlkJnfXWWaSMckU-u2NrC5re1_uJffHuScchD5TckYJ1-c5wciNEOoDOmBEyBnjjH3cmffRcc5rUksyI6j5hPaZJkQboQ_Qz0UsU8bXLsMFvgq4CwVWyRXwdVzGNLjSxYDHmIrrcX3A5RHwED30uIfVNADeKKzdGEPXTvkI7S1dn-H4tR-i33e3v27uZ4sf3x9urhazVhJRZo1TTmiuuAThldeqUXNNlqxhSsq5EV42nsuWirlhSnlPBRDWKA6UasOY5ofocqM7Ts0AvoVQkuvtmLrBpb82us6-34Tu0a7iHyupJlTzKvD1VSDFpwlysUOXW-h7FyBO2VItmdJCSFPRk3_QdZxSqN-rlDGCG6VeHH3bUG2Kucay3JqhxL5kZbdZVfbLrvst-ZZMBU43QK6rsIK0c_I_tWeuWJ0T</recordid><startdate>20161223</startdate><enddate>20161223</enddate><creator>Mun, Terry</creator><creator>Bachmann, Asger</creator><creator>Gupta, Vikas</creator><creator>Stougaard, Jens</creator><creator>Andersen, Stig U.</creator><general>Nature Publishing Group UK</general><general>Nature Publishing Group</general><scope>C6C</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>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20161223</creationdate><title>Lotus Base: An integrated information portal for the model legume Lotus japonicus</title><author>Mun, Terry ; Bachmann, Asger ; Gupta, Vikas ; Stougaard, Jens ; Andersen, Stig U.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c504t-ba7a483735e4d7d87b7680f2b2755694d5bd35c1469277dd14e02b73e11892283</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>38/70</topic><topic>45/91</topic><topic>631/114/129</topic><topic>631/114/2401</topic><topic>631/449/2491</topic><topic>Data interpretation</topic><topic>Data processing</topic><topic>Gene expression</topic><topic>Gene Expression - genetics</topic><topic>Genome, Plant - genetics</topic><topic>Genomes</topic><topic>Genomics - methods</topic><topic>Humanities and Social Sciences</topic><topic>Integration</topic><topic>Legumes</topic><topic>Lotus - genetics</topic><topic>multidisciplinary</topic><topic>Mutagenesis, Insertional - genetics</topic><topic>Mutation - genetics</topic><topic>Science</topic><topic>Web portals</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Mun, Terry</creatorcontrib><creatorcontrib>Bachmann, Asger</creatorcontrib><creatorcontrib>Gupta, Vikas</creatorcontrib><creatorcontrib>Stougaard, Jens</creatorcontrib><creatorcontrib>Andersen, Stig U.</creatorcontrib><collection>Springer Nature OA Free Journals</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database</collection><collection>Biological Science Database</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central Basic</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Scientific reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Mun, Terry</au><au>Bachmann, Asger</au><au>Gupta, Vikas</au><au>Stougaard, Jens</au><au>Andersen, Stig U.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Lotus Base: An integrated information portal for the model legume Lotus japonicus</atitle><jtitle>Scientific reports</jtitle><stitle>Sci Rep</stitle><addtitle>Sci Rep</addtitle><date>2016-12-23</date><risdate>2016</risdate><volume>6</volume><issue>1</issue><spage>39447</spage><epage>39447</epage><pages>39447-39447</pages><artnum>39447</artnum><issn>2045-2322</issn><eissn>2045-2322</eissn><abstract>Lotus japonicus
is a well-characterized model legume widely used in the study of plant-microbe interactions. However, datasets from various
Lotus
studies are poorly integrated and lack interoperability. We recognize the need for a comprehensive repository that allows comprehensive and dynamic exploration of
Lotus
genomic and transcriptomic data. Equally important are user-friendly in-browser tools designed for data visualization and interpretation. Here, we present
Lotus
Base, which opens to the research community a large, established
LORE1
insertion mutant population containing an excess of 120,000 lines, and serves the end-user tightly integrated data from
Lotus
, such as the reference genome, annotated proteins, and expression profiling data. We report the integration of expression data from the
L. japonicus
gene expression atlas project, and the development of tools to cluster and export such data, allowing users to construct, visualize, and annotate co-expression gene networks.
Lotus
Base takes advantage of modern advances in browser technology to deliver powerful data interpretation for biologists. Its modular construction and publicly available application programming interface enable developers to tap into the wealth of integrated
Lotus
data.
Lotus
Base is freely accessible at:
https://lotus.au.dk
.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>28008948</pmid><doi>10.1038/srep39447</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
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| ispartof | Scientific reports, 2016-12, Vol.6 (1), p.39447-39447, Article 39447 |
| issn | 2045-2322 2045-2322 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_5180183 |
| source | MEDLINE; Nature Free; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Alma/SFX Local Collection; Free Full-Text Journals in Chemistry; Springer Nature OA Free Journals |
| subjects | 38/70 45/91 631/114/129 631/114/2401 631/449/2491 Data interpretation Data processing Gene expression Gene Expression - genetics Genome, Plant - genetics Genomes Genomics - methods Humanities and Social Sciences Integration Legumes Lotus - genetics multidisciplinary Mutagenesis, Insertional - genetics Mutation - genetics Science Web portals |
| title | Lotus Base: An integrated information portal for the model legume Lotus japonicus |
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