{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T01:23:49Z","timestamp":1777512229026,"version":"3.51.4"},"reference-count":10,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2019,11,8]],"date-time":"2019-11-08T00:00:00Z","timestamp":1573171200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2019,11,8]],"date-time":"2019-11-08T00:00:00Z","timestamp":1573171200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["1R01AI123037-01"],"award-info":[{"award-number":["1R01AI123037-01"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"name":"National Science Foundation","award":["1645609"],"award-info":[{"award-number":["1645609"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2019,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n<jats:sec>\n<jats:title>Background<\/jats:title>\n<jats:p>The MG-RAST API provides search capabilities and delivers organism and function data as well as raw or annotated sequence data via the web interface and its RESTful API. For casual users, however, RESTful APIs are hard to learn and work with.<\/jats:p>\n<\/jats:sec>\n<jats:sec>\n<jats:title>Results<\/jats:title>\n<jats:p>We created the graphical MG-RAST API explorer to help researchers more easily build and export API queries; understand the data abstractions and indices available in MG-RAST; and use the results presented in-browser for exploration, development, and debugging.<\/jats:p>\n<\/jats:sec>\n<jats:sec>\n<jats:title>Conclusions<\/jats:title>\n<jats:p>The API explorer lowers the barrier to entry for occasional or first-time MG-RAST API users.<\/jats:p>\n<\/jats:sec>","DOI":"10.1186\/s12859-019-2993-0","type":"journal-article","created":{"date-parts":[[2019,11,8]],"date-time":"2019-11-08T15:36:12Z","timestamp":1573227372000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["The MG-RAST API explorer: an on-ramp for RESTful query composition"],"prefix":"10.1186","volume":"20","author":[{"given":"Tobias","family":"Paczian","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"William L.","family":"Trimble","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wolfgang","family":"Gerlach","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Travis","family":"Harrison","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andreas","family":"Wilke","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1112-2284","authenticated-orcid":false,"given":"Folker","family":"Meyer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2019,11,8]]},"reference":[{"issue":"1","key":"2993_CR1","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1186\/2042-5783-2-3","volume":"2","author":"T Thomas","year":"2012","unstructured":"Thomas T, Gilbert J, Meyer F. Metagenomics - a guide from sampling to data analysis. Microbial Inform Exp. 2012;2(1):3.","journal-title":"Microbial Inform Exp"},{"key":"2993_CR2","doi-asserted-by":"publisher","first-page":"356","DOI":"10.1186\/1471-2105-12-356","volume":"12","author":"SV Angiuoli","year":"2011","unstructured":"Angiuoli SV, Matalka M, Gussman A, Galens K, Vangala M, Riley DR, Arze C, White JR, White O, Fricke WF. CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing. BMC Bioinformatics [electronic resource]. 2011;12:356.","journal-title":"BMC Bioinformatics [electronic resource]"},{"issue":"1","key":"2993_CR3","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1038\/nmeth.3176","volume":"12","author":"B Buchfink","year":"2015","unstructured":"Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12(1):59\u201360.","journal-title":"Nat Methods"},{"issue":"11","key":"2993_CR4","doi-asserted-by":"publisher","first-page":"1026","DOI":"10.1038\/nbt.3988","volume":"35","author":"M Steinegger","year":"2017","unstructured":"Steinegger M, Soding J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat Biotechnol. 2017;35(11):1026\u20138.","journal-title":"Nat Biotechnol"},{"issue":"D1","key":"2993_CR5","doi-asserted-by":"publisher","first-page":"D595","DOI":"10.1093\/nar\/gkv1195","volume":"44","author":"A Mitchell","year":"2016","unstructured":"Mitchell A, Bucchini F, Cochrane G, Denise H, ten Hoopen P, Fraser M, Pesseat S, Potter S, Scheremetjew M, Sterk P, et al. EBI metagenomics in 2016--an expanding and evolving resource for the analysis and archiving of metagenomic data. Nucleic Acids Res. 2016;44(D1):D595\u2013603.","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"2993_CR6","doi-asserted-by":"publisher","first-page":"D507","DOI":"10.1093\/nar\/gkw929","volume":"45","author":"IA Chen","year":"2017","unstructured":"Chen IA, Markowitz VM, Chu K, Palaniappan K, Szeto E, Pillay M, Ratner A, Huang J, Andersen E, Huntemann M, et al. IMG\/M: integrated genome and metagenome comparative data analysis system. Nucleic Acids Res. 2017;45(D1):D507\u201316.","journal-title":"Nucleic Acids Res"},{"key":"2993_CR7","unstructured":"Fielding RT: Architectural styles and the Design of Network-based Software Architectures. University of California, Irvine.; 2000."},{"key":"2993_CR8","doi-asserted-by":"crossref","unstructured":"Meyer F, Bagchi S, Chaterji S, Gerlach W, Grama A, Harrison T, Paczian T, Trimble WL, Wilke A. MG-RAST version 4-lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis. Brief Bioinform. 2017.","DOI":"10.1093\/bib\/bbx105"},{"issue":"1","key":"2993_CR9","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1186\/1471-2105-13-141","volume":"13","author":"Andreas Wilke","year":"2012","unstructured":"Wilke A, Harrison T, Wilkening J, Field D, Glass EM, Kyrpides N, Mavrommatis K, Meyer F: The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools. BMC Bioinformatics [electronic resource] 2012, 13:141.","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"2993_CR10","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1186\/2047-217X-1-7","volume":"1","author":"D McDonald","year":"2012","unstructured":"McDonald D, Clemente JC, Kuczynski J, Rideout JR, Stombaugh J, Wendel D, Wilke A, Huse S, Hufnagle J, Meyer F, et al. The biological observation matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. Gigascience. 2012;1(1):7.","journal-title":"Gigascience"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-2993-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-019-2993-0\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-2993-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,11,7]],"date-time":"2020-11-07T00:09:52Z","timestamp":1604707792000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-019-2993-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,11,8]]},"references-count":10,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2019,12]]}},"alternative-id":["2993"],"URL":"https:\/\/doi.org\/10.1186\/s12859-019-2993-0","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,11,8]]},"assertion":[{"value":"11 December 2018","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 July 2019","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 November 2019","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests. Folker Meyer is currently acting as a member of the Editorial Board for BMC Bioinformatics.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"561"}}