{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:33:59Z","timestamp":1772138039664,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2020,7,31]],"date-time":"2020-07-31T00:00:00Z","timestamp":1596153600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"CGIAR CRP RICE"},{"name":"IRD DIADE UNIT"},{"name":"LMI RICE"},{"name":"ICTLab"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Currently, gene information available for Oryza sativa species is located in various online heterogeneous data sources. Moreover, methods of access are also diverse, mostly web-based and sometimes query APIs, which might not always be straightforward for domain experts. The challenge is to collect information quickly from these applications and combine it logically, to facilitate scientific research. We developed a Python package named PyRice, a unified programing API to access all supported databases at the same time with consistent output. PyRice design is modular and implements a smart query system, which fits the computing resources to optimize the query speed. As a result, PyRice is easy to use and produces intuitive results.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>https:\/\/github.com\/SouthGreenPlatform\/PyRice.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa694","type":"journal-article","created":{"date-parts":[[2020,7,24]],"date-time":"2020-07-24T07:32:22Z","timestamp":1595575942000},"page":"1037-1038","source":"Crossref","is-referenced-by-count":1,"title":["PyRice: a Python package for querying\n                    <i>Oryza sativa<\/i>\n                    databases"],"prefix":"10.1093","volume":"37","author":[{"given":"Quan","family":"Do","sequence":"first","affiliation":[{"name":"University of Science and Technology of Hanoi (USTH) , Hanoi, Vietnam"},{"name":"DIADE, Univ Montpellier, IRD , Montpellier, France"}]},{"given":"Ho","family":"Bich Hai","sequence":"additional","affiliation":[{"name":"Institute of Information Technology (IOIT), Vietnam Academy of Science and Technology , Hanoi, Vietnam"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2923-9790","authenticated-orcid":false,"given":"Pierre","family":"Larmande","sequence":"additional","affiliation":[{"name":"University of Science and Technology of Hanoi (USTH) , Hanoi, Vietnam"},{"name":"DIADE, Univ Montpellier, IRD , Montpellier, France"},{"name":"SouthGreen Bioinformatics Platform , Montpellier, France"}]}],"member":"286","published-online":{"date-parts":[[2020,7,31]]},"reference":[{"key":"2023051612143165900_btaa694-B1","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/j.cpb.2016.12.006","article-title":"Databases and bioinformatics tools for rice research","volume":"7\u20138","author":"Garg","year":"2016","journal-title":"Curr. 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An integrated biological and genome information database for rice","volume":"140","author":"Kurata","year":"2006","journal-title":"Plant Physiol"},{"key":"2023051612143165900_btaa694-B5","doi-asserted-by":"crossref","first-page":"D1075","DOI":"10.1093\/nar\/gkw1135","article-title":"Rice SNP-seek database update: new SNPs, indels, and queries","volume":"45","author":"Mansueto","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023051612143165900_btaa694-B6","doi-asserted-by":"crossref","first-page":"D246","DOI":"10.1093\/nar\/gkx1158","article-title":"Expression Atlas: gene and protein expression across multiple studies and organisms","volume":"46","author":"Papatheodorou","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023051612143165900_btaa694-B7","doi-asserted-by":"crossref","first-page":"D1181","DOI":"10.1093\/nar\/gkx1111","article-title":"Gramene 2018: unifying comparative genomics and pathway resources for plant research","volume":"46","author":"Tello-Ruiz","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023051612143165900_btaa694-B8","doi-asserted-by":"crossref","first-page":"D927","DOI":"10.1093\/nar\/gkz828","article-title":"GWAS Atlas: a curated resource of genome-wide variant-trait associations in plants and animals","volume":"48","author":"Tian","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2023051612143165900_btaa694-B10","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/gigascience\/gix119","article-title":"funRiceGenes dataset for comprehensive understanding and application of rice functional genes","volume":"7","author":"Yao","year":"2018","journal-title":"Gigascience"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa694\/34127025\/btaa694.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/7\/1037\/50341069\/btaa694.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/7\/1037\/50341069\/btaa694.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T08:16:39Z","timestamp":1684224999000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/7\/1037\/5879275"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,7,31]]},"references-count":9,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2021,5,17]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa694","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.04.20.049742","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,4,1]]},"published":{"date-parts":[[2020,7,31]]}}}