{"id":"https://openalex.org/W3046250769","doi":"https://doi.org/10.1093/bioinformatics/btaa694","title":"PyRice: a Python package for querying <i>Oryza sativa</i> databases","display_name":"PyRice: a Python package for querying <i>Oryza sativa</i> databases","publication_year":2020,"publication_date":"2020-07-24","ids":{"openalex":"https://openalex.org/W3046250769","doi":"https://doi.org/10.1093/bioinformatics/btaa694","mag":"3046250769","pmid":"https://pubmed.ncbi.nlm.nih.gov/32735312"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa694","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa694","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://hal-lirmm.ccsd.cnrs.fr/lirmm-03615370","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5073025832","display_name":"Do Quan","orcid":"https://orcid.org/0000-0002-7443-3760"},"institutions":[{"id":"https://openalex.org/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210117822","display_name":"Diversit\u00e9, adaptation et d\u00e9veloppement des plantes","ror":"https://ror.org/02banhz78","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I131077856","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I19894307","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210113730","https://openalex.org/I4210117822","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4405257220"]},{"id":"https://openalex.org/I4210166444","display_name":"Institut de Recherche pour le D\u00e9veloppement","ror":"https://ror.org/05q3vnk25","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210113730","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4405257220"]},{"id":"https://openalex.org/I94518387","display_name":"Hanoi University of Science and Technology","ror":"https://ror.org/04nyv3z04","country_code":"VN","type":"education","lineage":["https://openalex.org/I94518387"]}],"countries":["FR","VN"],"is_corresponding":false,"raw_author_name":"Quan Do","raw_affiliation_strings":["DIADE, Univ Montpellier, IRD , Montpellier, France","University of Science and Technology of Hanoi (USTH) , Hanoi, Vietnam"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"DIADE, Univ Montpellier, IRD , Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I4210166444","https://openalex.org/I4210117822"]},{"raw_affiliation_string":"University of Science and Technology of Hanoi (USTH) , Hanoi, Vietnam","institution_ids":["https://openalex.org/I94518387"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057313628","display_name":"Ho Bich Hai","orcid":null},"institutions":[{"id":"https://openalex.org/I70349855","display_name":"Vietnam Academy of Science and Technology","ror":"https://ror.org/02wsd5p50","country_code":"VN","type":"government","lineage":["https://openalex.org/I70349855"]}],"countries":["VN"],"is_corresponding":false,"raw_author_name":"Ho Bich Hai","raw_affiliation_strings":["Institute of Information Technology (IOIT), Vietnam Academy of Science and Technology , Hanoi, Vietnam"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Information Technology (IOIT), Vietnam Academy of Science and Technology , Hanoi, Vietnam","institution_ids":["https://openalex.org/I70349855"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063266192","display_name":"Pierre Larmande","orcid":"https://orcid.org/0000-0002-2923-9790"},"institutions":[{"id":"https://openalex.org/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210117822","display_name":"Diversit\u00e9, adaptation et d\u00e9veloppement des plantes","ror":"https://ror.org/02banhz78","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I131077856","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I19894307","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210113730","https://openalex.org/I4210117822","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4405257220"]},{"id":"https://openalex.org/I4210166444","display_name":"Institut de Recherche pour le D\u00e9veloppement","ror":"https://ror.org/05q3vnk25","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1327553481","https://openalex.org/I154202486","https://openalex.org/I2799535048","https://openalex.org/I2802818602","https://openalex.org/I4210088668","https://openalex.org/I4210090127","https://openalex.org/I4210113730","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4405257220"]},{"id":"https://openalex.org/I94518387","display_name":"Hanoi University of Science and Technology","ror":"https://ror.org/04nyv3z04","country_code":"VN","type":"education","lineage":["https://openalex.org/I94518387"]}],"countries":["FR","VN"],"is_corresponding":true,"raw_author_name":"Pierre Larmande","raw_affiliation_strings":["DIADE, Univ Montpellier, IRD , Montpellier, France","SouthGreen Bioinformatics Platform , Montpellier, France","University of Science and Technology of Hanoi (USTH) , Hanoi, Vietnam"],"raw_orcid":"https://orcid.org/0000-0002-2923-9790","affiliations":[{"raw_affiliation_string":"DIADE, Univ Montpellier, IRD , Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I4210166444","https://openalex.org/I4210117822"]},{"raw_affiliation_string":"SouthGreen Bioinformatics Platform , Montpellier, France","institution_ids":[]},{"raw_affiliation_string":"University of Science and Technology of Hanoi (USTH) , Hanoi, Vietnam","institution_ids":["https://openalex.org/I94518387"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5063266192"],"corresponding_institution_ids":["https://openalex.org/I19894307","https://openalex.org/I4210117822","https://openalex.org/I4210166444","https://openalex.org/I94518387"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.0709544,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"37","issue":"7","first_page":"1037","last_page":"1038"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.2337999939918518,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.2337999939918518,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.12359999865293503,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.07370000332593918,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.883204460144043},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8584938049316406},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.6645435094833374},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.6032438278198242},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.42572811245918274},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4036426246166229},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33910417556762695},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2144469916820526}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.883204460144043},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8584938049316406},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.6645435094833374},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.6032438278198242},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.42572811245918274},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4036426246166229},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33910417556762695},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2144469916820526}],"mesh":[{"descriptor_ui":"D012275","descriptor_name":"Oryza","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012275","descriptor_name":"Oryza","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012275","descriptor_name":"Oryza","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaa694","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa694","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32735312","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32735312","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:HAL:lirmm-03615370v1","is_oa":true,"landing_page_url":"https://hal-lirmm.ccsd.cnrs.fr/lirmm-03615370","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 2021, 37 (7), pp.1037-1038. &#x27E8;10.1093/bioinformatics/btaa694&#x27E9;","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"pmh:oai:HAL:lirmm-03615370v1","is_oa":true,"landing_page_url":"https://hal-lirmm.ccsd.cnrs.fr/lirmm-03615370","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 2021, 37 (7), pp.1037-1038. &#x27E8;10.1093/bioinformatics/btaa694&#x27E9;","raw_type":"info:eu-repo/semantics/article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6068764742","display_name":"Institut fran\u00e7ais de bioinformatique","funder_award_id":"ANR-11-INBS-0013","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":9,"referenced_works":["https://openalex.org/W2035806597","https://openalex.org/W2161069068","https://openalex.org/W2432508461","https://openalex.org/W2558561667","https://openalex.org/W2567407757","https://openalex.org/W2768308516","https://openalex.org/W2769591387","https://openalex.org/W2771667690","https://openalex.org/W2978057278"],"related_works":["https://openalex.org/W2341492732","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W1699080303","https://openalex.org/W4297799326","https://openalex.org/W3116064965","https://openalex.org/W4287027380","https://openalex.org/W3193760048","https://openalex.org/W2019887508","https://openalex.org/W3151146928"],"abstract_inverted_index":{"SUMMARY:":[0],"Currently,":[1],"gene":[2],"information":[3,44],"available":[4,121],"for":[5,36],"Oryza":[6],"sativa":[7],"species":[8],"is":[9,41,82,104],"located":[10],"in":[11],"various":[12],"online":[13],"heterogeneous":[14],"data":[15,119],"sources.":[16],"Moreover,":[17],"methods":[18],"of":[19],"access":[20,69],"are":[21,120],"also":[22],"diverse,":[23],"mostly":[24],"web-based":[25],"and":[26,49,84,108],"sometimes":[27],"query":[28,88,98],"APIs,":[29],"which":[30,90],"might":[31],"not":[32],"always":[33],"be":[34],"straightforward":[35],"domain":[37],"experts.":[38],"The":[39],"challenge":[40],"to":[42,53,68,95,106],"collect":[43],"quickly":[45],"from":[46],"these":[47],"applications":[48],"combine":[50],"it":[51],"logically,":[52],"facilitate":[54],"scientific":[55],"research.":[56],"We":[57],"developed":[58],"a":[59,64,86,101],"Python":[60],"package":[61],"named":[62],"PyRice,":[63],"unified":[65],"programing":[66],"API":[67],"all":[70],"supported":[71],"databases":[72],"at":[73,122],"the":[74,92,97],"same":[75],"time":[76],"with":[77],"consistent":[78],"output.":[79],"PyRice":[80,103],"design":[81],"modular":[83],"implements":[85],"smart":[87],"system,":[89],"fits":[91],"computing":[93],"resources":[94],"optimize":[96],"speed.":[99],"As":[100],"result,":[102],"easy":[105],"use":[107],"produces":[109],"intuitive":[110],"results.":[111],"AVAILABILITY":[112],"AND":[113],"IMPLEMENTATION:":[114],"https://github.com/SouthGreenPlatform/PyRice.":[115],"SUPPLEMENTARY":[116],"INFORMATION:":[117],"Supplementary":[118],"Bioinformatics":[123],"online.":[124]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-07-03T08:13:44.112507","created_date":"2020-08-07T00:00:00"}