{"id":"https://openalex.org/W2947954305","doi":"https://doi.org/10.1186/s12859-019-2874-6","title":"Solr-Plant: efficient extraction of plant names from text","display_name":"Solr-Plant: efficient extraction of plant names from text","publication_year":2019,"publication_date":"2019-05-22","ids":{"openalex":"https://openalex.org/W2947954305","doi":"https://doi.org/10.1186/s12859-019-2874-6","mag":"2947954305","pmid":"https://pubmed.ncbi.nlm.nih.gov/31117932"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-2874-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2874-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2874-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2874-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101538005","display_name":"Vivekanand Sharma","orcid":"https://orcid.org/0000-0003-1188-2312"},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vivekanand Sharma","raw_affiliation_strings":["Center for Biomedical Informatics, Brown University, Box G-R, Providence, RI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics, Brown University, Box G-R, Providence, RI, USA","institution_ids":["https://openalex.org/I27804330"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035376119","display_name":"Mar\u00eda Isabel Restrepo","orcid":"https://orcid.org/0000-0002-0436-8932"},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Maria Isabel Restrepo","raw_affiliation_strings":["Center for Biomedical Informatics, Brown University, Box G-R, Providence, RI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics, Brown University, Box G-R, Providence, RI, USA","institution_ids":["https://openalex.org/I27804330"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086602697","display_name":"Indra Neil Sarkar","orcid":"https://orcid.org/0000-0003-2054-7356"},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Indra Neil Sarkar","raw_affiliation_strings":["Center for Biomedical Informatics, Brown University, Box G-R, Providence, RI, USA. neil_sarkar@brown.edu","Center for Biomedical Informatics, Brown University, Box G-R, Providence, RI, USA"],"raw_orcid":"https://orcid.org/0000-0003-2054-7356","affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics, Brown University, Box G-R, Providence, RI, USA. neil_sarkar@brown.edu","institution_ids":["https://openalex.org/I27804330"]},{"raw_affiliation_string":"Center for Biomedical Informatics, Brown University, Box G-R, Providence, RI, USA","institution_ids":["https://openalex.org/I27804330"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5086602697"],"corresponding_institution_ids":["https://openalex.org/I27804330"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.5129,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.64401597,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"20","issue":"1","first_page":"263","last_page":"263"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.7139000296592712,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.7139000296592712,"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/T10895","display_name":"Species Distribution and Climate Change","score":0.055399999022483826,"subfield":{"id":"https://openalex.org/subfields/2302","display_name":"Ecological Modeling"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T13238","display_name":"Botanical Studies and Applications","score":0.03739999979734421,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7826045751571655},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.7022716999053955},{"id":"https://openalex.org/keywords/plant-identification","display_name":"Plant identification","score":0.5752213001251221},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4967501759529114},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.4805191457271576},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.4144400656223297},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3710845708847046},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.35359254479408264}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7826045751571655},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.7022716999053955},{"id":"https://openalex.org/C2776091240","wikidata":"https://www.wikidata.org/wiki/Q106238460","display_name":"Plant identification","level":2,"score":0.5752213001251221},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4967501759529114},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.4805191457271576},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.4144400656223297},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3710845708847046},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35359254479408264},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019992","descriptor_name":"Databases as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019992","descriptor_name":"Databases as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019992","descriptor_name":"Databases as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-019-2874-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2874-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2874-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31117932","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31117932","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:4bbfbdc22bc047208f21513d0fe32b02","is_oa":false,"landing_page_url":"https://doaj.org/article/4bbfbdc22bc047208f21513d0fe32b02","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 20, Iss 1, Pp 1-4 (2019)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6530169","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6530169","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-2874-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2874-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2874-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5211772393","display_name":null,"funder_award_id":"R01 LM011963","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G6943370894","display_name":null,"funder_award_id":"U54GM115467","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8371400083","display_name":null,"funder_award_id":"R01LM011963","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2947954305.pdf","grobid_xml":"https://content.openalex.org/works/W2947954305.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W2011875293","https://openalex.org/W2047116301","https://openalex.org/W2071879021","https://openalex.org/W2080019484","https://openalex.org/W2087064593","https://openalex.org/W2100627415","https://openalex.org/W2107347656","https://openalex.org/W2113514677","https://openalex.org/W2142678031","https://openalex.org/W2144917318","https://openalex.org/W2158833271","https://openalex.org/W2161661053","https://openalex.org/W2321769212","https://openalex.org/W2535170183","https://openalex.org/W2555753391","https://openalex.org/W4285719527","https://openalex.org/W6943765097"],"related_works":["https://openalex.org/W2357241418","https://openalex.org/W2789919619","https://openalex.org/W2086064646","https://openalex.org/W2119135658","https://openalex.org/W2115485936","https://openalex.org/W2293457016","https://openalex.org/W3022131925","https://openalex.org/W2349174110","https://openalex.org/W1597238586","https://openalex.org/W1536405386"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,117,179,194],"retrieval":[2],"of":[3,73,80,120,152,166,173,188,199],"plant-related":[4],"information":[5],"is":[6,124,137],"a":[7,66,202],"challenging":[8],"task":[9],"due":[10],"to":[11,41,65,184],"variations":[12],"in":[13,78,164,171],"species":[14,88,177,211],"name":[15,34,68],"mentions":[16,35],"as":[17,19,201],"well":[18],"spelling":[20],"or":[21],"typographical":[22],"errors":[23],"across":[24],"data":[25,203],"sources.":[26],"Scalable":[27],"solutions":[28],"are":[29,145],"needed":[30,146],"for":[31,61,100,135,147,206],"identifying":[32],"plant":[33,67,210],"from":[36,90],"text":[37,109],"and":[38,63,69,83,96,115,133,149,169,208],"resolving":[39],"them":[40],"accepted":[42],"taxonomic":[43,192],"names.":[44,158,212],"RESULTS:":[45],"An":[46],"Apache":[47],"Solr-based":[48],"fuzzy":[49],"matching":[50],"system":[51],"enhanced":[52],"with":[53,155],"the":[54,121,161],"Smith-Waterman":[55],"alignment":[56],"algorithm":[57],"(\"Solr-Plant\")":[58],"was":[59],"developed":[60],"mapping":[62],"resolution":[64],"synonym":[70],"thesaurus.":[71],"Evaluation":[72],"Solr-Plant":[74,136,159,200],"suggests":[75],"promising":[76],"results":[77,195],"terms":[79,165],"both":[81,167],"accuracy":[82,170],"processing":[84],"efficiency":[85,168],"on":[86],"misspelled":[87],"names":[89,174],"two":[91],"benchmark":[92],"datasets:":[93],"(1)":[94],"SALVIAS":[95],"(2)":[97],"National":[98],"Center":[99],"Biotechnology":[101],"Information":[102],"(NCBI)":[103],"Taxonomy.":[104],"Additional":[105],"evaluation":[106],"using":[107],"S800":[108],"corpus":[110],"also":[111],"reflects":[112],"high":[113],"precision":[114],"recall.":[116],"latest":[118],"version":[119],"source":[122],"code":[123],"available":[125],"at":[126,139,176,190],"https://github.com/bcbi/SolrPlantAPI":[127],".":[128,141],"A":[129],"REST-compliant":[130],"web":[131],"interface":[132],"service":[134],"hosted":[138],"http://bcbi.brown.edu/solrplant":[140],"CONCLUSION:":[142],"Automated":[143],"techniques":[144],"efficient":[148],"accurate":[150],"identification":[151,172],"knowledge":[153],"linked":[154],"biological":[156],"scientific":[157],"complements":[160],"current":[162],"state-of-the-art":[163],"restricted":[175],"level.":[178],"approach":[180],"can":[181],"be":[182],"extended":[183],"identify":[185],"broader":[186],"groups":[187],"organisms":[189],"different":[191],"levels.":[193],"reflect":[196],"potential":[197],"utility":[198],"mining":[204],"tool":[205],"extracting":[207],"correcting":[209]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2020,"cited_by_count":6}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}