{"id":"https://openalex.org/W2973233547","doi":"https://doi.org/10.1093/bioinformatics/btz707","title":"PPNID: a reference database and molecular identification pipeline for plant-parasitic nematodes","display_name":"PPNID: a reference database and molecular identification pipeline for plant-parasitic nematodes","publication_year":2019,"publication_date":"2019-09-11","ids":{"openalex":"https://openalex.org/W2973233547","doi":"https://doi.org/10.1093/bioinformatics/btz707","mag":"2973233547","pmid":"https://pubmed.ncbi.nlm.nih.gov/31529041"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz707","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz707","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://research.wur.nl/en/publications/ppnid-a-reference-database-and-molecular-identification-pipeline-","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5065765548","display_name":"Xue Qing","orcid":"https://orcid.org/0000-0002-0355-9956"},"institutions":[{"id":"https://openalex.org/I376102","display_name":"Agricultural Research Organization","ror":"https://ror.org/05hbrxp80","country_code":"IL","type":"government","lineage":["https://openalex.org/I376102"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"Xue Qing","raw_affiliation_strings":["Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), The Volcani Center , Rishon LeZion 7505101, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), The Volcani Center , Rishon LeZion 7505101, Israel","institution_ids":["https://openalex.org/I376102"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100377187","display_name":"Meng Wang","orcid":"https://orcid.org/0000-0002-7481-1856"},"institutions":[{"id":"https://openalex.org/I376102","display_name":"Agricultural Research Organization","ror":"https://ror.org/05hbrxp80","country_code":"IL","type":"government","lineage":["https://openalex.org/I376102"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Meng Wang","raw_affiliation_strings":["Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), The Volcani Center , Rishon LeZion 7505101, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), The Volcani Center , Rishon LeZion 7505101, Israel","institution_ids":["https://openalex.org/I376102"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112355230","display_name":"Gerrit Karssen","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Gerrit Karssen","raw_affiliation_strings":["National Plant Protection Organization, Wageningen Nematode Collection , Wageningen 6700 HC, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Plant Protection Organization, Wageningen Nematode Collection , Wageningen 6700 HC, The Netherlands","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079168972","display_name":"Patricia Bucki","orcid":"https://orcid.org/0000-0002-5988-8740"},"institutions":[{"id":"https://openalex.org/I376102","display_name":"Agricultural Research Organization","ror":"https://ror.org/05hbrxp80","country_code":"IL","type":"government","lineage":["https://openalex.org/I376102"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Patricia Bucki","raw_affiliation_strings":["Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), The Volcani Center , Rishon LeZion 7505101, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), The Volcani Center , Rishon LeZion 7505101, Israel","institution_ids":["https://openalex.org/I376102"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020667786","display_name":"Wim Bert","orcid":"https://orcid.org/0000-0002-5864-412X"},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Wim Bert","raw_affiliation_strings":["Department of Biology, Nematology Research Unit, Ghent University , Ghent 9000, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Nematology Research Unit, Ghent University , Ghent 9000, Belgium","institution_ids":["https://openalex.org/I32597200"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003941761","display_name":"Sigal Brown Miyara","orcid":"https://orcid.org/0000-0002-4888-4410"},"institutions":[{"id":"https://openalex.org/I376102","display_name":"Agricultural Research Organization","ror":"https://ror.org/05hbrxp80","country_code":"IL","type":"government","lineage":["https://openalex.org/I376102"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"Sigal Braun-Miyara","raw_affiliation_strings":["Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), The Volcani Center , Rishon LeZion 7505101, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), The Volcani Center , Rishon LeZion 7505101, Israel","institution_ids":["https://openalex.org/I376102"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5003941761","https://openalex.org/A5065765548"],"corresponding_institution_ids":["https://openalex.org/I376102"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.8759,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.87623006,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"36","issue":"4","first_page":"1052","last_page":"1056"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11179","display_name":"Nematode management and characterization studies","score":0.9819999933242798,"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"}},"topics":[{"id":"https://openalex.org/T11179","display_name":"Nematode management and characterization studies","score":0.9819999933242798,"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"}},{"id":"https://openalex.org/T10815","display_name":"Parasite Biology and Host Interactions","score":0.00430000014603138,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"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/T11074","display_name":"Helminth infection and control","score":0.0038999998942017555,"subfield":{"id":"https://openalex.org/subfields/3404","display_name":"Small Animals"},"field":{"id":"https://openalex.org/fields/34","display_name":"Veterinary"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.7250477075576782},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5543721914291382},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5341424345970154},{"id":"https://openalex.org/keywords/executable","display_name":"Executable","score":0.5285540819168091},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.4849293529987335},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.46740370988845825},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4543622136116028},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.4467346668243408},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3526553809642792},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.23499268293380737},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1508665382862091},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09010940790176392}],"concepts":[{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.7250477075576782},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5543721914291382},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5341424345970154},{"id":"https://openalex.org/C160145156","wikidata":"https://www.wikidata.org/wiki/Q778586","display_name":"Executable","level":2,"score":0.5285540819168091},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.4849293529987335},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.46740370988845825},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4543622136116028},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.4467346668243408},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3526553809642792},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.23499268293380737},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1508665382862091},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09010940790176392},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009348","descriptor_name":"Nematoda","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009348","descriptor_name":"Nematoda","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009348","descriptor_name":"Nematoda","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btz707","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz707","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:31529041","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31529041","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:library.wur.nl:wurpubs/592236","is_oa":true,"landing_page_url":"https://research.wur.nl/en/publications/ppnid-a-reference-database-and-molecular-identification-pipeline-","pdf_url":null,"source":{"id":"https://openalex.org/S4210201231","display_name":"Socio-Environmental Systems Modeling","issn_l":"2663-3027","issn":["2663-3027"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"ISSN: 1367-4803","raw_type":"Article/Letter to editor"},{"id":"pmh:oai:archive.ugent.be:8644432","is_oa":false,"landing_page_url":"http://hdl.handle.net/1854/LU-8644432","pdf_url":null,"source":{"id":"https://openalex.org/S4306400478","display_name":"Ghent University Academic Bibliography (Ghent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I32597200","host_organization_name":"Ghent University","host_organization_lineage":["https://openalex.org/I32597200"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BIOINFORMATICS","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"pmh:oai:library.wur.nl:wurpubs/592236","is_oa":true,"landing_page_url":"https://research.wur.nl/en/publications/ppnid-a-reference-database-and-molecular-identification-pipeline-","pdf_url":null,"source":{"id":"https://openalex.org/S4210201231","display_name":"Socio-Environmental Systems Modeling","issn_l":"2663-3027","issn":["2663-3027"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"ISSN: 1367-4803","raw_type":"Article/Letter to editor"},"sustainable_development_goals":[{"display_name":"Zero hunger","id":"https://metadata.un.org/sdg/2","score":0.5400000214576721}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":39,"referenced_works":["https://openalex.org/W36320680","https://openalex.org/W568958565","https://openalex.org/W1267673132","https://openalex.org/W1578260240","https://openalex.org/W1820060557","https://openalex.org/W2005176497","https://openalex.org/W2039824012","https://openalex.org/W2044876288","https://openalex.org/W2048784595","https://openalex.org/W2053885906","https://openalex.org/W2058186675","https://openalex.org/W2061354930","https://openalex.org/W2069445330","https://openalex.org/W2077441292","https://openalex.org/W2080887020","https://openalex.org/W2099901798","https://openalex.org/W2103546861","https://openalex.org/W2103961200","https://openalex.org/W2108973989","https://openalex.org/W2113206173","https://openalex.org/W2115387350","https://openalex.org/W2118179655","https://openalex.org/W2119083836","https://openalex.org/W2132297686","https://openalex.org/W2132926880","https://openalex.org/W2144361423","https://openalex.org/W2145397665","https://openalex.org/W2154819422","https://openalex.org/W2160388710","https://openalex.org/W2168105736","https://openalex.org/W2308066056","https://openalex.org/W2596897939","https://openalex.org/W2765311541","https://openalex.org/W2801815683","https://openalex.org/W2901833019","https://openalex.org/W4235612683","https://openalex.org/W6638423856","https://openalex.org/W6675224184","https://openalex.org/W6679995361"],"related_works":["https://openalex.org/W2174809885","https://openalex.org/W2598672065","https://openalex.org/W2883025420","https://openalex.org/W2057191541","https://openalex.org/W2949296710","https://openalex.org/W1992658754","https://openalex.org/W1993817217","https://openalex.org/W3120610872","https://openalex.org/W2111939425","https://openalex.org/W2065083790"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,83,131,153,182,204,224,235],"phylum":[2],"Nematoda":[3],"comprises":[4],"the":[5,19,30,48,61,75,107,112,136,194,229],"most":[6,20],"cosmopolitan":[7],"and":[8,13,42,60,78,114,141,159,172,193,199,216],"abundant":[9],"metazoans":[10],"on":[11,211],"Earth":[12],"plant-parasitic":[14],"nematodes":[15],"represent":[16],"one":[17],"of":[18,63,116,138,155],"significant":[21],"nematode":[22,34],"groups,":[23],"causing":[24],"severe":[25],"losses":[26],"in":[27,150,208,220],"agriculture.":[28],"Practically,":[29],"demands":[31],"for":[32,38,90,127],"accurate":[33],"identification":[35,69,115],"are":[36,148,249],"high":[37],"ecological,":[39],"agricultural,":[40],"taxonomic":[41],"phylogenetic":[43],"researches.":[44],"Despite":[45],"their":[46],"importance,":[47],"morphological":[49],"diagnosis":[50],"is":[51,70,197,226,241],"often":[52],"a":[53,96,117],"difficult":[54,72],"task":[55],"due":[56,73],"to":[57,74,87,187,218],"phenotypic":[58],"plasticity":[59],"absence":[62],"clear":[64],"diagnostic":[65],"characters":[66],"while":[67],"molecular":[68],"very":[71],"problematic":[76],"database":[77,98],"complex":[79],"genetic":[80,156],"background.":[81],"RESULTS:":[82],"present":[84],"study":[85],"attempts":[86],"make":[88],"up":[89],"currently":[91],"available":[92,242,250],"databases":[93],"by":[94],"creating":[95],"manually-curated":[97],"including":[99],"all":[100],"up-to-date":[101],"authentic":[102],"barcoding":[103],"sequences.":[104],"To":[105],"facilitate":[106,188],"laborious":[108],"process":[109],"associated":[110],"with":[111,239],"interpretation":[113,196],"given":[118],"query":[119],"sequence,":[120],"we":[121],"developed":[122,210],"an":[123],"automatic":[124],"software":[125],"pipeline":[126,183,205],"rapid":[128],"species":[129,151,174,180],"identification.":[130],"incorporated":[132],"alignment":[133],"function":[134],"facilitates":[135,173],"examination":[137],"mutation":[139],"distribution":[140],"therefore":[142],"also":[143],"reveals":[144],"nucleotide":[145],"autapomorphies,":[146],"which":[147],"important":[149],"delimitation.":[152],"implementation":[154],"distance,":[157],"plot":[158],"maximum":[160],"likelihood":[161],"phylogeny":[162,179],"analysis":[163],"provides":[164],"more":[165,189],"powerful":[166],"optimality":[167],"criteria":[168],"than":[169],"similarity":[170],"searching":[171],"delimitation":[175],"using":[176],"evolutionary":[177],"or":[178],"concepts.":[181],"streamlines":[184],"several":[185],"functions":[186],"precise":[190],"data":[191,248],"analyses,":[192],"subsequent":[195],"easy":[198],"straightforward.":[200],"AVAILABILITY":[201],"AND":[202],"IMPLEMENTATION:":[203],"was":[206],"written":[207],"vb.net,":[209],"Microsoft":[212],"Visual":[213],"Studio":[214],"2017":[215],"designed":[217],"work":[219],"any":[221],"Windows":[222],"environment.":[223],"PPNID":[225],"distributed":[227],"under":[228],"GNU":[230],"General":[231],"Public":[232],"License":[233],"(GPL).":[234],"executable":[236],"file":[237],"along":[238],"tutorials":[240],"at":[243,251],"https://github.com/xueqing4083/PPNID.":[244],"SUPPLEMENTARY":[245],"INFORMATION:":[246],"Supplementary":[247],"Bioinformatics":[252],"online.":[253]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":3}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
