{"id":"https://openalex.org/W4407843029","doi":"https://doi.org/10.21105/joss.07604","title":"Taxonomy Resolver: A Python package for building and filtering taxonomy trees","display_name":"Taxonomy Resolver: A Python package for building and filtering taxonomy trees","publication_year":2025,"publication_date":"2025-02-21","ids":{"openalex":"https://openalex.org/W4407843029","doi":"https://doi.org/10.21105/joss.07604"},"language":"en","primary_location":{"id":"doi:10.21105/joss.07604","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.07604","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.07604.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Open Source Software","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://joss.theoj.org/papers/10.21105/joss.07604.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5026860748","display_name":"F\u00e1bio Madeira","orcid":"https://orcid.org/0000-0001-8728-9449"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"F\u00e1bio Madeira","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom"],"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000103185","display_name":"Nandana Madhusoodanan","orcid":"https://orcid.org/0000-0001-5004-152X"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Nandana Madhusoodanan","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom"],"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078934360","display_name":"Joon Lee","orcid":"https://orcid.org/0000-0002-5760-2761"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Joonheung Lee","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom"],"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056742837","display_name":"Alberto Eusebi","orcid":"https://orcid.org/0000-0001-5179-7724"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Alberto Eusebi","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom"],"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035192006","display_name":"Ania Niewielska","orcid":"https://orcid.org/0000-0003-0989-3389"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Ania Niewielska","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom"],"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001416834","display_name":"Sarah Butcher","orcid":"https://orcid.org/0000-0002-4494-5124"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Sarah Butcher","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom"],"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5026860748"],"corresponding_institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.03030339,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"10","issue":"106","first_page":"7604","last_page":"7604"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9951000213623047,"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":0.9951000213623047,"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":0.991599977016449,"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/T10487","display_name":"Plant and animal studies","score":0.9696000218391418,"subfield":{"id":"https://openalex.org/subfields/1105","display_name":"Ecology, Evolution, Behavior and Systematics"},"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/python","display_name":"Python (programming language)","score":0.7521941065788269},{"id":"https://openalex.org/keywords/resolver","display_name":"Resolver","score":0.5938703417778015},{"id":"https://openalex.org/keywords/taxonomy","display_name":"Taxonomy (biology)","score":0.5654892325401306},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5563230514526367},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.42611074447631836},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23809337615966797},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.090767502784729}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.7521941065788269},{"id":"https://openalex.org/C80156102","wikidata":"https://www.wikidata.org/wiki/Q788036","display_name":"Resolver","level":3,"score":0.5938703417778015},{"id":"https://openalex.org/C58642233","wikidata":"https://www.wikidata.org/wiki/Q8269924","display_name":"Taxonomy (biology)","level":2,"score":0.5654892325401306},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5563230514526367},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.42611074447631836},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23809337615966797},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.090767502784729},{"id":"https://openalex.org/C165005293","wikidata":"https://www.wikidata.org/wiki/Q1074500","display_name":"Chip","level":2,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.21105/joss.07604","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.07604","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.07604.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Open Source Software","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.21105/joss.07604","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.07604","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.07604.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Open Source Software","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320313288","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4407843029.pdf","grobid_xml":"https://content.openalex.org/works/W4407843029.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W2142678478","https://openalex.org/W2401834729","https://openalex.org/W2513727910","https://openalex.org/W2917094250","https://openalex.org/W3021931899","https://openalex.org/W3048090444","https://openalex.org/W4386482833","https://openalex.org/W4394694796","https://openalex.org/W6713154993","https://openalex.org/W6911590169"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2121484818","https://openalex.org/W2142531896","https://openalex.org/W2804343227","https://openalex.org/W1526923327","https://openalex.org/W2158159993","https://openalex.org/W2207495067","https://openalex.org/W1906486629"],"abstract_inverted_index":{"Taxonomy":[0,71,106],"classification":[1,79],"provides":[2,76],"an":[3],"important":[4],"source":[5],"of":[6,19,38,56,59,131],"information":[7],"for":[8,16,67,82,116],"studying":[9],"biological":[10,20],"systems.It":[11],"is":[12],"a":[13,77,108],"key":[14],"component":[15],"many":[17],"areas":[18],"sciences":[21],"research,":[22],"particularly":[23],"genetics,":[24],"evolutionary":[25,54],"biology,":[26],"biodiversity":[27],"and":[28,36,40,80,102,111,118,139],"conservation":[29,37],"(Sandall":[30],"et":[31,62,73],"al.,":[32,63,74],"2023).Common":[33],"ancestry,":[34],"homology":[35],"sequence":[39,89],"structure":[41],"are":[42,49],"all":[43,83],"central":[44],"ideas":[45],"in":[46,86],"biology":[47],"that":[48],"directly":[50],"related":[51],"to":[52],"the":[53,84,87,92,124,129],"history":[55],"any":[57],"group":[58],"organisms":[60,85],"(Ochoterena":[61],"2019).The":[64],"National":[65],"Center":[66],"Biotechnology":[68],"Information":[69],"(NCBI)":[70],"(Schoch":[72],"2020)":[75],"curated":[78],"nomenclature":[81],"public":[88],"databases,":[90],"across":[91],"taxonomic":[93],"ranks":[94],"(i.e.Domain,":[95],"Kingdom,":[96],"Phylum,":[97],"Class,":[98],"Order,":[99],"Family,":[100],"Genus":[101],"Species).Here":[103],"we":[104],"describe":[105],"Resolver,":[107],"Python":[109],"module":[110],"command-line":[112],"interface":[113],"(CLI)":[114],"application":[115],"building":[117],"filtering":[119],"taxonomy":[120],"trees":[121],"based":[122],"on":[123],"NCBI":[125],"Taxonomy.Taxonomy":[126],"Resolver":[127],"streamlines":[128],"process":[130],"manipulating":[132],"trees,":[133],"enabling":[134],"fast":[135],"tree":[136],"traversal,":[137],"searching":[138],"filtering.":[140]},"counts_by_year":[],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
