{"id":"https://openalex.org/W2162050818","doi":"https://doi.org/10.1093/bioinformatics/btv276","title":"Phylesystem: a git-based data store for community-curated phylogenetic estimates","display_name":"Phylesystem: a git-based data store for community-curated phylogenetic estimates","publication_year":2015,"publication_date":"2015-05-04","ids":{"openalex":"https://openalex.org/W2162050818","doi":"https://doi.org/10.1093/bioinformatics/btv276","mag":"2162050818","pmid":"https://pubmed.ncbi.nlm.nih.gov/25940563"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv276","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv276","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"hybrid","oa_url":"https://doi.org/10.1093/bioinformatics/btv276","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031118780","display_name":"Emily Jane McTavish","orcid":"https://orcid.org/0000-0001-9766-5727"},"institutions":[{"id":"https://openalex.org/I71030271","display_name":"Heidelberg Institute for Theoretical Studies","ror":"https://ror.org/01f7bcy98","country_code":"DE","type":"facility","lineage":["https://openalex.org/I71030271"]},{"id":"https://openalex.org/I146416000","display_name":"University of Kansas","ror":"https://ror.org/001tmjg57","country_code":"US","type":"education","lineage":["https://openalex.org/I146416000"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Emily Jane McTavish","raw_affiliation_strings":["1 Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA,","2 Heidelberg Institute for Theoretical Studies, Heidelberg 69118, Germany,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA,","institution_ids":["https://openalex.org/I146416000"]},{"raw_affiliation_string":"2 Heidelberg Institute for Theoretical Studies, Heidelberg 69118, Germany,","institution_ids":["https://openalex.org/I71030271"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056794649","display_name":"Cody E. Hinchliff","orcid":"https://orcid.org/0000-0003-1298-5938"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cody E. Hinchliff","raw_affiliation_strings":["3 Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3 Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA,","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040539041","display_name":"James F. Allman","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"James F. Allman","raw_affiliation_strings":["4 Interrobang Corporation, Wake Forest, NC 27587, USA and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"4 Interrobang Corporation, Wake Forest, NC 27587, USA and","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031689741","display_name":"Joseph W. Brown","orcid":"https://orcid.org/0000-0002-3835-8062"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joseph W. Brown","raw_affiliation_strings":["3 Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3 Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA,","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077335670","display_name":"Karen Cranston","orcid":"https://orcid.org/0000-0002-4798-9499"},"institutions":[{"id":"https://openalex.org/I6002401","display_name":"National Evolutionary Synthesis Center","ror":"https://ror.org/001ykb961","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I6002401"]},{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Karen A. Cranston","raw_affiliation_strings":["5 National Evolutionary Synthesis Center, Duke University, Durham, NC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"5 National Evolutionary Synthesis Center, Duke University, Durham, NC, USA","institution_ids":["https://openalex.org/I6002401","https://openalex.org/I170897317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021006859","display_name":"Mark T. Holder","orcid":"https://orcid.org/0000-0001-5575-0536"},"institutions":[{"id":"https://openalex.org/I146416000","display_name":"University of Kansas","ror":"https://ror.org/001tmjg57","country_code":"US","type":"education","lineage":["https://openalex.org/I146416000"]},{"id":"https://openalex.org/I71030271","display_name":"Heidelberg Institute for Theoretical Studies","ror":"https://ror.org/01f7bcy98","country_code":"DE","type":"facility","lineage":["https://openalex.org/I71030271"]}],"countries":["DE","US"],"is_corresponding":true,"raw_author_name":"Mark T. Holder","raw_affiliation_strings":["1 Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA,","2 Heidelberg Institute for Theoretical Studies, Heidelberg 69118, Germany,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA,","institution_ids":["https://openalex.org/I146416000"]},{"raw_affiliation_string":"2 Heidelberg Institute for Theoretical Studies, Heidelberg 69118, Germany,","institution_ids":["https://openalex.org/I71030271"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069448726","display_name":"Jonathan Rees","orcid":"https://orcid.org/0000-0001-7694-8250"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]},{"id":"https://openalex.org/I6002401","display_name":"National Evolutionary Synthesis Center","ror":"https://ror.org/001ykb961","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I6002401"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan A. Rees","raw_affiliation_strings":["5 National Evolutionary Synthesis Center, Duke University, Durham, NC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"5 National Evolutionary Synthesis Center, Duke University, Durham, NC, USA","institution_ids":["https://openalex.org/I6002401","https://openalex.org/I170897317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019827410","display_name":"Stephen A. Smith","orcid":"https://orcid.org/0000-0003-2035-9531"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stephen A. Smith","raw_affiliation_strings":["3 Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3 Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA,","institution_ids":["https://openalex.org/I27837315"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5021006859"],"corresponding_institution_ids":["https://openalex.org/I146416000","https://openalex.org/I71030271"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.1082,"has_fulltext":false,"cited_by_count":65,"citation_normalized_percentile":{"value":0.87400416,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"31","issue":"17","first_page":"2794","last_page":"2800"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.7095000147819519,"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":0.7095000147819519,"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/T11354","display_name":"Evolution and Paleontology Studies","score":0.1014999970793724,"subfield":{"id":"https://openalex.org/subfields/1911","display_name":"Paleontology"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10895","display_name":"Species Distribution and Climate Change","score":0.038100000470876694,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7494439482688904},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.729443371295929},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5755512118339539},{"id":"https://openalex.org/keywords/transparency","display_name":"Transparency (behavior)","score":0.5280362367630005},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5086485147476196},{"id":"https://openalex.org/keywords/javascript","display_name":"JavaScript","score":0.49987363815307617},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.4575456976890564},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.4527107775211334},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.4450386166572571},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.36052072048187256},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3527017831802368},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32491928339004517},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.18776467442512512},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12914174795150757}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7494439482688904},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.729443371295929},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5755512118339539},{"id":"https://openalex.org/C2780233690","wikidata":"https://www.wikidata.org/wiki/Q535347","display_name":"Transparency (behavior)","level":2,"score":0.5280362367630005},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5086485147476196},{"id":"https://openalex.org/C544833334","wikidata":"https://www.wikidata.org/wiki/Q2005","display_name":"JavaScript","level":2,"score":0.49987363815307617},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.4575456976890564},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.4527107775211334},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.4450386166572571},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.36052072048187256},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3527017831802368},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32491928339004517},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.18776467442512512},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12914174795150757},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"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/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","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":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","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":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":9,"locations":[{"id":"doi:10.1093/bioinformatics/btv276","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv276","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25940563","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25940563","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:CiteSeerX.psu:10.1.1.778.9092","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.778.9092","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/1b/fc/btv276.PMC4547614.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.908.237","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.908.237","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2015/04/30/bioinformatics.btv276.full.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.912.4002","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.912.4002","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/31/17/2794.full.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.925.536","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.925.536","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2015/05/30/bioinformatics.btv276.full.pdf","raw_type":"text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:31/17/2794","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/17/2794","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:pubmedcentral.nih.gov:4547614","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4547614","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:kuscholarworks.ku.edu:1808/20061","is_oa":true,"landing_page_url":"http://hdl.handle.net/1808/20061","pdf_url":null,"source":{"id":"https://openalex.org/S4306400421","display_name":"KU ScholarWorks (The University of Kansas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I146416000","host_organization_name":"University of Kansas","host_organization_lineage":["https://openalex.org/I146416000"],"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":"","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv276","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv276","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.6200000047683716}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W1922832738","https://openalex.org/W2004267169","https://openalex.org/W2013410948","https://openalex.org/W2081488649","https://openalex.org/W2100412820","https://openalex.org/W2120375049","https://openalex.org/W2139097042","https://openalex.org/W2140896159","https://openalex.org/W2143176024","https://openalex.org/W2151577432","https://openalex.org/W2157025733","https://openalex.org/W2160393872","https://openalex.org/W2170041483","https://openalex.org/W2951002538","https://openalex.org/W4232313964","https://openalex.org/W6681219725"],"related_works":["https://openalex.org/W2362218761","https://openalex.org/W1997023990","https://openalex.org/W2062354928","https://openalex.org/W2113708670","https://openalex.org/W2795601048","https://openalex.org/W2403324299","https://openalex.org/W2621177934","https://openalex.org/W2088120817","https://openalex.org/W4286287737","https://openalex.org/W1844100222"],"abstract_inverted_index":{"MOTIVATION:":[0],"Phylogenetic":[1],"estimates":[2],"from":[3,305],"published":[4,92,261],"studies":[5],"can":[6,281],"be":[7,282],"archived":[8],"using":[9,211],"general":[10],"platforms":[11],"like":[12],"Dryad":[13],"(Vision,":[14],"2010)":[15],"or":[16],"TreeBASE":[17],"(Sanderson":[18],"et":[19],"al.,":[20],"1994).":[21],"Such":[22],"services":[23,254,294],"fulfill":[24],"a":[25,66,71,91,99,108,177,188,220,244],"crucial":[26,111],"role":[27],"in":[28,33,65,70],"ensuring":[29],"transparency":[30],"and":[31,51,68,122,170,231,242,251,258],"reproducibility":[32],"phylogenetic":[34,55,84,93,146,262],"research.":[35],"However,":[36],"digital":[37],"tree":[38,67,109,189],"data":[39,147,199,209,279],"files":[40],"often":[41],"require":[42],"some":[43],"editing":[44],"(e.g.":[45],"rerooting)":[46],"to":[47,82,107,116,129,140,176,187,207,214,255],"improve":[48],"the":[49,54,59,77,87,103,135,142,149,156,162,183,208,223,227,249,270,291],"accuracy":[50],"reusability":[52],"of":[53,79,89,102,105,137,145,151,155,166,182,185,236,260],"statements.":[56,263],"Furthermore,":[57],"establishing":[58],"mapping":[60],"between":[61],"tip":[62],"labels":[63],"used":[64],"taxa":[69],"single":[72],"common":[73],"taxonomy":[74],"dramatically":[75],"improves":[76],"ability":[78],"other":[80,252],"researchers":[81],"reuse":[83],"estimates.":[85],"As":[86],"process":[88],"curating":[90],"estimate":[94],"is":[95,110,190,274,295,303],"not":[96],"error-free,":[97],"retaining":[98],"full":[100],"record":[101,181],"provenance":[104],"edits":[106,186],"for":[112,119,161,269,300],"openness,":[113],"allowing":[114],"editors":[115],"receive":[117],"credit":[118],"their":[120],"work":[121],"making":[123,174],"errors":[124],"introduced":[125],"during":[126],"curation":[127,144,259],"easier":[128],"correct.":[130],"RESULTS:":[131],"Here,":[132],"we":[133],"report":[134],"development":[136],"software":[138],"infrastructure":[139],"support":[141],"open":[143,205],"by":[148,173,192],"community":[150],"biologists.":[152],"The":[153,180,233,278],"backend":[154],"system":[157],"provides":[158,204],"an":[159],"interface":[160],"standard":[163],"database":[164],"operations":[165],"creating,":[167],"reading,":[168],"updating":[169],"deleting":[171],"records":[172],"commits":[175],"git":[178,230],"repository.":[179],"history":[184],"preserved":[191],"git's":[193],"version":[194],"control":[195],"features.":[196],"Hosting":[197],"this":[198],"store":[200,210,280],"on":[201],"GitHub":[202],"(http://github.com/)":[203],"access":[206],"tools":[212],"familiar":[213],"many":[215],"developers.":[216],"We":[217],"have":[218],"deployed":[219,243,296],"server":[221],"running":[222],"'phylesystem-api',":[224],"which":[225],"wraps":[226],"interactions":[228],"with":[229],"GitHub.":[232],"Open":[234],"Tree":[235],"Life":[237],"project":[238],"has":[239],"also":[240],"developed":[241],"JavaScript":[245],"application":[246,288],"that":[247,289,301],"uses":[248,290],"phylesystem-api":[250],"web":[253,271,287,293],"enable":[256],"input":[257],"AVAILABILITY":[264],"AND":[265],"IMPLEMENTATION:":[266],"Source":[267],"code":[268],"service":[272],"layer":[273],"available":[275,304],"at":[276,297],"https://github.com/OpenTreeOfLife/phylesystem-api.":[277],"cloned":[283],"from:":[284],"https://github.com/OpenTreeOfLife/phylesystem.":[285],"A":[286],"phylesystem":[292],"http://tree.opentreeoflife.org/curator.":[298],"Code":[299],"tool":[302],"https://github.com/OpenTreeOfLife/opentree.":[306],"CONTACT:":[307],"mtholder@gmail.com.":[308]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":15},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":9},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}