{"id":"https://openalex.org/W2154425539","doi":"https://doi.org/10.1109/bibe.2003.1188940","title":"Requirements of phylogenetic databases","display_name":"Requirements of phylogenetic databases","publication_year":2003,"publication_date":"2003-11-21","ids":{"openalex":"https://openalex.org/W2154425539","doi":"https://doi.org/10.1109/bibe.2003.1188940","mag":"2154425539"},"language":"en","primary_location":{"id":"doi:10.1109/bibe.2003.1188940","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2003.1188940","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings.","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080534085","display_name":"Luay Nakhleh","orcid":"https://orcid.org/0000-0003-3288-6769"},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"L. Nakhleh","raw_affiliation_strings":["Department of Computer Sciences, University of Texas at Austin, Austin, TX"],"affiliations":[{"raw_affiliation_string":"Department of Computer Sciences, University of Texas at Austin, Austin, TX","institution_ids":["https://openalex.org/I86519309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083499808","display_name":"Daniel P. Miranker","orcid":"https://orcid.org/0009-0003-8838-2890"},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"D. Miranker","raw_affiliation_strings":["Department of Computer Sciences, University of Texas at Austin, Austin, TX"],"affiliations":[{"raw_affiliation_string":"Department of Computer Sciences, University of Texas at Austin, Austin, TX","institution_ids":["https://openalex.org/I86519309"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089076652","display_name":"Fran\u00e7ois Barban\u00e7on","orcid":null},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"F. Barbancon","raw_affiliation_strings":["Department of Computer Sciences, University of Texas at Austin, Austin, TX"],"affiliations":[{"raw_affiliation_string":"Department of Computer Sciences, University of Texas at Austin, Austin, TX","institution_ids":["https://openalex.org/I86519309"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5080534085"],"corresponding_institution_ids":["https://openalex.org/I86519309"],"apc_list":null,"apc_paid":null,"fwci":0.9151,"has_fulltext":false,"cited_by_count":28,"citation_normalized_percentile":{"value":0.72932266,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"141","last_page":"148"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9975000023841858,"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":0.9975000023841858,"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":0.9391999840736389,"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/T10012","display_name":"Genetic diversity and population structure","score":0.9381999969482422,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.8211665153503418},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6909308433532715},{"id":"https://openalex.org/keywords/transitive-relation","display_name":"Transitive relation","score":0.5943436622619629},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.581782341003418},{"id":"https://openalex.org/keywords/datalog","display_name":"Datalog","score":0.572540283203125},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5690785050392151},{"id":"https://openalex.org/keywords/sophistication","display_name":"Sophistication","score":0.5297015309333801},{"id":"https://openalex.org/keywords/database-theory","display_name":"Database theory","score":0.49090272188186646},{"id":"https://openalex.org/keywords/phylogenetic-relationship","display_name":"Phylogenetic relationship","score":0.4228660464286804},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.39216339588165283},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.38111475110054016},{"id":"https://openalex.org/keywords/relational-database","display_name":"Relational database","score":0.2607148587703705},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1305459439754486},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12382099032402039},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.06968426704406738}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.8211665153503418},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6909308433532715},{"id":"https://openalex.org/C191399111","wikidata":"https://www.wikidata.org/wiki/Q64861","display_name":"Transitive relation","level":2,"score":0.5943436622619629},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.581782341003418},{"id":"https://openalex.org/C148230440","wikidata":"https://www.wikidata.org/wiki/Q1172264","display_name":"Datalog","level":2,"score":0.572540283203125},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5690785050392151},{"id":"https://openalex.org/C168725872","wikidata":"https://www.wikidata.org/wiki/Q991663","display_name":"Sophistication","level":2,"score":0.5297015309333801},{"id":"https://openalex.org/C12439846","wikidata":"https://www.wikidata.org/wiki/Q4809258","display_name":"Database theory","level":3,"score":0.49090272188186646},{"id":"https://openalex.org/C2992072516","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetic relationship","level":4,"score":0.4228660464286804},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.39216339588165283},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.38111475110054016},{"id":"https://openalex.org/C5655090","wikidata":"https://www.wikidata.org/wiki/Q192588","display_name":"Relational database","level":2,"score":0.2607148587703705},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1305459439754486},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12382099032402039},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.06968426704406738},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","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/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C36289849","wikidata":"https://www.wikidata.org/wiki/Q34749","display_name":"Social science","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":[],"locations_count":3,"locations":[{"id":"doi:10.1109/bibe.2003.1188940","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2003.1188940","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings.","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.110.4281","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.110.4281","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.treebase.org/~piel/pdfs/bibe2003.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.13.3993","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.13.3993","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cs.utexas.edu/ftp/pub/techreports/tr02-64.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.44999998807907104}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W18601330","https://openalex.org/W92515953","https://openalex.org/W1497135357","https://openalex.org/W1569403765","https://openalex.org/W2033854905","https://openalex.org/W2037456534","https://openalex.org/W2056394944","https://openalex.org/W2082246635","https://openalex.org/W2146258444","https://openalex.org/W2154425539","https://openalex.org/W2162621793","https://openalex.org/W4205586278","https://openalex.org/W4249449737","https://openalex.org/W6682514920"],"related_works":["https://openalex.org/W2955734379","https://openalex.org/W2147472183","https://openalex.org/W1982619387","https://openalex.org/W2097324525","https://openalex.org/W2294787171","https://openalex.org/W39059914","https://openalex.org/W1552372479","https://openalex.org/W1600654507","https://openalex.org/W2940690142","https://openalex.org/W3217192861"],"abstract_inverted_index":{"We":[0,74,123],"examine":[1],"the":[2,9,13,24,27,101,107,129,134],"organizational":[3],"impact":[4],"on":[5],"phylogenetic":[6,18,42,70,114],"databases":[7,57],"of":[8,17,26,30,52,55,96,100,106,133],"increasing":[10],"sophistication":[11],"in":[12,32,40],"need":[14],"and":[15,48,58,131,139],"use":[16,25],"data.":[19],"A":[20],"primary":[21],"issue":[22],"is":[23],"unnormalized":[28],"representation":[29,136],"phylogenies":[31,91,108],"Newick":[33],"format":[34],"as":[35,94,120],"a":[36,50,69,86,142],"primitive":[37],"data":[38,88],"type":[39],"existing":[41],"databases.":[43],"In":[44],"particular":[45],"we":[46,109],"identify":[47],"enumerate":[49],"list":[51],"potential":[53],"applications":[54],"such":[56],"queries":[59,79,102,115],"(use-cases)":[60],"that":[61,80,112],"biologists":[62],"may":[63],"wish":[64],"to":[65,128],"see":[66],"integrated":[67],"into":[68],"database":[71],"management":[72],"system.":[73],"show":[75],"there":[76],"are":[77,92],"many":[78,99],"would":[81],"best":[82],"be":[83,117],"supported":[84],"by":[85,137],"normalized":[87,135],"model":[89],"where":[90],"stored":[93],"lists":[95],"edges.":[97],"Since":[98],"require":[103],"transitive":[104],"traversals":[105],"demonstrate,":[110],"constructively,":[111],"complex":[113],"can":[116],"conveniently":[118],"constructed":[119],"Datalog":[121],"programs.":[122],"address":[124],"concerns":[125],"with":[126],"respect":[127],"cost":[130],"performance":[132],"developing":[138],"empirically":[140],"evaluating":[141],"feasibility":[143],"prototype.":[144]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}