{"id":"https://openalex.org/W2798671114","doi":"https://doi.org/10.1017/s1471068418000236","title":"Phylotastic: An Experiment in Creating, Manipulating, and Evolving Phylogenetic Biology Workflows Using Logic Programming","display_name":"Phylotastic: An Experiment in Creating, Manipulating, and Evolving Phylogenetic Biology Workflows Using Logic Programming","publication_year":2018,"publication_date":"2018-07-01","ids":{"openalex":"https://openalex.org/W2798671114","doi":"https://doi.org/10.1017/s1471068418000236","mag":"2798671114"},"language":"en","primary_location":{"id":"doi:10.1017/s1471068418000236","is_oa":true,"landing_page_url":"https://doi.org/10.1017/s1471068418000236","pdf_url":"https://www.cambridge.org/core/services/aop-cambridge-core/content/view/202E5DB9473EB06448074C15036A0200/S1471068418000236a.pdf/div-class-title-phylotastic-an-experiment-in-creating-manipulating-and-evolving-phylogenetic-biology-workflows-using-logic-programming-div.pdf","source":{"id":"https://openalex.org/S59670734","display_name":"Theory and Practice of Logic Programming","issn_l":"1471-0684","issn":["1471-0684","1475-3081"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311721","host_organization_name":"Cambridge University Press","host_organization_lineage":["https://openalex.org/P4310311721","https://openalex.org/P4310311702"],"host_organization_lineage_names":["Cambridge University Press","University of Cambridge"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Theory and Practice of Logic Programming","raw_type":"journal-article"},"type":"preprint","indexed_in":["arxiv","crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://www.cambridge.org/core/services/aop-cambridge-core/content/view/202E5DB9473EB06448074C15036A0200/S1471068418000236a.pdf/div-class-title-phylotastic-an-experiment-in-creating-manipulating-and-evolving-phylogenetic-biology-workflows-using-logic-programming-div.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000357988","display_name":"Thanh Hai Nguyen","orcid":"https://orcid.org/0000-0001-9996-4720"},"institutions":[{"id":"https://openalex.org/I10052268","display_name":"New Mexico State University","ror":"https://ror.org/00hpz7z43","country_code":"US","type":"education","lineage":["https://openalex.org/I10052268"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"THANH HAI NGUYEN","raw_affiliation_strings":["Department of Computer Science, New Mexico State University, (e-mail:","New Mexico State University, "],"raw_orcid":"https://orcid.org/0000-0001-9996-4720","affiliations":[{"raw_affiliation_string":"Department of Computer Science, New Mexico State University, (e-mail:","institution_ids":["https://openalex.org/I10052268"]},{"raw_affiliation_string":"New Mexico State University, ","institution_ids":["https://openalex.org/I10052268"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024528910","display_name":"Enrico Pontelli","orcid":"https://orcid.org/0000-0002-7753-1737"},"institutions":[{"id":"https://openalex.org/I10052268","display_name":"New Mexico State University","ror":"https://ror.org/00hpz7z43","country_code":"US","type":"education","lineage":["https://openalex.org/I10052268"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"ENRICO PONTELLI","raw_affiliation_strings":["Department of Computer Science, New Mexico State University, (e-mail:","New Mexico State University, "],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, New Mexico State University, (e-mail:","institution_ids":["https://openalex.org/I10052268"]},{"raw_affiliation_string":"New Mexico State University, ","institution_ids":["https://openalex.org/I10052268"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063459912","display_name":"Tran Cao Son","orcid":"https://orcid.org/0000-0003-3689-8433"},"institutions":[{"id":"https://openalex.org/I10052268","display_name":"New Mexico State University","ror":"https://ror.org/00hpz7z43","country_code":"US","type":"education","lineage":["https://openalex.org/I10052268"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"TRAN CAO SON","raw_affiliation_strings":["Department of Computer Science, New Mexico State University, (e-mail:","New Mexico State University, "],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, New Mexico State University, (e-mail:","institution_ids":["https://openalex.org/I10052268"]},{"raw_affiliation_string":"New Mexico State University, ","institution_ids":["https://openalex.org/I10052268"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5000357988"],"corresponding_institution_ids":["https://openalex.org/I10052268"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.03896988,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"18","issue":"3-4","first_page":"656","last_page":"672"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10215","display_name":"Semantic Web and Ontologies","score":0.9937000274658203,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10215","display_name":"Semantic Web and Ontologies","score":0.9937000274658203,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10317","display_name":"Advanced Database Systems and Queries","score":0.9746999740600586,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11010","display_name":"Logic, Reasoning, and Knowledge","score":0.9634000062942505,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.8836007118225098},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6822711229324341},{"id":"https://openalex.org/keywords/workflow-management-system","display_name":"Workflow management system","score":0.529934823513031},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.5262481570243835},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.508188009262085},{"id":"https://openalex.org/keywords/reuse","display_name":"Reuse","score":0.470103919506073},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.44188961386680603},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.395953893661499},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3958480656147003},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.15504324436187744},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14810094237327576},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.13576984405517578},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.11767277121543884}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.8836007118225098},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6822711229324341},{"id":"https://openalex.org/C140824633","wikidata":"https://www.wikidata.org/wiki/Q2808660","display_name":"Workflow management system","level":3,"score":0.529934823513031},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.5262481570243835},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.508188009262085},{"id":"https://openalex.org/C206588197","wikidata":"https://www.wikidata.org/wiki/Q846574","display_name":"Reuse","level":2,"score":0.470103919506073},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.44188961386680603},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.395953893661499},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3958480656147003},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.15504324436187744},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14810094237327576},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.13576984405517578},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.11767277121543884},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1017/s1471068418000236","is_oa":true,"landing_page_url":"https://doi.org/10.1017/s1471068418000236","pdf_url":"https://www.cambridge.org/core/services/aop-cambridge-core/content/view/202E5DB9473EB06448074C15036A0200/S1471068418000236a.pdf/div-class-title-phylotastic-an-experiment-in-creating-manipulating-and-evolving-phylogenetic-biology-workflows-using-logic-programming-div.pdf","source":{"id":"https://openalex.org/S59670734","display_name":"Theory and Practice of Logic Programming","issn_l":"1471-0684","issn":["1471-0684","1475-3081"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311721","host_organization_name":"Cambridge University Press","host_organization_lineage":["https://openalex.org/P4310311721","https://openalex.org/P4310311702"],"host_organization_lineage_names":["Cambridge University Press","University of Cambridge"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Theory and Practice of Logic Programming","raw_type":"journal-article"},{"id":"doi:10.29007/nw9x","is_oa":true,"landing_page_url":"https://doi.org/10.29007/nw9x","pdf_url":"https://easychair.org/publications/preprint_open/RH47","source":{"id":"https://openalex.org/S4210223723","display_name":"EasyChair preprint","issn_l":"2516-2314","issn":["2516-2314"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"EasyChair Preprints","raw_type":"report-series"},{"id":"pmh:oai:arXiv.org:1805.00185","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1805.00185","pdf_url":"https://arxiv.org/pdf/1805.00185","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"mag:2798671114","is_oa":true,"landing_page_url":"https://arxiv.org/pdf/1805.00185.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null},{"id":"doi:10.48550/arxiv.1805.00185","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1805.00185","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"doi:10.1017/s1471068418000236","is_oa":true,"landing_page_url":"https://doi.org/10.1017/s1471068418000236","pdf_url":"https://www.cambridge.org/core/services/aop-cambridge-core/content/view/202E5DB9473EB06448074C15036A0200/S1471068418000236a.pdf/div-class-title-phylotastic-an-experiment-in-creating-manipulating-and-evolving-phylogenetic-biology-workflows-using-logic-programming-div.pdf","source":{"id":"https://openalex.org/S59670734","display_name":"Theory and Practice of Logic Programming","issn_l":"1471-0684","issn":["1471-0684","1475-3081"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311721","host_organization_name":"Cambridge University Press","host_organization_lineage":["https://openalex.org/P4310311721","https://openalex.org/P4310311702"],"host_organization_lineage_names":["Cambridge University Press","University of Cambridge"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Theory and Practice of Logic Programming","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.44999998807907104,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2798671114.pdf","grobid_xml":"https://content.openalex.org/works/W2798671114.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W170104878","https://openalex.org/W220331763","https://openalex.org/W1584110131","https://openalex.org/W1673404489","https://openalex.org/W1976373002","https://openalex.org/W1996816368","https://openalex.org/W2036507321","https://openalex.org/W2043164102","https://openalex.org/W2092211394","https://openalex.org/W2101165625","https://openalex.org/W2120375049","https://openalex.org/W2127779696","https://openalex.org/W2130247660","https://openalex.org/W2145252923","https://openalex.org/W2259225862","https://openalex.org/W2623761406","https://openalex.org/W2770613891","https://openalex.org/W2779166857","https://openalex.org/W2920807433","https://openalex.org/W6606926415","https://openalex.org/W6608727373","https://openalex.org/W6659458360","https://openalex.org/W6673541438","https://openalex.org/W6678976428","https://openalex.org/W6679125807","https://openalex.org/W6738900912","https://openalex.org/W6746514270"],"related_works":["https://openalex.org/W2889793151","https://openalex.org/W2782446504","https://openalex.org/W1992229674","https://openalex.org/W2182769893","https://openalex.org/W2154752825","https://openalex.org/W2147554562","https://openalex.org/W1946125831","https://openalex.org/W1586314608","https://openalex.org/W1487214958","https://openalex.org/W3043890729","https://openalex.org/W153286381","https://openalex.org/W2027209357","https://openalex.org/W2133504762","https://openalex.org/W2560127491","https://openalex.org/W2993124836","https://openalex.org/W2765426977","https://openalex.org/W2089482590","https://openalex.org/W2547927188","https://openalex.org/W2001427281","https://openalex.org/W1930308218"],"abstract_inverted_index":{"Abstract":[0],"Evolutionary":[1],"Biologists":[2],"have":[3,213],"long":[4],"struggled":[5],"with":[6,63,115],"the":[7,19,64,73,93,97,101,104,116,125,128,144,157,163,178,183,186,196,217,221],"challenge":[8],"of":[9,21,66,75,81,103,111,127,152,156,165,168,198,220],"developing":[10,67],"analysis":[11,77,203],"workflows":[12,136,204],"in":[13,92,106,124,137],"a":[14,32,55,85,109,173],"flexible":[15],"manner,":[16,140],"thus":[17],"facilitating":[18],"reuse":[20],"phylogenetic":[22,44,202],"knowledge.":[23],"An":[24],"evolutionary":[25,58,131],"biology":[26],"workflow":[27,175],"can":[28,39],"be":[29],"viewed":[30],"as":[31,54],"plan":[33],"which":[34],"composes":[35],"web":[36,82],"services":[37,83],"that":[38,87,176],"retrieve,":[40],"manipulate,":[41],"and":[42,60,121,200,209],"produce":[43],"trees.":[45],"The":[46],"Phylotastic":[47,107,193,222],"project":[48],"was":[49],"launched":[50],"two":[51],"years":[52],"ago":[53],"collaboration":[56],"between":[57],"biologists":[59,132],"computer":[61],"scientists,":[62],"goal":[65],"an":[68,138],"open":[69],"architecture":[70],"to":[71,118,134,162,171,185],"facilitate":[72],"creation":[74],"such":[76,211],"workflows.":[78],"While":[79],"composition":[80],"is":[84],"problem":[86,105],"has":[88,194],"been":[89,214],"extensively":[90],"explored":[91],"literature,":[94],"including":[95],"within":[96,216],"logic":[98,206],"programming":[99,207],"domain,":[100],"incarnation":[102],"provides":[108],"number":[110],"additional":[112],"challenges.":[113],"Along":[114],"need":[117,164],"integrate":[119],"preferences":[120],"formal":[122],"ontologies":[123],"description":[126],"desired":[129,148,158],"workflow,":[130,145],"tend":[133],"construct":[135],"incremental":[139,169],"by":[141,146],"successively":[142],"refining":[143,201],"indicating":[147],"changes":[149,180,184],"(e.g.,":[150],"exclusion":[151],"certain":[153],"services,":[154],"modifications":[155],"output).":[159],"This":[160,189],"leads":[161],"successive":[166],"iterations":[167],"replanning,":[170],"develop":[172],"new":[174],"integrates":[177],"requested":[179],"while":[181],"minimizing":[182],"original":[187],"workflow.":[188],"paper":[190],"illustrates":[191],"how":[192,210],"addressed":[195],"challenges":[197],"creating":[199],"using":[205],"technology":[208],"solutions":[212],"used":[215],"general":[218],"framework":[219],"project.":[223]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
