{"id":"https://openalex.org/W2394774943","doi":"https://doi.org/10.2390/biecoll-jib-2015-277","title":"Managing and Documenting Legacy Scientific Workflows","display_name":"Managing and Documenting Legacy Scientific Workflows","publication_year":2015,"publication_date":"2015-01-01","ids":{"openalex":"https://openalex.org/W2394774943","doi":"https://doi.org/10.2390/biecoll-jib-2015-277","mag":"2394774943","pmid":"https://pubmed.ncbi.nlm.nih.gov/26673793"},"language":"en","primary_location":{"id":"pmid:26673793","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26673793","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":"Journal of integrative bioinformatics","raw_type":null},"type":"article","indexed_in":["datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.2390/biecoll-jib-2015-277","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074536538","display_name":"Ruben Acu\u00f1a","orcid":"https://orcid.org/0000-0002-8405-8335"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Acuna, Ruben","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033642937","display_name":"Jacques Chomilier","orcid":"https://orcid.org/0000-0002-4250-0762"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Chomilier, Jacques","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5038915978","display_name":"Zo\u00e9 Lacroix","orcid":null},"institutions":[{"id":"https://openalex.org/I55732556","display_name":"Arizona State University","ror":"https://ror.org/03efmqc40","country_code":"US","type":"education","lineage":["https://openalex.org/I55732556"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lacroix, Zoe","raw_affiliation_strings":["Arizona State University**"],"affiliations":[{"raw_affiliation_string":"Arizona State University**","institution_ids":["https://openalex.org/I55732556"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5074536538"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":2.4089,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.92632064,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"12","issue":"3","first_page":"277","last_page":"277"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9969000220298767,"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/T11937","display_name":"Research Data Management Practices","score":0.9868999719619751,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"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":0.9352872967720032},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8103451728820801},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.715022087097168},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.6841290593147278},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.5689189434051514},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.44351357221603394},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.37321993708610535},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3645099997520447},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.2746541500091553}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.9352872967720032},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8103451728820801},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.715022087097168},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6841290593147278},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.5689189434051514},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.44351357221603394},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.37321993708610535},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3645099997520447},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2746541500091553}],"mesh":[{"descriptor_ui":"D001330","descriptor_name":"Electronic Data Processing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D001330","descriptor_name":"Electronic Data Processing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D001330","descriptor_name":"Electronic Data Processing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"pmid:26673793","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26673793","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":"Journal of integrative bioinformatics","raw_type":null},{"id":"doi:10.2390/biecoll-jib-2015-277","is_oa":true,"landing_page_url":"https://doi.org/10.2390/biecoll-jib-2015-277","pdf_url":null,"source":{"id":"https://openalex.org/S4306401670","display_name":"PUB \u2013 Publications at Bielefeld University (Bielefeld University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20121455","host_organization_name":"Bielefeld University","host_organization_lineage":["https://openalex.org/I20121455"],"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-journal"}],"best_oa_location":{"id":"doi:10.2390/biecoll-jib-2015-277","is_oa":true,"landing_page_url":"https://doi.org/10.2390/biecoll-jib-2015-277","pdf_url":null,"source":{"id":"https://openalex.org/S4306401670","display_name":"PUB \u2013 Publications at Bielefeld University (Bielefeld University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20121455","host_organization_name":"Bielefeld University","host_organization_lineage":["https://openalex.org/I20121455"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":50,"referenced_works":["https://openalex.org/W173717986","https://openalex.org/W179254938","https://openalex.org/W269919247","https://openalex.org/W1545590260","https://openalex.org/W1547370473","https://openalex.org/W1577450752","https://openalex.org/W1582747576","https://openalex.org/W1657123160","https://openalex.org/W1663021616","https://openalex.org/W1890786277","https://openalex.org/W1963570349","https://openalex.org/W1965154000","https://openalex.org/W1980240737","https://openalex.org/W1983833794","https://openalex.org/W1985036270","https://openalex.org/W1994698959","https://openalex.org/W2006505034","https://openalex.org/W2038733937","https://openalex.org/W2044334824","https://openalex.org/W2059109315","https://openalex.org/W2074760252","https://openalex.org/W2077925015","https://openalex.org/W2079083905","https://openalex.org/W2093721629","https://openalex.org/W2094201044","https://openalex.org/W2096474011","https://openalex.org/W2097284091","https://openalex.org/W2098295691","https://openalex.org/W2098982627","https://openalex.org/W2104512707","https://openalex.org/W2109525082","https://openalex.org/W2110417468","https://openalex.org/W2114083522","https://openalex.org/W2116783139","https://openalex.org/W2117543051","https://openalex.org/W2120886598","https://openalex.org/W2132177099","https://openalex.org/W2135621733","https://openalex.org/W2135645050","https://openalex.org/W2135729589","https://openalex.org/W2137653635","https://openalex.org/W2146917903","https://openalex.org/W2151680116","https://openalex.org/W2166608280","https://openalex.org/W2171995414","https://openalex.org/W2172218300","https://openalex.org/W2202708682","https://openalex.org/W2541372519","https://openalex.org/W2778936059","https://openalex.org/W2905761094"],"related_works":["https://openalex.org/W3140407034","https://openalex.org/W2235766367","https://openalex.org/W1582950852","https://openalex.org/W2551776835","https://openalex.org/W2905906027","https://openalex.org/W4250110356","https://openalex.org/W2976477659","https://openalex.org/W1852679760","https://openalex.org/W1971102487","https://openalex.org/W858026363"],"abstract_inverted_index":{"Scientific":[0],"legacy":[1,48],"workflows":[2,49,69],"are":[3],"often":[4],"developed":[5],"over":[6],"many":[7,61],"years,":[8],"poorly":[9],"documented":[10],"and":[11,53,84,94],"implemented":[12],"with":[13],"scripting":[14],"languages.":[15],"In":[16],"the":[17,25,35,92],"context":[18],"of":[19,27],"our":[20],"cross-disciplinary":[21],"projects":[22],"we":[23],"face":[24],"problem":[26],"maintaining":[28],"such":[29],"scientific":[30,100],"workflows.":[31,101],"This":[32],"paper":[33],"presents":[34],"Workflow":[36],"Instrumentation":[37],"for":[38],"Structure":[39],"Extraction":[40],"(WISE)":[41],"method":[42,93],"used":[43],"to":[44,70,82,87],"process":[45],"several":[46,99],"ad-hoc":[47],"written":[50],"in":[51,73],"Python":[52],"automatically":[54],"produce":[55],"their":[56],"workflow":[57,76],"structural":[58],"skeleton.":[59],"Unlike":[60],"existing":[62],"methods,":[63],"WISE":[64],"does":[65],"not":[66],"assume":[67],"input":[68],"be":[71],"preprocessed":[72],"a":[74],"known":[75],"formalism.":[77],"It":[78],"is":[79],"also":[80],"able":[81],"identify":[83],"analyze":[85],"calls":[86],"external":[88],"tools.":[89],"We":[90],"present":[91],"report":[95],"its":[96],"results":[97],"on":[98]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2025-11-06T06:51:31.235846","created_date":"2025-10-10T00:00:00"}