{"id":"https://openalex.org/W4309389067","doi":"https://doi.org/10.1007/s10664-022-10229-z","title":"Workflow analysis of data science code in public GitHub repositories","display_name":"Workflow analysis of data science code in public GitHub repositories","publication_year":2022,"publication_date":"2022-11-19","ids":{"openalex":"https://openalex.org/W4309389067","doi":"https://doi.org/10.1007/s10664-022-10229-z","pmid":"https://pubmed.ncbi.nlm.nih.gov/36420321"},"language":"en","primary_location":{"id":"doi:10.1007/s10664-022-10229-z","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10664-022-10229-z","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10664-022-10229-z.pdf","source":{"id":"https://openalex.org/S109852484","display_name":"Empirical Software Engineering","issn_l":"1382-3256","issn":["1382-3256","1573-7616"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Empirical Software Engineering","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s10664-022-10229-z.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5073190153","display_name":"Dhivyabharathi Ramasamy","orcid":"https://orcid.org/0009-0002-9056-6907"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Dhivyabharathi Ramasamy","raw_affiliation_strings":["Department of Informatics, University of Zurich, Zurich, Switzerland"],"affiliations":[{"raw_affiliation_string":"Department of Informatics, University of Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I202697423"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023061106","display_name":"Cristina Sarasua","orcid":"https://orcid.org/0000-0002-2076-9584"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Cristina Sarasua","raw_affiliation_strings":["Department of Informatics, University of Zurich, Zurich, Switzerland"],"affiliations":[{"raw_affiliation_string":"Department of Informatics, University of Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I202697423"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082720005","display_name":"Alberto Bacchelli","orcid":"https://orcid.org/0000-0003-0193-6823"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Alberto Bacchelli","raw_affiliation_strings":["Department of Informatics, University of Zurich, Zurich, Switzerland"],"affiliations":[{"raw_affiliation_string":"Department of Informatics, University of Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I202697423"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073592405","display_name":"Abraham Bernstein","orcid":"https://orcid.org/0000-0002-0128-4602"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Abraham Bernstein","raw_affiliation_strings":["Department of Informatics, University of Zurich, Zurich, Switzerland"],"affiliations":[{"raw_affiliation_string":"Department of Informatics, University of Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I202697423"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5073190153"],"corresponding_institution_ids":["https://openalex.org/I202697423"],"apc_list":{"value":2290,"currency":"EUR","value_usd":2890},"apc_paid":{"value":2290,"currency":"EUR","value_usd":2890},"fwci":7.4206,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.96692282,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"28","issue":"1","first_page":"7","last_page":"7"},"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/T11937","display_name":"Research Data Management Practices","score":0.9965999722480774,"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"}},{"id":"https://openalex.org/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.989300012588501,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.8029677867889404},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6938071250915527},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.5529944896697998},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.4727640748023987},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.41840285062789917},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.28984689712524414}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.8029677867889404},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6938071250915527},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.5529944896697998},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4727640748023987},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.41840285062789917},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.28984689712524414},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1007/s10664-022-10229-z","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10664-022-10229-z","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10664-022-10229-z.pdf","source":{"id":"https://openalex.org/S109852484","display_name":"Empirical Software Engineering","issn_l":"1382-3256","issn":["1382-3256","1573-7616"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Empirical Software Engineering","raw_type":"journal-article"},{"id":"pmid:36420321","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36420321","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":"Empirical software engineering","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9675706","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9675706","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Empir Softw Eng","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1007/s10664-022-10229-z","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10664-022-10229-z","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10664-022-10229-z.pdf","source":{"id":"https://openalex.org/S109852484","display_name":"Empirical Software Engineering","issn_l":"1382-3256","issn":["1382-3256","1573-7616"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Empirical Software Engineering","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"},{"id":"https://openalex.org/F4320323874","display_name":"Universit\u00e4t Z\u00fcrich","ror":"https://ror.org/02crff812"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4309389067.pdf","grobid_xml":"https://content.openalex.org/works/W4309389067.grobid-xml"},"referenced_works_count":76,"referenced_works":["https://openalex.org/W1487083903","https://openalex.org/W1555199703","https://openalex.org/W1970133304","https://openalex.org/W1973540172","https://openalex.org/W1973650376","https://openalex.org/W1974752004","https://openalex.org/W1979900513","https://openalex.org/W1980050552","https://openalex.org/W1987614102","https://openalex.org/W1996651333","https://openalex.org/W1998899601","https://openalex.org/W1999861206","https://openalex.org/W2001292754","https://openalex.org/W2010229520","https://openalex.org/W2032426551","https://openalex.org/W2044102377","https://openalex.org/W2046873602","https://openalex.org/W2053154970","https://openalex.org/W2058614593","https://openalex.org/W2099571428","https://openalex.org/W2102125164","https://openalex.org/W2102365548","https://openalex.org/W2109419450","https://openalex.org/W2118202495","https://openalex.org/W2120599119","https://openalex.org/W2123179704","https://openalex.org/W2140560937","https://openalex.org/W2153246402","https://openalex.org/W2182687482","https://openalex.org/W2241506117","https://openalex.org/W2293453852","https://openalex.org/W2437061623","https://openalex.org/W2506821214","https://openalex.org/W2507380695","https://openalex.org/W2529363007","https://openalex.org/W2587937998","https://openalex.org/W2610517421","https://openalex.org/W2724503592","https://openalex.org/W2771177173","https://openalex.org/W2784241156","https://openalex.org/W2787379525","https://openalex.org/W2796040126","https://openalex.org/W2900861633","https://openalex.org/W2903359694","https://openalex.org/W2907444226","https://openalex.org/W2909198760","https://openalex.org/W2913513779","https://openalex.org/W2940731426","https://openalex.org/W2941232686","https://openalex.org/W2941629559","https://openalex.org/W2941766203","https://openalex.org/W2943238809","https://openalex.org/W2950368691","https://openalex.org/W2954370766","https://openalex.org/W2962564927","https://openalex.org/W2968484890","https://openalex.org/W2971867419","https://openalex.org/W3012094108","https://openalex.org/W3032086959","https://openalex.org/W3042955694","https://openalex.org/W3043652335","https://openalex.org/W3080875002","https://openalex.org/W3089825883","https://openalex.org/W3089843629","https://openalex.org/W3090519803","https://openalex.org/W3100026183","https://openalex.org/W3125798375","https://openalex.org/W3163379266","https://openalex.org/W3193404501","https://openalex.org/W4207017378","https://openalex.org/W4213182250","https://openalex.org/W4245421756","https://openalex.org/W4286530314","https://openalex.org/W4288083705","https://openalex.org/W4288086169","https://openalex.org/W6602452458"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W1981780420","https://openalex.org/W2182707996","https://openalex.org/W45233828","https://openalex.org/W2964988449","https://openalex.org/W2397952901","https://openalex.org/W2029380707","https://openalex.org/W4255934811","https://openalex.org/W2465382974"],"abstract_inverted_index":{"Despite":[0],"the":[1,21,27,56,73,95,120,135,145,154,159,166,170,174,184,196,213,216,225,236,239,243,249,255,268],"ubiquity":[2],"of":[3,32,58,72,78,105,124,137,187,215,229,238,264],"data":[4,15,33,59,79,99,106,113,139,146,188,200,226,251,256,270],"science,":[5],"we":[6,36,82,130,164],"are":[7,203],"far":[8],"from":[9],"rigorously":[10],"understanding":[11,51,71],"how":[12],"coding":[13],"in":[14,48,89,198],"science":[16,34,80,107,140,147,189,201,227,271],"is":[17,52],"performed.":[18],"Even":[19],"though":[20],"scientific":[22],"literature":[23],"has":[24],"hinted":[25],"at":[26],"iterative":[28,74,205],"and":[29,45,75,115,122,168,206,253],"explorative":[30,76],"nature":[31,77],"coding,":[35,81,190],"need":[37],"further":[38],"empirical":[39],"evidence":[40,194],"to":[41,54,97,179,219,223,247],"understand":[42],"this":[43],"practice":[44],"its":[46],"workflows":[47],"detail.":[49],"Such":[50],"critical":[53],"recognise":[55],"needs":[57],"scientists":[60,100],"and,":[61],"for":[62,149,267],"instance,":[63],"inform":[64],"tooling":[65],"support.":[66],"To":[67],"obtain":[68],"a":[69,132,199,230],"deeper":[70,181],"analysed":[83,169],"470":[84,156],"Jupyter":[85],"notebooks":[86],"publicly":[87],"available":[88],"GitHub":[90],"repositories.":[91],"We":[92,210,234],"focused":[93],"on":[94],"extent":[96],"which":[98],"transition":[101,171],"between":[102,173],"different":[103,175],"types":[104],"activities,":[108],"or":[109],"<i>steps</i>":[110],"(such":[111],"as":[112,117,119],"preprocessing":[114],"modelling),":[116],"well":[118],"frequency":[121],"co-occurrence":[123],"such":[125],"transitions.":[126],"For":[127],"our":[128,191],"analysis,":[129],"developed":[131],"dataset":[133,218],"with":[134],"help":[136],"five":[138],"experts,":[141,260],"who":[142],"manually":[143],"annotated":[144,217],"steps":[148,197],"each":[150],"code":[151,232],"cell":[152],"within":[153],"aforementioned":[155],"notebooks.":[157],"Using":[158],"first-order":[160],"Markov":[161],"chain":[162],"model,":[163],"extracted":[165],"transitions":[167],"probabilities":[172],"steps.":[176],"In":[177],"addition":[178],"providing":[180],"insights":[182],"into":[183],"implementation":[185],"practices":[186],"results":[192],"provide":[193],"that":[195],"workflow":[202,244],"indeed":[204],"reveal":[207],"specific":[208],"patterns.":[209],"also":[211],"evaluated":[212],"use":[214],"train":[220],"machine-learning":[221],"classifiers":[222],"predict":[224],"step(s)":[228],"given":[231],"cell.":[233],"investigate":[235],"representativeness":[237],"classification":[240],"by":[241,259],"comparing":[242],"analysis":[245],"applied":[246],"(a)":[248],"predicted":[250],"set":[252,257],"(b)":[254],"labelled":[258],"finding":[261],"an":[262],"F1-score":[263],"about":[265],"71%":[266],"10-class":[269],"step":[272],"prediction":[273],"problem.":[274]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1}],"updated_date":"2026-04-02T15:55:50.835912","created_date":"2025-10-10T00:00:00"}
