{"id":"https://openalex.org/W4387167568","doi":"https://doi.org/10.1021/acs.jcim.3c00744","title":"LISTER: Semiautomatic Metadata Extraction from Annotated Experiment Documentation in eLabFTW","display_name":"LISTER: Semiautomatic Metadata Extraction from Annotated Experiment Documentation in eLabFTW","publication_year":2023,"publication_date":"2023-09-29","ids":{"openalex":"https://openalex.org/W4387167568","doi":"https://doi.org/10.1021/acs.jcim.3c00744","pmid":"https://pubmed.ncbi.nlm.nih.gov/37773594"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.3c00744","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c00744","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5071294345","display_name":"Fathoni A. Musyaffa","orcid":"https://orcid.org/0000-0003-4846-8051"},"institutions":[{"id":"https://openalex.org/I44260953","display_name":"Heinrich Heine University D\u00fcsseldorf","ror":"https://ror.org/024z2rq82","country_code":"DE","type":"education","lineage":["https://openalex.org/I44260953"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Fathoni A. Musyaffa","raw_affiliation_strings":["Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University D\u00fcsseldorf, 40225 D\u00fcsseldorf, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University D\u00fcsseldorf, 40225 D\u00fcsseldorf, Germany","institution_ids":["https://openalex.org/I44260953"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046022539","display_name":"Kirsten Rapp","orcid":null},"institutions":[{"id":"https://openalex.org/I44260953","display_name":"Heinrich Heine University D\u00fcsseldorf","ror":"https://ror.org/024z2rq82","country_code":"DE","type":"education","lineage":["https://openalex.org/I44260953"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Kirsten Rapp","raw_affiliation_strings":["Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University D\u00fcsseldorf, 40225 D\u00fcsseldorf, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University D\u00fcsseldorf, 40225 D\u00fcsseldorf, Germany","institution_ids":["https://openalex.org/I44260953"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063949219","display_name":"Holger Gohlke","orcid":"https://orcid.org/0000-0001-8613-1447"},"institutions":[{"id":"https://openalex.org/I171892758","display_name":"Forschungszentrum J\u00fclich","ror":"https://ror.org/02nv7yv05","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I171892758"]},{"id":"https://openalex.org/I44260953","display_name":"Heinrich Heine University D\u00fcsseldorf","ror":"https://ror.org/024z2rq82","country_code":"DE","type":"education","lineage":["https://openalex.org/I44260953"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Holger Gohlke","raw_affiliation_strings":["Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University D\u00fcsseldorf, 40225 D\u00fcsseldorf, Germany","Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum J\u00fclich GmbH, 52425 J\u00fclich, Germany"],"raw_orcid":"https://orcid.org/0000-0001-8613-1447","affiliations":[{"raw_affiliation_string":"Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University D\u00fcsseldorf, 40225 D\u00fcsseldorf, Germany","institution_ids":["https://openalex.org/I44260953"]},{"raw_affiliation_string":"Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum J\u00fclich GmbH, 52425 J\u00fclich, Germany","institution_ids":["https://openalex.org/I171892758"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5063949219"],"corresponding_institution_ids":["https://openalex.org/I171892758","https://openalex.org/I44260953"],"apc_list":null,"apc_paid":null,"fwci":1.7185,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.88109844,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"63","issue":"20","first_page":"6224","last_page":"6238"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11937","display_name":"Research Data Management Practices","score":0.9993000030517578,"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"}},"topics":[{"id":"https://openalex.org/T11937","display_name":"Research Data Management Practices","score":0.9993000030517578,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.9993000030517578,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9613999724388123,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.9226306676864624},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8317960500717163},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.7460899949073792},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.6447237730026245},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6266707181930542},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5879147052764893},{"id":"https://openalex.org/keywords/metadata-modeling","display_name":"Metadata modeling","score":0.5717600584030151},{"id":"https://openalex.org/keywords/metadata-repository","display_name":"Metadata repository","score":0.5515727996826172},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.5430954694747925},{"id":"https://openalex.org/keywords/json","display_name":"JSON","score":0.49938106536865234},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.4948658347129822},{"id":"https://openalex.org/keywords/interoperability","display_name":"Interoperability","score":0.4835633933544159},{"id":"https://openalex.org/keywords/data-element","display_name":"Data element","score":0.44976717233657837},{"id":"https://openalex.org/keywords/container","display_name":"Container (type theory)","score":0.4282735586166382},{"id":"https://openalex.org/keywords/data-curation","display_name":"Data curation","score":0.4270699918270111},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.38093864917755127},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12539070844650269},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.12406069040298462}],"concepts":[{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.9226306676864624},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8317960500717163},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.7460899949073792},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6447237730026245},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6266707181930542},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5879147052764893},{"id":"https://openalex.org/C110326360","wikidata":"https://www.wikidata.org/wiki/Q17149476","display_name":"Metadata modeling","level":4,"score":0.5717600584030151},{"id":"https://openalex.org/C153048206","wikidata":"https://www.wikidata.org/wiki/Q3454922","display_name":"Metadata repository","level":3,"score":0.5515727996826172},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.5430954694747925},{"id":"https://openalex.org/C2780416260","wikidata":"https://www.wikidata.org/wiki/Q2063","display_name":"JSON","level":2,"score":0.49938106536865234},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.4948658347129822},{"id":"https://openalex.org/C20136886","wikidata":"https://www.wikidata.org/wiki/Q749647","display_name":"Interoperability","level":2,"score":0.4835633933544159},{"id":"https://openalex.org/C30872290","wikidata":"https://www.wikidata.org/wiki/Q1172389","display_name":"Data element","level":3,"score":0.44976717233657837},{"id":"https://openalex.org/C2781018962","wikidata":"https://www.wikidata.org/wiki/Q5164884","display_name":"Container (type theory)","level":2,"score":0.4282735586166382},{"id":"https://openalex.org/C91632574","wikidata":"https://www.wikidata.org/wiki/Q15088675","display_name":"Data curation","level":2,"score":0.4270699918270111},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.38093864917755127},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12539070844650269},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.12406069040298462},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004282","descriptor_name":"Documentation","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":"D066289","descriptor_name":"Data Curation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.3c00744","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c00744","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:37773594","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37773594","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 chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1109129023","display_name":null,"funder_award_id":"267205415 / CRC 1208 INF","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W2048715559","https://openalex.org/W2109872885","https://openalex.org/W2131581981","https://openalex.org/W2302501749","https://openalex.org/W2332658296","https://openalex.org/W2406493898","https://openalex.org/W2414283705","https://openalex.org/W2481300999","https://openalex.org/W2523785361","https://openalex.org/W2607166384","https://openalex.org/W2619484455","https://openalex.org/W2760356275","https://openalex.org/W2766639721","https://openalex.org/W2789816182","https://openalex.org/W3025354823","https://openalex.org/W3044769325","https://openalex.org/W3128692456","https://openalex.org/W3128701936","https://openalex.org/W3136918052","https://openalex.org/W3197433610","https://openalex.org/W3207691511","https://openalex.org/W3211191624","https://openalex.org/W4210768918","https://openalex.org/W4221047533","https://openalex.org/W6602372667","https://openalex.org/W6606405422","https://openalex.org/W6820692689"],"related_works":["https://openalex.org/W2367786714","https://openalex.org/W3084772717","https://openalex.org/W2807292920","https://openalex.org/W4289754504","https://openalex.org/W2981561176","https://openalex.org/W3199469221","https://openalex.org/W202512329","https://openalex.org/W92613187","https://openalex.org/W2907247951","https://openalex.org/W2380261968"],"abstract_inverted_index":{"The":[0,212],"availability":[1],"of":[2,38,126,156],"scientific":[3,147],"methods,":[4],"code,":[5],"and":[6,31,64,73,78,106,142,190,194,196,251,263,266],"data":[7,15,40,48,121,243],"is":[8,43,239],"key":[9],"for":[10,246],"reproducing":[11],"an":[12],"experiment.":[13],"Research":[14],"should":[16,269],"be":[17,55,205,215,270],"made":[18],"available":[19],"following":[20],"the":[21,36,58,93,102,108,119,229,248],"FAIR":[22],"principle":[23],"(":[24,110],"f":[25],"indable,":[26],"a":[27,71,115,149,157,169,172,208,218,242],"ccessible,":[28],"i":[29,111],"nteroperable,":[30],"r":[32],"eusable).":[33],"For":[34],"that,":[35],"annotation":[37,129],"research":[39,47,231,252],"with":[41,163],"metadata":[42,54,80,133,155,179,186,213,250],"central.":[44],"However,":[45],"existing":[46,96],"management":[49],"workflows":[50],"often":[51],"require":[52],"that":[53,203],"created":[56],"by":[57,98],"corresponding":[59],"researchers,":[60],"which":[61],"takes":[62],"effort":[63],"time.":[65],"Here,":[66],"we":[67],"developed":[68],"LISTER":[69,124,184,256],"as":[70,101,118,217,241],"methodological":[72],"algorithmic":[74],"solution":[75],"to":[76,131,144,175,220,228,257,272],"create":[77,221],"extract":[79],"from":[81,181],"annotated,":[82],"template-based":[83],"experimental":[84],"documentation":[85],"using":[86,99,138],"minimum":[87],"effort.":[88],"We":[89,254],"focused":[90],"on":[91],"tailoring":[92],"integration":[94],"between":[95],"platforms":[97],"eLabFTW":[100,136,182],"electronic":[103],"lab":[104],"notebook":[105],"adopting":[107],"ISA":[109],"nvestigation,":[112],"s":[113],"tudy,":[114],"ssay)":[116],"model":[117,122],"abstract":[120],"framework.":[123],"consists":[125],"four":[127],"components:":[128],"language":[130],"support":[132],"extraction;":[134],"customized":[135],"entries":[137],"specific":[139],"hierarchies,":[140],"templates,":[141],"tags":[143],"structure":[145],"reusable":[146],"documentation;":[148],"\u201ccontainer\u201d":[150],"concept":[151,268],"in":[152,187,200,207],"eLabFTW,":[153],"making":[154],"particular":[158],"container":[159],"content":[160],"extractable":[161],"along":[162],"its":[164,236],"underlying,":[165],"related":[166],"experiments":[167],"via":[168],"single":[170],"click;":[171],"Python-based":[173],"app":[174],"enable":[176],"easy-to-use,":[177],"semiautomated":[178],"extraction":[180],"entries.":[183],"outputs":[185],"machine-readable":[188],".json":[189],"human-readable":[191],".xlsx":[192],"formats,":[193],"Material":[195],"Methods":[197],"(MM)":[198],"descriptions":[199],".docx":[201],"format":[202],"could":[204],"used":[206,216,240],"thesis":[209],"or":[210,222],"manuscript.":[211],"can":[214],"basis":[219],"extend":[223],"ontologies,":[224],"which,":[225],"when":[226],"applied":[227,255],"published":[230],"data,":[232],"will":[233],"significantly":[234],"enhance":[235],"value.":[237],"DSpace":[238],"cataloging":[244],"platform":[245],"hosting":[247],"extracted":[249],"data.":[253],"computational":[258],"biophysical":[259],"chemistry,":[260],"protein":[261],"biochemistry,":[262],"molecular":[264],"biology,":[265],"our":[267],"extendable":[271],"other":[273],"life":[274],"science":[275],"areas.":[276]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}