{"id":"https://openalex.org/W2125598012","doi":"https://doi.org/10.1186/1751-0473-8-3","title":"FCC \u2013 An automated rule-based processing tool for life science data","display_name":"FCC \u2013 An automated rule-based processing tool for life science data","publication_year":2013,"publication_date":"2013-01-11","ids":{"openalex":"https://openalex.org/W2125598012","doi":"https://doi.org/10.1186/1751-0473-8-3","mag":"2125598012","pmid":"https://pubmed.ncbi.nlm.nih.gov/23311610"},"language":"en","primary_location":{"id":"doi:10.1186/1751-0473-8-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-8-3","pdf_url":"https://link.springer.com/content/pdf/10.1186/1751-0473-8-3.pdf","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"Source Code for Biology and Medicine","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1186/1751-0473-8-3.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075728693","display_name":"Simon Barkow\u2010Oesterreicher","orcid":null},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Simon Barkow-Oesterreicher","raw_affiliation_strings":["Functional Genomics Center Zurich (FGCZ), Swiss Federal Institute of Technology Zurich (ETHZ)|University of Zurich (UZH), CH-8057 Zurich, Winterthurerstrasse 190, Switzerland. cp@fgcz.ethz.ch","Functional Genomics Center Zurich (FGCZ), Swiss Federal Institute of Technology Zurich (ETHZ)|University of Zurich (UZH), Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Functional Genomics Center Zurich (FGCZ), Swiss Federal Institute of Technology Zurich (ETHZ)|University of Zurich (UZH), CH-8057 Zurich, Winterthurerstrasse 190, Switzerland. cp@fgcz.ethz.ch","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Functional Genomics Center Zurich (FGCZ), Swiss Federal Institute of Technology Zurich (ETHZ)|University of Zurich (UZH), Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048758693","display_name":"Can T\u00fcrker","orcid":null},"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"]},{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Can T\u00fcrker","raw_affiliation_strings":["Functional Genomics Center Zurich (FGCZ), Swiss Federal Institute of Technology Zurich (ETHZ)|University of Zurich (UZH), CH-8057, Zurich, Winterthurerstrasse, 190, Switzerland","Functional Genomics Center Zurich (FGCZ), Swiss Federal Institute of Technology Zurich (ETHZ)|University of Zurich (UZH), Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Functional Genomics Center Zurich (FGCZ), Swiss Federal Institute of Technology Zurich (ETHZ)|University of Zurich (UZH), CH-8057, Zurich, Winterthurerstrasse, 190, Switzerland","institution_ids":["https://openalex.org/I202697423"]},{"raw_affiliation_string":"Functional Genomics Center Zurich (FGCZ), Swiss Federal Institute of Technology Zurich (ETHZ)|University of Zurich (UZH), Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002516811","display_name":"Christian Panse","orcid":"https://orcid.org/0000-0003-1975-3064"},"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"]},{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Christian Panse","raw_affiliation_strings":["Functional Genomics Center Zurich (FGCZ), Swiss Federal Institute of Technology Zurich (ETHZ)|University of Zurich (UZH), CH-8057, Zurich, Winterthurerstrasse, 190, Switzerland","Functional Genomics Center Zurich (FGCZ), Swiss Federal Institute of Technology Zurich (ETHZ)|University of Zurich (UZH), Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Functional Genomics Center Zurich (FGCZ), Swiss Federal Institute of Technology Zurich (ETHZ)|University of Zurich (UZH), CH-8057, Zurich, Winterthurerstrasse, 190, Switzerland","institution_ids":["https://openalex.org/I202697423"]},{"raw_affiliation_string":"Functional Genomics Center Zurich (FGCZ), Swiss Federal Institute of Technology Zurich (ETHZ)|University of Zurich (UZH), Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5002516811"],"corresponding_institution_ids":["https://openalex.org/I202697423","https://openalex.org/I35440088"],"apc_list":{"value":2040,"currency":"USD","value_usd":2040},"apc_paid":{"value":2040,"currency":"USD","value_usd":2040},"fwci":0.155,"has_fulltext":true,"cited_by_count":28,"citation_normalized_percentile":{"value":0.51106012,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"8","issue":"1","first_page":"3","last_page":"3"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.4424999952316284,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.4424999952316284,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.10809999704360962,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.07339999824762344,"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/computer-science","display_name":"Computer science","score":0.8382965326309204},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7157306671142578},{"id":"https://openalex.org/keywords/data-processing","display_name":"Data processing","score":0.6526594161987305},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.5528037548065186},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4651314616203308},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.45923125743865967},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4486267864704132},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3261234760284424},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2753239572048187},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10432097315788269}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8382965326309204},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7157306671142578},{"id":"https://openalex.org/C138827492","wikidata":"https://www.wikidata.org/wiki/Q6661985","display_name":"Data processing","level":2,"score":0.6526594161987305},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.5528037548065186},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4651314616203308},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.45923125743865967},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4486267864704132},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3261234760284424},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2753239572048187},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10432097315788269},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[],"locations_count":8,"locations":[{"id":"doi:10.1186/1751-0473-8-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-8-3","pdf_url":"https://link.springer.com/content/pdf/10.1186/1751-0473-8-3.pdf","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"Source Code for Biology and Medicine","raw_type":"journal-article"},{"id":"pmid:23311610","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23311610","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":"Source code for biology and medicine","raw_type":null},{"id":"pmh:oai:www.zora.uzh.ch:71742","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306401281","display_name":"Zurich Open Repository and Archive (University of Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I202697423","host_organization_name":"University of Zurich","host_organization_lineage":["https://openalex.org/I202697423"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Barkow-Oesterreicher, Simon; Tuerker, Can; Panse, Christian (2013). FCC \u2013 An automated rule-based processing tool for life science data. Source Code for Biology and Medicine, 8:3.","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:europepmc.org:2617042","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3614436","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3614436","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3614436","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"Source Code Biol Med","raw_type":"Text"},{"id":"pmh:oai:www.research-collection.ethz.ch:20.500.11850/62161","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11850/62161","pdf_url":null,"source":{"id":"https://openalex.org/S4306402302","display_name":"Repository for Publications and Research Data (ETH Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I35440088","host_organization_name":"ETH Zurich","host_organization_lineage":["https://openalex.org/I35440088"],"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":"Source code for biology and medicine, 8","raw_type":"info:eu-repo/semantics/article"},{"id":"doi:10.3929/ethz-b-000062161","is_oa":true,"landing_page_url":"https://doi.org/10.3929/ethz-b-000062161","pdf_url":null,"source":{"id":"https://openalex.org/S7407051236","display_name":"ETH Z\u00fcrich Research Collection","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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"},{"id":"doi:10.5167/uzh-71742","is_oa":true,"landing_page_url":"https://doi.org/10.5167/uzh-71742","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"JournalArticle"}],"best_oa_location":{"id":"doi:10.1186/1751-0473-8-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-8-3","pdf_url":"https://link.springer.com/content/pdf/10.1186/1751-0473-8-3.pdf","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"Source Code for Biology and Medicine","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Responsible consumption and production","id":"https://metadata.un.org/sdg/12","score":0.47999998927116394}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2125598012.pdf","grobid_xml":"https://content.openalex.org/works/W2125598012.grobid-xml"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W1491344747","https://openalex.org/W1556533941","https://openalex.org/W1835740130","https://openalex.org/W2027974246","https://openalex.org/W2050783490","https://openalex.org/W2110017950","https://openalex.org/W2335177920"],"related_works":["https://openalex.org/W1981780420","https://openalex.org/W2182707996","https://openalex.org/W2352265713","https://openalex.org/W2360242447","https://openalex.org/W2386554709","https://openalex.org/W3113494317","https://openalex.org/W2610098438","https://openalex.org/W2378356576","https://openalex.org/W2383657100","https://openalex.org/W2108408136"],"abstract_inverted_index":{"BACKGROUND:":[0],"Data":[1],"processing":[2,83,101,155,190,226,253],"in":[3,15,36,39,237],"the":[4,9,72,86,104,149,167,173,193,210,219,284],"bioinformatics":[5],"field":[6,19],"often":[7],"involves":[8],"handling":[10],"of":[11,24,74,85,95,122,126,143,195,221,235],"diverse":[12,196],"software":[13],"programs":[14,111,197],"one":[16],"workflow.":[17],"The":[18,49,181],"is":[20,51,183],"lacking":[21],"a":[22,92,128,184,199],"set":[23],"standards":[25],"for":[26,107,118,148,187,206,212,252,287,291],"file":[27,189],"formats":[28],"so":[29,262],"that":[30,52,80,191,267],"files":[31,261],"have":[32,272],"to":[33,41,45,63,134,198,218,278],"be":[34,216],"processed":[35],"different":[37,46],"ways":[38],"order":[40],"make":[42,124],"them":[43,123,159],"compatible":[44],"analysis":[47],"programs.":[48,102],"problem":[50],"mass":[53,258],"spectrometry":[54,259],"vendors":[55],"at":[56,172,250],"most":[57,121],"provide":[58],"only":[59,127],"closed-source":[60],"Windows":[61],"libraries":[62],"programmatically":[64],"access":[65],"their":[66],"proprietary":[67],"binary":[68],"formats.":[69],"This":[70],"prohibits":[71],"creation":[73],"an":[75,288],"efficient":[76,289],"and":[77,100,157,225,230,283],"unified":[78],"tool":[79,282],"fits":[81],"all":[82,213,240],"needs":[84,220],"users.":[87,150],"Therefore,":[88],"researchers":[89],"are":[90],"spending":[91],"significant":[93],"amount":[94],"time":[96,105,147],"using":[97,239],"GUI-based":[98],"conversion":[99],"Besides":[103],"needed":[106],"manual":[108],"usage,":[109],"such":[110],"also":[112],"can":[113,215,227],"show":[114],"long":[115],"running":[116],"times":[117],"processing,":[119],"because":[120],"use":[125],"single":[129,200,223],"CPU.":[130],"In":[131],"particular,":[132],"algorithms":[133],"enhance":[135],"data":[136,208],"quality,":[137],"e.g.":[138],"peak":[139],"picking":[140],"or":[141],"deconvolution":[142],"spectra,":[144],"add":[145],"waiting":[146],"RESULTS:":[151],"To":[152],"automate":[153],"these":[154],"tasks":[156,214],"let":[158],"run":[160,228],"continuously":[161],"without":[162],"user":[163],"interaction,":[164],"we":[165,265,275],"developed":[166],"FGCZ":[168,251],"Converter":[169],"Control":[170],"(FCC)":[171],"Functional":[174],"Genomics":[175],"Center":[176],"Zurich":[177],"(FGCZ)":[178],"core":[179],"facility.":[180],"FCC":[182,245],"rule-based":[185],"system":[186],"automated":[188],"reduces":[192],"operation":[194],"configuration":[201],"task.":[202],"Using":[203],"filtering":[204],"rules":[205],"raw":[207,260],"files,":[209],"parameters":[211],"custom-tailored":[217],"every":[222],"researcher":[224],"automatically":[229],"efficiently":[231],"on":[232,280],"any":[233],"number":[234],"servers":[236],"parallel":[238],"available":[241],"CPU":[242],"resources.":[243],"CONCLUSIONS:":[244],"has":[246],"been":[247],"used":[248],"intensively":[249],"more":[254],"than":[255],"hundred":[256],"thousand":[257],"far.":[263],"Since":[264],"know":[266],"many":[268],"other":[269],"research":[270],"facilities":[271],"similar":[273],"problems,":[274],"would":[276],"like":[277],"report":[279],"our":[281],"accompanying":[285],"ideas":[286],"set-up":[290],"potential":[292],"reuse.":[293]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1}],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2025-10-10T00:00:00"}
