{"id":"https://openalex.org/W2102768936","doi":"https://doi.org/10.1186/1471-2105-13-18","title":"Propagating semantic information in biochemical network models","display_name":"Propagating semantic information in biochemical network models","publication_year":2012,"publication_date":"2012-01-30","ids":{"openalex":"https://openalex.org/W2102768936","doi":"https://doi.org/10.1186/1471-2105-13-18","mag":"2102768936","pmid":"https://pubmed.ncbi.nlm.nih.gov/22289386"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-13-18","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-18","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-13-18","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-13-18","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079222008","display_name":"Marvin Schulz","orcid":"https://orcid.org/0009-0009-7565-9460"},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Marvin Schulz","raw_affiliation_strings":["Institut f\u00fcr Biologie, Theoretische Biophysik, Humboldt-Universit\u00e4t zu Berlin, Invalidenstr 42, 10115 Berlin, Germany. marvin.schulz@biologie.hu-berlin.de","Institut f\u00fcr Biologie, Theoretische Biophysik, Humboldt-Universit\u00e4t zu Berlin, Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Institut f\u00fcr Biologie, Theoretische Biophysik, Humboldt-Universit\u00e4t zu Berlin, Invalidenstr 42, 10115 Berlin, Germany. marvin.schulz@biologie.hu-berlin.de","institution_ids":["https://openalex.org/I39343248"]},{"raw_affiliation_string":"Institut f\u00fcr Biologie, Theoretische Biophysik, Humboldt-Universit\u00e4t zu Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003799374","display_name":"Edda Klipp","orcid":"https://orcid.org/0000-0002-0567-7075"},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Edda Klipp","raw_affiliation_strings":["Institut f\u00fcr Biologie, Theoretische Biophysik, Humboldt-Universit\u00e4t zu Berlin, Invalidenstr. 42, 10115, Berlin, Germany","Institut f\u00fcr Biologie, Theoretische Biophysik, Humboldt-Universit\u00e4t zu Berlin, Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Institut f\u00fcr Biologie, Theoretische Biophysik, Humboldt-Universit\u00e4t zu Berlin, Invalidenstr. 42, 10115, Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]},{"raw_affiliation_string":"Institut f\u00fcr Biologie, Theoretische Biophysik, Humboldt-Universit\u00e4t zu Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046914403","display_name":"Wolfram Liebermeister","orcid":"https://orcid.org/0000-0002-2568-2381"},"institutions":[{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"funder","lineage":["https://openalex.org/I7877124"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Wolfram Liebermeister","raw_affiliation_strings":["Institut f\u00fcr Biochemie, Charit\u00e9-Universit\u00e4tsmedizin Berlin, Seestr. 73, 13347, Berlin, Germany","Institut f\u00fcr Biochemie, Charit\u00e9\u2010Universit\u00e4tsmedizin Berlin, Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Institut f\u00fcr Biochemie, Charit\u00e9-Universit\u00e4tsmedizin Berlin, Seestr. 73, 13347, Berlin, Germany","institution_ids":["https://openalex.org/I7877124"]},{"raw_affiliation_string":"Institut f\u00fcr Biochemie, Charit\u00e9\u2010Universit\u00e4tsmedizin Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I7877124"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5079222008"],"corresponding_institution_ids":["https://openalex.org/I39343248"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.671,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.69099479,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"13","issue":"1","first_page":"18","last_page":"18"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9994999766349792,"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"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9994999766349792,"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"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9993000030517578,"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"}},{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9990000128746033,"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":0.597617506980896},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5314487218856812},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.488414466381073},{"id":"https://openalex.org/keywords/semantic-network","display_name":"Semantic network","score":0.42772069573402405},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.34699106216430664},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.3193244934082031},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.31024298071861267},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2677735686302185},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.16287961602210999},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.14405697584152222},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13068470358848572}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.597617506980896},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5314487218856812},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.488414466381073},{"id":"https://openalex.org/C85407183","wikidata":"https://www.wikidata.org/wiki/Q1045785","display_name":"Semantic network","level":2,"score":0.42772069573402405},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.34699106216430664},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3193244934082031},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.31024298071861267},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2677735686302185},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.16287961602210999},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.14405697584152222},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13068470358848572}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","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":"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":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-13-18","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-18","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-13-18","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22289386","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22289386","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:618d5fafeb6c4205af963bbe6944b067","is_oa":true,"landing_page_url":"https://doaj.org/article/618d5fafeb6c4205af963bbe6944b067","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 13, Iss 1, p 18 (2012)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3340317","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3340317","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-13-18","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-18","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-13-18","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2102768936.pdf","grobid_xml":"https://content.openalex.org/works/W2102768936.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W1533710340","https://openalex.org/W1539989627","https://openalex.org/W1557757161","https://openalex.org/W1966893452","https://openalex.org/W1970737407","https://openalex.org/W1979537657","https://openalex.org/W1985458980","https://openalex.org/W2017551827","https://openalex.org/W2020561965","https://openalex.org/W2028703400","https://openalex.org/W2033377040","https://openalex.org/W2056124433","https://openalex.org/W2070658593","https://openalex.org/W2072005960","https://openalex.org/W2096248361","https://openalex.org/W2097852199","https://openalex.org/W2098769288","https://openalex.org/W2100438221","https://openalex.org/W2103571314","https://openalex.org/W2104009289","https://openalex.org/W2107062718","https://openalex.org/W2120043685","https://openalex.org/W2121773288","https://openalex.org/W2123060905","https://openalex.org/W2126225210","https://openalex.org/W2127563440","https://openalex.org/W2128501050","https://openalex.org/W2134380650","https://openalex.org/W2150908245","https://openalex.org/W2156929407","https://openalex.org/W2157092888","https://openalex.org/W2167222948","https://openalex.org/W2171038145","https://openalex.org/W2171403830","https://openalex.org/W4240861547","https://openalex.org/W4290750029","https://openalex.org/W6678274143"],"related_works":["https://openalex.org/W2415545834","https://openalex.org/W2069695727","https://openalex.org/W1802639773","https://openalex.org/W2118505788","https://openalex.org/W4254166511","https://openalex.org/W2150084125","https://openalex.org/W1542823905","https://openalex.org/W172207243","https://openalex.org/W2183319312","https://openalex.org/W3112918607"],"abstract_inverted_index":{"Semantic":[0],"propagation":[1],"and":[2,20],"model":[3,18],"alignment":[4,19],"are":[5],"included":[6],"in":[7],"the":[8],"open-source":[9],"library":[10],"semanticSBML,":[11],"available":[12],"on":[13],"sourceforge.":[14],"Online":[15],"services":[16],"for":[17,21],"annotation":[22],"prediction":[23],"can":[24],"be":[25],"used":[26],"at":[27],"http://www.semanticsbml.org.":[28]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
