{"id":"https://openalex.org/W2766482558","doi":"https://doi.org/10.1093/bioinformatics/btx660","title":"PyBEL: a computational framework for Biological Expression Language","display_name":"PyBEL: a computational framework for Biological Expression Language","publication_year":2017,"publication_date":"2017-10-17","ids":{"openalex":"https://openalex.org/W2766482558","doi":"https://doi.org/10.1093/bioinformatics/btx660","mag":"2766482558","pmid":"https://pubmed.ncbi.nlm.nih.gov/29048466"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx660","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx660","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/4/703/25117260/btx660.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/4/703/25117260/btx660.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5065488553","display_name":"Charles Tapley Hoyt","orcid":"https://orcid.org/0000-0003-4423-4370"},"institutions":[{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]},{"id":"https://openalex.org/I4210098248","display_name":"Fraunhofer Institute for Algorithms and Scientific Computing","ror":"https://ror.org/00trw9c49","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210098248","https://openalex.org/I4923324"]},{"id":"https://openalex.org/I4210164149","display_name":"Bonn Aachen International Center for Information Technology","ror":"https://ror.org/054zhq066","country_code":"DE","type":"facility","lineage":["https://openalex.org/I135140700","https://openalex.org/I155417937","https://openalex.org/I4210164149","https://openalex.org/I4923324"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Charles Tapley Hoyt","raw_affiliation_strings":["Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany","Department of Life Science Informatics, Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn, Bonn, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany","institution_ids":["https://openalex.org/I4210098248"]},{"raw_affiliation_string":"Department of Life Science Informatics, Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn, Bonn, Germany","institution_ids":["https://openalex.org/I4210164149","https://openalex.org/I135140700"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031615313","display_name":"Andrej Konotopez","orcid":"https://orcid.org/0000-0002-0270-0284"},"institutions":[{"id":"https://openalex.org/I4210098248","display_name":"Fraunhofer Institute for Algorithms and Scientific Computing","ror":"https://ror.org/00trw9c49","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210098248","https://openalex.org/I4923324"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Andrej Konotopez","raw_affiliation_strings":["Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany","institution_ids":["https://openalex.org/I4210098248"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5034175020","display_name":"Christian Ebeling","orcid":"https://orcid.org/0000-0002-7560-6846"},"institutions":[{"id":"https://openalex.org/I4210098248","display_name":"Fraunhofer Institute for Algorithms and Scientific Computing","ror":"https://ror.org/00trw9c49","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210098248","https://openalex.org/I4923324"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Christian Ebeling","raw_affiliation_strings":["Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany","institution_ids":["https://openalex.org/I4210098248"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5065488553"],"corresponding_institution_ids":["https://openalex.org/I135140700","https://openalex.org/I4210098248","https://openalex.org/I4210164149"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.5822,"has_fulltext":false,"cited_by_count":55,"citation_normalized_percentile":{"value":0.90512456,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"34","issue":"4","first_page":"703","last_page":"704"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9988999962806702,"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":0.9988999962806702,"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":0.9962000250816345,"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":0.9961000084877014,"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/python","display_name":"Python (programming language)","score":0.9279791116714478},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.8946278691291809},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8231936693191528},{"id":"https://openalex.org/keywords/parsing","display_name":"Parsing","score":0.7951200008392334},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.6774308681488037},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.6675217747688293},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5596087574958801},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.5538507699966431},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.44544944167137146},{"id":"https://openalex.org/keywords/mac-os","display_name":"Mac OS","score":0.42894014716148376},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4174751043319702},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.330464243888855},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.15834054350852966}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.9279791116714478},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.8946278691291809},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8231936693191528},{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.7951200008392334},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.6774308681488037},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6675217747688293},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5596087574958801},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.5538507699966431},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.44544944167137146},{"id":"https://openalex.org/C522133331","wikidata":"https://www.wikidata.org/wiki/Q43627","display_name":"Mac OS","level":3,"score":0.42894014716148376},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4174751043319702},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.330464243888855},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.15834054350852966},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000544","descriptor_name":"Alzheimer Disease","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000544","descriptor_name":"Alzheimer Disease","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000544","descriptor_name":"Alzheimer Disease","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btx660","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx660","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/4/703/25117260/btx660.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29048466","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29048466","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:fraunhofer.de:N-484750","is_oa":true,"landing_page_url":"http://publica.fraunhofer.de/documents/N-484750.html","pdf_url":null,"source":{"id":"https://openalex.org/S4306400801","display_name":"Publikationsdatenbank der Fraunhofer-Gesellschaft (Fraunhofer-Gesellschaft)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4923324","host_organization_name":"Fraunhofer-Gesellschaft","host_organization_lineage":["https://openalex.org/I4923324"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Fraunhofer SCAI","raw_type":"Journal Article"},{"id":"pmh:oai:publica.fraunhofer.de:publica/251953","is_oa":false,"landing_page_url":"https://publica.fraunhofer.de/handle/publica/251953","pdf_url":null,"source":{"id":"https://openalex.org/S4306400318","display_name":"Fraunhofer-Publica (Fraunhofer-Gesellschaft)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4923324","host_organization_name":"Fraunhofer-Gesellschaft","host_organization_lineage":["https://openalex.org/I4923324"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"journal article"},{"id":"pmh:oai:pubmedcentral.nih.gov:5860616","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5860616","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx660","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx660","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/4/703/25117260/btx660.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6399999856948853,"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2766482558.pdf","grobid_xml":"https://content.openalex.org/works/W2766482558.grobid-xml"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W1871096589","https://openalex.org/W1969709265","https://openalex.org/W1989842786","https://openalex.org/W2060871034","https://openalex.org/W2069435157","https://openalex.org/W2146026944","https://openalex.org/W2150908245","https://openalex.org/W2178639092","https://openalex.org/W2656695974","https://openalex.org/W6682497444","https://openalex.org/W6685662141"],"related_works":["https://openalex.org/W2132241624","https://openalex.org/W4311683883","https://openalex.org/W4221030787","https://openalex.org/W4212902261","https://openalex.org/W2790811106","https://openalex.org/W2789551765","https://openalex.org/W3170192653","https://openalex.org/W4287775886","https://openalex.org/W4391006377","https://openalex.org/W3097598351"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":5}],"updated_date":"2026-04-12T07:58:50.170612","created_date":"2025-10-10T00:00:00"}