{"id":"https://openalex.org/W2913093503","doi":"https://doi.org/10.1371/journal.pcbi.1006791","title":"BioJava 5: A community driven open-source bioinformatics library","display_name":"BioJava 5: A community driven open-source bioinformatics library","publication_year":2019,"publication_date":"2019-02-08","ids":{"openalex":"https://openalex.org/W2913093503","doi":"https://doi.org/10.1371/journal.pcbi.1006791","mag":"2913093503","pmid":"https://pubmed.ncbi.nlm.nih.gov/30735498"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1006791","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006791","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006791&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006791&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031545090","display_name":"Aleix Lafita","orcid":"https://orcid.org/0000-0003-1549-3162"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Aleix Lafita","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK"],"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007217819","display_name":"Spencer Bliven","orcid":"https://orcid.org/0000-0002-1200-1698"},"institutions":[{"id":"https://openalex.org/I858936495","display_name":"ZHAW Zurich University of Applied Sciences","ror":"https://ror.org/05pmsvm27","country_code":"CH","type":"education","lineage":["https://openalex.org/I858936495"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Spencer Bliven","raw_affiliation_strings":["Zurich University of Applied Sciences (ZHAW), Zurich CH-8021, Switzerland"],"affiliations":[{"raw_affiliation_string":"Zurich University of Applied Sciences (ZHAW), Zurich CH-8021, Switzerland","institution_ids":["https://openalex.org/I858936495"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077634829","display_name":"Andreas Prli\u0107","orcid":"https://orcid.org/0000-0001-6346-6391"},"institutions":[{"id":"https://openalex.org/I181653535","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07","country_code":"US","type":"facility","lineage":["https://openalex.org/I181653535","https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andreas Prli\u0107","raw_affiliation_strings":["San Diego Supercomputer Center, UCSD, San Diego, CA 92093, USA"],"affiliations":[{"raw_affiliation_string":"San Diego Supercomputer Center, UCSD, San Diego, CA 92093, USA","institution_ids":["https://openalex.org/I181653535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013018624","display_name":"Dmytro Guzenko","orcid":"https://orcid.org/0000-0002-8688-7460"},"institutions":[{"id":"https://openalex.org/I181653535","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07","country_code":"US","type":"facility","lineage":["https://openalex.org/I181653535","https://openalex.org/I36258959"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dmytro Guzenko","raw_affiliation_strings":["Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA"],"affiliations":[{"raw_affiliation_string":"Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070583038","display_name":"Peter W. Rose","orcid":"https://orcid.org/0000-0001-9981-9750"},"institutions":[{"id":"https://openalex.org/I181653535","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07","country_code":"US","type":"facility","lineage":["https://openalex.org/I181653535","https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter W. Rose","raw_affiliation_strings":["Structural Bioinformatics Laboratory, San Diego Supercomputer Center, UCSD, San Diego, CA 92093, USA"],"affiliations":[{"raw_affiliation_string":"Structural Bioinformatics Laboratory, San Diego Supercomputer Center, UCSD, San Diego, CA 92093, USA","institution_ids":["https://openalex.org/I181653535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031260889","display_name":"A.R. Bradley","orcid":"https://orcid.org/0000-0002-0881-3490"},"institutions":[{"id":"https://openalex.org/I2802711169","display_name":"Diamond Light Source","ror":"https://ror.org/05etxs293","country_code":"GB","type":"facility","lineage":["https://openalex.org/I2802711169"]},{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]},{"id":"https://openalex.org/I4210151791","display_name":"Genomics (United Kingdom)","ror":"https://ror.org/053a6xa29","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210151791"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Anthony Bradley","raw_affiliation_strings":["Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK","Diamond Light Source Ltd., Didcot OX11 0DE, UK","Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"Diamond Light Source Ltd., Didcot OX11 0DE, UK","institution_ids":["https://openalex.org/I2802711169"]},{"raw_affiliation_string":"Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK","institution_ids":["https://openalex.org/I4210151791","https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031085866","display_name":"Paolo Pavan","orcid":"https://orcid.org/0000-0002-1424-4386"},"institutions":[{"id":"https://openalex.org/I4210158583","display_name":"D'Appolonia (Italy)","ror":"https://ror.org/050y0ba80","country_code":"IT","type":"company","lineage":["https://openalex.org/I4210158583"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Paolo Pavan","raw_affiliation_strings":["Genomnia srl, Bresso, Milan, Italy"],"affiliations":[{"raw_affiliation_string":"Genomnia srl, Bresso, Milan, Italy","institution_ids":["https://openalex.org/I4210158583"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001734787","display_name":"Douglas Myers-Turnbull","orcid":"https://orcid.org/0000-0003-3610-4808"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]},{"id":"https://openalex.org/I4210111938","display_name":"Institute for Neurodegenerative Disorders","ror":"https://ror.org/022hrs427","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210111938"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Douglas Myers-Turnbull","raw_affiliation_strings":["Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94143, USA"],"affiliations":[{"raw_affiliation_string":"Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94143, USA","institution_ids":["https://openalex.org/I4210111938","https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108116176","display_name":"Yana Valasatava","orcid":null},"institutions":[{"id":"https://openalex.org/I181653535","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07","country_code":"US","type":"facility","lineage":["https://openalex.org/I181653535","https://openalex.org/I36258959"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yana Valasatava","raw_affiliation_strings":["Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA"],"affiliations":[{"raw_affiliation_string":"Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090047444","display_name":"Michael Heuer","orcid":"https://orcid.org/0000-0002-9052-6000"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Heuer","raw_affiliation_strings":["RISELab, University of California Berkeley, Berkeley, CA, USA"],"affiliations":[{"raw_affiliation_string":"RISELab, University of California Berkeley, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101902745","display_name":"Matt Larson","orcid":"https://orcid.org/0000-0003-2116-5747"},"institutions":[{"id":"https://openalex.org/I4210140032","display_name":"DNASTAR (United States)","ror":"https://ror.org/0548qkv95","country_code":"US","type":"company","lineage":["https://openalex.org/I4210140032"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matt Larson","raw_affiliation_strings":["DNASTAR, Madison, WI, USA"],"affiliations":[{"raw_affiliation_string":"DNASTAR, Madison, WI, USA","institution_ids":["https://openalex.org/I4210140032"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068648875","display_name":"S.K. Burley","orcid":"https://orcid.org/0000-0002-2487-9713"},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]},{"id":"https://openalex.org/I181653535","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07","country_code":"US","type":"facility","lineage":["https://openalex.org/I181653535","https://openalex.org/I36258959"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I4390039325","display_name":"Rutgers Cancer Institute","ror":"https://ror.org/0060x3y55","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I102322142","https://openalex.org/I4390039302","https://openalex.org/I4390039325"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stephen K. Burley","raw_affiliation_strings":["Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA","Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA","Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA"],"affiliations":[{"raw_affiliation_string":"Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA","institution_ids":["https://openalex.org/I102322142"]},{"raw_affiliation_string":"Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"]},{"raw_affiliation_string":"Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA","institution_ids":["https://openalex.org/I102322142","https://openalex.org/I4390039325"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003460293","display_name":"Jos\u00e9 M. Duarte","orcid":"https://orcid.org/0000-0002-9544-5621"},"institutions":[{"id":"https://openalex.org/I181653535","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07","country_code":"US","type":"facility","lineage":["https://openalex.org/I181653535","https://openalex.org/I36258959"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jose M. Duarte","raw_affiliation_strings":["Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA"],"affiliations":[{"raw_affiliation_string":"Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":13,"corresponding_author_ids":["https://openalex.org/A5003460293"],"corresponding_institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":2.7482,"has_fulltext":true,"cited_by_count":48,"citation_normalized_percentile":{"value":0.91130774,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"15","issue":"2","first_page":"e1006791","last_page":"e1006791"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9983000159263611,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9983000159263611,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9952999949455261,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9937999844551086,"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":0.773263156414032},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.6917752027511597},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.682105302810669},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.6677228212356567},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.615337073802948},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.6007925868034363},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.5227218270301819},{"id":"https://openalex.org/keywords/structural-bioinformatics","display_name":"Structural bioinformatics","score":0.4543962776660919},{"id":"https://openalex.org/keywords/parsing","display_name":"Parsing","score":0.43380439281463623},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3695274591445923},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3549076318740845},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.34432440996170044},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.3156593441963196},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.18881499767303467},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12235310673713684}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.773263156414032},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.6917752027511597},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.682105302810669},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.6677228212356567},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.615337073802948},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.6007925868034363},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.5227218270301819},{"id":"https://openalex.org/C69131567","wikidata":"https://www.wikidata.org/wiki/Q2068215","display_name":"Structural bioinformatics","level":3,"score":0.4543962776660919},{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.43380439281463623},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3695274591445923},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3549076318740845},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.34432440996170044},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.3156593441963196},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.18881499767303467},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12235310673713684},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D022126","descriptor_name":"Access to Information","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D022126","descriptor_name":"Access to Information","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D022126","descriptor_name":"Access to Information","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":9,"locations":[{"id":"doi:10.1371/journal.pcbi.1006791","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006791","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006791&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:30735498","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30735498","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:osti.gov:1601670","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1601670","pdf_url":"https://www.osti.gov/servlets/purl/1601670","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null},{"id":"pmh:oai:alma.01RUT_INST:11664944150004646","is_oa":false,"landing_page_url":"https://scholarship.libraries.rutgers.edu/esploro/outputs/journalArticle/BioJava-5-A-community-driven-open-source/991031665658404646","pdf_url":null,"source":{"id":"https://openalex.org/S4210197018","display_name":"View","issn_l":"2688-268X","issn":["2688-268X","2688-3988"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:digitalcollection.zhaw.ch:11475/26200","is_oa":true,"landing_page_url":"https://hdl.handle.net/11475/26200","pdf_url":null,"source":{"id":"https://openalex.org/S4306401810","display_name":"Z\u00fcrcher Hochschule f\u00fcr Angewandte Wissenschaften digital collection (Zurich University of Applied Sciences)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I200744771","host_organization_name":"ZHAW Zurich University of Applied Sciences","host_organization_lineage":["https://openalex.org/I200744771"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:5c110558d5a8402a913e0beeea63fb8e","is_oa":true,"landing_page_url":"https://doaj.org/article/5c110558d5a8402a913e0beeea63fb8e","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 15, Iss 2, p e1006791 (2019)","raw_type":"article"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt9nz953cf","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/9nz953cf","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLOS Computational Biology, vol 15, iss 2","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5393751","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6383946","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:6383946","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6383946","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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1006791","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006791","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006791&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","score":0.4099999964237213,"display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G1485802007","display_name":null,"funder_award_id":"OGI-055","funder_id":"https://openalex.org/F4320319905","funder_display_name":"Ontario Genomics Institute"},{"id":"https://openalex.org/G2309620997","display_name":null,"funder_award_id":"115766","funder_id":"https://openalex.org/F4320319905","funder_display_name":"Ontario Genomics Institute"},{"id":"https://openalex.org/G2537093902","display_name":null,"funder_award_id":"1338415","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G2641904199","display_name":null,"funder_award_id":"NSF-DBI 1338415","funder_id":"https://openalex.org/F4320337398","funder_display_name":"Division of Biological Infrastructure"},{"id":"https://openalex.org/G2939136323","display_name":null,"funder_award_id":"115766","funder_id":"https://openalex.org/F4320310787","funder_display_name":"Genome Canada"},{"id":"https://openalex.org/G3619524234","display_name":null,"funder_award_id":"NSF-DBI 1338415","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G3719330294","display_name":null,"funder_award_id":"DBI 1338415","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3880306168","display_name":"PDB Management by the Research Collaboratory for Structural Bioinformatics","funder_award_id":"1338415","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4565528198","display_name":null,"funder_award_id":"U01 CA198942","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G5921281487","display_name":null,"funder_award_id":"number","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G644439380","display_name":null,"funder_award_id":"CA198942","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7116188982","display_name":null,"funder_award_id":"grants","funder_id":"https://openalex.org/F4320307765","funder_display_name":"Pfizer"},{"id":"https://openalex.org/G7122601629","display_name":null,"funder_award_id":"grant","funder_id":"https://openalex.org/F4320307765","funder_display_name":"Pfizer"},{"id":"https://openalex.org/G7181657240","display_name":null,"funder_award_id":"U01 CA198942","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7669079602","display_name":null,"funder_award_id":"115766","funder_id":"https://openalex.org/F4320314178","funder_display_name":"European Federation of Pharmaceutical Industries and Associations"},{"id":"https://openalex.org/G8348572397","display_name":null,"funder_award_id":"OGI-055","funder_id":"https://openalex.org/F4320310787","funder_display_name":"Genome Canada"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320307765","display_name":"Pfizer","ror":"https://ror.org/01xdqrp08"},{"id":"https://openalex.org/F4320310787","display_name":"Genome Canada","ror":"https://ror.org/029s29983"},{"id":"https://openalex.org/F4320311647","display_name":"Merck KGaA","ror":"https://ror.org/04b2dty93"},{"id":"https://openalex.org/F4320314024","display_name":"Ontario Genomics","ror":null},{"id":"https://openalex.org/F4320314178","display_name":"European Federation of Pharmaceutical Industries and Associations","ror":"https://ror.org/00g1x4v36"},{"id":"https://openalex.org/F4320316545","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07"},{"id":"https://openalex.org/F4320319905","display_name":"Ontario Genomics Institute","ror":"https://ror.org/00c68jz96"},{"id":"https://openalex.org/F4320320997","display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","ror":"https://ror.org/02ddkpn78"},{"id":"https://openalex.org/F4320321886","display_name":"Ontario Ministry of Research, Innovation and Science","ror":"https://ror.org/03zr1tg88"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332736","display_name":"Novartis Pharma","ror":"https://ror.org/0013shd50"},{"id":"https://openalex.org/F4320337269","display_name":"Z\u00fcrcher Hochschule f\u00fcr Angewandte Wissenschaften","ror":"https://ror.org/05pmsvm27"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337398","display_name":"Division of Biological Infrastructure","ror":"https://ror.org/04qn9mx93"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2913093503.pdf","grobid_xml":"https://content.openalex.org/works/W2913093503.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W1977984247","https://openalex.org/W1979300931","https://openalex.org/W1985810115","https://openalex.org/W1992102171","https://openalex.org/W2001900040","https://openalex.org/W2008708467","https://openalex.org/W2100827887","https://openalex.org/W2105803236","https://openalex.org/W2114850508","https://openalex.org/W2132247062","https://openalex.org/W2146728635","https://openalex.org/W2150934173","https://openalex.org/W2156678798","https://openalex.org/W2160697532","https://openalex.org/W2237150576","https://openalex.org/W2531396638","https://openalex.org/W2561361862","https://openalex.org/W2589205199","https://openalex.org/W2604075160","https://openalex.org/W2766157941","https://openalex.org/W2766737008","https://openalex.org/W2791740716","https://openalex.org/W2797669016","https://openalex.org/W2800648160","https://openalex.org/W2950192635","https://openalex.org/W2950466381","https://openalex.org/W4293241248"],"related_works":["https://openalex.org/W2036021480","https://openalex.org/W2546377002","https://openalex.org/W4285209474","https://openalex.org/W22571951","https://openalex.org/W2046541848","https://openalex.org/W2791776396","https://openalex.org/W4384009753","https://openalex.org/W2964820744","https://openalex.org/W3081674575","https://openalex.org/W4287673983"],"abstract_inverted_index":{"BioJava":[0,67,100,117],"is":[1,74,84],"an":[2],"open-source":[3],"project":[4,15,83],"that":[5,53],"provides":[6],"a":[7],"Java":[8,69],"library":[9,49],"for":[10,28],"processing":[11],"biological":[12],"data.":[13,66],"The":[14,82],"aims":[16],"to":[17,58,111],"simplify":[18],"bioinformatic":[19],"analyses":[20],"by":[21],"implementing":[22],"parsers,":[23],"data":[24],"structures,":[25],"and":[26,37,51,73,92,103],"algorithms":[27],"common":[29],"tasks":[30],"in":[31],"genomics,":[32],"structural":[33],"biology,":[34],"ontologies,":[35],"phylogenetics,":[36],"more.":[38],"Since":[39],"2012,":[40],"we":[41],"have":[42],"released":[43],"two":[44],"major":[45],"versions":[46],"of":[47],"the":[48,78,99,112,116],"(4":[50],"5)":[52],"include":[54],"many":[55],"new":[56],"features":[57],"tackle":[59],"challenges":[60],"with":[61],"increasingly":[62],"complex":[63],"macromolecular":[64],"structure":[65],"requires":[68],"8":[70],"or":[71,115],"higher":[72],"freely":[75],"available":[76],"under":[77],"LGPL":[79],"2.1":[80],"license.":[81],"hosted":[85],"on":[86,98],"GitHub":[87,113],"at":[88],"https://github.com/biojava/biojava.":[89],"More":[90],"information":[91],"documentation":[93],"can":[94],"be":[95,109],"found":[96],"online":[97],"website":[101],"(http://www.biojava.org)":[102],"tutorial":[104],"(https://github.com/biojava/biojava-tutorial).":[105],"All":[106],"inquiries":[107],"should":[108],"directed":[110],"page":[114],"mailing":[118],"list":[119],"(http://lists.open-bio.org/mailman/listinfo/biojava-l).":[120]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":11},{"year":2019,"cited_by_count":6}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
