{"id":"https://openalex.org/W2525009482","doi":"https://doi.org/10.1142/s0219720016500359","title":"phraSED-ML: A paraphrased, human-readable adaptation of SED-ML","display_name":"phraSED-ML: A paraphrased, human-readable adaptation of SED-ML","publication_year":2016,"publication_date":"2016-09-30","ids":{"openalex":"https://openalex.org/W2525009482","doi":"https://doi.org/10.1142/s0219720016500359","mag":"2525009482","pmid":"https://pubmed.ncbi.nlm.nih.gov/27774871"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720016500359","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720016500359","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5009998609","display_name":"Kiri Choi","orcid":"https://orcid.org/0000-0002-0156-8410"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kiri Choi","raw_affiliation_strings":["University of Washington, Department of Bioengineering, Seattle, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Washington, Department of Bioengineering, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067339679","display_name":"Lucian P. Smith","orcid":"https://orcid.org/0000-0001-7002-6386"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lucian P. Smith","raw_affiliation_strings":["University of Washington, Department of Bioengineering, Seattle, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Washington, Department of Bioengineering, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035478017","display_name":"Kyle Medley","orcid":"https://orcid.org/0000-0002-9135-0844"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J. Kyle Medley","raw_affiliation_strings":["University of Washington, Department of Bioengineering, Seattle, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Washington, Department of Bioengineering, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044484291","display_name":"Herbert M. Sauro","orcid":"https://orcid.org/0000-0002-3659-6817"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Herbert M. Sauro","raw_affiliation_strings":["University of Washington, Department of Bioengineering, Seattle, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Washington, Department of Bioengineering, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5009998609"],"corresponding_institution_ids":["https://openalex.org/I201448701"],"apc_list":null,"apc_paid":null,"fwci":2.2367,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.89355302,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"14","issue":"06","first_page":"1650035","last_page":"1650035"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11195","display_name":"Simulation Techniques and Applications","score":0.7738999724388123,"subfield":{"id":"https://openalex.org/subfields/1803","display_name":"Management Science and Operations Research"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},"topics":[{"id":"https://openalex.org/T11195","display_name":"Simulation Techniques and Applications","score":0.7738999724388123,"subfield":{"id":"https://openalex.org/subfields/1803","display_name":"Management Science and Operations Research"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T13286","display_name":"Modeling and Simulation Systems","score":0.14090000092983246,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.015300000086426735,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7930104732513428},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.7403557300567627},{"id":"https://openalex.org/keywords/sed","display_name":"sed","score":0.6520307064056396},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.5927702188491821},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5273008346557617},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5040435194969177},{"id":"https://openalex.org/keywords/simple","display_name":"Simple (philosophy)","score":0.49423959851264954},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.48756998777389526},{"id":"https://openalex.org/keywords/adaptation","display_name":"Adaptation (eye)","score":0.4839618504047394},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.44664886593818665},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.4346504211425781},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.3745045065879822},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3294844329357147},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.2837616205215454},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.20320042967796326}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7930104732513428},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.7403557300567627},{"id":"https://openalex.org/C126707884","wikidata":"https://www.wikidata.org/wiki/Q305876","display_name":"sed","level":2,"score":0.6520307064056396},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.5927702188491821},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5273008346557617},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5040435194969177},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.49423959851264954},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.48756998777389526},{"id":"https://openalex.org/C139807058","wikidata":"https://www.wikidata.org/wiki/Q352374","display_name":"Adaptation (eye)","level":2,"score":0.4839618504047394},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.44664886593818665},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.4346504211425781},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3745045065879822},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3294844329357147},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.2837616205215454},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.20320042967796326},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","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":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":true},{"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":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D048049","descriptor_name":"Extracellular Signal-Regulated MAP Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D048049","descriptor_name":"Extracellular Signal-Regulated MAP Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D048049","descriptor_name":"Extracellular Signal-Regulated MAP Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","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}],"locations_count":3,"locations":[{"id":"doi:10.1142/s0219720016500359","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720016500359","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:27774871","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27774871","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of bioinformatics and computational biology","raw_type":null},{"id":"pmh:oai:europepmc.org:4621895","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5313123","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","score":0.6200000047683716,"display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W1576664335","https://openalex.org/W2042880070","https://openalex.org/W2078574757","https://openalex.org/W2098367419","https://openalex.org/W2102653059","https://openalex.org/W2117364474","https://openalex.org/W2123783513","https://openalex.org/W2125615370","https://openalex.org/W2129659530","https://openalex.org/W2134221731","https://openalex.org/W2136970290","https://openalex.org/W2141394518","https://openalex.org/W2145435867","https://openalex.org/W2150908245","https://openalex.org/W2161088429","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2468279273","https://openalex.org/W4385386698","https://openalex.org/W2606446052","https://openalex.org/W2354198838","https://openalex.org/W2036021480","https://openalex.org/W1989130879","https://openalex.org/W4247057290","https://openalex.org/W2293871408","https://openalex.org/W2053798630","https://openalex.org/W4235604569"],"abstract_inverted_index":{"MOTIVATION:":[0],"Model":[1],"simulation":[2],"exchange":[3],"has":[4],"been":[5],"standardized":[6],"with":[7],"the":[8],"Simulation":[9],"Experiment":[10],"Description":[11],"Markup":[12],"Language":[13],"(SED-ML),":[14],"but":[15],"specialized":[16],"software":[17],"is":[18],"needed":[19],"to":[20,30,42,52,57,72,82],"generate":[21],"simulations":[22],"in":[23,68,86],"this":[24,80],"format.":[25,46],"Text-based":[26],"languages":[27],"allow":[28],"researchers":[29],"create":[31],"and":[32,37,39,66,74,95],"modify":[33],"experimental":[34],"protocols":[35],"quickly":[36],"easily,":[38],"export":[40],"them":[41],"a":[43,69],"common":[44],"machine-readable":[45],"RESULTS:":[47],"phraSED-ML":[48,90],"language":[49,91],"allows":[50],"modelers":[51],"use":[53,85],"simple":[54],"text":[55],"commands":[56],"encode":[58],"various":[59],"elements":[60],"of":[61],"SED-ML":[62,83],"(models,":[63],"tasks,":[64],"simulations,":[65],"results)":[67],"format":[70],"easy":[71],"read":[73],"modify.":[75],"The":[76],"library":[77],"can":[78],"translate":[79],"script":[81],"for":[84],"other":[87],"softwares.":[88],"AVAILABILITY:":[89],"specification,":[92],"libphrasedml":[93],"library,":[94],"source":[96],"code":[97],"are":[98],"available":[99],"under":[100],"BSD":[101],"license":[102],"from":[103],"http://phrasedml.sourceforge.net/":[104],".":[105]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
