{"id":"https://openalex.org/W2124577331","doi":"https://doi.org/10.1109/bibe.2004.1317397","title":"Semantic analysis and synthesis of complex biological systems","display_name":"Semantic analysis and synthesis of complex biological systems","publication_year":2004,"publication_date":"2004-11-30","ids":{"openalex":"https://openalex.org/W2124577331","doi":"https://doi.org/10.1109/bibe.2004.1317397","mag":"2124577331"},"language":"en","primary_location":{"id":"doi:10.1109/bibe.2004.1317397","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2004.1317397","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. Fourth IEEE Symposium on Bioinformatics and Bioengineering","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5111414210","display_name":"Fei Xie","orcid":null},"institutions":[{"id":"https://openalex.org/I4210140791","display_name":"Irvine University","ror":"https://ror.org/04ysmca02","country_code":"US","type":"education","lineage":["https://openalex.org/I4210140791"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Fei Xie","raw_affiliation_strings":["Dept. of Electr. Eng. & Comput. Sci. & Biomedical Eng., California Univ., Irvine, CA, USA"],"affiliations":[{"raw_affiliation_string":"Dept. of Electr. Eng. & Comput. Sci. & Biomedical Eng., California Univ., Irvine, CA, USA","institution_ids":["https://openalex.org/I4210140791"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076927567","display_name":"Phillip C.\u2010Y. Sheu","orcid":"https://orcid.org/0000-0003-2036-850X"},"institutions":[{"id":"https://openalex.org/I4210140791","display_name":"Irvine University","ror":"https://ror.org/04ysmca02","country_code":"US","type":"education","lineage":["https://openalex.org/I4210140791"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"P. C-y Sheu","raw_affiliation_strings":["Dept. of Electr. Eng. & Comput. Sci. & Biomedical Eng., California Univ., Irvine, CA, USA"],"affiliations":[{"raw_affiliation_string":"Dept. of Electr. Eng. & Comput. Sci. & Biomedical Eng., California Univ., Irvine, CA, USA","institution_ids":["https://openalex.org/I4210140791"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030125759","display_name":"Arthur D. Lander","orcid":"https://orcid.org/0000-0002-4380-5525"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"A. Lander","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5069378948","display_name":"V. Christini","orcid":null},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"V. Christini","raw_affiliation_strings":["Departments of Biomedical Engineering, University of California, Irvine, USA"],"affiliations":[{"raw_affiliation_string":"Departments of Biomedical Engineering, University of California, Irvine, USA","institution_ids":["https://openalex.org/I204250578"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5111414210"],"corresponding_institution_ids":["https://openalex.org/I4210140791"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.10694776,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"23","issue":null,"first_page":"600","last_page":"610"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9945999979972839,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9945999979972839,"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":0.9890000224113464,"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":0.9872000217437744,"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":0.7719948291778564},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.6872564554214478},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.6497609615325928},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.6383224129676819},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.5334326028823853},{"id":"https://openalex.org/keywords/user-interface","display_name":"User interface","score":0.5180292725563049},{"id":"https://openalex.org/keywords/natural-language","display_name":"Natural language","score":0.4895261228084564},{"id":"https://openalex.org/keywords/term","display_name":"Term (time)","score":0.4880343973636627},{"id":"https://openalex.org/keywords/complex-system","display_name":"Complex system","score":0.4798264503479004},{"id":"https://openalex.org/keywords/modelling-biological-systems","display_name":"Modelling biological systems","score":0.47900933027267456},{"id":"https://openalex.org/keywords/natural","display_name":"Natural (archaeology)","score":0.4579024314880371},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.42791491746902466},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.40978604555130005},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.3504433035850525},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.3484402894973755},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2678837180137634},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.10570824146270752}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7719948291778564},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.6872564554214478},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.6497609615325928},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.6383224129676819},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.5334326028823853},{"id":"https://openalex.org/C89505385","wikidata":"https://www.wikidata.org/wiki/Q47146","display_name":"User interface","level":2,"score":0.5180292725563049},{"id":"https://openalex.org/C195324797","wikidata":"https://www.wikidata.org/wiki/Q33742","display_name":"Natural language","level":2,"score":0.4895261228084564},{"id":"https://openalex.org/C61797465","wikidata":"https://www.wikidata.org/wiki/Q1188986","display_name":"Term (time)","level":2,"score":0.4880343973636627},{"id":"https://openalex.org/C47822265","wikidata":"https://www.wikidata.org/wiki/Q854457","display_name":"Complex system","level":2,"score":0.4798264503479004},{"id":"https://openalex.org/C137866125","wikidata":"https://www.wikidata.org/wiki/Q4299308","display_name":"Modelling biological systems","level":3,"score":0.47900933027267456},{"id":"https://openalex.org/C2776608160","wikidata":"https://www.wikidata.org/wiki/Q4785462","display_name":"Natural (archaeology)","level":2,"score":0.4579024314880371},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.42791491746902466},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.40978604555130005},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3504433035850525},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.3484402894973755},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2678837180137634},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.10570824146270752},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"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/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","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/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibe.2004.1317397","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2004.1317397","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. Fourth IEEE Symposium on Bioinformatics and Bioengineering","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Quality Education","score":0.8399999737739563,"id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":38,"referenced_works":["https://openalex.org/W157111480","https://openalex.org/W1538450113","https://openalex.org/W1810305467","https://openalex.org/W1835045972","https://openalex.org/W1963861745","https://openalex.org/W1964615735","https://openalex.org/W1973546194","https://openalex.org/W1974158461","https://openalex.org/W1975230522","https://openalex.org/W1976974479","https://openalex.org/W1984632132","https://openalex.org/W1986837879","https://openalex.org/W1988163242","https://openalex.org/W1989462530","https://openalex.org/W2000878171","https://openalex.org/W2013743651","https://openalex.org/W2022842799","https://openalex.org/W2036212055","https://openalex.org/W2040890820","https://openalex.org/W2048195900","https://openalex.org/W2060402190","https://openalex.org/W2068258896","https://openalex.org/W2076868976","https://openalex.org/W2088024191","https://openalex.org/W2089441381","https://openalex.org/W2090683259","https://openalex.org/W2091931537","https://openalex.org/W2111682035","https://openalex.org/W2122407134","https://openalex.org/W2128584428","https://openalex.org/W2131067724","https://openalex.org/W2138321569","https://openalex.org/W2147764898","https://openalex.org/W2150908245","https://openalex.org/W2151170651","https://openalex.org/W2154209639","https://openalex.org/W2190236061","https://openalex.org/W4249569159"],"related_works":["https://openalex.org/W4386563820","https://openalex.org/W631732704","https://openalex.org/W1968058641","https://openalex.org/W2155261113","https://openalex.org/W1748979965","https://openalex.org/W3199870583","https://openalex.org/W1593256703","https://openalex.org/W4254550161","https://openalex.org/W1497779830","https://openalex.org/W2057769265"],"abstract_inverted_index":{"In":[0],"general":[1],"biologists":[2,94,123],"are":[3,16,43],"not":[4],"accustomed":[5],"to":[6,18,57,87,95,109,148,166],"formulating":[7,127],"biological":[8,98,129,159],"problems":[9,130,160],"in":[10,46,126,131,144],"the":[11,47,63,105,111,117,141,164],"precise":[12],"mathematical":[13,113],"terms":[14,133],"that":[15,38,74,92,116,154,161,181],"required":[17],"solve":[19],"them":[20],"analytically":[21],"or":[22],"numerically.":[23],"Although":[24],"many":[25,39],"computational":[26],"tools":[27,42,64],"for":[28],"systems":[29,99],"biology":[30],"have":[31,65],"been":[32],"developed":[33],"recently,":[34],"our":[35],"observations":[36],"indicate":[37],"of":[40,49,79,177,184,195],"these":[41],"powerful":[44],"only":[45],"hands":[48],"those":[50],"who":[51],"know":[52],"a":[53,66,89,150,196],"lot":[54],"about":[55],"how":[56],"use":[58],"them.":[59],"For":[60],"most":[61],"biologists,":[62],"protracted":[67],"learning":[68],"curve":[69],"and":[70,104,124,198],"unfriendly":[71],"user":[72],"interface":[73],"often":[75,118],"diminish":[76],"their":[77],"likelihood":[78],"being":[80],"used.":[81],"Our":[82],"long":[83],"term":[84],"goal":[85,143],"is":[86,107,147,182],"build":[88,149],"knowledge":[90,151],"system":[91,106,152,180],"allows":[93],"synthesize":[96],"complex":[97,128,191],"via":[100],"natural":[101,199],"language":[102,200],"interactions,":[103],"able":[108],"generate":[110],"corresponding":[112],"descriptions":[114],"so":[115],"cumbersome":[119],"communication":[120],"process":[121],"between":[122],"mathematicians/engineers":[125],"mathematic":[132],"can":[134],"be":[135],"performed":[136],"more":[137,190],"easily.":[138],"To":[139],"focus,":[140],"first":[142],"this":[145],"research":[146],"prototype":[153],"focuses":[155],"on":[156],"transport":[157],"related":[158],"occur":[162],"from":[163],"cellular":[165],"tissue":[167],"level.":[168],"We":[169],"address":[170],"specifically":[171],"two":[172],"inter-related":[173],"problems:":[174],"(1)":[175],"provision":[176,194],"an":[178],"intelligent":[179],"capable":[183],"automatically":[185],"synthesizing":[186],"smaller":[187],"components":[188],"into":[189],"systems;":[192],"(2)":[193],"user-friendly":[197],"interface.":[201]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
