{"id":"https://openalex.org/W604810289","doi":null,"title":"A framework for annotating and visualizing cellML models","display_name":"A framework for annotating and visualizing cellML models","publication_year":2009,"publication_date":"2009-01-01","ids":{"openalex":"https://openalex.org/W604810289","mag":"604810289"},"language":"en","primary_location":{"id":"pmh:oai:researchspace.auckland.ac.nz:2292/5606","doi":null,"is_oa":false,"landing_page_url":"https://hdl.handle.net/2292/5606","pdf_url":null,"source":{"id":"https://openalex.org/S7407055463","display_name":"ResearchSpace (University of Auckland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I154130895","host_organization_name":"University of Auckland","host_organization_lineage":["https://openalex.org/I154130895"],"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":"Thesis"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"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/A5034436640","display_name":"Sarala Wimalaratne","orcid":"https://orcid.org/0000-0002-5355-2576","observed_orcids":["https://orcid.org/0000-0002-5355-2576"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Sarala Wimalaratne","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-5355-2576","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5034436640"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.5131999850273132,"subfield":{"id":"https://openalex.org/subfields/2718","display_name":"Health Informatics"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.5131999850273132,"subfield":{"id":"https://openalex.org/subfields/2718","display_name":"Health Informatics"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.13429999351501465,"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"}},{"id":"https://openalex.org/T10215","display_name":"Semantic Web and Ontologies","score":0.0754999965429306,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/cellml","display_name":"CellML","score":0.9919999837875366},{"id":"https://openalex.org/keywords/model-annotation","display_name":"model annotation","score":0.8610000014305115},{"id":"https://openalex.org/keywords/ontology-information-science","display_name":"ontology (information science)","score":0.6759999990463257},{"id":"https://openalex.org/keywords/physiome-project","display_name":"Physiome Project","score":0.8240000009536743},{"id":"https://openalex.org/keywords/mathematical-biology","display_name":"mathematical biology","score":0.4519999921321869},{"id":"https://openalex.org/keywords/composite-model","display_name":"composite model","score":0.3160000145435333}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6912256479263306},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.46110209822654724},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.34330713748931885}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:researchspace.auckland.ac.nz:2292/5606","doi":null,"is_oa":false,"landing_page_url":"https://hdl.handle.net/2292/5606","pdf_url":null,"source":{"id":"https://openalex.org/S7407055463","display_name":"ResearchSpace (University of Auckland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I154130895","host_organization_name":"University of Auckland","host_organization_lineage":["https://openalex.org/I154130895"],"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":"Thesis"},{"id":"mag:604810289","doi":null,"is_oa":false,"landing_page_url":"http://europepmc.org/theses/ETH/795","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,"listed_in":[],"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":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":54,"referenced_works":["https://openalex.org/W188614979","https://openalex.org/W1487338715","https://openalex.org/W1489737525","https://openalex.org/W1499796720","https://openalex.org/W1500325068","https://openalex.org/W1541343226","https://openalex.org/W1570740602","https://openalex.org/W1654805921","https://openalex.org/W1965014786","https://openalex.org/W1978486653","https://openalex.org/W1981021538","https://openalex.org/W1985940938","https://openalex.org/W2028307228","https://openalex.org/W2031631803","https://openalex.org/W2033377040","https://openalex.org/W2040890820","https://openalex.org/W2042880070","https://openalex.org/W2044639106","https://openalex.org/W2045478141","https://openalex.org/W2047480488","https://openalex.org/W2069157810","https://openalex.org/W2085377104","https://openalex.org/W2085949935","https://openalex.org/W2087308849","https://openalex.org/W2087779040","https://openalex.org/W2089562567","https://openalex.org/W2099007946","https://openalex.org/W2100525485","https://openalex.org/W2102653059","https://openalex.org/W2103017472","https://openalex.org/W2105922907","https://openalex.org/W2108036176","https://openalex.org/W2110025254","https://openalex.org/W2114211768","https://openalex.org/W2117364474","https://openalex.org/W2121642757","https://openalex.org/W2121905803","https://openalex.org/W2131067724","https://openalex.org/W2133429395","https://openalex.org/W2133938042","https://openalex.org/W2134050761","https://openalex.org/W2135290856","https://openalex.org/W2139383813","https://openalex.org/W2140205166","https://openalex.org/W2147990117","https://openalex.org/W2148329459","https://openalex.org/W2149991291","https://openalex.org/W2150281351","https://openalex.org/W2150908245","https://openalex.org/W2159675211","https://openalex.org/W2160845726","https://openalex.org/W2161749893","https://openalex.org/W2163670493","https://openalex.org/W2170122529"],"related_works":["https://openalex.org/W2114211768","https://openalex.org/W2139383813","https://openalex.org/W1541343226","https://openalex.org/W2054759025","https://openalex.org/W3033481214","https://openalex.org/W2089562567","https://openalex.org/W2613280671","https://openalex.org/W2161749893","https://openalex.org/W7093075855","https://openalex.org/W2133451142"],"abstract_inverted_index":{"The":[0,24,47,82,144,235],"Physiome":[1],"Project":[2],"was":[3,27,305],"established":[4],"to":[5,31,38,66,104,125,148,156,177,189,214,219,225,257,274,282,287,316,337,355,362],"develop":[6],"tools":[7],"for":[8,34,53,136,162,201,301],"international":[9],"collaboration":[10],"and":[11,21,40,76,88,122,184,211,270,289,313,323,330],"sharing":[12],"physiological":[13],"knowledge":[14],"in":[15,29,142,154,207,223,261,327,334],"the":[16,32,55,68,74,85,89,93,106,110,119,126,138,158,196,208,216,220,227,248,251,259,267,310,314,321,344,356],"form":[17],"of":[18,44,57,229,232,238,250,295],"biological":[19,45,58,70,86,94,107,120,139,152,185,193,324,345,372],"models":[20,43,80,146,181,253,304,329,342,367],"experimental":[22],"data.":[23],"CellML":[25,111,128,145,180,209,252,303,328,341,366],"language":[26,37,48,200,218,312],"developed":[28,169],"response":[30],"need":[33,147],"a":[35,50,132,164,187,191,198,212,233,242,262,283,293,298],"high-level":[36],"represent":[39],"exchange":[41],"mathematical":[42,90],"processes.":[46],"provides":[49],"flexible":[51],"framework":[52,115,172,222,357],"describing":[54,92],"dynamics":[56],"processes":[59,77,205],"but":[60],"does":[61],"not":[62],"explicitly":[63,178],"lend":[64],"itself":[65],"capturing":[67],"underlying":[69,127],"concepts":[71,108,121,140,153,269,325],"such":[72],"as":[73],"entities":[75],"that":[78,244,264,279,319],"these":[79],"represent.":[81,113,348],"relationship":[83,124],"between":[84],"process":[87,95],"model":[91,129,239,260],"is":[96,245,278],"also":[97],"often":[98],"complex.":[99],"This":[100,307],"makes":[101],"it":[102,358],"difficult":[103],"see":[105],"which":[109,116,173,254],"structures":[112],"A":[114],"supports":[117],"visualizing":[118,302],"its":[123],"would":[130,359],"provide":[131,157],"very":[133],"useful":[134],"toolset":[135],"understanding":[137],"modeled":[141],"CellML.":[143],"be":[149,175,360],"annotated":[150],"with":[151,182,352],"order":[155,224],"machine":[159],"interpretable":[160],"data":[161],"generating":[163],"visual":[165,199,217,230,311],"representation.":[166],"We":[167],"have":[168],"an":[170],"ontological":[171,221],"can":[174],"used":[176],"annotate":[179],"physical":[183,322],"concepts,":[186],"method":[188,213,237],"derive":[190],"simplified":[192],"view":[194],"from":[195],"annotations,":[197],"representing":[202],"all":[203],"biophysical":[204,268],"captured":[206,326],"models,":[210],"map":[215],"automate":[226],"generation":[228],"representations":[231],"model.":[234],"proposed":[236],"visualization":[240],"produces":[241],"result":[243],"dependent":[246],"on":[247],"structure":[249,258],"requires":[255],"modelers":[256],"way":[263],"best":[265,284],"describes":[266],"abstractions":[271],"they":[272,347],"wish":[273],"demonstrate.":[275],"Our":[276],"argument":[277],"this":[280,296],"leads":[281],"practice":[285],"approach":[286],"building":[288],"organizing":[290],"models.":[291],"As":[292,349],"part":[294],"research,":[297],"software":[299],"tool":[300,308],"developed.":[306],"combines":[309],"ontologies":[315],"generate":[317],"visualizations":[318],"depict":[320],"enables":[331],"different":[332],"communities":[333],"diverse":[335],"disciplines":[336],"more":[338],"easily":[339],"understand":[340],"within":[343],"domain":[346],"research":[350],"continues,":[351],"further":[353],"improvement":[354],"possible":[361],"visually":[363],"construct":[364],"composite":[365],"by":[368],"selecting":[369],"high":[370],"level":[371],"concepts.":[373]},"counts_by_year":[],"updated_date":"2026-11-06T12:05:46.655746","created_date":"2016-06-24T00:00:00"}
