{"id":"https://openalex.org/W2157541442","doi":"https://doi.org/10.1109/bibm.2007.5","title":"Using a Novel Data Transformation Technique to Provide the EMBOSS Software Suite as Semantic Web Services","display_name":"Using a Novel Data Transformation Technique to Provide the EMBOSS Software Suite as Semantic Web Services","publication_year":2007,"publication_date":"2007-11-01","ids":{"openalex":"https://openalex.org/W2157541442","doi":"https://doi.org/10.1109/bibm.2007.5","mag":"2157541442"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2007.5","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2007.5","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007)","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/A5032104010","display_name":"Paul M. K. Gordon","orcid":"https://orcid.org/0000-0003-2881-1713"},"institutions":[{"id":"https://openalex.org/I168635309","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39","country_code":"CA","type":"education","lineage":["https://openalex.org/I168635309"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Paul M. K. Gordon","raw_affiliation_strings":["Sun Center of Excellence for Visual Genomics, University of Calgary, Canada"],"affiliations":[{"raw_affiliation_string":"Sun Center of Excellence for Visual Genomics, University of Calgary, Canada","institution_ids":["https://openalex.org/I168635309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049642797","display_name":"Edward Kawas","orcid":null},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Edward Kawas","raw_affiliation_strings":["James Hogg iCAPTURE Centre, University of British Columbia, Canada"],"affiliations":[{"raw_affiliation_string":"James Hogg iCAPTURE Centre, University of British Columbia, Canada","institution_ids":["https://openalex.org/I141945490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067974158","display_name":"Mark D. Wilkinson","orcid":"https://orcid.org/0000-0001-6960-357X"},"institutions":[{"id":"https://openalex.org/I168635309","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39","country_code":"CA","type":"education","lineage":["https://openalex.org/I168635309"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Mark Wilkinson","raw_affiliation_strings":["Sun Center of Excellence for Visual Genomics, University of Calgary, Canada"],"affiliations":[{"raw_affiliation_string":"Sun Center of Excellence for Visual Genomics, University of Calgary, Canada","institution_ids":["https://openalex.org/I168635309"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009552437","display_name":"Christoph W. Sensen","orcid":"https://orcid.org/0000-0001-9604-8962"},"institutions":[{"id":"https://openalex.org/I168635309","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39","country_code":"CA","type":"education","lineage":["https://openalex.org/I168635309"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Christoph W. Sensen","raw_affiliation_strings":["Sun Center of Excellence for Visual Genomics, University of Calgary, Canada"],"affiliations":[{"raw_affiliation_string":"Sun Center of Excellence for Visual Genomics, University of Calgary, Canada","institution_ids":["https://openalex.org/I168635309"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5032104010"],"corresponding_institution_ids":["https://openalex.org/I168635309"],"apc_list":null,"apc_paid":null,"fwci":5.2337,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.95244839,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":null,"biblio":{"volume":"1","issue":null,"first_page":"117","last_page":"124"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9987000226974487,"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"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9987000226974487,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9944999814033508,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9897000193595886,"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":0.8801584839820862},{"id":"https://openalex.org/keywords/xslt","display_name":"XSLT","score":0.712549090385437},{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.6571491956710815},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.506846010684967},{"id":"https://openalex.org/keywords/web-service","display_name":"Web service","score":0.4536842107772827},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.4404629170894623},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4335518777370453},{"id":"https://openalex.org/keywords/codebase","display_name":"Codebase","score":0.432861328125},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.4323180317878723},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.43031638860702515},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.4084034860134125},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3689078092575073}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8801584839820862},{"id":"https://openalex.org/C150569060","wikidata":"https://www.wikidata.org/wiki/Q32110","display_name":"XSLT","level":3,"score":0.712549090385437},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.6571491956710815},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.506846010684967},{"id":"https://openalex.org/C35578498","wikidata":"https://www.wikidata.org/wiki/Q193424","display_name":"Web service","level":2,"score":0.4536842107772827},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.4404629170894623},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4335518777370453},{"id":"https://openalex.org/C51929080","wikidata":"https://www.wikidata.org/wiki/Q2425187","display_name":"Codebase","level":3,"score":0.432861328125},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.4323180317878723},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.43031638860702515},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.4084034860134125},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3689078092575073},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","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/bibm.2007.5","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2007.5","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320310787","display_name":"Genome Canada","ror":"https://ror.org/029s29983"},{"id":"https://openalex.org/F4320326646","display_name":"Genome Alberta","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W587796778","https://openalex.org/W1594031697","https://openalex.org/W1602702994","https://openalex.org/W1649804825","https://openalex.org/W1969423031","https://openalex.org/W1973948212","https://openalex.org/W1980731367","https://openalex.org/W1983833794","https://openalex.org/W1986729473","https://openalex.org/W1996902131","https://openalex.org/W1998613372","https://openalex.org/W2017900294","https://openalex.org/W2042029298","https://openalex.org/W2048985087","https://openalex.org/W2050829396","https://openalex.org/W2067970576","https://openalex.org/W2071286514","https://openalex.org/W2083822241","https://openalex.org/W2113182242","https://openalex.org/W2113745093","https://openalex.org/W2125055259","https://openalex.org/W2135884466","https://openalex.org/W2142356762","https://openalex.org/W2151512984","https://openalex.org/W2161679242","https://openalex.org/W2162897441","https://openalex.org/W2168103533","https://openalex.org/W2336952649","https://openalex.org/W2797502950","https://openalex.org/W3085162807","https://openalex.org/W6677313179"],"related_works":["https://openalex.org/W2724352767","https://openalex.org/W2170279083","https://openalex.org/W2418011696","https://openalex.org/W1868164859","https://openalex.org/W4288685592","https://openalex.org/W1584033423","https://openalex.org/W2353223204","https://openalex.org/W2504958673","https://openalex.org/W2390876725","https://openalex.org/W2359720645"],"abstract_inverted_index":{"The":[0,117,167,218],"EMBOSS":[1,53,77,111,149],"software":[2],"suite":[3,78],"is":[4,220,224],"a":[5,55,85,164,174],"well":[6],"established":[7],"package":[8],"consists":[9],"of":[10,48,62,68,88,120,154,183,213],"over":[11],"200":[12],"command":[13,70],"line":[14],"programs":[15,112,150],"that":[16,158],"can":[17,103,128],"be":[18,34,104,160],"strung":[19],"together":[20],"to":[21,106,135,187,205],"perform":[22],"many":[23,131],"common":[24],"tasks":[25],"in":[26,97,162],"Bioinformatics.":[27],"To":[28,58],"date,":[29],"its":[30],"users":[31],"must":[32,45],"either":[33],"proficient":[35],"at":[36],"the":[37,60,66,69,75,98,107,152,189,192,203,228],"command-line":[38],"for":[39,52,123],"batch":[40],"data":[41,96],"processing,":[42],"or":[43],"they":[44,127,144],"use":[46],"one":[47],"several":[49],"Web-form":[50],"wrappers":[51],"on":[54],"one-off":[56],"basis.":[57],"combine":[59],"simplicity":[61],"Web-based":[63],"forms":[64],"with":[65],"power":[67],"line,":[71],"we":[72],"are":[73,125],"wrapping":[74],"entire":[76],"as":[79],"semantic":[80],"Web":[81,190],"Services":[82],"(SWS)":[83],"using":[84,171],"novel":[86,175],"framework":[87,219],"declarative":[89,168],"rules.":[90],"These":[91,195],"rules":[92,169],"describe":[93],"how":[94],"ontology-driven":[95],"BioMOBY":[99,132,156,229],"SWS":[100],"XML":[101],"format":[102],"converted":[105],"various":[108],"text":[109],"formats":[110],"use,":[113],"and":[114,137,142,151,173,191,208,216,223],"vice":[115],"versa.":[116],"chief":[118],"benefits":[119],"this":[121],"approach":[122],"end-users":[124],"1)":[126],"chose":[129],"between":[130,148],"client":[133,207],"GUIs":[134],"create":[136],"run":[138],"EMBOSS-based":[139],"analysis":[140],"pipelines":[141],"2)":[143],"get":[145],"automatic":[146],"interoperability":[147],"100's":[153],"other":[155],"services":[157],"may":[159],"useful":[161],"answering":[163],"research":[165],"question.":[166],"approach,":[170],"XSLT":[172],"\"anti-XSLT\"":[176],"language,":[177],"promotes":[178],"creating":[179],"modular,":[180],"reusable":[181],"pieces":[182],"domain":[184],"technical":[185],"knowledge":[186],"bridge":[188],"Semantic":[193],"Web.":[194],"rule":[196],"systems":[197],"have":[198],"successfully":[199],"been":[200],"applied":[201],"\"in":[202],"wild\"":[204],"both":[206],"server-side":[209],"software,":[210],"facilitating":[211],"integration":[212],"bioinformatics":[214],"tools":[215],"data.":[217],"Open":[221],"Source":[222],"freely":[225],"available":[226],"from":[227],"code":[230],"repository.":[231]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
