{"id":"https://openalex.org/W2169589518","doi":"https://doi.org/10.1186/1471-2105-10-251","title":"SNAD: sequence name annotation-based designer","display_name":"SNAD: sequence name annotation-based designer","publication_year":2009,"publication_date":"2009-08-14","ids":{"openalex":"https://openalex.org/W2169589518","doi":"https://doi.org/10.1186/1471-2105-10-251","mag":"2169589518","pmid":"https://pubmed.ncbi.nlm.nih.gov/19682364"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-10-251","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-251","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-251","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-251","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078566855","display_name":"Igor A. Sidorov","orcid":"https://orcid.org/0000-0001-6519-4983"},"institutions":[{"id":"https://openalex.org/I2800006345","display_name":"Leiden University Medical Center","ror":"https://ror.org/05xvt9f17","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2800006345"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Igor A Sidorov","raw_affiliation_strings":["Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands. i.a.sidorov@lumc.nl","Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, PO Box 9600, E4-P, 2300, RC, Leiden, Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands. i.a.sidorov@lumc.nl","institution_ids":["https://openalex.org/I2800006345"]},{"raw_affiliation_string":"Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, PO Box 9600, E4-P, 2300, RC, Leiden, Netherlands","institution_ids":["https://openalex.org/I2800006345"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050895140","display_name":"Denis A. Reshetov","orcid":"https://orcid.org/0000-0001-5609-389X"},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Denis A Reshetov","raw_affiliation_strings":["Faculty of Bioengineering and Bioinformatics, Moscow State University, 119899, Moscow, Russia","Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Bioengineering and Bioinformatics, Moscow State University, 119899, Moscow, Russia","institution_ids":["https://openalex.org/I19880235"]},{"raw_affiliation_string":"Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia","institution_ids":["https://openalex.org/I19880235"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038215233","display_name":"Alexander E. Gorbalenya","orcid":"https://orcid.org/0000-0002-4967-7341"},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]},{"id":"https://openalex.org/I2800006345","display_name":"Leiden University Medical Center","ror":"https://ror.org/05xvt9f17","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2800006345"]}],"countries":["NL","RU"],"is_corresponding":false,"raw_author_name":"Alexander E Gorbalenya","raw_affiliation_strings":["Faculty of Bioengineering and Bioinformatics, Moscow State University, 119899, Moscow, Russia","Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia","Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands","Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, PO Box 9600, E4-P, 2300, RC, Leiden, Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Bioengineering and Bioinformatics, Moscow State University, 119899, Moscow, Russia","institution_ids":["https://openalex.org/I19880235"]},{"raw_affiliation_string":"Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia","institution_ids":["https://openalex.org/I19880235"]},{"raw_affiliation_string":"Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands","institution_ids":["https://openalex.org/I2800006345"]},{"raw_affiliation_string":"Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, PO Box 9600, E4-P, 2300, RC, Leiden, Netherlands","institution_ids":["https://openalex.org/I2800006345"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.3777,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.6216888,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"10","issue":"1","first_page":"251","last_page":"251"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.45399999618530273,"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":0.45399999618530273,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.25690001249313354,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.07079999893903732,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/annotation","display_name":"Annotation","score":0.7924454212188721},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6136576533317566},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4616585671901703},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4614924192428589},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.37212812900543213},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3668052554130554},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.36353060603141785},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3331493139266968},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23501303791999817},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1998036801815033}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7924454212188721},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6136576533317566},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4616585671901703},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4614924192428589},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.37212812900543213},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3668052554130554},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.36353060603141785},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3331493139266968},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23501303791999817},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1998036801815033}],"mesh":[{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","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":"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}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-10-251","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-251","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-251","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19682364","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19682364","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:196e99ba484640e9a8cf358822ddbc6a","is_oa":true,"landing_page_url":"https://doaj.org/article/196e99ba484640e9a8cf358822ddbc6a","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 10, Iss 1, p 251 (2009)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2739203","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2739203","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-10-251","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-251","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-251","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320929","display_name":"Universiteit Leiden","ror":"https://ror.org/027bh9e22"},{"id":"https://openalex.org/F4320323080","display_name":"Leids Universitair Medisch Centrum","ror":"https://ror.org/05xvt9f17"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2169589518.pdf","grobid_xml":"https://content.openalex.org/works/W2169589518.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W1554361839","https://openalex.org/W1953939973","https://openalex.org/W1975292664","https://openalex.org/W1981646999","https://openalex.org/W1997831273","https://openalex.org/W2001674944","https://openalex.org/W2023367724","https://openalex.org/W2039240110","https://openalex.org/W2048053704","https://openalex.org/W2049905679","https://openalex.org/W2058991511","https://openalex.org/W2077103006","https://openalex.org/W2095897227","https://openalex.org/W2099373309","https://openalex.org/W2100412820","https://openalex.org/W2117486769","https://openalex.org/W2122694512","https://openalex.org/W2131320300","https://openalex.org/W2132202407","https://openalex.org/W2134889157","https://openalex.org/W2139703939","https://openalex.org/W2145719673","https://openalex.org/W2149557149","https://openalex.org/W2150261709","https://openalex.org/W2150934173","https://openalex.org/W2154139219","https://openalex.org/W2161271012","https://openalex.org/W2170479957","https://openalex.org/W4240231372","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2358755282","https://openalex.org/W2625833328","https://openalex.org/W1533177136","https://openalex.org/W4380994516","https://openalex.org/W2556260348"],"abstract_inverted_index":{"BACKGROUND:":[0],"A":[1,147],"growing":[2],"diversity":[3],"of":[4,51,84,118,124,153,173,178],"biological":[5],"data":[6,22],"is":[7,56,108],"tagged":[8],"with":[9,14,88],"unique":[10],"identifiers":[11],"(UIDs)":[12],"associated":[13],"polynucleotides":[15],"and":[16,25,49,69,104,160,165,176,180],"proteins":[17],"to":[18,46,67,137],"ensure":[19],"efficient":[20],"computer-mediated":[21],"storage,":[23],"maintenance,":[24],"processing.":[26],"These":[27],"identifiers,":[28],"which":[29],"are":[30,36],"not":[31],"informative":[32],"for":[33,140,149],"most":[34],"people,":[35],"often":[37],"substituted":[38],"by":[39,110],"biologically":[40,101,157],"meaningful":[41,102,158],"names":[42,103,139,159],"in":[43,121,144],"various":[44],"presentations":[45],"facilitate":[47],"utilization":[48],"dissemination":[50,182],"sequence-based":[52],"knowledge.":[53],"This":[54,106],"substitution":[55],"commonly":[57],"done":[58],"manually":[59],"that":[60,80,115],"may":[61],"be":[62,135],"a":[63],"tedious":[64],"exercise":[65],"prone":[66],"mistakes":[68],"omissions.":[70],"RESULTS:":[71],"Here":[72],"we":[73,129],"introduce":[74],"SNAD":[75],"(Sequence":[76],"Name":[77],"Annotation-based":[78],"Designer)":[79],"mediates":[81],"automatic":[82],"conversion":[83,107,152],"sequence":[85,154,174],"UIDs":[86,155],"(associated":[87],"multiple":[89],"alignment":[90],"or":[91,94,112],"phylogenetic":[92],"tree,":[93],"supplied":[95],"as":[96],"plain":[97],"text":[98],"list)":[99],"into":[100,156,167],"acronyms.":[105],"directed":[109],"precompiled":[111],"user-defined":[113],"templates":[114],"exploit":[116],"wealth":[117],"annotation":[119],"available":[120],"cognate":[122],"entries":[123],"external":[125],"databases.":[126],"Using":[127],"examples,":[128],"demonstrate":[130],"how":[131],"this":[132],"tool":[133,148],"can":[134],"used":[136],"generate":[138],"practical":[141],"purposes,":[142],"particularly":[143],"virology.":[145],"CONCLUSION:":[146],"controllable":[150],"annotation-based":[151],"acronyms":[161],"has":[162],"been":[163],"developed":[164],"placed":[166],"service,":[168],"fostering":[169],"links":[170],"between":[171],"quality":[172],"annotation,":[175],"efficiency":[177],"communication":[179],"knowledge":[181],"among":[183],"researchers.":[184]},"counts_by_year":[{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2015,"cited_by_count":2}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
