{"id":"https://openalex.org/W2130523733","doi":"https://doi.org/10.1186/1751-0473-8-4","title":"BlaSTorage: a fast package to parse, manage and store BLAST results","display_name":"BlaSTorage: a fast package to parse, manage and store BLAST results","publication_year":2013,"publication_date":"2013-01-30","ids":{"openalex":"https://openalex.org/W2130523733","doi":"https://doi.org/10.1186/1751-0473-8-4","mag":"2130523733","pmid":"https://pubmed.ncbi.nlm.nih.gov/23363699"},"language":"en","primary_location":{"id":"doi:10.1186/1751-0473-8-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-8-4","pdf_url":"https://scfbm.biomedcentral.com/counter/pdf/10.1186/1751-0473-8-4","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"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":"Source Code for Biology and Medicine","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://scfbm.biomedcentral.com/counter/pdf/10.1186/1751-0473-8-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080977250","display_name":"Massimiliano Orsini","orcid":"https://orcid.org/0000-0003-0087-3349"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Massimiliano Orsini","raw_affiliation_strings":["CRS4, Bioinformatics Group, Loc Pixina Manna, Pula 09010, ITALY. orsini@crs4.it"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CRS4, Bioinformatics Group, Loc Pixina Manna, Pula 09010, ITALY. orsini@crs4.it","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071939577","display_name":"Simone Carcangiu","orcid":null},"institutions":[{"id":"https://openalex.org/I2800759272","display_name":"Center for Advanced Studies Research and Development in Sardinia","ror":"https://ror.org/03jdxdk20","country_code":"IT","type":"facility","lineage":["https://openalex.org/I2800759272"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Simone Carcangiu","raw_affiliation_strings":["CRS4, Bioinformatics Group, Loc Pixina Manna, Pula, 09010, ITALY"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CRS4, Bioinformatics Group, Loc Pixina Manna, Pula, 09010, ITALY","institution_ids":["https://openalex.org/I2800759272"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5080977250"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.2992,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.62992624,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"8","issue":"1","first_page":"4","last_page":"4"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.26649999618530273,"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":0.26649999618530273,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.22689999639987946,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.10980000346899033,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/parsing","display_name":"Parsing","score":0.8948839902877808},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8820639848709106},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.8240589499473572},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.4322546124458313},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3435746431350708}],"concepts":[{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.8948839902877808},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8820639848709106},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8240589499473572},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.4322546124458313},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3435746431350708}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/1751-0473-8-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-8-4","pdf_url":"https://scfbm.biomedcentral.com/counter/pdf/10.1186/1751-0473-8-4","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"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":"Source Code for Biology and Medicine","raw_type":"journal-article"},{"id":"pmid:23363699","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23363699","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":"Source code for biology and medicine","raw_type":null},{"id":"pmh:oai:europepmc.org:2571676","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3571973","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3571973","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3571973","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":"Source Code Biol Med","raw_type":"Text"},{"id":"pmh:oai:www.p-arch.it:11050/605","is_oa":true,"landing_page_url":"http://hdl.handle.net/11050/605","pdf_url":null,"source":{"id":"https://openalex.org/S4306401595","display_name":"P-arch (Science and Technology Park of Sardinia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210098674","host_organization_name":"Sardegna Ricerche (Italy)","host_organization_lineage":["https://openalex.org/I4210098674"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Articolo"}],"best_oa_location":{"id":"doi:10.1186/1751-0473-8-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-8-4","pdf_url":"https://scfbm.biomedcentral.com/counter/pdf/10.1186/1751-0473-8-4","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"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":"Source Code for Biology and Medicine","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2130523733.pdf","grobid_xml":"https://content.openalex.org/works/W2130523733.grobid-xml"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W2103148772","https://openalex.org/W2105550995","https://openalex.org/W2137075133","https://openalex.org/W2147618358","https://openalex.org/W2150782408","https://openalex.org/W2158714788"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2341492732","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W4287027380","https://openalex.org/W1699080303","https://openalex.org/W4297799326","https://openalex.org/W3116064965","https://openalex.org/W2207495067","https://openalex.org/W1906486629"],"abstract_inverted_index":{"BACKGROUND:":[0],"Large-scale":[1],"sequence":[2],"studies":[3],"requiring":[4],"BLAST-based":[5],"analysis":[6],"produce":[7],"huge":[8],"amounts":[9],"of":[10,79,86,103],"data":[11,96],"to":[12,40,93],"be":[13,115],"parsed.":[14],"BLAST":[15,35,59,71,80],"parsers":[16],"are":[17,21],"available,":[18],"but":[19],"they":[20],"often":[22],"missing":[23],"some":[24],"important":[25],"features,":[26],"such":[27],"as":[28,111],"keeping":[29],"all":[30,77,94],"information":[31],"from":[32],"the":[33,95],"raw":[34],"output,":[36],"allowing":[37],"direct":[38],"access":[39,92],"single":[41],"results,":[42,81],"and":[43,61,75,113],"performing":[44],"logical":[45],"operations":[46],"over":[47],"them.":[48],"FINDINGS:":[49],"We":[50],"implemented":[51],"BlaSTorage,":[52],"a":[53,65,88],"Python":[54],"package":[55],"that":[56],"parses":[57],"multi":[58],"results":[60],"returns":[62],"them":[63],"in":[64,108],"purpose-built":[66],"object-database":[67],"format.":[68],"Unlike":[69],"other":[70],"parsers,":[72],"BlaSTorage":[73,99],"retains":[74],"stores":[76],"parts":[78],"including":[82],"alignments,":[83],"without":[84],"loss":[85],"information;":[87],"complete":[89],"API":[90],"allows":[91],"components.":[97],"CONCLUSIONS:":[98],"shows":[100],"comparable":[101],"speed":[102],"more":[104],"basic":[105],"parser":[106],"written":[107],"compiled":[109],"languages":[110],"C++":[112],"can":[114],"easily":[116],"integrated":[117],"into":[118],"web":[119],"applications":[120],"or":[121],"software":[122],"pipelines.":[123]},"counts_by_year":[{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
