{"id":"https://openalex.org/W2921218152","doi":"https://doi.org/10.1093/bioinformatics/btz186","title":"ECOGEMS: efficient compression and retrieve of SNP data of 2058 rice accessions with integer sparse matrices","display_name":"ECOGEMS: efficient compression and retrieve of SNP data of 2058 rice accessions with integer sparse matrices","publication_year":2019,"publication_date":"2019-03-13","ids":{"openalex":"https://openalex.org/W2921218152","doi":"https://doi.org/10.1093/bioinformatics/btz186","mag":"2921218152","pmid":"https://pubmed.ncbi.nlm.nih.gov/30873546"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz186","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz186","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"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/A5015085832","display_name":"Wen Yao","orcid":"https://orcid.org/0000-0002-0643-506X"},"institutions":[{"id":"https://openalex.org/I4750791","display_name":"Henan Agricultural University","ror":"https://ror.org/04eq83d71","country_code":"CN","type":"education","lineage":["https://openalex.org/I4750791"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Wen Yao","raw_affiliation_strings":["College of Life Sciences, Henan Agricultural University , Zhengzhou, China","National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University , Zhengzhou, China"],"raw_orcid":"https://orcid.org/0000-0002-0643-506X","affiliations":[{"raw_affiliation_string":"College of Life Sciences, Henan Agricultural University , Zhengzhou, China","institution_ids":["https://openalex.org/I4750791"]},{"raw_affiliation_string":"National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University , Zhengzhou, China","institution_ids":["https://openalex.org/I4750791"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050089664","display_name":"Fangfang Huang","orcid":"https://orcid.org/0000-0001-5398-7978"},"institutions":[{"id":"https://openalex.org/I4750791","display_name":"Henan Agricultural University","ror":"https://ror.org/04eq83d71","country_code":"CN","type":"education","lineage":["https://openalex.org/I4750791"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fangfang Huang","raw_affiliation_strings":["College of Life Sciences, Henan Agricultural University , Zhengzhou, China","National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University , Zhengzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Sciences, Henan Agricultural University , Zhengzhou, China","institution_ids":["https://openalex.org/I4750791"]},{"raw_affiliation_string":"National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University , Zhengzhou, China","institution_ids":["https://openalex.org/I4750791"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008794919","display_name":"Xuehai Zhang","orcid":"https://orcid.org/0000-0001-7734-706X"},"institutions":[{"id":"https://openalex.org/I4750791","display_name":"Henan Agricultural University","ror":"https://ror.org/04eq83d71","country_code":"CN","type":"education","lineage":["https://openalex.org/I4750791"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuehai Zhang","raw_affiliation_strings":["Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University , Zhengzhou, China","College of Agronomy, Henan Agricultural University , Zhengzhou, China","National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University , Zhengzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University , Zhengzhou, China","institution_ids":["https://openalex.org/I4750791"]},{"raw_affiliation_string":"College of Agronomy, Henan Agricultural University , Zhengzhou, China","institution_ids":["https://openalex.org/I4750791"]},{"raw_affiliation_string":"National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University , Zhengzhou, China","institution_ids":["https://openalex.org/I4750791"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5069050873","display_name":"Jihua Tang","orcid":"https://orcid.org/0000-0002-8623-6828"},"institutions":[{"id":"https://openalex.org/I4750791","display_name":"Henan Agricultural University","ror":"https://ror.org/04eq83d71","country_code":"CN","type":"education","lineage":["https://openalex.org/I4750791"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jihua Tang","raw_affiliation_strings":["Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University , Zhengzhou, China","College of Agronomy, Henan Agricultural University , Zhengzhou, China","National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University , Zhengzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University , Zhengzhou, China","institution_ids":["https://openalex.org/I4750791"]},{"raw_affiliation_string":"College of Agronomy, Henan Agricultural University , Zhengzhou, China","institution_ids":["https://openalex.org/I4750791"]},{"raw_affiliation_string":"National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University , Zhengzhou, China","institution_ids":["https://openalex.org/I4750791"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5015085832","https://openalex.org/A5069050873"],"corresponding_institution_ids":["https://openalex.org/I4750791"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.58,"has_fulltext":false,"cited_by_count":20,"citation_normalized_percentile":{"value":0.65187327,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"35","issue":"20","first_page":"4181","last_page":"4183"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.38609999418258667,"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":0.38609999418258667,"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/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.21089999377727509,"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"}},{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.0575999990105629,"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/computer-science","display_name":"Computer science","score":0.6023457646369934},{"id":"https://openalex.org/keywords/integer","display_name":"Integer (computer science)","score":0.5935064554214478},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5525776743888855},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.36414164304733276},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.09378525614738464}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6023457646369934},{"id":"https://openalex.org/C97137487","wikidata":"https://www.wikidata.org/wiki/Q729138","display_name":"Integer (computer science)","level":2,"score":0.5935064554214478},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5525776743888855},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36414164304733276},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.09378525614738464}],"mesh":[{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012275","descriptor_name":"Oryza","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012275","descriptor_name":"Oryza","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012275","descriptor_name":"Oryza","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044962","descriptor_name":"Data Compression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D044962","descriptor_name":"Data Compression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D044962","descriptor_name":"Data Compression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btz186","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz186","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30873546","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30873546","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":6,"referenced_works":["https://openalex.org/W1906974606","https://openalex.org/W2006066143","https://openalex.org/W2016705673","https://openalex.org/W2090639763","https://openalex.org/W2130774313","https://openalex.org/W2558561667"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2068608913","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W3124914020","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2130043461"],"abstract_inverted_index":{"SUMMARY:":[0],"We":[1],"proposed":[2],"to":[3],"store":[4],"large-scale":[5],"genotype":[6,29,45],"data":[7,30,46,84,106,128],"as":[8],"integer":[9,36],"sparse":[10,37],"matrices,":[11],"which":[12,89],"consumed":[13],"much":[14],"fewer":[15],"computing":[16],"resources":[17],"for":[18,77,95,122],"storage":[19],"and":[20,53,80,105,119],"analysis":[21,79],"than":[22],"traditional":[23],"approaches.":[24],"In":[25],"addition,":[26],"the":[27,44,66],"raw":[28],"could":[31],"be":[32],"readily":[33],"recovered":[34],"from":[35],"matrices.":[38],"Utilizing":[39],"this":[40],"approach,":[41],"we":[42],"stored":[43],"of":[47,72,82,107],"1612":[48],"Asian":[49,55],"cultivated":[50],"rice":[51,57,96],"accessions":[52,58],"446":[54],"wild":[56],"across":[59],"8":[60],"584":[61],"244":[62],"SNP":[63,83],"sites":[64],"in":[65,87],"ECOGEMS":[67,108,114],"database":[68],"with":[69],"310":[70],"MB":[71],"disk":[73],"usage.":[74],"Graphical":[75],"interface":[76],"visualization,":[78],"download":[81],"were":[85],"implemented":[86],"ECOGEMS,":[88],"made":[90],"it":[91],"a":[92],"valuable":[93],"resource":[94],"functional":[97],"genomic":[98],"studies.":[99],"AVAILABILITY":[100],"AND":[101],"IMPLEMENTATION:":[102],"The":[103],"code":[104],"are":[109,129],"freely":[110],"available":[111,130],"at":[112,117,131],"https://github.com/venyao/ECOGEMS.":[113],"is":[115],"deployed":[116],"http://ecogems.ncpgr.cn":[118],"http://150.109.59.144:":[120],"3838/ECOGEMS/":[121],"online":[123],"use.":[124],"SUPPLEMENTARY":[125],"INFORMATION:":[126],"Supplementary":[127],"Bioinformatics":[132],"online.":[133]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
