{"id":"https://openalex.org/W4403436119","doi":"https://doi.org/10.1186/s12859-024-05898-0","title":"Be-dataHIVE: a base editing database","display_name":"Be-dataHIVE: a base editing database","publication_year":2024,"publication_date":"2024-10-15","ids":{"openalex":"https://openalex.org/W4403436119","doi":"https://doi.org/10.1186/s12859-024-05898-0","pmid":"https://pubmed.ncbi.nlm.nih.gov/39407093"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-024-05898-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05898-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05898-0","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/s12859-024-05898-0","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014974142","display_name":"Lucas Schneider","orcid":"https://orcid.org/0000-0003-2596-6621"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]},{"id":"https://openalex.org/I4210146410","display_name":"Science Oxford","ror":"https://ror.org/04j8yhy50","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I4210146410"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Lucas Schneider","raw_affiliation_strings":["Department of Computer Science, University of Oxford, Parks Road, Oxford, OX1 3QD, UK. lucas.schneider@cs.ox.ac.uk","Department of Computer Science, University of Oxford, Parks Road, Oxford, OX1 3QD, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Oxford, Parks Road, Oxford, OX1 3QD, UK. lucas.schneider@cs.ox.ac.uk","institution_ids":["https://openalex.org/I40120149","https://openalex.org/I4210146410"]},{"raw_affiliation_string":"Department of Computer Science, University of Oxford, Parks Road, Oxford, OX1 3QD, UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5022118838","display_name":"P\u00e9ter Min\u00e1ry","orcid":"https://orcid.org/0000-0002-1779-6741"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]},{"id":"https://openalex.org/I4210146410","display_name":"Science Oxford","ror":"https://ror.org/04j8yhy50","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I4210146410"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Peter Minary","raw_affiliation_strings":["Department of Computer Science, University of Oxford, Parks Road, Oxford, OX1 3QD, UK. peter.minary@cs.ox.ac.uk","Department of Computer Science, University of Oxford, Parks Road, Oxford, OX1 3QD, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Oxford, Parks Road, Oxford, OX1 3QD, UK. peter.minary@cs.ox.ac.uk","institution_ids":["https://openalex.org/I40120149","https://openalex.org/I4210146410"]},{"raw_affiliation_string":"Department of Computer Science, University of Oxford, Parks Road, Oxford, OX1 3QD, UK","institution_ids":["https://openalex.org/I40120149"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5014974142","https://openalex.org/A5022118838"],"corresponding_institution_ids":["https://openalex.org/I40120149","https://openalex.org/I4210146410"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.1866,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.5467902,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"25","issue":"1","first_page":"330","last_page":"330"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","score":1.0,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":1.0,"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9987999796867371,"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/T12610","display_name":"RNA regulation and disease","score":0.986299991607666,"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":0.791700005531311},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.6283098459243774},{"id":"https://openalex.org/keywords/base","display_name":"Base (topology)","score":0.5884949564933777},{"id":"https://openalex.org/keywords/relational-database","display_name":"Relational database","score":0.5246931910514832},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.4949185252189636},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.44537076354026794},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4178510904312134},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3766513466835022},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.34568554162979126},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.18994346261024475},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12324801087379456},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09342780709266663}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.791700005531311},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.6283098459243774},{"id":"https://openalex.org/C42058472","wikidata":"https://www.wikidata.org/wiki/Q810214","display_name":"Base (topology)","level":2,"score":0.5884949564933777},{"id":"https://openalex.org/C5655090","wikidata":"https://www.wikidata.org/wiki/Q192588","display_name":"Relational database","level":2,"score":0.5246931910514832},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.4949185252189636},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.44537076354026794},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4178510904312134},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3766513466835022},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.34568554162979126},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.18994346261024475},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12324801087379456},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09342780709266663},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072669","descriptor_name":"Gene Editing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000072669","descriptor_name":"Gene Editing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000072669","descriptor_name":"Gene Editing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000072669","descriptor_name":"Gene Editing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000094704","descriptor_name":"RNA, Guide, CRISPR-Cas Systems","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000094704","descriptor_name":"RNA, Guide, CRISPR-Cas Systems","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000094704","descriptor_name":"RNA, Guide, CRISPR-Cas Systems","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000094704","descriptor_name":"RNA, Guide, CRISPR-Cas Systems","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-024-05898-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05898-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05898-0","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:39407093","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39407093","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:pubmedcentral.nih.gov:11476525","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11476525","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11476525/pdf/12859_2024_Article_5898.pdf","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"},{"id":"pmh:oai:doaj.org/article:e85239b22bf2436fa0a03d996747b522","is_oa":false,"landing_page_url":"https://doaj.org/article/e85239b22bf2436fa0a03d996747b522","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 25, Iss 1, Pp 1-18 (2024)","raw_type":"article"},{"id":"pmh:oai:ora.ox.ac.uk:uuid:55b15c89-738b-46b6-9e02-90adc79c192d","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402636","display_name":"Oxford University Research Archive (ORA) (University of Oxford)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I40120149","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/I40120149"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Jisc Publications Router","raw_type":"Journal article"}],"best_oa_location":{"id":"doi:10.1186/s12859-024-05898-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05898-0","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05898-0","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":[{"score":0.6200000047683716,"display_name":"Decent work and economic growth","id":"https://metadata.un.org/sdg/8"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4403436119.pdf","grobid_xml":"https://content.openalex.org/works/W4403436119.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W2072605585","https://openalex.org/W2112796928","https://openalex.org/W2114850508","https://openalex.org/W2154241726","https://openalex.org/W2336828812","https://openalex.org/W2806980026","https://openalex.org/W2898360779","https://openalex.org/W2916230551","https://openalex.org/W2950114027","https://openalex.org/W3035700080","https://openalex.org/W3039159245","https://openalex.org/W3093632917","https://openalex.org/W3174716159","https://openalex.org/W3190858414","https://openalex.org/W3194369599","https://openalex.org/W3197375931","https://openalex.org/W4214553676","https://openalex.org/W4311588643","https://openalex.org/W4379768365","https://openalex.org/W4382881322"],"related_works":["https://openalex.org/W2770593030","https://openalex.org/W3154990682","https://openalex.org/W2560201613","https://openalex.org/W2171975302","https://openalex.org/W2022352247","https://openalex.org/W4312219546","https://openalex.org/W2377538627","https://openalex.org/W2107220315","https://openalex.org/W306357984","https://openalex.org/W4299841221"],"abstract_inverted_index":{"Base":[0],"editing":[1,6,43,66,106],"is":[2,30,80,88,134,168],"an":[3],"enhanced":[4],"gene":[5],"approach":[7],"that":[8,115],"enables":[9],"the":[10,18,72,86,104],"precise":[11],"transformation":[12],"of":[13,27,77,125,128],"single":[14],"nucleotides":[15],"and":[16,32,48,75,96,133,139,152,167,173],"has":[17,44],"potential":[19],"to":[20,45,55,63,84,89],"cure":[21],"rare":[22],"diseases.":[23],"The":[24,122,156],"design":[25],"process":[26],"base":[28,42,65,105],"editors":[29],"labour-intensive":[31],"outcomes":[33,67],"are":[34,153],"not":[35,101],"easily":[36],"predictable.":[37],"For":[38],"any":[39,51],"clinical":[40],"use,":[41],"be":[46,56,159],"accurate":[47],"efficient.":[49],"Thus,":[50],"bystander":[52],"mutations":[53],"have":[54,68],"minimized.":[57],"In":[58],"recent":[59],"years,":[60],"computational":[61],"models":[62,79,91],"predict":[64],"been":[69],"developed.":[70],"However,":[71],"overall":[73],"robustness":[74],"performance":[76,87],"those":[78],"limited.":[81],"One":[82],"way":[83],"improve":[85],"train":[90],"on":[92],"a":[93,112],"diverse,":[94],"feature-rich,":[95],"large":[97],"dataset,":[98],"which":[99],"does":[100],"exist":[102],"for":[103,147,171],"field.":[107],"Hence,":[108],"we":[109],"develop":[110],"BE-dataHIVE,":[111],"mySQL":[113],"database":[114,157],"covers":[116],"over":[117],"460,000":[118],"gRNA":[119],"target":[120],"combinations.":[121],"current":[123],"version":[124],"BE-dataHIVE":[126],"consists":[127],"data":[129,145],"from":[130],"five":[131],"studies":[132],"enriched":[135],"with":[136],"melting":[137],"temperatures":[138],"energy":[140],"terms.":[141],"Furthermore,":[142],"multiple":[143],"different":[144],"structures":[146],"machine":[148,174],"learning":[149,175],"were":[150],"computed":[151],"directly":[154],"available.":[155],"can":[158],"accessed":[160],"via":[161],"our":[162],"website":[163],"https://be-datahive.com/":[164],"or":[165],"API":[166],"therefore":[169],"suitable":[170],"practitioners":[172],"researchers.":[176]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-06-17T06:14:20.161405","created_date":"2025-10-10T00:00:00"}