{"id":"https://openalex.org/W4205530110","doi":"https://doi.org/10.1093/bioinformatics/btab834","title":"CellMeSH: probabilistic cell-type identification using indexed literature","display_name":"CellMeSH: probabilistic cell-type identification using indexed literature","publication_year":2021,"publication_date":"2021-12-06","ids":{"openalex":"https://openalex.org/W4205530110","doi":"https://doi.org/10.1093/bioinformatics/btab834","pmid":"https://pubmed.ncbi.nlm.nih.gov/34893819"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab834","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab834","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1093/bioinformatics/btab834","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5019154579","display_name":"Shunfu Mao","orcid":"https://orcid.org/0000-0002-8203-0507"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shunfu Mao","raw_affiliation_strings":["Electrical and Computer Engineering Department, University of Washington , Seattle, WA 98195, USA"],"raw_orcid":"https://orcid.org/0000-0002-8203-0507","affiliations":[{"raw_affiliation_string":"Electrical and Computer Engineering Department, University of Washington , Seattle, WA 98195, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069771612","display_name":"Y Zhang","orcid":"https://orcid.org/0000-0001-6533-5563"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yue Zhang","raw_affiliation_strings":["Paul G. Allen School of Computer Science and Engineering, University of Washington , Seattle, WA 98195, USA"],"raw_orcid":"https://orcid.org/0000-0001-6533-5563","affiliations":[{"raw_affiliation_string":"Paul G. Allen School of Computer Science and Engineering, University of Washington , Seattle, WA 98195, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021731745","display_name":"Georg Seelig","orcid":"https://orcid.org/0000-0002-3163-8782"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Georg Seelig","raw_affiliation_strings":["Electrical and Computer Engineering Department, University of Washington , Seattle, WA 98195, USA","Paul G. Allen School of Computer Science and Engineering, University of Washington , Seattle, WA 98195, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Electrical and Computer Engineering Department, University of Washington , Seattle, WA 98195, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Paul G. Allen School of Computer Science and Engineering, University of Washington , Seattle, WA 98195, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100722219","display_name":"Sreeram Kannan","orcid":"https://orcid.org/0000-0001-8843-2964"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sreeram Kannan","raw_affiliation_strings":["Electrical and Computer Engineering Department, University of Washington , Seattle, WA 98195, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Electrical and Computer Engineering Department, University of Washington , Seattle, WA 98195, USA","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5021731745","https://openalex.org/A5100722219"],"corresponding_institution_ids":["https://openalex.org/I201448701"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.5924,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.64747761,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"38","issue":"5","first_page":"1393","last_page":"1402"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9990000128746033,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9990000128746033,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.0003000000142492354,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T10885","display_name":"Gene expression and cancer classification","score":0.00019999999494757503,"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":0.7907319068908691},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.7123132944107056},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.6866364479064941},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.6034638285636902},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.45531165599823},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.44063708186149597},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4020635485649109},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.34109988808631897},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.24218007922172546},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08722367882728577}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7907319068908691},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7123132944107056},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.6866364479064941},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.6034638285636902},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.45531165599823},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.44063708186149597},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4020635485649109},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.34109988808631897},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.24218007922172546},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08722367882728577},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"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":"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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btab834","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab834","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34893819","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34893819","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},{"id":"pmh:oai:pubmedcentral.nih.gov:8826164","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8826164","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab834","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab834","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5400000214576721,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G2346146521","display_name":null,"funder_award_id":"1R01HG008164","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4113855631","display_name":null,"funder_award_id":"R01HG009892","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G4404837078","display_name":null,"funder_award_id":"R01HG008164","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G5413168500","display_name":null,"funder_award_id":"R21 CA246358","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G6472985349","display_name":null,"funder_award_id":"R21CA246358","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7262935159","display_name":null,"funder_award_id":"R01HG009892","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":55,"referenced_works":["https://openalex.org/W1736726159","https://openalex.org/W1874466506","https://openalex.org/W1979283544","https://openalex.org/W1984883254","https://openalex.org/W1999574084","https://openalex.org/W2005097381","https://openalex.org/W2020278455","https://openalex.org/W2033072655","https://openalex.org/W2069089843","https://openalex.org/W2070050178","https://openalex.org/W2071010503","https://openalex.org/W2099851046","https://openalex.org/W2135937351","https://openalex.org/W2140729960","https://openalex.org/W2149573463","https://openalex.org/W2152692691","https://openalex.org/W2159707944","https://openalex.org/W2164683872","https://openalex.org/W2169456326","https://openalex.org/W2231058499","https://openalex.org/W2323326409","https://openalex.org/W2344887288","https://openalex.org/W2407916594","https://openalex.org/W2523620612","https://openalex.org/W2541820485","https://openalex.org/W2598326928","https://openalex.org/W2747545374","https://openalex.org/W2760692740","https://openalex.org/W2788348358","https://openalex.org/W2792647356","https://openalex.org/W2794083495","https://openalex.org/W2794480084","https://openalex.org/W2796170779","https://openalex.org/W2800392236","https://openalex.org/W2804150826","https://openalex.org/W2811512420","https://openalex.org/W2885376126","https://openalex.org/W2894687190","https://openalex.org/W2895456557","https://openalex.org/W2907514116","https://openalex.org/W2931036699","https://openalex.org/W2942380588","https://openalex.org/W2951506174","https://openalex.org/W2952303649","https://openalex.org/W2952568226","https://openalex.org/W2953251392","https://openalex.org/W2964643116","https://openalex.org/W2966569571","https://openalex.org/W2971398276","https://openalex.org/W2973034691","https://openalex.org/W3005127469","https://openalex.org/W4213009331","https://openalex.org/W4320800138","https://openalex.org/W6655443941","https://openalex.org/W6759704670"],"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/W2251519152"],"abstract_inverted_index":{"MOTIVATION:":[0],"Single-cell":[1],"RNA":[2],"sequencing":[3],"(scRNA-seq)":[4],"is":[5,114,138,142,168],"widely":[6],"used":[7],"for":[8,92,109,180],"analyzing":[9],"gene":[10,55,119],"expression":[11,56],"in":[12,33],"multi-cellular":[13],"systems":[14],"and":[15,27,43,120,141,187,195,212],"provides":[16],"unprecedented":[17],"access":[18],"to":[19,25,49,88,133,171],"cellular":[20],"heterogeneity.":[21],"scRNA-seq":[22],"experiments":[23],"aim":[24],"identify":[26],"quantify":[28],"all":[29],"cell":[30,50,90],"types":[31,51,91],"present":[32],"a":[34,70,100,106,191],"sample.":[35],"Measured":[36],"single-cell":[37],"transcriptomes":[38],"are":[39,47,165,199,220],"grouped":[40],"by":[41,116],"similarity":[42],"the":[44,59,158,163],"resulting":[45],"clusters":[46,63,93],"mapped":[48],"based":[52,94],"on":[53,95,190],"cluster-specific":[54],"patterns.":[57],"While":[58],"process":[60],"of":[61,102,125,193],"generating":[62],"has":[64],"become":[65],"largely":[66],"automated,":[67],"annotation":[68,182],"remains":[69],"laborious":[71],"ad":[72],"hoc":[73],"effort":[74],"that":[75,198],"requires":[76],"expert":[77],"biological":[78],"knowledge.":[79],"RESULTS:":[80],"Here,":[81],"we":[82],"introduce":[83],"CellMeSH-a":[84],"new":[85,146],"automated":[86],"approach":[87],"identifying":[89],"prior":[96,174],"literature.":[97],"CellMeSH":[98,137,167,184],"combines":[99],"database":[101,110,113],"gene-cell-type":[103,159],"associations":[104,160],"with":[105,145],"probabilistic":[107,149],"method":[108,151],"querying.":[111],"The":[112,148],"constructed":[115,135],"automatically":[117],"linking":[118],"cell-type":[121],"information":[122,154],"from":[123,162],"millions":[124],"publications":[126],"using":[127],"existing":[128,203],"indexed":[129],"literature":[130,164],"resources.":[131],"Compared":[132],"manually":[134],"databases,":[136],"more":[139],"comprehensive":[140],"easily":[143],"updated":[144],"data.":[147],"query":[150],"enables":[152],"reliable":[153],"retrieval":[155],"even":[156],"though":[157],"extracted":[161],"noisy.":[166],"also":[169],"able":[170],"optionally":[172],"utilize":[173],"knowledge":[175],"about":[176],"tissues":[177],"or":[178],"cells":[179],"further":[181],"improvement.":[183],"achieves":[185],"top-one":[186],"top-three":[188],"accuracies":[189],"number":[192],"mouse":[194],"human":[196],"datasets":[197],"consistently":[200],"better":[201],"than":[202],"approaches.":[204],"AVAILABILITY":[205],"AND":[206],"IMPLEMENTATION:":[207],"Web":[208],"server":[209],"at":[210,214,222],"https://uncurl.cs.washington.edu/db_query":[211],"API":[213],"https://github.com/shunfumao/cellmesh.":[215],"SUPPLEMENTARY":[216],"INFORMATION:":[217],"Supplementary":[218],"data":[219],"available":[221],"Bioinformatics":[223],"online.":[224]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2020,"cited_by_count":1}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}