{"id":"https://openalex.org/W4412711097","doi":"https://doi.org/10.1186/s12859-025-06236-8","title":"PuMA: PubMed gene/cell type-relation Atlas","display_name":"PuMA: PubMed gene/cell type-relation Atlas","publication_year":2025,"publication_date":"2025-07-29","ids":{"openalex":"https://openalex.org/W4412711097","doi":"https://doi.org/10.1186/s12859-025-06236-8","pmid":"https://pubmed.ncbi.nlm.nih.gov/40731310"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06236-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06236-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06236-8","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/s12859-025-06236-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091980022","display_name":"Lucas Bickmann","orcid":"https://orcid.org/0000-0001-9043-7844"},"institutions":[{"id":"https://openalex.org/I95793202","display_name":"Otto-von-Guericke-Universit\u00e4t Magdeburg","ror":"https://ror.org/00ggpsq73","country_code":"DE","type":"education","lineage":["https://openalex.org/I95793202"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Lucas Bickmann","raw_affiliation_strings":["Institute of Medical Data Science, Otto-von-Guericke University Magdeburg, Magdeburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Medical Data Science, Otto-von-Guericke University Magdeburg, Magdeburg, Germany","institution_ids":["https://openalex.org/I95793202"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050708741","display_name":"Sarah Sandmann","orcid":"https://orcid.org/0000-0002-5011-0641"},"institutions":[{"id":"https://openalex.org/I95793202","display_name":"Otto-von-Guericke-Universit\u00e4t Magdeburg","ror":"https://ror.org/00ggpsq73","country_code":"DE","type":"education","lineage":["https://openalex.org/I95793202"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Sarah Sandmann","raw_affiliation_strings":["Institute of Medical Data Science, Otto-von-Guericke University Magdeburg, Magdeburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Medical Data Science, Otto-von-Guericke University Magdeburg, Magdeburg, Germany","institution_ids":["https://openalex.org/I95793202"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102955927","display_name":"Carolin Walter","orcid":"https://orcid.org/0000-0002-5155-7728"},"institutions":[{"id":"https://openalex.org/I22465464","display_name":"University of M\u00fcnster","ror":"https://ror.org/00pd74e08","country_code":"DE","type":"education","lineage":["https://openalex.org/I22465464"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Carolin Walter","raw_affiliation_strings":["Institute of Medical Informatics, University of M\u00fcnster, M\u00fcnster, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Medical Informatics, University of M\u00fcnster, M\u00fcnster, Germany","institution_ids":["https://openalex.org/I22465464"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033176798","display_name":"Julian Varghese","orcid":"https://orcid.org/0000-0002-7206-3719"},"institutions":[{"id":"https://openalex.org/I95793202","display_name":"Otto-von-Guericke-Universit\u00e4t Magdeburg","ror":"https://ror.org/00ggpsq73","country_code":"DE","type":"education","lineage":["https://openalex.org/I95793202"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Julian Varghese","raw_affiliation_strings":["Institute of Medical Data Science, Otto-von-Guericke University Magdeburg, Magdeburg, Germany. julian.varghese@med.ovgu.de"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Medical Data Science, Otto-von-Guericke University Magdeburg, Magdeburg, Germany. julian.varghese@med.ovgu.de","institution_ids":["https://openalex.org/I95793202"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5033176798"],"corresponding_institution_ids":["https://openalex.org/I95793202"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.3894,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.59245853,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"26","issue":"1","first_page":"201","last_page":"201"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.4523000121116638,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.4523000121116638,"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":0.20800000429153442,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.20250000059604645,"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/annotation","display_name":"Annotation","score":0.7943980097770691},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.742304265499115},{"id":"https://openalex.org/keywords/relation","display_name":"Relation (database)","score":0.5731514096260071},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5627228617668152},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4959445893764496},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4856668710708618},{"id":"https://openalex.org/keywords/gene-annotation","display_name":"Gene Annotation","score":0.46803879737854004},{"id":"https://openalex.org/keywords/online-database","display_name":"Online database","score":0.4577547311782837},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.43029719591140747},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.42432743310928345},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.26715195178985596},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.25492769479751587},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.24695715308189392},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.22808918356895447},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13980117440223694},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.09702259302139282}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7943980097770691},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.742304265499115},{"id":"https://openalex.org/C25343380","wikidata":"https://www.wikidata.org/wiki/Q277521","display_name":"Relation (database)","level":2,"score":0.5731514096260071},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5627228617668152},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4959445893764496},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4856668710708618},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.46803879737854004},{"id":"https://openalex.org/C2777715827","wikidata":"https://www.wikidata.org/wiki/Q7094076","display_name":"Online database","level":2,"score":0.4577547311782837},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.43029719591140747},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.42432743310928345},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.26715195178985596},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.25492769479751587},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.24695715308189392},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.22808918356895447},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13980117440223694},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.09702259302139282},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D030541","descriptor_name":"Databases, Genetic","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":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-025-06236-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06236-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06236-8","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:40731310","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40731310","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:12308971","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12308971","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"},{"id":"pmh:oai:doaj.org/article:7e5cbe99da13451081b2994088f9ddec","is_oa":true,"landing_page_url":"https://doaj.org/article/7e5cbe99da13451081b2994088f9ddec","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 26, Iss 1, Pp 1-13 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06236-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06236-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06236-8","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":[{"display_name":"Quality Education","score":0.7200000286102295,"id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320335829","display_name":"Otto von Guericke University Magdeburg","ror":"https://ror.org/00ggpsq73"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4412711097.pdf"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W2101746535","https://openalex.org/W2140947746","https://openalex.org/W2159583324","https://openalex.org/W2169528473","https://openalex.org/W2462007197","https://openalex.org/W2528405651","https://openalex.org/W2788348358","https://openalex.org/W2894687190","https://openalex.org/W2902122549","https://openalex.org/W2931036699","https://openalex.org/W2951506174","https://openalex.org/W2954952794","https://openalex.org/W3082330004","https://openalex.org/W3124814274","https://openalex.org/W4205530110","https://openalex.org/W4221142212","https://openalex.org/W4285175792","https://openalex.org/W4307432965","https://openalex.org/W4320800138","https://openalex.org/W4322718191","https://openalex.org/W4385605341","https://openalex.org/W4393936594","https://openalex.org/W6713748237"],"related_works":["https://openalex.org/W2059565715","https://openalex.org/W2901823680","https://openalex.org/W2009940763","https://openalex.org/W4386637333","https://openalex.org/W2946410450","https://openalex.org/W4361192415","https://openalex.org/W2126804125","https://openalex.org/W2162782320","https://openalex.org/W2137318037","https://openalex.org/W1760213857"],"abstract_inverted_index":{"BACKGROUND:":[0],"Rapid":[1],"extraction":[2],"and":[3,102,111,130,160,176,198,201,209],"visualization":[4,138],"of":[5,53],"cell-specific":[6],"gene":[7,101,113,174],"expression":[8],"is":[9,22,144,185,206],"important":[10],"for":[11,128,139,214],"automatic":[12],"cell":[13,19,41,83,103,115,131,162],"type":[14,42,84,104,116,163],"annotation,":[15],"e.g.":[16],"in":[17,26,97],"single":[18],"analysis.":[20],"There":[21],"an":[23,135,188],"emerging":[24],"field":[25],"which":[27,74],"tools":[28],"such":[29,59],"as":[30,60],"curated":[31,172,191],"databases":[32,175],"or":[33],"machine":[34,90],"learning":[35,91],"methods":[36],"are":[37,62],"used":[38],"to":[39,47,80,99,114,158],"support":[40],"annotation.":[43,85],"However,":[44],"complementing":[45],"approaches":[46],"efficiently":[48],"incorporate":[49],"the":[50,68,149],"latest":[51],"knowledge":[52,216],"free-text":[54],"articles":[55],"from":[56,106],"literature":[57],"databases,":[58],"PubMed,":[61,107],"understudied.":[63],"RESULTS:":[64],"This":[65,154],"work":[66,155],"introduces":[67],"PubMed":[69,151,167],"Gene/Cell":[70],"type-Relation":[71],"Atlas":[72],"(PuMA)":[73],"provides":[75],"a":[76,88,120,125],"local,":[77],"easy-to-use":[78],"web-interface":[79],"facilitate":[81],"literature-driven":[82],"It":[86,123,169],"utilizes":[87],"pretrained":[89],"based":[92,118,165],"named":[93],"entity":[94],"recognition":[95],"model":[96],"order":[98],"extract":[100],"concepts":[105],"links":[108],"biomedical":[109],"ontologies,":[110],"suggests":[112],"relations":[117],"on":[119,166],"ranking":[121],"score.":[122],"includes":[124],"search":[126],"tool":[127],"genes":[129],"types,":[132],"additionally":[133],"providing":[134],"interactive":[136,178],"graph":[137],"exploring":[140],"cross-relations.":[141],"Each":[142],"result":[143],"fully":[145],"traceable":[146],"by":[147],"linking":[148],"relevant":[150],"articles.":[152,168],"CONCLUSIONS:":[153],"enables":[156,177,210],"researchers":[157],"analyse":[159],"automatize":[161],"annotation":[164],"complements":[170],"manual":[171,190],"marker":[173],"visualizations.":[179],"The":[180,203],"evaluation":[181],"shows":[182],"that":[183],"PuMA":[184],"competitive":[186],"against":[187],"extensive":[189],"database":[192],"across":[193],"three":[194],"gold":[195],"standard":[196],"datasets":[197],"two":[199],"species-mouse":[200],"human.":[202],"software":[204],"framework":[205],"freely":[207],"available":[208],"regular":[211],"article":[212],"imports":[213],"incremental":[215],"updates.GitLab:":[217],"https://imigitlab.uni-muenster.de/published/PuMA/.":[218]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
