{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,30]],"date-time":"2026-03-30T18:54:05Z","timestamp":1774896845448,"version":"3.50.1"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2019,5,22]],"date-time":"2019-05-22T00:00:00Z","timestamp":1558483200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100008333","name":"University of Alabama at Birmingham","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008333","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008523","name":"Center for Clinical and Translational Science","doi-asserted-by":"publisher","award":["1TL1TR001418\u201301"],"award-info":[{"award-number":["1TL1TR001418\u201301"]}],"id":[{"id":"10.13039\/100008523","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["U01CA223976"],"award-info":[{"award-number":["U01CA223976"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>BEERE (Biomedical Entity Expansion, Ranking and Explorations) is a new web-based data analysis tool to help biomedical researchers characterize any input list of genes\/proteins, biomedical terms or their combinations, i.e. \u2018biomedical entities\u2019, in the context of existing literature. Specifically, BEERE first aims to help users examine the credibility of known entity-to-entity associative or semantic relationships supported by database or literature references from the user input of a gene\/term list. Then, it will help users uncover the relative importance of each entity\u2014a gene or a term\u2014within the user input by computing the ranking scores of all entities. At last, it will help users hypothesize new gene functions or genotype\u2013phenotype associations by an interactive visual interface of constructed global entity relationship network. The output from BEERE includes: a list of the original entities matched with known relationships in databases; any expanded entities that may be generated from the analysis; the ranks and ranking scores reported with statistical significance for each entity; and an interactive graphical display of the gene or term network within data provenance annotations that link to external data sources. The web server is free and open to all users with no login requirement and can be accessed at http:\/\/discovery.informatics.uab.edu\/beere\/.<\/jats:p>","DOI":"10.1093\/nar\/gkz428","type":"journal-article","created":{"date-parts":[[2019,5,20]],"date-time":"2019-05-20T19:18:23Z","timestamp":1558379903000},"page":"W578-W586","source":"Crossref","is-referenced-by-count":13,"title":["BEERE: a web server for biomedical entity expansion, ranking and explorations"],"prefix":"10.1093","volume":"47","author":[{"given":"Zongliang","family":"Yue","sequence":"first","affiliation":[{"name":"Informatics Institute, School of Medicine, the University of Alabama at Birmingham, AL 35233, USA"}]},{"given":"Christopher D","family":"Willey","sequence":"additional","affiliation":[{"name":"Department of Radiation Oncology, School of Medicine, the University of Alabama at Birmingham, AL 35233, USA"}]},{"given":"Anita B","family":"Hjelmeland","sequence":"additional","affiliation":[{"name":"Department of Cell, Developmental and Integrative Biology, School of Medicine, the University of Alabama at Birmingham, AL 35233, USA"}]},{"given":"Jake Y","family":"Chen","sequence":"additional","affiliation":[{"name":"Informatics Institute, School of Medicine, the University of Alabama at Birmingham, AL 35233, USA"}]}],"member":"286","published-online":{"date-parts":[[2019,5,22]]},"reference":[{"key":"2019062808323586100_B1","first-page":"367","article-title":"Mining Alzheimer disease relevant proteins from integrated protein interactome data","volume":"11","author":"Chen","year":"2006","journal-title":"Pac. Symp. Biocomput."},{"key":"2019062808323586100_B2","doi-asserted-by":"crossref","first-page":"46598","DOI":"10.1038\/srep46598","article-title":"A large-scale benchmark of gene prioritization methods","volume":"7","author":"Guala","year":"2017","journal-title":"Sci. Rep."},{"key":"2019062808323586100_B3","doi-asserted-by":"crossref","first-page":"W334","DOI":"10.1093\/nar\/gkr289","article-title":"PINTA: a web server for network-based gene prioritization from expression data","volume":"39","author":"Nitsch","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2019062808323586100_B4","doi-asserted-by":"crossref","first-page":"W305","DOI":"10.1093\/nar\/gkp427","article-title":"ToppGene Suite for gene list enrichment analysis and candidate gene prioritization","volume":"37","author":"Chen","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2019062808323586100_B5","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1093\/bioinformatics\/btk031","article-title":"SUSPECTS: enabling fast and effective prioritization of positional candidates","volume":"22","author":"Adie","year":"2006","journal-title":"Bioinformatics"},{"key":"2019062808323586100_B6","doi-asserted-by":"crossref","first-page":"528","DOI":"10.1186\/1471-2105-9-528","article-title":"Gene Prospector: an evidence gateway for evaluating potential susceptibility genes and interacting risk factors for human diseases","volume":"9","author":"Yu","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2019062808323586100_B7","doi-asserted-by":"crossref","first-page":"W377","DOI":"10.1093\/nar\/gkn325","article-title":"ENDEAVOUR update: a web resource for gene prioritization in multiple species","volume":"36","author":"Tranchevent","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2019062808323586100_B8","doi-asserted-by":"crossref","first-page":"1181","DOI":"10.1056\/NEJMoa0908094","article-title":"Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy","volume":"362","author":"Lupski","year":"2010","journal-title":"N. Engl. J. Med."},{"key":"2019062808323586100_B9","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1002\/wsbm.1177","article-title":"Recent approaches to the prioritization of candidate disease genes","volume":"4","author":"Doncheva","year":"2012","journal-title":"Wiley Interdiscip. Rev. Syst. Biol. Med."},{"key":"2019062808323586100_B10","doi-asserted-by":"crossref","first-page":"3081","DOI":"10.1093\/bioinformatics\/bts581","article-title":"An unbiased evaluation of gene prioritization tools","volume":"28","author":"Bornigen","year":"2012","journal-title":"Bioinformatics"},{"key":"2019062808323586100_B11","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1038\/nrg3253","article-title":"Computational tools for prioritizing candidate genes: boosting disease gene discovery","volume":"13","author":"Moreau","year":"2012","journal-title":"Nat. Rev. Genet."},{"key":"2019062808323586100_B12","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1007\/978-1-61779-176-5_12","article-title":"Web tools for the prioritization of candidate disease genes","volume":"760","author":"Oti","year":"2011","journal-title":"Methods Mol. Biol."},{"key":"2019062808323586100_B13","doi-asserted-by":"crossref","first-page":"678","DOI":"10.1111\/j.1742-4658.2012.08471.x","article-title":"Computational approaches to disease-gene prediction: rationale, classification and successes","volume":"279","author":"Piro","year":"2012","journal-title":"FEBS J."},{"key":"2019062808323586100_B14","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1093\/bib\/bbq007","article-title":"A guide to web tools to prioritize candidate genes","volume":"12","author":"Tranchevent","year":"2011","journal-title":"Brief Bioinform."},{"key":"2019062808323586100_B15","doi-asserted-by":"crossref","first-page":"D362","DOI":"10.1093\/nar\/gkw937","article-title":"The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible","volume":"45","author":"Szklarczyk","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2019062808323586100_B16","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1186\/s12864-017-3512-1","article-title":"HAPPI-2: a comprehensive and high-quality map of human annotated and predicted protein interactions","volume":"18","author":"Chen","year":"2017","journal-title":"BMC Genomics"},{"key":"2019062808323586100_B17","doi-asserted-by":"crossref","first-page":"17417","DOI":"10.1038\/srep17417","article-title":"Drug target prioritization by perturbed gene expression and network information","volume":"5","author":"Isik","year":"2015","journal-title":"Sci. Rep."},{"key":"2019062808323586100_B18","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1517\/14728222.11.3.411","article-title":"Pathway analysis software as a tool for drug target selection, prioritization and validation of drug mechanism","volume":"11","author":"Sivachenko","year":"2007","journal-title":"Expert Opin. Ther. Targets"},{"key":"2019062808323586100_B19","doi-asserted-by":"crossref","first-page":"532","DOI":"10.1186\/s12859-017-1889-0","article-title":"Repositioning drugs by targeting network modules: a Parkinson's disease case study","volume":"18","author":"Yue","year":"2017","journal-title":"BMC Bioinformatics"},{"key":"2019062808323586100_B20","doi-asserted-by":"crossref","first-page":"425","DOI":"10.3414\/ME0508","article-title":"Semantic structuring of and information extraction from medical documents using the UMLS","volume":"47","author":"Denecke","year":"2008","journal-title":"Methods Inf. Med."},{"key":"2019062808323586100_B21","doi-asserted-by":"crossref","first-page":"949","DOI":"10.1136\/jclinpath-2016-203872","article-title":"Natural language processing in pathology: a scoping review","volume":"69","author":"Burger","year":"2016","journal-title":"J. Clin. Pathol."},{"key":"2019062808323586100_B22","first-page":"521","article-title":"Scholarly information extraction is going to make a quantum leap with pubmed central (PMC)","volume":"245","author":"Matthies","year":"2017","journal-title":"Stud. Health Technol. Inform."},{"key":"2019062808323586100_B23","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1038\/nmeth.3484","article-title":"Phenolyzer: phenotype-based prioritization of candidate genes for human diseases","volume":"12","author":"Yang","year":"2015","journal-title":"Nat Methods"},{"key":"2019062808323586100_B24","doi-asserted-by":"crossref","first-page":"2794","DOI":"10.1093\/bioinformatics\/bti414","article-title":"POSBIOTM-NER: a trainable biomedical named-entity recognition system","volume":"21","author":"Song","year":"2005","journal-title":"Bioinformatics"},{"key":"2019062808323586100_B25","doi-asserted-by":"crossref","first-page":"1745","DOI":"10.1093\/bioinformatics\/bty869","article-title":"Cross-type biomedical named entity recognition with deep multi-task learning","volume":"35","author":"Wang","year":"2018","journal-title":"Bioinformatics"},{"key":"2019062808323586100_B26","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1186\/s12920-017-0316-8","article-title":"Disease named entity recognition from biomedical literature using a novel convolutional neural network","volume":"10","author":"Zhao","year":"2017","journal-title":"BMC Med. Genomics"},{"key":"2019062808323586100_B27","doi-asserted-by":"crossref","first-page":"e0164680","DOI":"10.1371\/journal.pone.0164680","article-title":"BEST: next-generation biomedical entity search tool for knowledge discovery from biomedical literature","volume":"11","author":"Lee","year":"2016","journal-title":"PLoS One"},{"key":"2019062808323586100_B28","doi-asserted-by":"crossref","first-page":"D36","DOI":"10.1093\/nar\/gku1055","article-title":"Gene: a gene-centered information resource at NCBI","volume":"43","author":"Brown","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2019062808323586100_B29","first-page":"533","article-title":"Using UMLS Concept Unique Identifiers (CUIs) for word sense disambiguation in the biomedical domain","volume":"2007","author":"McInnes","year":"2007","journal-title":"AMIA Annu. Symp. Proc."},{"key":"2019062808323586100_B30","doi-asserted-by":"crossref","first-page":"3158","DOI":"10.1093\/bioinformatics\/bts591","article-title":"SemMedDB: a PubMed-scale repository of biomedical semantic predications","volume":"28","author":"Kilicoglu","year":"2012","journal-title":"Bioinformatics"},{"key":"2019062808323586100_B31","first-page":"587","article-title":"Using SemRep to label semantic relations extracted from clinical text","volume":"2012","author":"Liu","year":"2012","journal-title":"AMIA Annu. Symp. Proc."},{"key":"2019062808323586100_B32","doi-asserted-by":"crossref","first-page":"W518","DOI":"10.1093\/nar\/gkt441","article-title":"PubTator: a web-based text mining tool for assisting biocuration","volume":"41","author":"Wei","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2019062808323586100_B33","first-page":"164","article-title":"Semantic MEDLINE for discovery browsing: using semantic predications and the literature-based discovery paradigm to elucidate a mechanism for the obesity paradox","volume":"2013","author":"Cairelli","year":"2013","journal-title":"AMIA Annu. Symp. Proc."},{"key":"2019062808323586100_B34","doi-asserted-by":"crossref","first-page":"D789","DOI":"10.1093\/nar\/gku1205","article-title":"OMIM.org: online mendelian inheritance in man (OMIM(R)), an online catalog of human genes and genetic disorders","volume":"43","author":"Amberger","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2019062808323586100_B35","doi-asserted-by":"crossref","first-page":"baw030","DOI":"10.1093\/database\/baw030","article-title":"Genic insights from integrated human proteomics in GeneCards","volume":"2016","author":"Fishilevich","year":"2016","journal-title":"Database"},{"key":"2019062808323586100_B36","doi-asserted-by":"crossref","first-page":"5355","DOI":"10.1158\/0008-5472.CAN-14-3689","article-title":"Targeting a Plk1-controlled polarity checkpoint in therapy-resistant glioblastoma-propagating cells","volume":"75","author":"Lerner","year":"2015","journal-title":"Cancer Res"},{"key":"2019062808323586100_B37","doi-asserted-by":"crossref","first-page":"D733","DOI":"10.1093\/nar\/gkv1189","article-title":"Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation","volume":"44","author":"O\u2019Leary","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2019062808323586100_B38","doi-asserted-by":"crossref","first-page":"3176","DOI":"10.1158\/0008-5472.CAN-17-3470","article-title":"Differential Effects of Estrogen Receptor \u03b2 Isoforms on Glioblastoma Progression","volume":"78","author":"Liu","year":"2018","journal-title":"Cancer Res."},{"key":"2019062808323586100_B39","doi-asserted-by":"crossref","first-page":"eaao5253","DOI":"10.1126\/scitranslmed.aao5253","article-title":"Sex differences in GBM revealed by analysis of patient imaging, transcriptome, and survival data","volume":"11","author":"Yang","year":"2019","journal-title":"Sci. Transl. Med."},{"key":"2019062808323586100_B40","doi-asserted-by":"crossref","first-page":"D668","DOI":"10.1093\/nar\/gkx1040","article-title":"PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology","volume":"46","author":"Yue","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2019062808323586100_B41","doi-asserted-by":"crossref","first-page":"D1060","DOI":"10.1093\/nar\/gkr901","article-title":"GeneSigDB: a manually curated database and resource for analysis of gene expression signatures","volume":"40","author":"Culhane","year":"2012","journal-title":"Nucleic Acids Res."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/advance-article-pdf\/doi\/10.1093\/nar\/gkz428\/28684556\/gkz428.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/47\/W1\/W578\/28880313\/gkz428.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,18]],"date-time":"2022-09-18T09:19:14Z","timestamp":1663492754000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/47\/W1\/W578\/5494748"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,5,22]]},"references-count":41,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2019,5,22]]},"published-print":{"date-parts":[[2019,7,2]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkz428","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,7,2]]},"published":{"date-parts":[[2019,5,22]]}}}