title: AAgAtlas 1.0: a human autoantigen database.
abstract: Autoantibodies refer to antibodies that target self-antigens, which can play pivotal roles in maintaining homeostasis, distinguishing normal from tumor tissue and trigger autoimmune diseases. In the last three decades, tremendous efforts have been devoted to elucidate the generation, evolution and functions of autoantibodies, as well as their target autoantigens. However, reports of these countless previously identified autoantigens are randomly dispersed in the literature. Here, we constructed an AAgAtlas database 1.0 using text-mining and manual curation. We extracted 45 830 autoantigen-related abstracts and 94 313 sentences from PubMed using the keywords of either 'autoantigen' or 'autoantibody' or their lexical variants, which were further refined to 25 520 abstracts, 43 253 sentences and 3984 candidates by our bio-entity recognizer based on the Protein Ontology. Finally, we identified 1126 genes as human autoantigens and 1071 related human diseases, with which we constructed a human autoantigen database (AAgAtlas database 1.0). The database provides a user-friendly interface to conveniently browse, retrieve and download human autoantigens as well as their associated diseases. The database is freely accessible at http://biokb.ncpsb.org/aagatlas/ We believe this database will be a valuable resource to track and understand human autoantigens as well as to investigate their functions in basic and translational research.
authors.affiliation: State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Radiation Medicine, Beijing 102206, China.
authors.forename: Dan
authors.initials: D
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Radiation Medicine, Beijing 102206, China.
authors.forename: Liuhui
authors.initials: L
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Radiation Medicine, Beijing 102206, China.
authors.forename: Ping
authors.initials: P
authors.lastname: Zhang
authors.affiliation: The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
authors.forename: Joshua
authors.initials: J
authors.lastname: LaBaer
authors.affiliation: State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Radiation Medicine, Beijing 102206, China hhe@ebi.ac.uk.|European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Henning
authors.initials: H
authors.lastname: Hermjakob
authors.affiliation: State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Radiation Medicine, Beijing 102206, China lidong.bprc@foxmail.com.
authors.forename: Dong
authors.initials: D
authors.lastname: Li
authors.affiliation: State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Radiation Medicine, Beijing 102206, China xiaobo.yu@hotmail.com.
authors.forename: Xiaobo
authors.initials: X
authors.lastname: Yu
mesh_terms: D001324:Autoantigens; D019295:Computational Biology / Q000379:methods*; D066289:Data Curation; D016208:Databases, Factual; D006801:Humans; D057386:Search Engine; D014584:User-Computer Interface; D064878:Web Browser
chemical_list: D001324:Autoantigens