TY - JOUR
T1 - AAgAtlas 1.0
T2 - A human autoantigen database
AU - Wang, Dan
AU - Yang, Liuhui
AU - Zhang, Ping
AU - LaBaer, Joshua
AU - Hermjakob, Henning
AU - Li, Dong
AU - Yu, Xiaobo
N1 - Funding Information:
National Natural Science Foundation of China [81673040 to X.Y.]; Beijing Municipal Human Resources and Social Security Bureau [grant for Overseas Scholars to X.Y.]; Guangdong Science and Technology Department [2016A020215004 to X.Y.]; International S&T Cooperation Program [2014DFB30020 to D.L.]; Program of Precision Medicine [2016YFC0901905 to D.L.]; Early Detection Research Network [5U01CA117374 to J.L.]; Funding for open access charge: National Natural Science Foundation of China [81673040 to X.Y.].
Publisher Copyright:
© The Author(s) 2016.
PY - 2017/1/1
Y1 - 2017/1/1
N2 - Autoantibodies refer to antibodies that target selfantigens, 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 whichwe 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.
AB - Autoantibodies refer to antibodies that target selfantigens, 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 whichwe 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.
UR - http://www.scopus.com/inward/record.url?scp=85015989421&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85015989421&partnerID=8YFLogxK
U2 - 10.1093/nar/gkw946
DO - 10.1093/nar/gkw946
M3 - Article
C2 - 27924021
AN - SCOPUS:85015989421
SN - 0305-1048
VL - 45
SP - D769-D776
JO - Nucleic acids research
JF - Nucleic acids research
IS - D1
ER -