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论文范文
1. A High-Level Overview of the IEDB The Immune Epitope Database (IEDB) is a free online resource that catalogs and makes accessible to the scientific community epitope-related data derived from allergic diseases, infectious diseases, apart from HIV which is captured separately in the Los Alamos HIV database [1], autoimmune diseases, and diseases associated with transplantation and alloantigens. The IEDB [2] contains both T cell and B cell epitopes, as well as MHC ligand data. The epitopes are derived from humans, nonhuman primates, mice, and all other studied hosts. The curation of scientific literature started in 2004, requiring the curation of past and current relevant epitope literature in available peer-reviewed journals [3, 4]. As the IEDB evolved, it has been necessary to change how biological concepts are captured in order to maximize accuracy. In addition, automated validation is continuously added. Consequently, there is a significant ongoing “recuration” effort of revising existing entries to improve data quality and consistency. The IEDB is now current with the published literature, and targeted PubMed queries are run biweekly, with the goal of making the data available in the IEDB within eight weeks of publication. As of November 2016, the IEDB data were derived from over 18,000 papers. In addition, the IEDB contains nearly 300 submissions (corresponding to approximately 20% of the total data) from several NIH-funded large-scale epitope discovery programs and from researchers that directly approach the IEDB to deposit their data, including negative data, which might typically appear in supplemental tables or might not be published at all. Slightly more than half of the references in the IEDB relate to infectious diseases and about a quarter relate to autoimmune diseases. The remainder includes allergy, transplant, and other categories. Because the data in the IEDB reside in the public domain, researchers can freely access, analyze, and publish works using these data. When initially designing the IEDB, we realized that different researchers had different views on what should be included in an epitope database, based largely on their area of research. While each scientist’s specific interests and epitope definitions might vary, ultimately every epitope is defined by an experiment or specific assay. To provide a general yet accurate epitope database, we utilized an assay-centric design, capturing the experiments (assays) that characterize and define each epitope. This required translation of the data typically described in the methods and results sections of a scientific paper into a generic data structure in which epitope data are entered and stored in a format that allows users to query for the characteristics of these epitopes. The IEDB website has undergone two major revisions since its introduction in early 2006, each improving its features and usability [2, 5]. The current IEDB 3.0, deployed in February 2015, incorporated feedback from immunologists and bioinformaticians, collected at user workshops, help desk requests, and user observation sessions, to make searching the database more intuitive and to deliver results in a more useful format. The home page prominently features the query interface, which contains the fields that address over 80% of the typical queries. The query concept is similar to a travel website where users specify basic information and can then filter or refine the results with additional fields. In the following sections, we will present a detailed account of the IEDB query and reporting and also provide several specific examples. 
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