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VaximmutorDB DocumentationThe VaximmutorDB website is user-friendly and easy to use and explore. 1. VaximmutorDB data curation The vaximmuntor bioinformatics curation was achieved through an internally developed, web-based Limix literature curation and analysis system. Specifically, the papers annotated came from the PubMed literature database. The annotation of the data in the papers was achieved based on pre-defined database schema (or categories). With a PubMed paper ID or a Gene ID, our system is able to to retrieve all related information about the literature citation or the gene, respectively. The system also allows an annotator to submit data and a reviewer to double check, edit if needed, and approve the submitted annotations. Only after the review and approval by a domain expert, the information is available in the VaximmuntorDB website for users to query and browse. See more information on the VIOLIN account registration and data submission tutorial website.
2. Website query Querying the VaximmutorDB is straightforward. Figure 1 provides a good example of querying vaximmutor information in the VaximmutorDB web site.
Figure 1. VaximmuntorDB data query. (A) Search VaximmutorDB for influenza virus vaccines and gene names containing “IFN”. (B) Two genes results found and each gene is associated with two influenza vaccines. (C) The detailed vaccine information and how the gene was regulated in vaccinated hosts are provided in another VaximmutorDB page. (D) A click of the VO ID leads to an Ontobee page showing the information about this vaccine. For example, after clicking, the VO ID (VO_0000044) points to the Ontobee web page: http://purl.obolibrary.org/obo/VO_0000044.
3. BLAST analysis The VaximmutorDB BLAST analysis supports the BLAST sequence similarity analysis using a customized BLAST data library based on the data stored in the VaximmutorDB database.
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