What is "refdb"

RefDB is a client/server reference database and bibliography tool for markup languages like SGML, XML, and LaTeX. It is suitable for standalone use for the purpose of self-archiving, but can be used as an institutional repository as well. Data storage proper is done in one of several supported SQL database engines. RefDB runs on Unix-like operating systems ( Linux, FreeBSD, NetBSD, Mac OS X, Solaris) and on Windows/ Cygwin. RefDB is licensed under the GPL.

The data storage is managed by an application server accessed through command-line clients with a query language, a PHP-based web interface, a SRU interface, or by custom programs using one of the available client libraries.

RefDB supports such bibliographic formats as BibTeX, Endnote, RIS, ISI, MODS XML, PubMed, Medline, MARC, and Copac and can create output in these formats, or as TEI, DocBook, HTML, or XHTML documents. RefDB can process DocBook, TEI, or LaTeX documents and automatically insert and format bibliographies according to the specifications of a journal or a publisher.

Text editor extensions are provided for Emacs and for Vim to integrate editing, searching, and citing references as well as transforming your documents into your familiar XML, SGML, or LaTeX authoring environment.

The Re-referenced Protein Chemical shift Database (RefDB) is a NMR spectroscopy database of carefully corrected or re-referenced chemical shifts, derived from the BioMagResBank (BMRB) (Fig. 1). The database was assembled by using a structure-based chemical shift calculation program (called SHIFTX) to calculate expected protein (1)H, (13)C and (15)N chemical shifts from X-ray or NMR coordinate data of previously assigned proteins reported in the BMRB. The comparison is automatically performed by a program called SHIFTCOR. The RefDB database currently provides reference-corrected chemical shift data on more than 2000 assigned peptides and proteins. Data from the database indicates that nearly 25% of BMRB entries with (13)C protein assignments and 27% of BMRB entries with (15)N protein assignments require significant chemical shift reference readjustments. Additionally, nearly 40% of protein entries deposited in the BioMagResBank appear to have at least one assignment error. Users may download, search or browse the database through a number of methods available through the RefDB website. RefDB provides a standard chemical shift resource for biomolecular NMR spectroscopists, wishing to derive or compute chemical shift trends in peptides and proteins.

RefDB may refer to:

• RefDB, a client/server reference database and bibliography tool for markup languages like SGML, XML, and LaTeX.
• RefDB (chemistry), the Re-referenced Protein Chemical shift Database.