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blue bulletWhat is the NCBI ToolBox?

The NCBI ToolBox consists of three major parts:

  • Data Model - An explicit data model of biological sequences, structures, bibliographic data, and associated annotations.
  • Data Encoding - A formal specification and encoding rules. The telecommunications standard, ASN.1, has been used for this. Recently it has been mapped to a similar language, XML.
  • Programming Libraries - Originally written in a portable dialect of C. Recently a new generation is being written in C++.
The ToolBox model and code is used extensively within NCBI for the internal pipelines and tools such as GenBank, Entrez, BLAST, Sequin, OMIM, RefSeq, and others. We make the same tools available to the public domain for whatever purposes the community may desire. These tools are supported in the sense that they are designed to work in many environments outside NCBI, and as such we feel we can fix any bugs or answer questions about using them. Unfortunately they are not supported in the sense of a turnkey system with extensive documentation. However, there are applications set up in the distribution with standard makefiles, such as Sequin, BLAST, a program to convert ASN.1 data to XML, and others. But this distribution is primarily for serious programmers.

NCBI Data in XML
NCBI software tools can now automatically produce data as either ASN.1, as before, or as XML. This provides developers access to the full internal NCBI data set using a variety of OpenSource tools. In addition, a number of new specifications are being developed to present simpler views of the data in XML, specifically for use by applications developers outside NCBI. Entrez can display and download data in XML, and a standalone tool, asn2xml, can convert ASN.1 daily update files into XML on your site. More..

blue bulletContacting Us

Information is made available on this page to ToolBox programmers. In addition, you may ask questions by email to .

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Revised April 9, 2001

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