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NCBI ToolBox
Supported software tools from IEB
Research within IEB
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ToolBox FTP site
download data and software
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 What 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.. |
| Contacting Us |
Information is made available on this page to ToolBox programmers. In addition, you
may ask questions by email to [email protected]
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Disclaimer
Privacy statement
Revised April 9, 2001
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What is the NCBI ToolBox?
DataModel and C Toolkit Docs