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NCBI ToolBox
Supported software tools from IEB
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ToolBox FTP site
download data and software
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 What is the NCBI ToolBox? |
Internally NCBI stores data in a variety of ways most appropriate to the flow of the data
and its semantics. These may include normalized relational databases (eg. for ESTs), ASN.1
(eg. for other types of sequences), or XML (eg. for journal articles). NCBI also distributes
the same data in a number of formats such as GenBank, FASTA, ASN.1, and XML, no matter how
they are natively stored.
For a particular nucleotide sequence of the human beta globin locus, options are:
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GenBank format
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FASTA format
- ASN.1 format
- Data Encoding - A formal specification and encoding rules. The
telecommunications standard, ASN.1, has been used for this.
This has also been mapped to XML.
- Programming Libraries - Originally written in a portable dialect of
C. This has also been 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 open source tools. In addition, a number of specifications
have been 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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Revised May 8, 2003
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DataModel and C Toolkit Docs