DATATOOL - NCBI data conversion tool

Program Description

DATATOOL is a utility program designed to convert ASN.1 specifications into XML DTD and vice versa, and to convert data between ASN.1 and XML formats. DATATOOL makes it possible to convert ASN.1 specification into XML DTD or schema, DTD into ASN.1 (with limitations), and DTD into XML schema. Also, once the specification is known, DATATOOL can convert data from ASN.1 to XML, or from XML to ASN.1 format.

DATATOOL is a part of NCBI C++ toolkit that can be freely downloaded from:
ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/CURRENT/
For more information please refer to:
http://ncbi.github.io/cxx-toolkit/pages/ch_app

Prebuilt DATATOOL for some platforms can be found at:
ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/BIN/CURRENT/datatool/

Basic instructions

DATATOOL can be used to formally convert any ASN.1 or XML data or data specification. For the list of command line arguments please refer to
http://ncbi.github.io/cxx-toolkit/pages/ch_app

Important Note

As DATATOOL performs only formal data conversion so it cannot be used to perform any additional processing on the converted data. If you need an additional data processing you can either:

Write your own code using DATATOOL and NCBI serialization library (or any other XML or ASN.1 framework), or
For bio-sequence data in XML, ASN.1 and other formats use one of specialized tools such as the NCBI ones described at https://www.ncbi.nlm.nih.gov/Web/Newsltr/V14N1/toolkit.html

Example

Converting GenBank ASN.1 data file to XML:

Obtain GenBank ASN.1 data file at: ftp://ftp.ncbi.nlm.nih.gov/ncbi-asn1/. Here daily-nc directory contains individual files for each day's new or updated entries since close-of-data for the last GenBank Release in ASN.1 format.
Additional documentation:
/ncbi-asn1/README.asn1
/ncbi-asn1/daily-nc/README.asn1.daily-nc
Download the appropriate datatool binary for your platform:
ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/BIN/CURRENT/datatool/
Download NCBI data specification file:
https://ncbi.nlm.nih.gov/data_specs/asn/NCBI_all.asn
Run the program:
```
./datatool -m NCBI_all.asn -d gbest225.aso -t Bioseq-set -px gbest225.xml
```
Here:

gbest225.aso

is the name of the source GenBank data file in ASN binary format

Bioseq-set

is the name of the data type in the source file

gbest225.xml

is the name of the output file in XML format

PLEASE NOTE:

The uncompressed XML file is about 10 times the size of the compressed binary ASN.1 file, so it can be extremely big.
The ASN.1 usually contains more than the GenBank files; it includes other databases like PDB and RefSeq, gaps of HTG records, and shows the quality scores of HTG records. For further information, read: ftp://ftp.ncbi.nlm.nih.gov/ncbi-asn1/README.asn1

Please email questions at: [email protected]

Last updated: Mar 30, 2006