Who is NCBI?
What is ASN.1?
ASN.1 is a telecommunications standard used primarily by to exchange messages. Microsoft Internet Explorer and Outlook use ASN.1 to structure data. Nokia and Motorola use ASN.1 for wireless communications. The official ASN.1 standards site is at http://www.asn1.org
A free downloadable definitive book on the ASN.1 standard is available at http://www.oss.com/asn1/dubuisson.html
. "ASN.1 - Communication between heterogeneous systems" by Olivier Dubuisson translated by Philippe Fouquart justrequires user registration to download.
NCBI also lists a summary of ASN.1 references at http://www.ncbi.nlm.nih.gov/Sitemap/Summary/asn1.html
The National Center for Biotechnology Informaton (NCBI) (http://www.ncbi.nlm.nih.gov
) was established in 1988 as a division of the National Library of Medicine (NLM) at the National Institutes of Health (NIH) as a resource for molecular biology information. NCBI serves as a repository for molecular data in the United States of America.
What do ASN.1 and NCBI have in common?
The Information Engineering Branch (IEB) at NCBI is responsible for designing and building NCBI's software and databases. IEB uses ASN.1 to structure the molecular data housed in the NCBI data repository. The ASN.1 data model's inherent infinite extendibility has proven to be a good choice for the NCBI data model.
How Can I View the NCBI ASN.1 Data?
The IEB maintains a software suite call the NCBI ToolBox. The ToolBox is a programming library written in the C and C++ programming languages that provides the software tools required for decoding the NCBI ASN.1 data model. The ToolBox also contains the source code for NCBI sequence analysis tools such as BLAST, and sequence submission tools such as Sequin. The ToolBox provides the asntool that converts the ASN.1 data model into C/C++ header files (*.h) and C/C++ object wrappers. Another tool, asn2xml, converts data stored in ASN.1 files into eXtensible Markup Language (XML).
What is LARTS?
LARTS stands for LifeFomulae ASN.1 Reader Toolset. It is an ASN.1 to XML parser written in Java. LARTS converts NCBI ASN.1 binary or ASCII files into XML. LARTS can also produce GenBank output and FASTA-formatted sequence files from ASN.1 input.
We provide a "roadmap" to the NCBI ASN.1 data model as a download. (Link to ASN.1 roadmap). We also provide a "click-able" NCBI ASN.1 cross reference HTML file that enables the user to navigate the NCBI ASN.1 data model the "Uses" and "Used By" links.
The World Wide Web Consortium (W3C) has a comprehensive XML tutorial at
Why Use LARTS?
The XML produced by the NCBI ToolBox is not always well-formed. This means that NCBI XMLis does not always conform to the W3C XML 1.0 standard.
The main purpose of XML is to allow information systems to share data across the internet by encoding data as XML elements according to a user-defined schema or Document Type Definition (DTD). LARTS uses XML Schema to define encoded data. NCBI uses the older DTD format which uses a custom non-XML syntax that is limited in its ability to express some aspects of the XML documents. With the NCBI DTD scenario, data field default values are not displayed, and all NCBI ASN.1 data elements must have a unique DTD defined for that element. This means a large number *.dtd files. Any change in the NCBI ASN.1 data definition means these files must be updated.
With LARTS, you never have to worry about changes to the NCBI ASN.1 data model, as we handle it all for you.
How Do I Use LARTS?
LARTS is a "Software As Service" application. This means the LARTS application is presented as a service over the internet and is accessed by means of a web browser such as FireFox, Internet Explorer, Opera, and Safari. The web browser is the only local application required.
Even in binary format, an average NCBI ASN.1 data file size is around 50 Mb and there are hundreds of files. There are no local disk storage requirements, other that the data you personally select through the LARTS interface.
LARTS allows keyword, element path, and keyword with an associated element path searches.
What Keywords Can I Search With in LARTS?
A keyword is composed of numbers and letters, but no punctuation characters are allowed.
How Do I Determine an XML Element Path?
For an XML element path search, as asterisk followed by the last 4 element path components is sufficient to produce a viable search. For example, */Author/names/name/last is a common element path search.
To output a complete list of NCBI XML element paths, use the Unique XML elements paths without text format as the Output formats selection on the Output page.
To find the values associated with XML element paths, select the XML element paths with text Output format option.
How Do I Combine a Keyword with an Element Path for a Search?
To combine a keyword with an XML element path, use the following format:
‘keyword:element path’. For example: Smith:*/Author/names/name/last.
How Do I Obtain An Archive of My Searches and Resulting Output?
From User Profile page, click the "Transactions" tab to get a list of searches and search results which can be sorted by field name. The sorted list is then available for output in Excel, Word, and other formats.
How can I get a history longer than the default 3 month retention?
From User Profile page, click the "Transactions" tab to get a list of searches and search results which can be sorted by field name. The sorted list is then available for output in Excel, Word, and other formats. If you need to retain a history longer that the 3 month retention on the website, you should export your transaction history into one of the available formats and retain it in your own system for historical purposes.