[Bioperl-l] Fw: [Gene-announce] Announcing gene2xml to facilitate conversion of Entrez Gene ASN.1 to XML and more...

[Sean Davis]

Forwarded from a colleague:

----- Original Message ----- 
Sent: Thursday, March 24, 2005 6:33 PM
Subject: Fwd: [Gene-announce] Announcing gene2xml to facilitate conversion 
of Entrez Gene ASN.1 to XML and more...


>>Sender: gene-announce-bounces at ncbi.nlm.nih.gov
>>
>>Contents:
>>   1. new directory on the ftp site
>>   2. release of gene2xml to convert the files in the new directory to XML
>>   3. modifications in Entrez Gene displays
>>   4. modifications in Entrez Gene content
>>   5. Gene chapter in the NCBI handbook
>>
>>1. the new ASN_BINARY subdirectory
>>
>>   We would like to announce that Entrez Gene has added a new subdirectory 
>> to
>>its ftp site, namely /DATA/ASN_BINARY. The subdirectories and files in
>>ASN_BINARY have the same scope as the files in the /DATA/ASN subdirectory,
>>namely comprensive extractions of Entrez Gene records.  The difference in
>>the
>>directories is that the format of files in ASN_BINARY is binary, and the
>>organization of the records is as an Entrezgene set.  The files in the ASN
>>directory are ASN.1 text and the records are concatenated.
>>
>>
>>2. gene2xml
>>
>>   The ASN_BINARY format is being introduced in conjunction with the tool
>>gene2xml, which readily converts the binary ASN.1 to XML.
>>The tool is available from
>>
>>        ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/cmdline/
>>
>>for multiple platforms.
>>
>>   gene2xml.Darwin-7.8.0-Power_Macintosh.gz
>>   gene2xml.Linux-2.4.23-P3-4G-i686.gz
>>   gene2xml.OSF1-V5.1-alpha.gz
>>   gene2xml.SunOS-5.8-sun4u.gz
>>   gene2xml.win32.exe.gz
>>
>>
>>The documentation for this program is provided in this README file:
>>
>>        ftp://ftp.ncbi.nlm.nih.gov/gene/tools/README.
>>
>>   We would like to draw your attention to some of the functions of 
>> gene2xml.
>>If you are interested in Gene records for only one species or strain, and
>>records for that species or strain have not already been provided in a
>>separate file, there is an option (-t) that extracts records based on the
>>NCBI
>>Taxonomy identifier for that species or strain.
>>
>>  There is also an option (-x) to convert the binary ASN.1 Entrezgene set
>>into
>>the concatenated ASN.1 text we have been providing.
>>
>>  Our plan is to provide both formats for an indeterminate period, but 
>> then
>>discontinue production of the files in the ASN directory, because that
>>format
>>can be (and is by us) be reproduced from the gene2xml tool.
>>
>>Please be reminded that the Entrezgene specification is here:
>>
>>http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entre
>>zgene/entrezgene.asn
>>
>>and the DTD for Entrez Gene is here:
>>
>>         http://www.ncbi.nlm.nih.gov/dtd/
>>
>>
>>3. changes in Entrez Gene display
>>
>>    In the next few days, we will be adding limited context-specific help 
>> to
>>subdivisions of the Entrez Gene graphic (default) display.  This means 
>>that
>>question marks (?) will occur at the far right of the blue bar. These will
>>anchor links to the appropriate subsection of the Entrez Gene help 
>>document.
>>
>>4. changes in content
>>
>>    In the next few days, we will be adding a new subsection to the 
>> record,
>>'Alleles'. This section reports the general characteristics of alleles 
>>that
>>have been described for a gene, and provides links to more detailed
>>information. This function is being phased in gradually; the current set 
>>is
>>for mouse and is being developed from information supplied by Mouse Genome
>>Informatics.
>>
>>
>>5. NCBI Handbook chapter 19
>>
>>
>>The LocusLink chapter of the NCBI handbook
>>
>>http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=handbook
>>.TOC&depth=2
>>
>>has now been replaced with a chapter describing Entrez Gene.
>>
>>http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=handbook.chapter.ch19
>>
>>We hope this chapter helps answer your questions.  If not, you can email
>>your questions to info at ncbi.nlm.nih.gov or lodge your comments here:
>>
>>         http://www.ncbi.nlm.nih.gov/RefSeq/update.cgi
>>
>>_______________________________________________
>>Gene-announce mailing list
>>Gene-announce at ncbi.nlm.nih.gov
>>http://www.ncbi.nlm.nih.gov/mailman/listinfo/gene-announce
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