[Bioperl-l] Fw: [Gene-announce] Announcing gene2xml to facilitate
conversion of Entrez Gene ASN.1 to XML and more...
sdavis2 at mail.nih.gov
Thu Mar 24 20:42:34 EST 2005
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
>> 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
>>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
>>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.
>> 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
>>for multiple platforms.
>>The documentation for this program is provided in this README file:
>> We would like to draw your attention to some of the functions of
>>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
>>Taxonomy identifier for that species or strain.
>> There is also an option (-x) to convert the binary ASN.1 Entrezgene set
>>the concatenated ASN.1 text we have been providing.
>> Our plan is to provide both formats for an indeterminate period, but
>>discontinue production of the files in the ASN directory, because that
>>can be (and is by us) be reproduced from the gene2xml tool.
>>Please be reminded that the Entrezgene specification is here:
>>and the DTD for Entrez Gene is here:
>>3. changes in Entrez Gene display
>> In the next few days, we will be adding limited context-specific help
>>subdivisions of the Entrez Gene graphic (default) display. This means
>>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
>>4. changes in content
>> In the next few days, we will be adding a new subsection to the
>>'Alleles'. This section reports the general characteristics of alleles
>>have been described for a gene, and provides links to more detailed
>>information. This function is being phased in gradually; the current set
>>for mouse and is being developed from information supplied by Mouse Genome
>>5. NCBI Handbook chapter 19
>>The LocusLink chapter of the NCBI handbook
>>has now been replaced with a chapter describing Entrez Gene.
>>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:
>>Gene-announce mailing list
>>Gene-announce at ncbi.nlm.nih.gov
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