GENE2XML CONVERTER PROGRAM

gene2xml is a stand-alone program that converts Entrez Gene ASN.1 into XML.
It is available for several computer platforms (Alpha, Linux, Macintosh,
Solaris, and Windows) and is distributed in the asn1-converters area of the
NCBI public ftp site. From asn1-converters, navigate into by_program and
then gene2xml, and download and extract the appropriate file.

The following versions of gene2xml have been made available:

  Version 1.5  March 23, 2015

    Added RNA-ref field to Gene-commentary

  Version 1.4  September 16, 2013

    Removed Gene-track.status value 'newentry'

  Version 1.3  March 1, 2010

    Report write failures

  Version 1.2  February 1, 2010

    Adds new choices with these values:
      ncRNA (8)
      tmRNA (9)
      miscRNA (10)
    Adds elements RNA-gen, RNA-qual, RNA-qual-set

Entrez Gene data are stored as compressed binary Entrezgene-Set ASN.1 files
on the NCBI ftp site, and have the suffix .ags.gz. These are several-fold
smaller than compressed XML files, resulting in a significant savings of
disk storage and network bandwidth. Normal processing by gene2xml produces
text XML files with the same name but with .xgs as the suffix.

The command-line arguments to gene2xml are described below.

  -   Version and Argument Display

Displays the version of the gene2xml program and its arguments and their
descriptions.

  -p  Path to Files [String]  Optional

Use -p if you want to process a entire directory of files. In this case,
gene2xml ignores the -i and -o arguments. Otherwise it takes -a as the
single input file, regardless of suffix.

  -r  Path for Results [String]  Optional

If -p is given but no -r results path is provided, results are written in
the same directory as the input file. The -p argument recursively explores
any subdirectories, so there can be multiple places where output is written.

  -i  Single Input File [File In]  Optional
    default = stdin

  -o  Single Output File [File Out]  Optional
    default = stdout

If -p is not given, -i is used for the input file, and -o is used for the
output file. Suffix conventions are ignored in this case.

  -b  File is Binary [T/F]  Optional
    default = F

  -c  File is Compressed [T/F]  Optional
    default = F

On UNIX platforms you can decompress .ags.gz files on-the-fly by using both
-b and -c. On the PC you will need to manually decompress into .ags files
and then only use the -b flag.

  -t  Taxon ID to Filter [Integer]  Optional
    default = 0

If you want to extract only records for a particular organism, pass the
NCBI taxon database number with the -t argument.  For example

  gene2xml -i All_Mammalia.ags.gz -b -c -t 9685 -o cats.xgs

will only send gene records for cats (taxonomy ID 9685) to the file
cats.xgs.

  -l  Log Processing [T/F]  Optional
    default = F

When you are processing an entire directory of files, passing -l on the
command-line causes gene2xml to print the current file name as it
progresses through the directory.

The following arguments, -x, -y, and -z, are normally not used, and
gene2xml will default to writing Entrezgene-Set XML, which is the normal
situation.

  -x  Extract .ags -> text .agc [T/F]  Optional
    default = F

To accommodate existing programs, the -x argument will convert .ags files
to the catenated Entrezgene text ASN.1 files that were previously
distributed.

  -y  Combine .agc -> text .ags (for testing) [T/F]  Optional
    default = F

  -z  Combine .agc -> binary .ags, then gzip [T/F]  Optional
    default = F

NCBI uses gene2xml with the -y or -z arguments to process internal data
into the compressed binary Entrezgene-Set ASN.1 files that are placed on
the NCBI ftp site. It is not expected that anyone outside of NCBI would use
these arguments.

A sample record that illustrates the structure of Entrezgene-Set XML is
shown below. Ellipses (...) are used where blocks of text have been removed
for brevity in this documentation.

<?xml version="1.0"?>
<!DOCTYPE Entrezgene-Set PUBLIC "-//NCBI//NCBI Entrezgene/EN"
"http://www.ncbi.nlm.nih.gov/dtd/NCBI_Entrezgene.dtd">
<Entrezgene-Set>
  <Entrezgene>
    <Entrezgene_track-info>
      <Gene-track>
        <Gene-track_geneid>2652</Gene-track_geneid>
        <Gene-track_status value="live">0</Gene-track_status>
        <Gene-track_create-date>
          <Date>
            <Date_std>
              <Date-std>
                <Date-std_year>2003</Date-std_year>
                <Date-std_month>8</Date-std_month>
                <Date-std_day>28</Date-std_day>
                <Date-std_hour>20</Date-std_hour>
                <Date-std_minute>30</Date-std_minute>
                <Date-std_second>0</Date-std_second>
              </Date-std>
            </Date_std>
          </Date>
        </Gene-track_create-date>
        <Gene-track_update-date>
          <Date>
            <Date_std>
              <Date-std>
                <Date-std_year>2005</Date-std_year>
                <Date-std_month>4</Date-std_month>
                <Date-std_day>27</Date-std_day>
                <Date-std_hour>21</Date-std_hour>
                <Date-std_minute>45</Date-std_minute>
                <Date-std_second>0</Date-std_second>
              </Date-std>
            </Date_std>
          </Date>
        </Gene-track_update-date>
      </Gene-track>
    </Entrezgene_track-info>
    <Entrezgene_type value="protein-coding">6</Entrezgene_type>
    <Entrezgene_source>
      <BioSource>
        <BioSource_genome value="genomic">1</BioSource_genome>
        <BioSource_origin value="natural">1</BioSource_origin>
        <BioSource_org>
          <Org-ref>
            <Org-ref_taxname>Homo sapiens</Org-ref_taxname>
            <Org-ref_common>human</Org-ref_common>
            <Org-ref_db>
              <Dbtag>
                <Dbtag_db>taxon</Dbtag_db>
                <Dbtag_tag>
                  <Object-id>
                    <Object-id_id>9606</Object-id_id>
                  </Object-id>
                </Dbtag_tag>
              </Dbtag>
            </Org-ref_db>
            <Org-ref_syn>
              <Org-ref_syn_E>man</Org-ref_syn_E>
            </Org-ref_syn>
            <Org-ref_orgname>
              <OrgName>
                <OrgName_name>
                  <OrgName_name_binomial>
                    <BinomialOrgName>
                      <BinomialOrgName_genus>Homo</BinomialOrgName_genus>
                      <BinomialOrgName_species>sapiens
</BinomialOrgName_species>
                    </BinomialOrgName>
                  </OrgName_name_binomial>
                </OrgName_name>
                <OrgName_lineage>Eukaryota; Metazoa; Chordata; Craniata;
Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates;
Catarrhini; Hominidae; Homo</OrgName_lineage>
                <OrgName_gcode>1</OrgName_gcode>
                <OrgName_mgcode>2</OrgName_mgcode>
                <OrgName_div>PRI</OrgName_div>
              </OrgName>
            </Org-ref_orgname>
          </Org-ref>
        </BioSource_org>
        <BioSource_subtype>
          <SubSource>
            <SubSource_subtype value="chromosome">1</SubSource_subtype>
            <SubSource_name>X</SubSource_name>
          </SubSource>
        </BioSource_subtype>
      </BioSource>
    </Entrezgene_source>
    <Entrezgene_gene>
      <Gene-ref>
        <Gene-ref_locus>OPN1MW</Gene-ref_locus>
        <Gene-ref_desc>opsin 1 (cone pigments), medium-wave-sensitive (color
blindness, deutan)</Gene-ref_desc>
        <Gene-ref_maploc>Xq28</Gene-ref_maploc>
        <Gene-ref_db>
          <Dbtag>
            <Dbtag_db>MIM</Dbtag_db>
            <Dbtag_tag>
              <Object-id>
                <Object-id_id>303800</Object-id_id>
              </Object-id>
            </Dbtag_tag>
          </Dbtag>
        </Gene-ref_db>
        <Gene-ref_syn>
          <Gene-ref_syn_E>CBD</Gene-ref_syn_E>
          <Gene-ref_syn_E>DCB</Gene-ref_syn_E>
          <Gene-ref_syn_E>GCP</Gene-ref_syn_E>
          <Gene-ref_syn_E>CBBM</Gene-ref_syn_E>
        </Gene-ref_syn>
        <Gene-ref_locus-tag>HGNC:4206</Gene-ref_locus-tag>
      </Gene-ref>
    </Entrezgene_gene>
    <Entrezgene_prot>
      <Prot-ref>
        <Prot-ref_name>
          <Prot-ref_name_E>opsin 1 (cone pigments), medium-wave-sensitive
(color blindness, deutan)</Prot-ref_name_E>
          <Prot-ref_name_E>green cone pigment</Prot-ref_name_E>
        </Prot-ref_name>
      </Prot-ref>
    </Entrezgene_prot>
    <Entrezgene_location>
      <Maps>
        <Maps_display-str>Xq28</Maps_display-str>
        <Maps_method>
          <Maps_method_map-type value="cyto"/>
        </Maps_method>
      </Maps>
    </Entrezgene_location>
    <Entrezgene_gene-source>
      <Gene-source>
        <Gene-source_src>LocusLink</Gene-source_src>
        <Gene-source_src-int>2652</Gene-source_src-int>
        <Gene-source_src-str2>2652</Gene-source_src-str2>
      </Gene-source>
    </Entrezgene_gene-source>
    <Entrezgene_locus>
      <Gene-commentary>
        <Gene-commentary_type value="genomic">1</Gene-commentary_type>
        <Gene-commentary_heading>Reference</Gene-commentary_heading>
        <Gene-commentary_accession>NC_000023</Gene-commentary_accession>
        <Gene-commentary_version>8</Gene-commentary_version>
        <Gene-commentary_seqs>
          <Seq-loc>
            <Seq-loc_int>
              <Seq-interval>
                <Seq-interval_from>152969013</Seq-interval_from>
                <Seq-interval_to>152982377</Seq-interval_to>
                <Seq-interval_strand>
                  <Na-strand value="plus"/>
                </Seq-interval_strand>
                <Seq-interval_id>
                  <Seq-id>
                    <Seq-id_gi>51511752</Seq-id_gi>
                  </Seq-id>
                </Seq-interval_id>
              </Seq-interval>
            </Seq-loc_int>
          </Seq-loc>
        </Gene-commentary_seqs>
        <Gene-commentary_products>
          <Gene-commentary>
            <Gene-commentary_type value="mRNA">3</Gene-commentary_type>
            <Gene-commentary_heading>Reference</Gene-commentary_heading>
            <Gene-commentary_accession>NM_000513</Gene-commentary_accession>
            <Gene-commentary_version>1</Gene-commentary_version>
            <Gene-commentary_genomic-coords>
              <Seq-loc>
                <Seq-loc_mix>
                  <Seq-loc-mix>
                    <Seq-loc>
                      <Seq-loc_int>
                        <Seq-interval>
                          <Seq-interval_from>152969013</Seq-interval_from>
                          <Seq-interval_to>152969124</Seq-interval_to>
                          <Seq-interval_strand>
                            <Na-strand value="plus"/>
                          </Seq-interval_strand>
                          <Seq-interval_id>
                            <Seq-id>
                              <Seq-id_gi>51511752</Seq-id_gi>
                            </Seq-id>
                          </Seq-interval_id>
                        </Seq-interval>
                      </Seq-loc_int>
                    </Seq-loc>
                    ...
                  </Seq-loc-mix>
                </Seq-loc_mix>
              </Seq-loc>
            </Gene-commentary_genomic-coords>
            <Gene-commentary_seqs>
              <Seq-loc>
                <Seq-loc_whole>
                  <Seq-id>
                    <Seq-id_gi>4503964</Seq-id_gi>
                  </Seq-id>
                </Seq-loc_whole>
              </Seq-loc>
            </Gene-commentary_seqs>
            <Gene-commentary_products>
              <Gene-commentary>
                <Gene-commentary_type value="peptide">8</Gene-commentary_type>
                <Gene-commentary_heading>Reference</Gene-commentary_heading>
                <Gene-commentary_accession>NP_000504
</Gene-commentary_accession>
                <Gene-commentary_version>1</Gene-commentary_version>
                <Gene-commentary_genomic-coords>
                  <Seq-loc>
                    <Seq-loc_packed-int>
                      <Packed-seqint>
                        <Seq-interval>
                          <Seq-interval_from>152969013</Seq-interval_from>
                          <Seq-interval_to>152969124</Seq-interval_to>
                          <Seq-interval_strand>
                            <Na-strand value="plus"/>
                          </Seq-interval_strand>
                          <Seq-interval_id>
                            <Seq-id>
                              <Seq-id_gi>51511752</Seq-id_gi>
                            </Seq-id>
                          </Seq-interval_id>
                        </Seq-interval>
                        ...
                      </Packed-seqint>
                    </Seq-loc_packed-int>
                  </Seq-loc>
                </Gene-commentary_genomic-coords>
                <Gene-commentary_seqs>
                  <Seq-loc>
                    <Seq-loc_whole>
                      <Seq-id>
                        <Seq-id_gi>4503965</Seq-id_gi>
                      </Seq-id>
                    </Seq-loc_whole>
                  </Seq-loc>
                </Gene-commentary_seqs>
              </Gene-commentary>
            </Gene-commentary_products>
          </Gene-commentary>
        </Gene-commentary_products>
      </Gene-commentary>
      ...
    </Entrezgene_locus>
    <Entrezgene_properties>
      <Gene-commentary>
        <Gene-commentary_type value="comment">254</Gene-commentary_type>
        <Gene-commentary_label>Nomenclature</Gene-commentary_label>
        <Gene-commentary_source>
          <Other-source>
            <Other-source_anchor>HUGO Gene Nomenclature Committee
</Other-source_anchor>
          </Other-source>
        </Gene-commentary_source>
        <Gene-commentary_properties>
          <Gene-commentary>
            <Gene-commentary_type value="property">16</Gene-commentary_type>
            <Gene-commentary_label>Official Symbol</Gene-commentary_label>
            <Gene-commentary_text>OPN1MW</Gene-commentary_text>
          </Gene-commentary>
          <Gene-commentary>
            <Gene-commentary_type value="property">16</Gene-commentary_type>
            <Gene-commentary_label>Official Full Name</Gene-commentary_label>
            <Gene-commentary_text>opsin 1 (cone pigments),
medium-wave-sensitive (color blindness, deutan)</Gene-commentary_text>
          </Gene-commentary>
        </Gene-commentary_properties>
      </Gene-commentary>
      ...
    </Entrezgene_properties>
    <Entrezgene_comments>
      <Gene-commentary>
        <Gene-commentary_type value="comment">254</Gene-commentary_type>
        <Gene-commentary_heading>LocusTagLink</Gene-commentary_heading>
        <Gene-commentary_source>
          <Other-source>
            <Other-source_src>
              <Dbtag>
                <Dbtag_db>HGNC</Dbtag_db>
                <Dbtag_tag>
                  <Object-id>
                    <Object-id_id>4206</Object-id_id>
                  </Object-id>
                </Dbtag_tag>
              </Dbtag>
            </Other-source_src>
          </Other-source>
        </Gene-commentary_source>
      </Gene-commentary>
      ...
    </Entrezgene_comments>
    <Entrezgene_unique-keys>
      <Dbtag>
        <Dbtag_db>LocusID</Dbtag_db>
        <Dbtag_tag>
          <Object-id>
            <Object-id_id>2652</Object-id_id>
          </Object-id>
        </Dbtag_tag>
      </Dbtag>
      <Dbtag>
        <Dbtag_db>MIM</Dbtag_db>
        <Dbtag_tag>
          <Object-id>
            <Object-id_id>303800</Object-id_id>
          </Object-id>
        </Dbtag_tag>
      </Dbtag>
    </Entrezgene_unique-keys>
    <Entrezgene_xtra-index-terms>
      <Entrezgene_xtra-index-terms_E>LOC2652</Entrezgene_xtra-index-terms_E>
    </Entrezgene_xtra-index-terms>
    <Entrezgene_xtra-properties>
      <Xtra-Terms>
        <Xtra-Terms_tag>PROP</Xtra-Terms_tag>
        <Xtra-Terms_value>phenotype</Xtra-Terms_value>
      </Xtra-Terms>
    </Entrezgene_xtra-properties>
  </Entrezgene>
</Entrezgene-Set>

