BRC Central

Overview

The BRC Internal Documentation area is a collection of information providing access to a number of resources used and needed by the BRCs. Please click on the links in the left menu to navigate to an area of interest.

FTP Site

ftp://ftp.brc-central.org

There are two important locations on the BRC Central FTP site. One is the location of the GFF3 files, the other is the location of the Genome Sources XML files.

The GFF3 files are located underneath the individual BRC acronym. You can then click further in to the organism directories to get to the associated GFF3 file.

The XML files are located underneath the "xml" directory and separated by each BRC. Click into the BRC and the XML files will be sorted by organism.

Usage Conventions

The GFF3 format for the BRCs contains differences from the "standard" GFF3 format. You can see the BRC usage of GFF3 here.

Dbxref Submissions

The Dbxref Listings Page allows users to view the list of BRC approved Dbxref accessions they are permitted to use when referencing external databases in GFF3 files. In addition to viewing the current list, the page allows users to submit new Dbxref databases and accessions for approval by the Dbxref Approval Committee.

The committee is responsible for reviewing the Dbxref for completeness, suggesting modifications, and submitting the new database to GO so they can add it to their official list.

Dbxref Request Form

New Database Name
A short name of the database you plan on submitting.
Database Abbreviation
A compact neumonic for the database that will be used to identify it when used as a GFF3 column nine tag, e.g.: "Dbxref=RefSeq:NC_004310".
Example Dbxref
A bonafied identifier exemplar, suitable for testing purposes. In the GO list, example IDs are preceeded with the database abbreviation and a colon. To reduce confusion, I recommend we either discontinue this practice or rigorously enforce the : syntax.
Generic URL
A URL for a webpage providing descriptive information for the database, its content and source(s).
URL Syntax
A basic URL to which an identifier can be added to form a URL that returns the object of interest. Typically, the identifier is simply appended to url_syntax string to generate a valid URL. When this is not possible, the token ##id## can be used in the url_syntax string and its value substituted at run time.
URL Example
In the typical case, the URL example should consist of the concatenation of the url_syntax and example_id strings. In cases of unusual url_syntax, the url_example should simply be a valid URL generated as described.
Description
A concise description of the referenced database including any specifics implied by the URL or identifier syntax.
Contact Person
The full name of the person requesting the new Dbxref
Contact Email
The email address of the Contact Person
Requesting BRC
The BRC the Contact Person is representing

BRC URLs

<urls>
<service name='genome_page'>
   <urlBase>http://www.apidb.org/cgi-bin/redirect.cgi</urlBase>
   <parameter name='taxon'>
     <key>taxon_id</key>
   </parameter>
</service>
<service name='gene_page'>
<urlBase>http://www.apidb.org/cgi-bin/redirect.cgi</urlBase>
   <parameter name='Name'>
     <key>source_id</key>
   </parameter>
   <parameter name='taxon'>
     <key>taxon_id</key>
   </parameter>
</service>
<service name='brc_page'>
    <urlBase>http://apidb.org</urlBase>
</service>
</urls>

<urls>
<service name="genome_page">
    <urlBase>http://www.biohealthbase.org/GSearch/statsAutomation.do</urlBase>
    <parameter name="organism_name">
      <key>decorator</key>
    </parameter>
</service>

<service name="gene_page">
    <urlBase>http://www.biohealthbase.org/GSearch/statsAutomation.do</urlBase>
    <parameter name="organism_name">
      <key>decorator</key>
    </parameter>
</service>

<service name="brc_page">
    <urlBase>http://www.biohealthbase.org</urlBase>
</service>
</urls>

<urls>
<service name='genome_page'>
  <urlBase>http://www.ericbrc.org/portal/eric/enteropathogens?id=enteropathogens</urlBase>
</service>
<service name='gene_page'>
  <urlBase>http://www.ericbrc.org/asap/feature_info.php</urlBase>
  <parameter name='web_id'>
    <key>FeatureID</key>
  </parameter>
</service>
<service name='brc_page'>
    <urlBase>http://www.ericbrc.org/</urlBase>
</service>
</urls>

<urls>
<service name='genome_page'>
    <urlBase>http://www.nmpdr.org</urlBase>
</service>
<service name='gene_page'>
    <urlBase>http://www.nmpdr.org/linkin.cgi</urlBase>
    <parameter name='web_id'>
      <key>id</key>
    </parameter>
</service>
<service name='brc_page'>
    <urlBase>http://www.nmpdr.org</urlBase>
</service>
</urls>

<urls>
<service name='genome_page'>
    <urlBase>http://patric.vbi.vt.edu/genome/overview.php</urlBase>
    <parameter name='ID'>
      <key>seqId</key>
    </parameter>
</service>
<service name='gene_page'>
    <urlBase>http://patric.vbi.vt.edu/gene/overview.php</urlBase>
    <parameter name='web_id'>
      <key>fid</key>
    </parameter>
</service> 
<service name='brc_page'>
    <urlBase>http://patric.vbi.vt.edu</urlBase>
</service>
</urls>

<urls>
<service name='genome_page'>
    <urlBase>http://pathema.jcvi.org/tigr-scripts/Burkholderia/GenomePage.cgi?</urlBase>
    <parameter name='taxon'>
      <key>taxon_id</key>
    </parameter>
</service>
<service name='gene_page'>
    <urlBase>http://pathema.jcvi.org/tigr-scripts/Burkholderia/shared/GenePage.cgi</urlBase>
    <parameter name='locus'>
      <key>locus</key>
    </parameter>
</service>
<service name='sop_gene'>
    <urlBase>http://pathema.jcvi.org/pathema/TigrAnnotationSops.shtml</urlBase>
</service>
<service name='brc_page'>
    <urlBase>http://pathema.jcvi.org</urlBase>
</service>
</urls>

<urls>
<service name='genome_page'>
   <urlBase>http://www.vbrc.org/query.asp</urlBase>
   <parameter name='ID'>
     <key>web_id</key>
   </parameter>
</service>

<service name='gene_page'>
   <urlBase>http://www.vbrc.org/query.asp</urlBase>
   <parameter name='web_id'>
     <key>web_id</key>
   </parameter>
</service>

<service name='brc_page'>
   <urlBase>http://www.vbrc.org</urlBase>
</service>

<service name='feature_page'>
   <urlBase>http://www.vbrc.org/query.asp</urlBase>
   <parameter name='web_id'>
     <key>web_id</key>
   </parameter>
</service>
</urls>

<urls>
<service name='genome_page'>
    <urlBase>http://www.vectorbase.org/Genome/BRCGenome</urlBase>
    <parameter name='taxon'>
      <key>taxon_id</key>
    </parameter>
</service>
<service name='gene_page'>
    <urlBase>http://www.vectorbase.org</urlBase>
</service>
<service name='brc_page'>
    <urlBase>http://www.vectorbase.org</urlBase>
</service>
</urls>

Software Pages XML Spec

<software>
  <description name="Software Name"></description>

  <description name="Institution"></description>

  <description name="Description"></description>

  <description name="Headline"></description>

  <description name="Developer"></description>

  <description name="Contact"></description>

  <description name="Web Site"></description>

  <description name="Open Source"></description>

  <description name="Download Site"></description>

  <description name="Current Version"></description>

  <description name="Current Version Release Date"></description>

  <description name="Relevant Publications"></description>

  <description name="Platforms"></description>

  <description name="Requirements"></description>

  <description name="Other Information"></description>

  <description name="Keywords"></description>

  <description name="Listing Last Updated"></description>

</software>

Genome Sources XML Spec Descriptions

1. brc - contains the BRC name and acronym

Parameters:

name - the full name of the BRC
acronym - the current acronym of the BRC

2. organism - information on the organism represented in the file

Parameters:

name - name of the organism (same as what is in the GFF3 file)
strain - strain of the organism (same as what is in the GFF3 file)
taxon_id - taxon id of the organism (same as what is in the GFF3 file)

3. gff3 - the GFF3 file and FTP location that corresponds to the organism

Parameters:

corresponding_gff3_file - the GFF3 file name
ftp_url - the direct FTP URL to the GFF3 file

4. submission - boolean for stating if BRC Central will submit the data to RefSeq

Parameters:

brc_central_submits_to_refseq - Yes/No

5. sequence_info - this is the main section of the XML file. It hold four main sections. The first is required and allows the BRC to place an internal sequence identifier onto the sequence. The second deals with GenBank accessions. The third allows for RefSeq accessions, and the last section describes whether the BRC has modified the sequence. The category allows for multiple sequences by enclosing these four subcategories into a "sequence" tag that can be repeated as many times as needed to describe each sequence.

internal Subcategory Parameters:

sequence_identifier - BRC internal sequence identifier (ID field in GFF3)

genbank Subcategory Parameters:

latest_accession - latest GenBank accession that exists for the sequence
latest_version - latest GenBank version for that accession
owner - owner of the sequence corresponding to the latest_accession

refseq Subcategory Parameters:

latest_accession - latest RefSeq accession that exists for the sequence
latest_version - latest RefSeq version for that accession

modified Subcategory Parameters:

sequence_changed - has the sequence been changed from the original
submitted_to_genbank - has the sequence been submitted to GenBank

6. curatorship - this category describes who is responsible for curation of a few features of the sequence

Parameters:

annotation - who is responsible for annotation of this genome
gene_ends - who is responsible for modifying gene structure
gene_families - who is responsible for adding gene families
changing_dna_sequence - is the BRC changing the DNA sequence for any reason
changing_gene_ends - is the BRC modifying gene boundaries

7. ownership - if the data is available and/or easily accessible, the BRCs should provide informatiion about sequence ownership in this category

Parameters:

current_genbank_control - who has full control over the genome in GenBank
original_source - what organization did the original sequence come from
original_sequence - who owns the original sequence now
original_annotation - who was responsible for the original annotation
downloaded_from - where was the sequence downloaded from
date_of_download - when was the sequence downloaded
owner_url - what is the URL of the owner of the original sequence

8. evidence - this category is used to describe any type of literature or experimental evidence that the BRCs will be attaching to the annotation

literature Subcategory Parameters:

providing_pmid - will the BRC be attaching PMIDs to their annotations

experimental Subcategory Parameters:

type - if any, describe the type of experiments that will be done and attached to annotations here. This parameter can be repeated if more than one exists.

Genome Sources Skeleton XML Spec

<source>
  <category name="brc">
    <parameter name="name">REQUIRED</parameter>
    <parameter name="acronym">REQUIRED</parameter>
  </category>

  <category name="organism">
    <parameter name="name">REQUIRED</parameter>
    <parameter name="strain"></parameter>
    <parameter name="taxon_id">REQUIRED</parameter>
  </category>

  <category name="gff3">
    <parameter name="corresponding_gff3_file">REQUIRED</parameter>
    <parameter name="ftp_url">REQUIRED</parameter>
  </category>

  <category name="submission">
    <parameter name="brc_central_submits_to_refseq">REQUIRED</parameter>
  </category>

  <category name="sequence_info">
    <sequence>
      <internal>
        <parameter name="sequence_identifier">REQUIRED</parameter>
      </internal>
      <genbank>
        <parameter name="latest_accession"></parameter>
        <parameter name="latest_version"></parameter>
        <parameter name="owner"></parameter>
      </genbank>
      <refseq>
        <parameter name="latest_accession"></parameter>
        <parameter name="latest_version"></parameter>
      </refseq>
      <modified>
        <parameter name="sequence_changed">REQUIRED</parameter> 
        <parameter name="submitted_to_genbank">REQUIRED</parameter> 
      </modified>
    </sequence>
  </category>

  <category name="curatorship">
    <parameter name="annotation">REQUIRED</parameter>
    <parameter name="gene_ends">REQUIRED</parameter>
    <parameter name="gene_families"></parameter>
    <parameter name="changing_dna_sequence">REQUIRED</parameter>
    <parameter name="changing_gene_ends">REQUIRED</parameter>
  </category>

  <category name="ownership">
    <parameter name="current_genbank_control">REQUIRED</parameter>
    <parameter name="original_source"></parameter>
    <parameter name="original_sequence"></parameter>
    <parameter name="original_annotation"></parameter>
    <parameter name="downloaded_from"></parameter>
    <parameter name="date_of_download"></parameter>
    <parameter name="owner_url"></parameter>
  </category>

  <category name="evidence">
    <literature>
      <parameter name="providing_pmid">REQUIRED</parameter>
    </literature>
    <experimental>
      <parameter name="type"></parameter>
    </experimental>
  </category>
</source>

Genome Sources Sample XML

<source>
  <category name="brc">
    <parameter name="name">Pathema</parameter>
    <parameter name="acronym">Pathema</parameter>
  </category>
  <category name="organism">
    <parameter name="name">Bacillus anthracis</parameter>
    <parameter name="strain">Ames Ancestor</parameter>
    <parameter name="taxon_id">261594</parameter>
  </category>
  <category name="gff3">
    <parameter name="corresponding_gff3_file">b_anthracis_ames_ancestor.gff3</parameter>
    <parameter name="ftp_url">ftp://ftp.brc-central.org/Pathema/bacillus_anthracis/b_anthracis_ames_ancestor.gff3</parameter>
  </category>
  <category name="submission">
    <parameter name="brc_central_submits_to_refseq">Yes</parameter>
  </category>
  <category name="sequence_info">
    <sequence>
      <internal>
        <parameter name="sequence_identifier">gb6.contig.2480</parameter>
      </internal>
      <genbank>
        <parameter name="latest_accession">AE017336</parameter>
        <parameter name="latest_version">2</parameter>
        <parameter name="owner">TIGR</parameter>
      </genbank>
      <refseq>
        <parameter name="latest_accession">NC_007322</parameter>
        <parameter name="latest_version">2</parameter>
      </refseq>
      <modified>
        <parameter name="sequence_changed">Yes</parameter>
        <parameter name="submitted_to_genbank">Yes</parameter>
      </modified>
    </sequence>
    <sequence>
      <internal>
        <parameter name="sequence_identifier">gb6.contig.2481</parameter>
      </internal>
      <genbank>
        <parameter name="latest_accession">AE017334</parameter>
        <parameter name="latest_version">2</parameter>
        <parameter name="owner">TIGR</parameter>
      </genbank>
      <refseq>
        <parameter name="latest_accession">NC_007530</parameter>
        <parameter name="latest_version">2</parameter>
      </refseq>
      <modified>
        <parameter name="sequence_changed">Yes</parameter>
        <parameter name="submitted_to_genbank">Yes</parameter>
      </modified>
    </sequence>
    <sequence>
      <internal>
        <parameter name="sequence_identifier">gb6.contig.2479</parameter>
      </internal>
      <genbank>
        <parameter name="latest_accession">AE017335</parameter>
        <parameter name="latest_version">3</parameter>
        <parameter name="owner">TIGR</parameter>
      </genbank>
      <refseq>
        <parameter name="latest_accession">NC_007323</parameter>
        <parameter name="latest_version">3</parameter>
      </refseq>
      <modified>
        <parameter name="sequence_changed">Yes</parameter>
        <parameter name="submitted_to_genbank">Yes</parameter>
      </modified>
    </sequence>
  </category>
  <category name="curatorship">
    <parameter name="annotation">Pathema</parameter>
    <parameter name="gene_ends">Pathema</parameter>
    <parameter name="gene_families"></parameter>
    <parameter name="changing_dna_sequence">No</parameter>
    <parameter name="changing_gene_ends">No</parameter>
  </category>
  <category name="ownership">
    <parameter name="current_genbank_control">Pathema</parameter>
    <parameter name="original_source">TIGR</parameter>
    <parameter name="original_sequence">TIGR</parameter>
    <parameter name="original_annotation">TIGR</parameter>
    <parameter name="downloaded_from"></parameter>
    <parameter name="date_of_download"></parameter>
    <parameter name="owner_url">http://www.tigr.org</parameter>
  </category>
  <category name="evidence">
    <literature>
      <parameter name="providing_pmid">Yes</parameter>
    </literature>
    <experimental>
      <parameter name="type"></parameter>
    </experimental>
  </category>
</source>

IOWG List

The Interoperability Working Group (IOWG) is comprised of members from NIAID's Bioinformatics Resource Centers. The IOWG's core purpose is to facilitate interoperation amongst the BRCs. This site will serve as a repository of discussions, files, and documentation generated by the IOWG. It is meant to complement the IOWG mailing list.

Mailing List Archives - View past threads

Send Mail to the IOWG

RefSeq Working Group

The refseq mailing list is used to discuss issues involving submission of data to RefSeq. All submission requests should be posted through this list. To subscribe to this list, please go to the list adminstration page and enter in your email address and name. A message will be sent to you once your request has been processed.

Mailing List Archives - View past threads

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