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
ApiDB |
BHB |
ERIC |
NMPDR |
PATRIC |
Pathema |
VBRC |
VectorBase
<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.
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