BIGSdb
Concepts and terms
BIGSdb
Loci
Alleles
Schemes
Profiles
Sequence tags
Sets
BIGSdb dependencies
Required packages
Linux packages
Perl modules
Optional packages
Installation and configuration of BIGSdb
Software installation
Configuring PostgreSQL
Site-specific configuration
Setting up the offline job manager
Setting up the submission system
Periodically delete temporary files
Prevent preference database getting too large
Purging old jobs from the jobs database
Log file rotation
Upgrading BIGSdb
Running the BIGSdb RESTful interface
Proxying the API to use a standard web port
Database setup
Creating databases
Database-specific configuration
XML configuration attributes used in config.xml
Isolate database XML attributes
Special values
Sequence definition database XML attributes
User authentication
Apache authentication
Built-in authentication
Setting up the admin user
Updating PubMed citations
Administrator’s guide
Types of user
User groups
Curator permissions
Locus and scheme permissions (sequence definition database)
Controlling access
Restricting particular configurations to specific user accounts
Setting user passwords
Setting the first user password
Enabling plugins
Temporarily disabling database updates
Global
Database-specific
Host mapping
Improving performance
Use mod_perl
Cache scheme definitions within an isolate database
Use materialized views for scheme definitions
Use a ramdisk for the secure temporary directory
Dataset partitioning
Sets
Configuration of sets
Set metadata
Set views
Using only defined sets
Adding new loci
Sequence definition databases
Single locus
Batch adding
Isolate databases
Single locus
Batch adding
Defining locus extended attributes
Defining schemes
Sequence definition databases
Isolate databases
Organizing schemes into hierarchical groups
Setting up client databases
Look up isolates with given allele
Look up isolates with a given scheme primary key
Look up specific isolate database fields linked to a given allele
Rule-based sequence queries
Example rule code
Rule files
Linking to the rule query
Adding descriptive text
Workflow for setting up a MLST scheme
Defining new loci based on annotated reference genome
Genome filtering
Filtering by
in silico
PCR
Filtering by
in silico
hybridization
Setting locus genome positions
Defining composite fields
Extended provenance attributes (lookup tables)
Sequence bin attributes
Checking external database configuration settings
Exporting table configurations
Authorizing third-party client software to access authenticated resources
Curator’s guide
Adding new sender details
Adding new allele sequence definitions
Single allele
Batch adding multiple alleles
Upload using a spreadsheet
Upload using a FASTA file
Updating and deleting allele sequence definitions
Updating locus descriptions
Adding new scheme profile definitions
Updating and deleting scheme profile definitions
Adding isolate records
Updating and deleting single isolate records
Batch updating multiple isolate records
Deleting multiple isolate records
Uploading sequence contigs linked to isolate records
Select isolate from drop-down list
Select from isolate query
Upload options
Automated web-based sequence tagging
Projects
Creating the project
Explicitly adding isolates to a project
Isolate record versioning
Curating submitted data
Alleles
Individual allele curation
Batch allele curation
Rejecting sequences
Closing the submission
Profiles
Individual profile curation
Batch profile curation
Rejecting profiles
Closing the submission
Isolates
Closing the submission
Offline curation tools
Automated offline sequence tagging
Automated offline allele definition
Cleanly interrupting offline curation
Uploading contigs from the command line
Definition downloads
Allele sequence definitions
Scheme tree
Alphabetical list
All loci by scheme
Download locus table
Scheme profile definitions
Data records
Isolate records
Projects
Provenance metadata
Publications
Sequence bin summary
Scheme and locus data
Allele definition records
Sequence tag records
Profile records
Sequence bin records
Querying data
Querying sequences to determine allele identity
Querying whole genome data
Searching for specific allele definitions
Locus-specific attributes
Browsing scheme profile definitions
Querying scheme profile definitions
Investigating allele differences
Sequence similarity
Sequence comparison
Querying isolate data
Query by allele_designation/scheme field
Query by allele designation status
Query by tagged sequence status
Query filters
Querying by allelic profile
Retrieving list of isolates or profiles
Retrieving isolates by linked publication
User-configurable options
General options
Main results table
Isolate record display
Provenance field display
Query filters
Modifying locus and scheme display options
Data analysis plugins
Locus explorer
Polymorphic site analysis
Codon usage
Aligned translations
Field breakdown
Two field breakdown
Scheme and allele breakdown
Sequence bin breakdown
Genome comparator
Analysis using defined loci
Analysis using annotated reference genome
Include in identifiers fieldset
Reference genome fieldset
Parameters/options fieldset
Distance matrix calculation fieldset
Alignments fieldset
Core genome analysis fieldset
Filter fieldset
Understanding the output
Distance matrix
Unique strains
BLAST
Include in results table fieldset
Parameters fieldset
No matches
Filter fieldset
BURST
Codon usage
Unique combinations
Polymorphisms
Presence/absence
Options
Tag status
Data export plugins
Isolate record export
Advanced options
Molecular weight calculation
Sequence export
Aligning sequences
Contig export
Filtering by tagged status of contigs
Submitting data using the submission system
Registering a user account
Allele submission
Start
Select the submission locus
Enter details of sequencing method
Paste in sequence(s)
Add message to curator
Add supporting files
Finalize submission
Profile submission
Start
Paste in profile(s)
Add message to curator
Add supporting files
Finalize submission
Isolate submission
Start
Paste in isolate data
Add message to curator
Add supporting files
Finalize submission
RESTful Application Programming Interface (API)
Passing optional parameters
Resources
/ or /db
/db/{database}
/db/{database}/loci
/db/{database}/loci/{locus}
/db/{database}/loci/{locus}/alleles
/db/{database}/loci/{locus}/alleles_fasta
/db/{database}/loci/{locus}/alleles/{allele_id}
/db/{database}/schemes
/db/{database}/schemes/{scheme_id}
/db/{database}/schemes/{scheme_id}/fields/{field}
/db/{database}/schemes/{scheme_id}/profiles
/db/{database}/schemes/{scheme_id}/profiles_csv
/db/{database}/schemes/{scheme_id}/profiles/{profile_id}
/db/{database}/isolates
/db/{database}/isolates/{isolate_id}
/db/{database}/isolates/{isolate_id}/allele_designations
/db/{database}/isolates/{isolate_id}/allele_designations/{locus}
/db/{database}/isolates/{isolate_id}/allele_ids
/db/{database}/isolates/{isolate_id}/schemes/{scheme_id}/allele_designations
/db/{database}/isolates/{isolate_id}/schemes/{scheme_id}/allele_ids
/db/{database}/isolates/{isolate_id}/contigs
/db/{database}/isolates/{isolate_id}/contigs_fasta
/db/{database}/contigs/{contig_id}
/db/{database}/fields
/db/{database}/users/{user_id}
Authentication
Developer sign up to get a consumer key
Getting a request token
Getting user authorization
Getting an access token
Getting a session token
Accessing protected resources
Frequently asked questions (FAQs)
General
Installation
Administration
Appendix
Query operators
Sequence tag flags
Allele sequence flags
Database schema
BIGSdb
Docs
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Database schema
Edit on GitHub
Database schema
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Sequence
definition
database
Isolate
database