Database setup

There are two types of BIGSdb database:

  • sequence definition databases, containing
    • allele sequences and their identifiers
    • scheme data, e.g. MLST profile definitions
  • isolate databases, containing
    • isolate provenance metadata
    • genome sequences
    • allele designations for loci defined in sequence definition databases.

These two databases are independent but linked. A single isolate database can communicate with multiple sequence definition databases and vice versa. Different access restrictions can be placed on different databases.

Databases are described in XML files telling BIGSdb everything it needs to know about them. Isolate databases can have any fields defined for the isolate table,allowing customisation of metadata - these fields are described in the XML file (config.xml) and must match the fields defined in the database itself.

Creating databases

There are templates available for the sequence definition and isolate databases. These are SQL scripts found in the sql directory.

To create a database, you will need to log in as the postgres user and use these templates. For example to create a new sequence definition database called bigsdb_test_seqdef, navigate to the sql directory and log in as the postgres user, e.g.

sudo su postgres

then

createdb bigsdb_test_seqdef
psql -f seqdef.sql bigsdb_test_seqdef

Create an isolate database the same way:

createdb bigsdb_test_isolates
psql -f isolatedb.sql bigsdb_test_isolates

The standard fields in the isolate table are limited to essential fields required by the system. To add new fields, you need to log in to the database and alter this table. For example, to add fields for country and year, first log in to the newly created isolate database as the postgres user:

psql bigsdb_test_isolates

and alter the isolate table:

ALTER TABLE isolates ADD country text;
ALTER TABLE isolates ADD year int;

Remember that any fields added to the table need to be described in the config.xml file for this database.

Database-specific configuration

Each BIGSdb database on a system has its own configuration directory, by default in /etc/bigsdb/dbases. The database has a short configuration name used to specify it in a web query and this matches the name of the configuration sub-directory, e.g. http://pubmlst.org/cgi-bin/bigsdb/bigsdb.pl?db=pubmlst_neisseria_isolates is the URL of the front page of the PubMLST Neisseria isolate database whose configuration settings are stored in /etc/bigsdb/dbases/pubmlst_neisseria_isolates. This database sub-directory contains a number of files (hyperlinks lead to the files used on the Neisseria database):

  • config.xml - the database configuration file. Fields defined here correspond to fields in the isolate table of the database.
  • banner.html - optional file containing text that will appear as a banner within the database index pages. HTML markup can be used within this text.
  • header.html - HTML markup that is inserted at the top of all pages. This can be used to set up site-specific menubars and logos.
  • footer.html - HTML markup that is inserted at the bottom of all pages.
  • curate_header.html - HTML markup that is inserted at the top of all curator’s interface pages.
  • curate_footer.html - HTML markup that is inserted at the bottom of all curator’s interface pages.
  • profile_submit.html - HTML markup for text that is inserted in to the submission interface prior to profile submission finalization. This can be used to add specific instructions such as the requirement to make an isolate submission.
  • allele_submit.html - HTML markup for text that is inserted in to the submission interface prior to allele submission finalization. This can be used to add specific instructions such as the requirement to attach Sanger trace files.

The header and footer files can alternatively be placed in the root directory of the web site for site-wide use.

There are four additional files, site_header.html, site_footer.html, curate_site_header.html and curate_site_footer.html which are used when either bigsdb.pl or bigscurate.pl are called without a database configuration. These should be placed in the root directory of the web site.

You can also add HTML meta attributes (such as a favicon) by including a file called meta.html in the database configuration directory. For example to set a favicon this file can contain something like the following:

<link rel="shortcut icon" href="/favicon.ico" type="image/ico" />

These attributes will appear in the <head> section of the HTML page.

XML configuration attributes used in config.xml

The following lists describes the attributes used in the config.xml file that is used to describe databases.

Isolate database XML attributes

Please note that database structure described by the field and sample elements must match the physical structure of the database isolate and sample tables respectively. Required attributes are in bold:

<db>

Top level element. Contains child elements: system, field and sample.:

<system>

Any value set here can be overridden in a system.overrides file.

  • authentication
  • db
    • Name of database on system.
  • dbtype
    • Type of database: either ‘isolates’ or ‘sequences’.
  • description
    • Description of database used throughout interface.
  • align_limit
    • Overrides the sequence export record alignment limit in the Sequence Export plugin. Default: ‘200’.
  • all_plugins
    • Enable all appropriate plugins for database: either ‘yes’ or ‘no’, default ‘no’.
  • annotation
    • Semi-colon separated list of accession numbers with descriptions (separated by a |), eg. ‘AL157959|Z2491;AM421808|FAM18;NC_002946|FA 1090;NC_011035|NCCP11945;NC_014752|020-06’. Currently used only by Genome Comparator plugin.
  • cache_schemes
    • Enable automatic refreshing of scheme field caches when batch adding new isolates: either ‘yes’ or ‘no’, default ‘no’.
    • See scheme caching.
  • codon_usage_limit
    • Overrides the record limit for the Codon Usage plugin. Default: ‘500’.
  • contig_analysis_limit
    • Overrides the isolate number limit for the Contig Export plugin. Default: ‘1000’.
  • curate_config
    • The database configuration that should be used for curation if different from the current configuration. This is used when the submission system is being used so that curation links in the ‘Manage submissions’ pages for curators load the correct database configuration.
  • curate_link
    • URL to curator’s interface, which can be relative or absolute. This will be used to create a link in the public interface dropdown menu.
  • curate_path_includes
    • Partial path of the bigscurate.pl script used to curate the database. See user authentication.
  • curate_script
    • Relative web path to curation script. Default ‘bigscurate.pl’ (version 1.11+).
    • This is only needed if automated submissions are enabled. If bigscurate.pl is in a different directory from bigsdb.pl, you need to include the whole web path, e.g. /cgi-bin/private/bigsdb/bigscurate.pl.
  • curator_home
    • URL of curator’s index page, which can be relative or absolute. This will be used to add a link in the dropdown menu.
  • curators_only
    • Set to ‘yes’ to prevent ordinary authenticated users having access to database configuration. This is only effective if read_access is set to ‘authenticated_users’. This may be useful if you have different configurations for curation and querying with some data hidden in the configuration used by standard users. Default ‘no’.
  • daily_pending_submissions
    • Overrides the daily limit on pending submissions that a user can submit via the web submission system. Default: ‘15’.
  • daily_rest_submissions_limit
    • Overrides the limit on number of submissions that can be made to the database via the RESTful interface. This is useful to prevent flooding of the submission system by aberrant scripts. Default: ‘100’.
  • default_access
    • The default access to the database configuration, either ‘allow’ or ‘deny’. If ‘allow’, then specific users can be denied access by creating a file called ‘users.deny’ containing usernames (one per line) in the configuration directory. If ‘deny’ then specific users can be allowed by creating a file called ‘users.allow’ containing usernames (one per line) in the configuration directory. See default access.
  • default_private_records
    • The default number of private isolate records that a user can upload. The user account must have a status of either ‘submitter’, ‘curator’, or ‘admin’. This value is used to set the private_quota field when creating a new user record (which can be overridden for individual users). Changing it will not affect the quotas of existing users. Default: ‘0’.
  • default_seqdef_config
    • Isolate databases only: Name of the default seqdef database configuration used with this database. Used to automatically fill in details when adding new loci.
  • default_seqdef_dbase
    • Isolate databases only: Name of the default seqdef database used with this database. Used to automatically fill in details when adding new loci.
  • default_seqdef_script
    • Isolate databases only: URL of BIGSdb script running the seqdef database (default: ‘/cgi-bin/bigsdb/bigsdb.pl’).
  • export_limit
    • Overrides the default allowed number of data points (isolates x columns) to export. Default: ‘25000000’.
  • fast_scan
    • Sets whether fast mode scanning is enabled via the web interface. This will scan all loci together, using exemplar sequences. In cases where multiple loci are being scanned this should be significantly faster than the standard locus-by-locus scan, but it will take longer for the first results to appear. Allele exemplars should be defined if you enable this option. Set to ‘yes’ to enable. Default: ‘no’.
  • fieldgroup1 - fieldgroup10
    • Allows multiple fields to be queried as a group. Value should be the name of the group followed by a colon (:) followed by a comma-separated list of fields to group, e.g. identifiers:id,strain,other_name.
  • genome_comparator_limit
    • Overrides the isolate number limit for the Genome Comparator plugin. Default: ‘1000’.
  • genome_comparator_max_ref_loci
    • Overrides the limit on number of loci allowed in a reference genome. Default: ‘10000’.
  • genome_comparator_threads
    • The number of threads to use for data gathering (BLAST, database queries) to populate data structure for Genome Comparator analysis. You should not set this to less than 2 as this will prevent job cancelling due to the way isolates are queued. Default: ‘2’.
  • hide_unused_schemes
    • Sets whether a scheme is shown in a main results table if none of the isolates on that page have any data for the specific scheme: either ‘yes’ or ‘no’, default ‘no’.
  • host
    • Host name/IP address of machine hosting isolate database, default ‘localhost’.
  • job_priority
    • Integer with default job priority for offline jobs (default:5).
  • job_quota
    • Integer with number of offline jobs that can be queued or currently running for this database.
  • labelfield
    • Field that is used to describe record in isolate info page, default ‘isolate’.
  • locus_aliases
    • Display locus aliases and use them in dropdown lists by default: must be either ‘yes’ or ‘no’, default ‘no’. This option can be overridden by a user preference.
  • locus_superscript_prefix
    • Superscript the first letter of a locus name if it is immediately following by an underscore, e.g. f_abcZ would be displayed as fabcZ within the interface: must be either ‘yes’ or ‘no’, default ‘no’. This can be used to designate gene fragments (or any other meaning you like).
  • maindisplay_aliases
    • Default setting for whether isolates aliases are displayed in main results tables: either ‘yes’ or ‘no’, default ‘no’. This setting can be overridden by individual user preferences.
  • noshow
    • Comma-separated list of fields not to use in breakdown statistic plugins.
  • no_publication_filter
    • Isolate databases only: Switches off display of publication filter in isolate query form by default: either ‘yes’ or ‘no’, default ‘no’.
  • only_sets
    • Don’t allow option to view the ‘whole database’ - only list sets that have been defined: either ‘yes’ or ‘no’, default ‘no’.
  • password
    • Password for access to isolates database, default ‘remote’.
  • port
    • Port number that the isolate host is listening on, default ‘5432’.
  • privacy
    • Displays E-mail address for sender in isolate information page if set to ‘no’. Default ‘yes’.
  • public_login
    • Optionally allow users to log in to a public database - this is useful as any jobs will be associated with the user and their preferences will also be linked to the account. Set to ‘no’ to disable. Default ‘yes’.
  • query_script
    • Relative web path to bigsdb script. Default ‘bigsdb.pl’ (version 1.11+).
    • This is only needed if automated submissions are enabled. If bigsdb.pl is in a different directory from bigscurate.pl, you need to include the whole web path, e.g. /cgi-bin/bigsdb/bigsdb.pl.
  • read_access
    • Describes who can view data: either ‘public’ for everybody or ‘authenticated_users’ for anybody who has been able to log in. Default ‘public’.
  • related_databases
    • Semi-colon separated list of links to related BIGSdb databases on the system. This should be in the form of database configuration name followed by a ‘|’ and the description, e.g. ‘pubmlst_neisseria_seqdef|Sequence and profile definitions’. This is used to populate the dropdown menu.
  • script_path_includes
  • seqbin_size_threshold
    • Sets the size values in Mbp to enable for the seqbin filter.
    • Example: seqbin_size_threshold=”0.5,1,2,4”.
  • seq_export_limit
    • Overrides the sequence export limit (records x loci) in the Sequence Export plugin. Default: ‘1000000’.
  • sets
    • Use sets: either ‘yes’ or ‘no’, default ‘no’.
  • set_id
    • Force the use of a specific set when accessing database via this XML configuration: Value is the name of the set.
  • start_id
    • Defines the minimum record id to be used when uploading new isolate records. This can be useful when it is anticipated that two databases may be merged and it would be easier to do so if the id numbers in the two databases were different. Default: ‘1’.
  • submissions
    • Enable automated submission system: either ‘yes’ or ‘no’, default ‘no’ (version 1.11+).
    • The curate_script and query_script paths should also be set, either in the bigsdb.conf file (for site-wide configuration) or within the system attribute of config.xml.
  • submissions_deleted_days
    • Overrides the default number of days before closed submissions are deleted from the system. Default: ‘90’.
  • tblastx_tagging
    • Sets whether tagging can be performed using TBLASTX: either ‘yes’ or ‘no’, default ‘no’.
  • total_pending_submissions
    • Overrides the total limit on pending submissions that a user can submit via the web submission system. Default: ‘20’.
  • user
    • Username for access to isolates database, default ‘apache’.
  • user_job_quota
    • Integer with number of offline jobs that can be queued or currently running for this database by any specific user - this parameter is only effective if users have to log in.
  • user_projects
    • Sets whether authenticated users can create their own projects in order to group isolates: either ‘yes’ or ‘no’, default ‘no’.
  • view
    • Database view containing isolate data, default ‘isolates’.
  • views
    • Comma-separated list of views of the isolate table defined in the database. This is used to set a view for a set.
  • webroot
    • URL of web root, which can be relative or absolute. This is used to provide a hyperlinked item in the dropdown menu. Default ‘/’.
<field>

Element content: Field name + optional list <optlist> of allowed values, e.g.:

<field type="text" required="no" length="40" maindisplay="no"
   web="http://somewebsite.com/cgi-bin/script.pl?id=[?]" optlist="yes">epidemiology
  <optlist>
   <option>carrier</option>
   <option>healthy contact</option>
   <option>sporadic case</option>
   <option>endemic</option>
   <option>epidemic</option>
   <option>pandemic</option>
  </optlist>
</field>
  • type
    • Data type: int, text, float, bool, or date.
  • comments * optional
    • Comments about the field. These will be displayed in the field description plugin and as tooltips within the curation interface.
  • curate_only
    • Set to ‘yes’ to hide field on an isolate information page in the standard interface. The field will be visible if the page is accessed via the curator’s interface (version 1.10.0+).
  • default
    • Default value. This will be entered automatically in the web form but can be overridden.
  • dropdown
    • Select if you want this field to have its own dropdown filter box on the query page. If the field has an option list it will use the values in it, otherwise all values defined in the database will be included: ‘yes’ or ‘no’, default ‘no’. This setting can be overridden by individual user preferences.
  • length
    • Length of field, default 12.
  • maindisplay
    • Sets if field is displayed in the main table after a database search, ‘yes’ or ‘no’, default ‘yes’. This setting can be overridden by individual user preferences.
  • max
    • Maximum value for integer and date types. Special values such as CURRENT_YEAR and CURRENT_DATE can be used.
  • min
    • Minimum value for integer and date types.
  • no_curate
    • Setting this will hide the field in the curator interface and prevent it from being manually modified. This is useful for fields that are populated by automated scripts or database triggers. Can be ‘yes’ or ‘no’, default ‘no’.
  • optlist
    • Sets if this field has a list of allowed values, default ‘no’. Surround each option with an <option> tag.
  • regex
    • Regular expression used to constrain field values, e.g. regex=”^[A-Z].*$” forces the first letter of the value to be capitalized.
  • required
    • Sets if data is required for this field, ‘yes’ or ‘no’, default ‘yes’.
  • userfield
    • Select if you want this field to have its own dropdown filter box of users (populated from the users table): ‘yes’ or ‘no’, default ‘no’.
  • web
    • URL that will be used to hyperlink field values. If [?] is included in the URL, this will be substituted for the actual field value.

Special values

The following special variables can be used in place of an actual value:

  • CURRENT_DATE: current date in yyyy-mm-dd format
  • CURRENT_YEAR: the 4 digit value of the current year
<sample>

Element content: Sample field name + optional list <optlist> of allowed values. Attributes are essentially the same as isolate field attributes, but refer to the samples table rather than the isolates table.

The sample table, if defined, must include isolate_id and sample_id fields, which must also be described in the XML file. These must be set as integer fields.

Sequence definition database XML attributes

Required attributes are in bold.

<db>

Top level element. Contains child elements: system, field and sample.

<system>

Any value set here can be overridden in a system.overrides file.

  • authentication
  • db
    • Name of database on system.
  • dbtype
    • Type of database: either ‘isolates’ or ‘sequences’.
  • description
    • Description of database used throughout interface.
  • align_limit
    • Overrides the sequence export record alignment limit in the Sequence Export plugin. Default: ‘200’.
  • allele_comments
    • Enable comments on allele sequences: either ‘yes’ or ‘no’, default ‘no’.
    • This is not enabled by default to discourage the practice of adding isolate information to allele definitions (this sort of information belongs in an isolate database).
  • allele_flags
    • Enable flags to be set for alleles: either ‘yes’ or ‘no’, default ‘no’.
  • curate_config
    • The database configuration that should be used for curation if different from the current configuration. This is used when the submission system is being used so that curation links in the ‘Manage submissions’ pages for curators load the correct database configuration.
  • curate_path_includes
    • Partial path of the bigscurate.pl script used to curate the database. See user authentication.
  • curate_script
    • Relative web path to curation script. Default ‘bigscurate.pl’ (version 1.11+).
    • This is only needed if automated submissions are enabled. If bigscurate.pl is in a different directory from bigsdb.pl, you need to include the whole web path, e.g. /cgi-bin/private/bigsdb/bigscurate.pl.
  • curator_home
    • URL of curator’s index page, which can be relative or absolute. This will be used to add a link in the dropdown menu.
  • curators_only
    • Set to ‘yes’ to prevent ordinary authenticated users having access to database configuration. This is only effective if read_access is set to ‘authenticated_users’. This may be useful if you have different configurations for curation and querying with some data hidden in the configuration used by standard users. Default ‘no’.
  • daily_pending_submissions
    • Overrides the daily limit on pending submissions that a user can submit via the web submission system. Default: ‘15’.
  • daily_rest_submissions_limit
    • Overrides the limit on number of submissions that can be made to the database via the RESTful interface. This is useful to prevent flooding of the submission system by aberrant scripts. Default: ‘100’.
  • diploid
    • Allow IUPAC 2-nuclotide ambiguity codes in allele definitions for use with diploid typing schemes: either ‘yes’ or ‘no’, default ‘no’.
  • disable_seq_downloads
    • Prevent users or curators from downloading all alleles for a locus (admins always can). ‘yes’ or ‘no’, default ‘no’.
  • exemplars
    • Use exemplar sequences in the BLAST caches used for the sequence query pages. This is useful on larger databases as it speeds up the query significantly. Exemplar alleles MUST be defined otherwise sequence queries will fail. ‘yes’ or ‘no’, default ‘no’.
  • isolate_database
    • The config name of the isolate database. This is used to provide a link to isolate submissions. You also need to set isolate_submissions=”yes”.
  • isolate_submissions
    • Set to yes to provide a link to isolate submissions. The isolate_database attribute also needs to be set. Default: ‘no’.
  • job_priority
    • Integer with default job priority for offline jobs (default:5).
  • job_quota
    • Integer with number of offline jobs that can be queued or currently running for this database.
  • profile_submissions
    • Enable profile submissions (automated submission system): either ‘yes’ or ‘no’, default ‘no’ (version 1.11+).
    • To enable, you will also need to set submissions=”yes”. By default, profile submissions are disabled since generally new profiles should be accompanied by representative isolate data, and the profile can be extracted from that.
  • public_login
    • Optionally allow users to log in to a public database - this is useful as any jobs will be associated with the user and their preferences will also be linked to the account. Set to ‘no’ to disable. Default ‘yes’.
  • query_script
    • Relative web path to bigsdb script. Default ‘bigsdb.pl’ (version 1.11+).
    • This is only needed if automated submissions are enabled. If bigsdb.pl is in a different directory from bigscurate.pl, you need to include the whole web path, e.g. /cgi-bin/bigsdb/bigsdb.pl.
  • read_access
    • Describes who can view data: either ‘public’ for everybody, or ‘authenticated_users’ for anybody who has been able to log in. Default ‘public’.
  • related_databases
    • Semi-colon separated list of links to related BIGSdb databases on the system. This should be in the form of database configuration name followed by a ‘|’ and the description, e.g. ‘pubmlst_neisseria_isolates|Isolates’. This is used to populate the dropdown menu.
  • script_path_includes
  • seq_export_limit
    • Overrides the sequence export limit (records x loci) in the Sequence Export plugin. Default: ‘1000000’.
  • sets
    • Use sets: either ‘yes’ or ‘no’, default ‘no’.
  • set_id
    • Force the use of a specific set when accessing database via this XML configuration: Value is the name of the set.
  • submissions
    • Enable automated submission system: either ‘yes’ or ‘no’, default ‘no’ (version 1.11+).
    • The curate_script and query_script paths should also be set, either in the bigsdb.conf file (for site-wide configuration) or within the system attribute of config.xml.
  • submissions_deleted_days
    • Overrides the default number of days before closed submissions are deleted from the system. Default: ‘90’.
  • total_pending_submissions
    • Overrides the total limit on pending submissions that a user can submit via the web submission system. Default: ‘20’.
  • user_job_quota
    • Integer with number of offline jobs that can be queued or currently running for this database by any specific user - this parameter is only effective if users have to log in.
  • webroot
    • URL of web root, which can be relative or absolute. This is used to provide a hyperlinked item in the dropdown menu. Default ‘/’.

Over-riding global defaults set in bigsdb.conf

Certain values set in bigsdb.conf can be over-ridden by corresponding values set in a database-specific config.xml file. These can be set within the system tag like other attributes:

  • query_script
    • Relative web path to bigsdb script.
  • curate_script
    • Relative web path to curation script.
  • prefs_db
    • The name of the preferences database.
  • auth_db
    • The name of the authentication database.
  • tmp_dir
    • Path to the web-accessible temporary directory.
  • secure_tmp_dir
    • Path to the web-inaccessible (secure) temporary directory.
  • ref_db
    • The name of the references database.

Over-riding values set in config.xml

Any attribute used in the system tag of the database config.xml file can be over-ridden using a file called system.overrides, placed in the same directory as config.xml. This is very useful as it allows you to set up multiple configs for a database, with the config.xml files symlinked so that any changes to one will be seen in each database configuration. An example of why you may wish to do this would be if you create separate public and private views of the isolate table that filters on some attribute. The system.overrides file uses key value pairs separated by = with the values quoted, e.g.

view="private"
read_access="authenticated_users"
description="Private view of database"

User authentication

You can choose whether to allow Apache to handle your authentication or use built-in authentication.

Apache authentication

Using apache to provide your authentication allows a flexible range of methods and back-ends (see the Apache authentication HowTo for a start, or any number of tutorials on the web).

At its simplest, use a .htaccess file in the directory containing the bigscurate.pl (and bigsdb.pl for restriction of read-access) script or by equivalent protection of the directory in the main Apache server configuration. It is important to note however that, by default, any BIGSdb database can be accessed by any instance of the BIGSdb script (including one which may not be protected by a .htaccess file, allowing public access). To ensure that only a particular instance (protected by a specific htaccess directive) can access the database, the following attributes can be set in the system tag of the database XML description file:

  • script_path_includes: the BIGSdb script path must contain the value set.
  • curate_path_includes: the BIGSdb curation script path must contain the value set.

For public databases, the ‘script_path_includes’ attribute need not be set.

To use apache authentication you need to set the authentication attribute in the system tag of the database XML configuration to ‘apache’.

Built-in authentication

BIGSdb has its own built-in authentication, using a separate database to store password and session hashes. The advantages of using this over many forms of apache authentication are:

  • Users are able to update their own passwords.
  • Passwords are not transmitted over the Internet in plain text.

When a user logs in, the server provides a random one-time session variable and the user is prompted to enter their username and password. The password is encrypted within the browser using a Javscript one-way hash algorithm, and this is combined with the session variable and hashed again. This hash is passed to the server. The server compares this hash with its own calculated hash of the stored encrypted password and session variable that it originally sent to the browser. Implementation is based on perl-md5-login.

To use built-in authentication you need to set the authentication attribute in the system tag of the database XML configuration to ‘builtin’.

Setting up the admin user

The first admin user needs to be manually added to the users table of the database. Connect to the database using psql and add the following (changing details to suit the user).:

INSERT INTO users (id, user_name, surname, first_name, email, affiliation, status, date_entered,
datestamp, curator) VALUES (1, 'keith', 'Jolley', 'Keith', 'keith.jolley@zoo.ox.ac.uk',
'University of Oxford, UK', 'admin', 'now', 'now', 1);

If you are using built-in authentication, set the password for this user using the add_user.pl script. This hashes the password and stores this within the authentication database. Other users can be added by the admin user from the curation interface accessible from http://your_website/cgi-bin/private/bigscurate.pl?db=test_db (or wherever you have located your bigscurate.pl script).

Updating PubMed citations

Publications listed in PubMed can be associated with individual isolate records, profiles, loci and sequences. Full citations for these are stored within a local reference database, enabling these to be displayed within isolate records and searching by publication and author. This local database is populated by a script that looks in BIGSdb databases for PubMed records not locally stored and then requests the full citation record from the PubMed database.

The script is called getrefs.pl and can be found in the scripts/maintenance directory. This script needs to know which BIGSdb databases and tables it needs to search for PubMed ids. These are listed in a configuration file (usually called getrefs.conf) which contains two columns - the first is the name of the database, the second is a comma-separated list of tables to search, e.g.

pubmlst_bigsdb_neisseria_isolates          refs
pubmlst_bigsdb_neisseria_seqdef            profile_refs,sequence_refs,locus_refs

The script can be called as follows:

getrefs.pl getrefs.conf

Run either as the ‘postgres’ user or an account that is allowed to connect as the postgres user.

This should be run periodically from a CRON job, e.g. every hour.