Database XML description
The following list describes the allowed attributes for an isolate database. A profile database is similar but generally the only standard fields included are 'st' and 'clonal_complex'. See hp_profiles.xml and nm_isolates.xml for example files.
Use the online configurator tool to design your databases and generate the corresponding XML file.
Isolate database XML attributes
<mlst>
Top level element. Contains child elements: system, locus, field.
<system>
Element content: Brief description to appear on web pages.
| Attribute | Description | Required | Example |
|---|---|---|---|
| longcode | database name | required | nm_isolates |
| webroot | URL of web root, default '/' | optional | /neisseria |
| description | database description | optional | |
| indexpage | home page name, default 'index.html' | optional | index.html |
| dbprof | name of profiles database | required | nm_profiles |
| profhome | URL of profiles database home page | required | http://pubmlst.org/cgi-bin/ mlstdbnet/mlstdbnet.pl? file=nm_profiles.xml |
| dbtype | either 'profiles' if allelic profile is stored in database or 'st' if sequence type is stored, default 'st' | required | |
| profiles_host | host name/IP address of machine hosting profile database, default '127.0.0.1' | optional | 163.1.73.11 |
| profiles_port | port number that the profiles host is listening on, default '5432' | optional | 5432 |
| profiles_user | remote username for read-only access to profiles database, default 'remote' | optional | |
| profiles_pass | remote password for read-only access to profiles database, default 'remote' | optional | |
| host | host name/IP address of machine hosting isolate database, default '127.0.0.1' | optional | 163.1.73.11 |
| port | port number that the isolate host is listening on, default '5432' | optional | 5432 |
| user | username for access to isolates database, default 'apache' | optional | |
| pass | password for access to isolates database, default 'remote' | optional | |
| view | database view to query, default 'isolates' | optional | |
| nocomplex | set to 'nocomplex' if profiles database lacks a clonal_complex field | optional | |
| seqdl | set to 'seqdl' if you would like to be able to download allele sequence files by isolate | optional | |
| noshow | comma separated list of fields not to use in breakdown statistics | optional | |
| 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 | optional | identifiers:id,strain,other_name |
| treelist | field to be used as key for drawing trees | optional | |
| complex_maindisplay | determines whether the clonal complex field from the profile database is displayed in the isolates main results table | optional | |
| reftable | determines if the database contains a table for linking isolate records to PubMed ids. | optional | yes |
| multiviews | set to 'multiviews' to restrict users to different database views. Further details. | optional | multiviews |
<locus>
Element content: Locus abbreviation
| Attribute | Description | Required | Example |
|---|---|---|---|
| fullname | full name of gene | optional | ABC transporter |
| length | (standard) length of gene | required | 433 |
| varying | set to 'yes' if some alleles vary from standard length | optional | yes |
| orf | open reading frame, set to '2' or '3' if ORF doesn't start at first nucleotide, or '4', '5' or '6' if you have a reverse reading frame (the software will reverse complement the sequence when generating in-frame concatenated sequences) | optional | 2 |
| nocoding | set to 'yes' if alleles do not code for a protein | optional | yes |
<field>
Element content: Field name + optional list <optlist> of allowed values
| Attribute | Description | Required | Example |
|---|---|---|---|
| type | data type - integer, text, real or date | required | int |
| required | is data required for this field? default 'yes' | optional | no |
| maindisplay | is field displayed in main table after database search? default 'yes' | optional | no |
| userupdate | can a database user (curator) update this field - generally only the id number can not be updated, default 'yes' | optional | no |
| length | length of field | required | 12 |
| optlist | does this field have a list of allowed values? default 'no'. Surround each option with an <option> tag | optional | yes |
| dropdown | select if you want this field to have its own dropdown box on the query page. If the field has an option list and you prefer to use the list from the XML file set a value of 'list'. Set as 'yes' to use the values from the database. | optional | yes |
| comments | comments about the field | optional | |
| dbpep | set to name of database if this field returns an antigen peptide (or short sequence) from a remote database | optional | poravr |
| dbnuc | set to name of database if this field returns an antigen nucleotide (or long peptide) sequence from a remote database | optional | pora_alleles |
| host | host name/IP number of machine hosting antigen database | optional | 163.1.73.11 |
| port | port number that the antigen database host is listening on | optional | 5432 |
| user | remote username for access to antigen database | optional | |
| pass | remote password for access to antigen database | optional | |
| table | database table to query | optional | pora |
| qryname | database field to query | optional | id |
| seq | database sequence field to return | optional | seq |
| web | URL that hyperlinked peptide sequence points to | optional | http://neisseria.org/nm/ typing/pora/vr1.shtml |
| composite | Composite field made up of any number of other fields. The composite field itself does not appear in the database. To include another field use a dollar sign ($) immediately followed by the field name (which can come from either the profile or isolate database). Use any other characters you like in the string. | optional | ST-$ST($clonal_complex): $serogroup: P1.$porA_VR1,$porA_VR2: $fetA_VR (will display a field like 'ST-11(cc11):B:P1.5,2:F1-2) |
| composite_empties | To be used with 'composite' attribute. Use to set the display value of fields that make up a composite field when the real value is empty. This is a comma-separated list. | optional | composite_empties="$porA_VR1:ND, $porA_VR2:ND, $clonal_complex:-, $fetA_VR:ND" |
| composite_ clonal_ complex_ format | Set the format for clonal complex in composite field 1: as database 2: number part of field | optional | 2 |