Special Access Feature: If your team also uses Dotmatics Bioregister, you may be eligible to turn on the Bioregister integration for your Biologics organization. This allows you to register and pull across data from Biologics directly into Bioregister.
Steps for setting up Dotmatics Bioregister
1. Turn on Bioregister Integration
Reach out to us here notifying our team to turn on integrations with Dotmatics Bioregister.
2. Configure your Bioregister Settings
Ask us here or reach out to your Dotmatics Representative to assist in the configuration settings below
Part 1: Set the URL and the entity ID’s
The organization settings need to be set so that Biologics knows where to send and register sequences. This can be done by any logged in user of the organization, by navigating to the Bioregister Configuration page on the left hand panel.
Requirements:
- The URL must end with /bioregister/api
- One of "Sequence Entity Name", or "Sequence Entity ID" must be set.
- One of "Complex Entity Name", or "Complex Entity ID" must be set.
- ID fields must be a number
Entity and complex information for the given URL can be viewed by going to the <hostname>/bioregister/resourceType/list. For example, with the below URL, it would be http://example-bioregister.com/
Part 2: Setup the mapping configuration
The mapping configuration specifies what Geneious Biologics column values should map to what Bioregister fields. For example, when registering a light chain sequence, the Light CDR1 column in Biologics should map to the cdr1 field in Bioregister.
This config is currently just a plain JSON object, a simplified version looks like this:
{
"Light Chain": [
{
"BxColumnName": "Light CDR1",
"BioregisterField": "cdr1"
},
],
"Heavy Chain": [
{
"BxColumnName": "Heavy CDR1",
"BioregisterField": "cdr1"
},
]
}
The object must have a Light Chain and a Heavy Chain section (for registering either a light or heavy chain). Each section contains an array of mappings which have two fields:
- The BxColumnName specifies the id name (which is usually, but not always the display name) of the Biologics column.
- The BioregisterField specifies the bioregister field to send the value of the BxColumnName to
The default mappings are below
{
"Light Chain": [
{
"BxColumnName": "Light CDR1",
"BioregisterField": "cdr1"
},
{
"BxColumnName": "Light CDR2",
"BioregisterField": "cdr2"
},
{
"BxColumnName": "Light CDR3",
"BioregisterField": "cdr3"
},
{
"BxColumnName": "VJ Region",
"BioregisterField": "sequence"
},
{
"BxColumnName": "Light V Gene",
"BioregisterField": "vGene"
},
{
"BxColumnName": "Light J Gene",
"BioregisterField": "jGene"
},
{
"BxColumnName": "Light V Gene ID",
"BioregisterField": "vIdentity"
},
{
"BxColumnName": "Light J Gene ID",
"BioregisterField": "jIdentity"
}
],
"Heavy Chain": [
{
"BxColumnName": "Heavy CDR1",
"BioregisterField": "cdr1"
},
{
"BxColumnName": "Heavy CDR2",
"BioregisterField": "cdr2"
},
{
"BxColumnName": "Heavy CDR3",
"BioregisterField": "cdr3"
},
{
"BxColumnName": "VDJ Region",
"BioregisterField": "sequence"
},
{
"BxColumnName": "Heavy V Gene",
"BioregisterField": "vGene"
},
{
"BxColumnName": "Heavy J Gene",
"BioregisterField": "jGene"
},
{
"BxColumnName": "Heavy V Gene ID",
"BioregisterField": "vIdentity"
},
{
"BxColumnName": "Heavy J Gene ID",
"BioregisterField": "jIdentity"
}
]
}
Notes:
-
If an attempt is made to register a sequence which doesn’t have the specified BxColumnName, that mapping will be skipped.
-
If an attempt is made to register a sequence where BioregisterField doesn’t exist, then it is likely that the configuration is wrong and jobs will fail.
-
BxColumnName must be the name of the column, this is not always the display name. To see a column’s real name: find a document with that column, right click a value in the column and select Filter ..., in the filter box, the column’s real name should be printed.
-
When registering as a nucleotide sequence, applicable columns will attempt to prioritize using the column name with the Nucleotides appended to it.
-
These configuration options (and the format) may change in the future depending on how integration evolves.