Enterobase MCP connector

Enterobase is an online resource for uploading sequencing data, performing de novo assembly, and conducting genotyping comparisons using MLST and wgMLST. The Enterobase MCP connector allows AI agents to authenticate users, query and filter genomic assemblies, and manage lookup tables for genetic typing schemes. It also supports retrieving scheme definitions and performing comparative genomics operations across bacterial strain databases.

Authentication type

• Basic Auth - Requires a username and password to be configured for the agent to access the service.

Uses

Use the Enterobase MCP connector to perform the following actions:

• Upload and assemble microbial sequencing data for genomic analysis
• Compare bacterial strains using multilocus sequence typing (MLST) and whole-genome MLST profiles
• Track strain metadata and genotyping schemes across microbiology research projects
• Retrieve allele sequences and loci information for genotyping comparisons
• Manage sequence-read traces and genome assembly records in a centralized database
• Monitor strain versions and historical metadata changes for audit and compliance
• Automate barcode lookups and strain identification across Enterobase databases
• Build epidemiological workflows that correlate strain data with outbreak investigations

Example prompts

Use the following example prompts to invoke Enterobase MCP connector tools from your AI assistant or Boomi Connect workflow:

• Show me all strains uploaded to Enterobase in the last 30 days.
• Find genome assemblies for Salmonella with a quality score above 95.
• What genotyping schemes are available in Enterobase for my research database?
• Retrieve the ST profile data for strain barcode SAL-12345 in Enterobase.
• List all sequence-read traces associated with our recent outbreak investigation.
• Get the previous versions of metadata for strain SAL-67890 to see what changed.
• Search for alleles matching locus STM_001 in our Enterobase instance.
• Pull a lookup of all barcodes from Enterobase that match my sample batch.
• Update strain metadata for 50 isolates at once in Enterobase.
• Create a new genotyping scheme in Enterobase for my custom MLST panel.

Enterobase MCP connector tools

The Enterobase MCP connector provides the following tools. Each tool maps to a specific action you can invoke from your AI agent or automation.

Tool	Description
getApiV20	Retrieves information from the Enterobase version 2.0 service.
getApiV20Login	Authenticates a user and provides access credentials for the service.
getApiV20Lookup	Searches for and retrieves matching records from the database.
getApiV20Lookup2	Performs an alternative search query to find and retrieve records.
createApiV20Lookup	Creates a new search query for finding records in the database.
getApiV20Assemblies	Retrieves genomic assembly records and their associated information.
getApiV20Assemblies2	Retrieves additional genomic assembly records with alternative parameters.
createApiV20Assemblies	Creates a new genomic assembly record in the database.
updateApiV20Assemblies	Modifies existing genomic assembly records with new information.
getApiV20Schemes	Retrieves classification scheme records used for bacterial typing.
getApiV20Schemes2	Retrieves additional classification scheme records with alternative parameters.
createApiV20Schemes	Creates a new classification scheme for bacterial typing.
updateApiV20Schemes	Modifies existing classification scheme records with new data.
getApiV20Straindata	Retrieves detailed data associated with specific bacterial strains.
getApiV20Strains	Retrieves bacterial strain records and their metadata.
getApiV20Strains2	Retrieves additional bacterial strain records with alternative parameters.
createApiV20Strains	Creates a new bacterial strain record in the database.
updateApiV20Strains	Modifies existing bacterial strain records with updated information.
getApiV20Strainsversion	Retrieves version history and changes for specific bacterial strains.
getApiV20Traces	Retrieves sequencing trace files and their associated data.
getApiV20Traces2	Retrieves additional sequencing trace files with alternative parameters.
createApiV20Traces	Creates a new sequencing trace record in the database.
updateApiV20Traces	Modifies existing sequencing trace records with new data.
getApiV20Alleles	Retrieves allele variants and their sequence information.
getApiV20Loci	Retrieves genetic loci records used in typing schemes.
getApiV20Sts	Retrieves sequence type records from multilocus typing data.