eggnog-mcp
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
| PYTHONPATH | No | Path to the src directory, needed only when running from a source install without adding the package to PATH (e.g. "/path/to/eggNOG-MCP/src"). |
Instructions
Guidance the server publishes about itself, which clients place ahead of the tool catalog so the model reads it before choosing anything.
This server publishes no instructions, or was last inspected before Glama recorded them.
Capabilities
Features and capabilities supported by this server
Protocol revision2025-11-25
| Capability | Details |
|---|---|
| tools | {
"listChanged": false
} |
| prompts | {
"listChanged": false
} |
| resources | {
"subscribe": false,
"listChanged": false
} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| get_proteinB | Look up detailed information for a protein in the eggNOG database. Retrieves protein family membership, predicted functions (KEGG KO terms and GO terms with confidence scores), and the list of orthologous groups (OGs) associated with the protein. Parametersprotein_id : str
The eggNOG protein identifier in the format Returnsstr JSON string with protein family, function predictions, and OG list. |
| get_orthologous_groupA | Look up information for an orthologous group (OG) in eggNOG. Retrieves the evolutionary origin, protein count, species count, functional annotation (KEGG KO and GO slim terms), and the list of all OGs in the same protein family. Parametersog_id : str
The orthologous group identifier in the format
Returnsstr JSON string with OG details including evolutionary origin, counts, and functional annotation. |
| get_og_contentA | Retrieve the list of proteins within an orthologous group. Returns the species and their protein members for the specified OG.
The result is capped at Parametersog_id : str
The orthologous group identifier in Returnsstr JSON string with species list, protein counts, and protein IDs. |
| get_orthologsB | Retrieve pairwise orthologs for a protein. Returns the orthologous proteins grouped by species for the given eggNOG protein ID. Parametersprotein_id : str
The eggNOG protein identifier in Returnsstr JSON string with orthologs grouped by species. |
| search_eggnogA | Search the eggNOG database for proteins or protein families. Performs a text search across the eggNOG database. The query must be
at least 3 characters long. The query can be a protein name
(e.g. Parametersquery : str
Search query string (minimum 3 characters).
Examples:
- Returnsstr JSON string with a list of search results (type, ID, label, URL). |
| annotate_proteinA | Annotate a protein with functional information from eggNOG. Returns a structured functional annotation for the given protein,
including KEGG KO terms, GO slim terms, protein family, Pfam domains,
and orthologous groups. This is a higher-level convenience wrapper
around Parametersprotein_id : str
The eggNOG protein identifier in the format Returnsstr JSON string with KEGG KO terms, GO terms, and cross-references. |
| get_protein_familyB | Retrieve protein family (cluster) content from eggNOG. Returns the list of species and proteins grouped under the given protein family name (also called a cluster). Parametersfamily_name : str
The protein family / cluster name.
Examples: Returnsstr JSON string with species list, protein counts, and protein IDs. |
| get_database_statsA | Retrieve summary statistics of the eggNOG 7 database. Returns the number of annotated species, protein sequences, phylogenetic trees, and orthologous groups in the current eggNOG release. Returnsstr JSON string with database statistics. |
| list_downloadsA | List downloadable data files from the eggNOG 7 database. Returns a list of all bulk-downloadable files (protein sequences, OG info, phylogenetic trees, taxonomic info, etc.) with their URLs and descriptions. Returnsstr JSON string with download file information. |
| get_taxid_infoA | Look up taxonomic information for an NCBI taxonomy ID. Provides guidance on retrieving taxonomic information for a given
NCBI taxonomy ID from the eggNOG database. The full taxonomic
data is available in the downloadable Parameterstaxid : int
NCBI taxonomy ID.
Examples:
- Returnsstr JSON string with taxonomic lookup information and download URL. |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
| version_info | Return the eggNOG-MCP server version. |
| database_stats_resource | Return cached database statistics. |
| database_downloads_resource | Return the list of downloadable files. |
TDQS
Scored across 10 tools
Most tools target distinct resources (protein, OG, family, taxid, stats, downloads, search), and descriptions give concrete examples. However, annotate_protein is explicitly a 'convenience wrapper around get_protein' returning overlapping data for the same protein_id, and get_og_content vs get_orthologs/get_protein_family all return species/protein lists with similar shapes, creating mild risk of misselection.
Consistent snake_case verb_noun pattern throughout (get_*, list_*, search_*, annotate_*). Minor terminology drift between 'orthologous_group' and 'orthologs' but the convention is clear and predictable.
10 tools is well-scoped for a read-only database API, with each tool covering a distinct lookup or listing need. No bloat and nothing obviously trivial.
Core lifecycle is well covered: search, protein annotation, OG detail, OG content, orthologs, family, stats, and downloads. Minor gaps remain (no sequence/FASTA retrieval), and get_taxid_info is effectively a stub that only points to a downloadable file rather than returning the taxonomy data.