Embl Mcp Server — independently scanned and version-tracked by SaferSkills.
SaferSkills independently audited Embl Mcp Server (Agent Skill) and scored it 100/100 (green). The audit ran 55 deterministic rules across Security, Supply Chain, Maintenance, Transparency, and Community; it found 0 high-severity and 0 lower-severity findings. The full rule-by-rule trace and per-finding evidence are below. Free, methodology-open.
Findings & checks · 0 flagged
Every scanned point with the score it earned and what moved between them.
First recorded scan — no prior version to compare against.
The primary manifest — the file an agent reads to learn what this artifact does.
Model Context Protocol (MCP) server for EMBL-EBI bioinformatics APIs — InterPro protein domains, Pfam families, protein sequence features, and taxonomy.
embl_data) with 6 methodscd embl-mcp-server
npm install
npm run build{
"mcpServers": {
"embl": {
"command": "node",
"args": ["/path/to/embl-mcp-server/build/index.js"]
}
}
}Single unified tool with multiple methods accessed via the method parameter.
#### 1. search_interpro
Search InterPro protein families and domains.
{
"method": "search_interpro",
"query": "kinase",
"limit": 10
}Returns: accession, name, type (family/domain/repeat), description.
#### 2. get_interpro_entry
Get full InterPro entry details.
{
"method": "get_interpro_entry",
"accession": "IPR000719"
}Returns: name, type, description, GO terms, literature references.
#### 3. get_protein_domains
Get all InterPro domains mapped to a UniProt protein.
{
"method": "get_protein_domains",
"uniprot_id": "P04637"
}Returns: domain entries with positions on the protein sequence.
#### 4. search_pfam
Search Pfam protein families.
{
"method": "search_pfam",
"query": "SH2 domain",
"limit": 10
}Returns: Pfam accession, name, type, description.
#### 5. get_protein_features
Get all sequence features for a UniProt protein.
{
"method": "get_protein_features",
"uniprot_id": "P04637"
}Returns: features array with type, description, location (begin/end), evidence.
#### 6. search_taxonomy
Search NCBI taxonomy via EBI.
{
"method": "search_taxonomy",
"query": "homo sapiens",
"limit": 5
}Returns: taxId, scientificName, displayName.
MIT
~30 seconds. Free. No account. Every finding cites a rule and a line of evidence.