Skip to main content
Glama

search_records

Read-only

Search the sequence archives by free text (a gene name, a protein, an organism, a phrase) across NCBI Nucleotide and Protein, ENA (plain records, WGS and TSA/TLS assembly sets, and annotated coding/non-coding features), UniProtKB and the iGEM Registry at once, and hand back the matching accessions.

Input Schema

NameRequiredDescriptionDefault
limitNohow many hits to ask each source for. The panel pages at this size, and every source is asked for the same number.
queryYesthe words to search for. Archive query syntax is accepted where the archive accepts it, but plain words are the normal case: "beta-lactamase Escherichia coli", "GFP", "pUC19".
_filesNoThe project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
sourcesNowhich archives to ask. Each is searched independently and the hits are interleaved, so asking more costs time rather than accuracy. Defaults to the nucleotide pair the panel opens on.
_subjectNoThe record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.

Output Schema

NameRequiredDescriptionDefault
hitsYesthe full result rows: accession, title, source, organism, length, molecule kind and the archive’s own reported fields
sourceYeswhich archive the top hit came from, ready for the same node's $source where the two vocabularies agree
hitCountYeshow many records came back across every source asked
accessionYesthe top hit's accession, ready for a fetch_record node's $accession. This is the seam between searching and fetching
accessionsYesevery hit’s accession, newline-separated, in the order they are ranked
unavailableYesthe sources that could not answer, each with the reason: empty when every source answered. A search is not a failure because one archive is down, and hiding that would make a short list read as a small literature

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A3.8/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint/openWorldHint/destructiveHint=false, so safety is covered. The description adds genuine behavioral context beyond them: each archive is queried independently and hits are interleaved, so adding sources costs latency rather than accuracy, and the result is accessions rather than full records. It still omits rate limits and per-source failure behavior.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

A single front-loaded sentence led by the verb and resource, with the archive list as parenthetical detail. It is dense but every clause carries scope information; the nested parenthetical for ENA sub-sources is the only mildly heavy section.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a read-only federated search with an output schema and fully documented parameters, the description supplies what is needed to call it correctly: what is searched, at what granularity, and what comes back. The missing piece is routing guidance against the many sibling lookup/blast tools, which is a usage rather than completeness gap.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100%, so 3 is the baseline. The description earns above baseline by giving the query parameter real semantics — free text may be a gene name, protein, organism, or phrase — which tells an agent the intended input style better than the schema's example list alone. The _subject/_files project-reference parameters are left entirely to the schema.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb and resource ('Search the sequence archives by free text') and enumerates the exact corpora searched (NCBI Nucleotide/Protein, ENA plain/WGS/TSA/features, UniProtKB, iGEM) plus the return shape ('matching accessions'). That is far clearer than a generic 'search'. It stops short of naming the siblings it competes with (find_accessions, blast_search, fetch_record, query_database), so it earns a 4 rather than a 5.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

There is no explicit when-to-use or when-not-to-use statement. Usage is only implied: the tool returns accessions, which signals a discovery step that precedes fetch_record/load_record. The only real selection guidance lives in the schema ('asking more costs time rather than accuracy'), not in the description.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

Try in Browser

Glama MCP Gateway

Add one secure layer between your agents and this server.

Resources