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Glama

Ensembl

by io.github.pipeworx-io

Search Within a Source

search_within
Read-onlyIdempotent

Semantic search INSIDE a fetched record. Pass the text you already pulled (e.g. a SEC 10-K body, an article, a long tool result) plus a natural-language query; get back the top-N passages with character offsets and similarity scores. Use when the record is too big to cram into the prompt — search_within saves context, returns only the passages that matter, and every passage carries an offset so the agent can verify a verbatim quote. Pairs with ask_pipeworx_grounded: fetch with the gateway, ground over the relevant passages instead of the whole document. BGE-base-en embeddings + cosine over 500-char overlapping windows; cap is 200K chars (longer inputs are truncated and flagged).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
textYesThe document text to search inside (max ~200K chars).
limitNoMax passages to return (1-20, default 5).
queryYesNatural-language query — what passages do you want? E.g. "supply-chain risk", "fiscal year 2024 revenue", "drug interactions with warfarin".

Schema Changelog

Changes observed during successful MCP inspections. Dates show when Glama detected each change.

  1. Added

TDQS

A4.9/5.0
Behavior5/5

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

Beyond the annotations (readOnly, openWorld, idempotent, non-destructive), the description discloses the embedding model (BGE-base-en), the retrieval method (cosine over 500-char overlapping windows), and the hard 200K char cap with truncation-flag behavior. This is exactly the kind of implementation detail that helps an agent reason about input limits and result quality.

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

Conciseness5/5

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

The description is compact but information-dense: a one-sentence purpose, a usage rationale, a sibling pairing, and a technical behavior clause. Every sentence serves a distinct role with no padding or repetition.

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

Completeness5/5

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

Even without an output schema, the description specifies what the agent gets back: 'top-N passages with character offsets and similarity scores.' It covers input constraints, output shape, and failure behavior (truncation flag), making the tool fully usable from the description alone.

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 the baseline is 3. The description adds value by giving concrete example queries ('supply-chain risk', 'fiscal year 2024 revenue') and clarifying that 'text' is the already-fetched record content. It also reinforces the limit defaults and the top-N passage output, going slightly beyond the schema's bare descriptions.

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

Purpose5/5

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

The description opens with 'Semantic search INSIDE a fetched record' — a specific verb, resource, and clear scope. It explicitly contrasts with ask_pipeworx_grounded, telling the agent this is the tool for searching within text you've already pulled, not for grounding over a whole document.

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

Usage Guidelines5/5

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

The description says 'Use when the record is too big to cram into the prompt' and explains that it 'saves context, returns only the passages that matter.' It also names a sibling tool (ask_pipeworx_grounded) and describes the intended pairing, giving clear when-to-use and when-not-to-use guidance.

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

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TDQS

A3.6/5.0
Disambiguation2/5

There is heavy overlap in the ask_pipeworx family (ask_pipeworx, ask_pipeworx_beta, ask_pipeworx_grounded, deep_research, bet_research, validate_claim) — several are near-identical 'route a natural-language question to a source' tools differing only by small qualifiers. ai_visibility_check vs scan_competitor_ai_presence and entity_profile vs compare_entities vs recent_changes also blur together. An agent could easily misselect among these.

Naming Consistency4/5

The dominant convention is snake_case verb_noun/noun_verb (list_subscriptions, scan_dependency, validate_claim, resolve_entity) which is fairly consistent, but there are several bare single-word verbs (lookup, sequence, variation, vep, xrefs, recall, remember, forget) that break the pattern. No camelCase is present, so the inconsistency is minor rather than chaotic.

Tool Count2/5

38 tools is heavy, and the overwhelming majority (~31) are Pipeworx meta-tools (subscriptions, memory, feedback, trend, discovery, llms.txt generation) that have nothing to do with the server's declared Ensembl identity. Only about 7 tools are actually genomics-related, so the count is inflated by off-domain additions that dilute the surface.

Completeness2/5

For the Ensembl domain, the surface covers gene lookup, symbol resolution, sequence retrieval, orthologs, SNPs, variant effect prediction, and xrefs — but misses major Ensembl capabilities like gene trees/families, regulatory features, comparative/multi-species alignments, expression data, phenotypes, GO/ontology annotations, and region/overlap queries. Conversely the Pipeworx tools are complete for their own domain but irrelevant here, leaving the declared domain notably incomplete.

Resources