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Jean — Molecular Biology & Genomics

find_accessions

Read-only

Find the sequence accessions a text names (a paper's methods, a notebook, a report) and resolve each against its archive: identifiers.org's own pattern for every namespace a fetch target serves, scanned over the text, then one batched search per archive.

Input Schema

NameRequiredDescriptionDefault
textYesthe text to scan, e.g. the markdown fetch_article returns.
_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.
_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
foundYeseach resolved accession with the record it names (archive, title, organism, length) and how often the text mentions it
summaryYeshow many accessions resolved, at which archives, and how many spans did not
accessionsYesevery resolved accession as the text writes it, in text order
namespacesYesthe identifiers.org namespaces read, by prefix and registry name
unresolvedYesspans a pattern admitted that no archive holds

Schema Changelog

Changes observed during successful MCP inspections.

  1. Added

TDQS

A3.7/5.0
Behavior4/5

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

Annotations already declare readOnly, openWorld and non-destructive, but the description adds real mechanism: it scans identifiers.org patterns per namespace and issues one batched search per archive, which tells the agent this makes multiple external calls rather than a local lookup. It stops short of describing failure handling when an accession fails to resolve or any rate/cost limits.

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?

One sentence, verb-first, with the key scope up front and mechanism after the colon. The clause 'identifiers.org's own pattern for every namespace a fetch target serves' is dense jargon that costs some readability, but nothing is redundant.

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?

An output schema exists, so return shape need not be explained, and the three parameters are fully covered by the schema. The description conveys input domain and the two-stage resolution behavior; only the role of the project context parameters in the finding process is left implicit.

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

Parameters3/5

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

Schema description coverage is 100%, so the nested text/_files/_subject semantics are already documented in the schema. The description adds only that scanning happens over the text and that archives are namespaces served by a fetch target, without clarifying how _subject or _files influence resolution. Baseline 3 applies.

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: find sequence accessions named in free text and resolve each against its archive. The parenthetical examples (paper's methods, notebook, report) pin down the input domain well. It does not explicitly contrast with nearby siblings such as fetch_record or search_records, which keeps it from 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?

Usage is implied rather than stated: the text examples and the schema note that the input is 'e.g. the markdown fetch_article returns' suggest a chaining pattern after fetch_article. There is no explicit when-to-use/when-not or named alternative such as fetch_record for a single known accession.

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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