plant-genomics-mcp

Overview Schema Source Related Servers Discussions Admin

Literature (Europe PMC)

locus_literature

Read-onlyIdempotent

Search Europe PMC for articles mentioning a plant locus. Returns publication metadata, abstracts, citation counts, and links, with species disambiguation for non-Arabidopsis genes.

Instructions

Search Europe PMC for literature mentioning a plant locus. Free, no API key. Returns up to size results (default 10, capped at 25) with title, authors, journal, year, DOI, PMID, open-access status, citation count, abstract, and the article's web_url (a link for the client to open; no tool on this server retrieves it). For non-Arabidopsis species the species common name is appended to the query to disambiguate locus IDs (rice, maize, ...). Pair with resolve_locus_to_uniprot or ensembl_plants_lookup_locus to ground the locus before fanning out to the literature.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`size`	No	Max results (1–25, default 10)
`locus`	Yes	e.g. AT1G01010 (Arabidopsis), Os01g0100100 (rice)
`cursor`	No	next_cursor from the previous page; omit for the first (#123)
`organism`	No	Plant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxid	arabidopsis_thaliana
`include_abstract`	No	Set false to null out abstractText, which is ~67% of this payload. The response echoes 'abstracts_included' so a null abstract is not mistaken for an article that has none.

Output Schema

TableJSON Schema

Name	Required	Description
`hits`	Yes
`locus`	Yes
`query`	Yes	Final query string sent to Europe PMC
`total`	Yes	How many papers (Europe PMC hitCount) exist upstream for this query, all pages (pre-cap) (#123)
`hitCount`	Yes	Total hits available upstream (may exceed returned)
`organism`	Yes
`returned`	Yes	Rows in this payload (#123)
`truncated`	Yes	True when total > returned: more exist upstream than came back (#123)
`next_cursor`	No	Pass back as cursor= to get the rows after this page; null on the last page. Opaque, and bound to this tool and query (#123)
`upstream_version`	No	Europe PMC release that produced THIS response, — always null today: this backend states no release on its responses; upstream_release(backend='europe_pmc') reports the release its own endpoint calls current at query time, or why there is none. null means Europe PMC did not state one — never that no release exists, and never inferred from a separate metadata call, which can describe a different release than the one that answered.
`abstracts_included`	No	False when include_abstract=False was passed, in which case every abstractText is null because it was not requested — not because the article lacks one. Abstracts are ~67% of this payload.

Schema Changelog

Changes observed during successful MCP inspections.

Changed1 schema field changedv1.27.0Sep 27, 2026

changedOutput schema / properties / upstream_version / description

Previous value: -"Europe PMC release that produced THIS response, — always null today: this backend states no release on its responses. null means Europe PMC did not state one — never that no release exists, and never inferred from a separate metadata call, which can describe a different release than the one that answered."New value: +"Europe PMC release that produced THIS response, — always null today: this backend states no release on its responses; upstream_release(backend='europe_pmc') reports the release its own endpoint calls current at query time, or why there is none. null means Europe PMC did not state one — never that no release exists, and never inferred from a separate metadata call, which can describe a different release than the one that answered."

Changed6 schema fields changedv1.24.0Sep 26, 2026

changedOutput schema / $defs / LiteratureHit / properties / hasPDF / anyOf

Previous value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]New value: +[
+  {
+    "type": "boolean"
+  },
+  {
+    "type": "null"
+  }
+]

changedOutput schema / $defs / LiteratureHit / properties / hasPDF / description

Previous value: -"\"Y\" or \"N\""New value: +"A PDF is available (upstream Y/N)"

changedOutput schema / $defs / LiteratureHit / properties / isOpenAccess / anyOf

Previous value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]New value: +[
+  {
+    "type": "boolean"
+  },
+  {
+    "type": "null"
+  }
+]

changedOutput schema / $defs / LiteratureHit / properties / isOpenAccess / description
```
Previous value: -"\"Y\" or \"N\""New value: +"Open access (upstream Y/N)"
```

changedOutput schema / $defs / LiteratureHit / properties / pubYear / anyOf

Previous value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]New value: +[
+  {
+    "type": "integer"
+  },
+  {
+    "type": "null"
+  }
+]

changedOutput schema / $defs / LiteratureHit / properties / pubYear / description

Previous value: -"String — wire format is untyped"New value: +"Publication year"

Changed8 schema fields changedv1.22.0Sep 24, 2026

addedInput schema / properties / cursor

Added value: +{
+  "description": "next_cursor from the previous page; omit for the first (#123)",
+  "type": "string"
+}

changedOutput schema / $defs / LiteratureHit / properties / web_url / description

Previous value: -"europepmc.org article URL"New value: +"europepmc.org article URL — a link for the client to open or fetch; no tool on this server dereferences it"

addedOutput schema / properties / next_cursor

Added value: +{
+  "anyOf": [
+    {
+      "type": "string"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "description": "Pass back as cursor= to get the rows after this page; null on the last page. Opaque, and bound to this tool and query (#123)",
+  "title": "Next Cursor"
+}

changedOutput schema / properties / returned / description

Previous value: -"Number of hits actually in hits[]"New value: +"Rows in this payload (#123)"

addedOutput schema / properties / total

Added value: +{
+  "description": "How many papers (Europe PMC hitCount) exist upstream for this query, all pages (pre-cap) (#123)",
+  "title": "Total",
+  "type": "integer"
+}

addedOutput schema / properties / truncated

Added value: +{
+  "description": "True when total > returned: more exist upstream than came back (#123)",
+  "title": "Truncated",
+  "type": "boolean"
+}

addedOutput schema / properties / upstream_version

Added value: +{
+  "anyOf": [
+    {
+      "type": "string"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "description": "Europe PMC release that produced THIS response, — always null today: this backend states no release on its responses. null means Europe PMC did not state one — never that no release exists, and never inferred from a separate metadata call, which can describe a different release than the one that answered.",
+  "title": "Upstream Version"
+}

changedOutput schema / required

Previous value: -[
-  "locus",
-  "organism",
-  "query",
-  "hitCount",
-  "returned",
-  "hits"
-]New value: +[
+  "total",
+  "truncated",
+  "locus",
+  "organism",
+  "query",
+  "hitCount",
+  "returned",
+  "hits"
+]

Changed2 schema fields changedv1.20.0Jul 28, 2026

addedInput schema / properties / include_abstract

Added value: +{
+  "default": true,
+  "description": "Set false to null out abstractText, which is ~67% of this payload. The response echoes 'abstracts_included' so a null abstract is not mistaken for an article that has none.",
+  "type": "boolean"
+}

addedOutput schema / properties / abstracts_included

Added value: +{
+  "default": true,
+  "description": "False when include_abstract=False was passed, in which case every abstractText is null because it was not requested — not because the article lacks one. Abstracts are ~67% of this payload.",
+  "title": "Abstracts Included",
+  "type": "boolean"
+}

Addedv1.19.4Jul 28, 2026
Removedv1.18.2Jul 24, 2026
First observedv1.8.0May 30, 2026

TDQS

A4.5/5.0

Behavior4/5

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

Annotations already declare readOnlyHint, openWorldHint, idempotentHint, and destructiveHint=false. The description adds value by stating 'Free, no API key' (cost/access), clarifying that 'web_url' is merely a link and 'no tool on this server retrieves it' (does not fetch content), and explaining the disambiguation behavior for non-Arabidopsis species. These are behavioral traits beyond the annotations, though the overall safety profile is covered by annotations.

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 four sentences with no redundancy. It front-loads the core action, then lists return fields and a caveat, then explains disambiguation and pairing. Every sentence earns its place, and the structure flows logically from main purpose to details to usage context.

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?

Given the tool's complexity (5 parameters, rich return fields) and that annotations cover safety, the description is complete. It explains the returned fields, the pagination-related 'size' behavior, the disambiguation for organism, and the absence of article retrieval via web_url. The output schema exists, so no need to repeat return structures. No critical information is missing.

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 description coverage is 100%, so the baseline is 3. The description adds meaning beyond the schema by explaining the effect of the 'organism' parameter: 'For non-Arabidopsis species the species common name is appended to the query to disambiguate locus IDs.' It also reiterates the 'size' cap and default. This clarifies behavior not present in the parameter descriptions, justifying a score above baseline.

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 states a specific action and resource: 'Search Europe PMC for literature mentioning a plant locus.' It clearly distinguishes from sibling tools like tair_locus_info or plantcyc_locus_info which are not about literature, and names companion tools (resolve_locus_to_uniprot, ensembl_plants_lookup_locus) for context. The verb 'search' and the resource 'Europe PMC' are unambiguous.

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

Usage Guidelines4/5

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

The description gives clear context on when to use this tool: 'Pair with resolve_locus_to_uniprot or ensembl_plants_lookup_locus to ground the locus before fanning out to the literature.' It does not explicitly mention when not to use it or alternatives like batch_locus_literature, but it implies a workflow that justifies its use. This is a clear context without explicit exclusions, fitting a score of 4.

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

Deploy Server