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interpro-mcp-server

by io.github.cyanheads
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InterPro entry metadata

interpro_get_entry
Read-onlyIdempotent

Retrieve one InterPro or member-database entry with full metadata by default. Select optional sections while retaining core and unknown metadata, or supply overlapLimit to page whole overlap records in upstream order; offsets are not a snapshot across calls.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "accession": "<accession>"
    },
    "name": "interpro_get_entry"
  }
}

Input Schema

NameRequiredDescriptionDefault
sectionsNoRetain these named sections and all core or unknown metadata; omitted means full detail, and an empty array retains core metadata only.
accessionYesInterPro or member-database entry accession, such as IPR011615 or PF00870; no URL syntax.
overlapLimitNoPositive safe integer number of whole overlap records; supplying it enables overlap paging.
overlapOffsetNoNonnegative safe integer overlap offset; requires overlapLimit, defaults to zero.
sourceDatabaseNoDatabase slug; inferred from standard accession prefixes when omitted.
includeThumbnailNoInclude each Wikipedia thumbnail image, base64 data often hundreds of KB; defaults to false.

Output Schema

NameRequiredDescriptionDefault
urlNoCanonical InterPro website URL.
entryNoUpstream metadata after explicit section selection and overlap paging, with readable descriptionText when description is retained; raw description shapes and sparse annotations survive. Wikipedia thumbnails are omitted unless includeThumbnail is true.
errorNoPresent when the call failed. Absent on success.
noticeNoSection selection, overlap page continuation or availability, and omitted Wikipedia thumbnail guidance.
sectionsNoCanonical selected sections, when explicitly selected.
accessionNoCanonical requested accession.
sourceUrlNoOfficial API source URL.
totalCountNoTotal upstream overlap records when explicit paging has an available array.
overlapsPageNoExplicit overlap paging state; unavailable arrays have no fabricated total.
sourceDatabaseNoInterPro entry API database slug.
omittedSectionsNoNamed sections actually removed from upstream metadata.

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed11 schema fields changed
    • addedInput schema / properties / overlapLimit
      Added value: +{
+  "description": "Positive safe integer number of whole overlap records; supplying it enables overlap paging.",
+  "exclusiveMinimum": 0,
+  "maximum": 9007199254740991,
+  "type": "integer"
+}
    • addedInput schema / properties / overlapOffset
      Added value: +{
+  "description": "Nonnegative safe integer overlap offset; requires overlapLimit, defaults to zero.",
+  "maximum": 9007199254740991,
+  "minimum": 0,
+  "type": "integer"
+}
    • addedInput schema / properties / sections
      Added value: +{
+  "description": "Retain these named sections and all core or unknown metadata; omitted means full detail, and an empty array retains core metadata only.",
+  "items": {
+    "description": "Optional metadata section to retain.",
+    "enum": [
+      "description",
+      "hierarchy",
+      "member_databases",
+      "go_terms",
+      "literature",
+      "cross_references",
+      "wikipedia",
+      "counters",
+      "overlaps_with"
+    ],
+    "type": "string"
+  },
+  "type": "array"
+}
    • changedOutput schema / properties / entry / description
      Previous value: -"Complete upstream metadata with readable descriptionText, preserving raw description shapes and sparse annotations; Wikipedia thumbnails are omitted unless includeThumbnail is true."New value: +"Upstream metadata after explicit section selection and overlap paging, with readable descriptionText when description is retained; raw description shapes and sparse annotations survive. Wikipedia thumbnails are omitted unless includeThumbnail is true."
    • changedOutput schema / properties / error / properties / data / properties / reason / description
      Previous value: -"Machine-readable failure mode. Declared by this tool: `database_mismatch`: Explicit database conflicts with accession routing. `accession_source_unknown`: Accession has no inferred or explicit database. `entry_not_found`: Entry detail returns 204 or 404, or the accession is a set accession. `entry_withdrawn`: Entry or set returns 410. `upstream_shape_invalid`: Upstream JSON, structure, or continuation is incompatible. `upstream_response_too_large`: An upstream response exceeds 4 MiB. `upstream_rejected`: InterPro returns an unhandled redirect or client rejection. `upstream_unavailable`: InterPro has a network or server failure; HTTP 501 is not retryable. `upstream_timeout`: InterPro returns HTTP 408/504 or an attempt exceeds its deadline. `upstream_rate_limited`: InterPro returns HTTP 429. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `overlap_limit_required`: overlapOffset is supplied without overlapLimit. `overlaps_not_selected`: Overlap paging is requested but sections excludes overlaps_with. `database_mismatch`: Explicit database conflicts with accession routing. `accession_source_unknown`: Accession has no inferred or explicit database. `entry_not_found`: Entry detail returns 204 or 404, or the accession is a set accession. `entry_withdrawn`: Entry or set returns 410. `upstream_shape_invalid`: Upstream JSON, structure, or continuation is incompatible. `upstream_response_too_large`: An upstream response exceeds 4 MiB. `upstream_rejected`: InterPro returns an unhandled redirect or client rejection. `upstream_unavailable`: InterPro has a network or server failure; HTTP 501 is not retryable. `upstream_timeout`: InterPro returns HTTP 408/504 or an attempt exceeds its deadline. `upstream_rate_limited`: InterPro returns HTTP 429. Other values are possible when a failure originates below the handler."
    • changedOutput schema / properties / error / properties / data / properties / reason / examples
      Previous value: -[
-  "database_mismatch",
-  "accession_source_unknown",
-  "entry_not_found",
-  "entry_withdrawn",
-  "upstream_shape_invalid",
-  "upstream_response_too_large",
-  "upstream_rejected",
-  "upstream_unavailable",
-  "upstream_timeout",
-  "upstream_rate_limited"
-]New value: +[
+  "overlap_limit_required",
+  "overlaps_not_selected",
+  "database_mismatch",
+  "accession_source_unknown",
+  "entry_not_found",
+  "entry_withdrawn",
+  "upstream_shape_invalid",
+  "upstream_response_too_large",
+  "upstream_rejected",
+  "upstream_unavailable",
+  "upstream_timeout",
+  "upstream_rate_limited"
+]
    • changedOutput schema / properties / notice / description
      Previous value: -"Omitted Wikipedia thumbnail size and how to include it."New value: +"Section selection, overlap page continuation or availability, and omitted Wikipedia thumbnail guidance."
    • addedOutput schema / properties / omittedSections
      Added value: +{
+  "description": "Named sections actually removed from upstream metadata.",
+  "items": {
+    "description": "Omitted source section.",
+    "enum": [
+      "description",
+      "hierarchy",
+      "member_databases",
+      "go_terms",
+      "literature",
+      "cross_references",
+      "wikipedia",
+      "counters",
+      "overlaps_with"
+    ],
+    "type": "string"
+  },
+  "type": "array"
+}
    • addedOutput schema / properties / overlapsPage
      Added value: +{
+  "description": "Explicit overlap paging state; unavailable arrays have no fabricated total.",
+  "oneOf": [
+    {
+      "additionalProperties": false,
+      "description": "Page of complete upstream overlap records.",
+      "properties": {
+        "available": {
+          "const": true,
+          "description": "Overlap array was supplied.",
+          "type": "boolean"
+        },
+        "hasMore": {
+          "description": "More overlap records remain.",
+          "type": "boolean"
+        },
+        "nextOffset": {
+          "description": "Next offset when more records remain.",
+          "maximum": 9007199254740991,
+          "minimum": 0,
+          "type": "integer"
+        },
+        "offset": {
+          "description": "Requested record offset.",
+          "maximum": 9007199254740991,
+          "minimum": 0,
+          "type": "integer"
+        },
+        "returned": {
+          "description": "Complete records returned.",
+          "maximum": 9007199254740991,
+          "minimum": 0,
+          "type": "integer"
+        },
+        "total": {
+          "description": "Complete upstream overlap count.",
+          "maximum": 9007199254740991,
+          "minimum": 0,
+          "type": "integer"
+        }
+      },
+      "required": [
+        "available",
+        "total",
+        "offset",
+        "returned",
+        "hasMore"
+      ],
+      "type": "object"
+    },
+    {
+      "additionalProperties": false,
+      "description": "Overlap paging unavailable for a missing or null source section.",
+      "properties": {
+        "available": {
+          "const": false,
+          "description": "Overlap array was not supplied.",
+          "type": "boolean"
+        },
+        "offset": {
+          "description": "Requested record offset.",
+          "maximum": 9007199254740991,
+          "minimum": 0,
+          "type": "integer"
+        }
+      },
+      "required": [
+        "available",
+        "offset"
+      ],
+      "type": "object"
+    }
+  ]
+}
    • addedOutput schema / properties / sections
      Added value: +{
+  "description": "Canonical selected sections, when explicitly selected.",
+  "items": {
+    "description": "Retained optional section.",
+    "enum": [
+      "description",
+      "hierarchy",
+      "member_databases",
+      "go_terms",
+      "literature",
+      "cross_references",
+      "wikipedia",
+      "counters",
+      "overlaps_with"
+    ],
+    "type": "string"
+  },
+  "type": "array"
+}
    • addedOutput schema / properties / totalCount
      Added value: +{
+  "description": "Total upstream overlap records when explicit paging has an available array.",
+  "maximum": 9007199254740991,
+  "minimum": 0,
+  "type": "integer"
+}
  2. First observed

TDQS

A3.7/5.0
Behavior4/5

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

Annotations already declare readOnly, idempotent, openWorld, so the safety profile is covered. The description still adds real behavioral context beyond them: default full metadata, section retention preserving core/unknown fields, and the caveat that offsets are not a snapshot across calls, which matters for paging correctness.

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?

Two dense sentences with no filler, and the default behavior (full metadata) is front-loaded. The paging caveat is slightly compressed but still lands in the same sentence as its trigger parameter.

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?

With an output schema present, return values need not be explained, and the description covers default behavior, section selection, paging mode, and a non-obvious paging caveat. What remains missing is any upstream/error behavior context or sibling routing, keeping it at 4 rather than 5.

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 schema already documents sections, overlapLimit/overlapOffset, sourceDatabase inference, and thumbnail cost. The description restates the section-retention and paging behavior at a high level but adds no syntax or format detail beyond the schema, so 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 ('Retrieve one InterPro or member-database entry') and a default scope ('full metadata by default'), which differentiates it from list/search siblings like interpro_search_entries. It doesn't explicitly name a sibling or exclusion, so it falls just short of 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?

It describes how to use the options ('select optional sections while retaining core and unknown metadata, or supply overlapLimit to page whole overlap records'), which implies when to use those modes. However, it never states when to call this versus interpro_search_entries or interpro_get_clan, so usage is inferred rather than guided.

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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