plant-genomics-mcp

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PANTHER: Protein Family

panther_family

Read-onlyIdempotent

Fetch PANTHER family classification and functional annotations for a plant locus. Get family/subfamily IDs, GO terms, protein class, and pathways to interpret gene function across 12 organisms.

Instructions

Fetch the PANTHER protein-family classification for a locus (pantherdb.org; free, no key). Returns the PANTHER family and subfamily (id + name) plus curated GO terms grouped by aspect (molecular_function / biological_process / cellular_component), the PANTHER protein class, and pathways. found=false when PANTHER cannot map the locus; a mapped locus can still have a null family or subfamily, which means PANTHER assigns it none. Complements the sequence-homology tools (gramene_homologs / consensus_homologs) with an evolutionary-family view. Works for all 12 organisms. Defaults to arabidopsis_thaliana; pass organism= for other species.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`locus`	Yes	e.g. AT1G01060 (Arabidopsis), Os01g0100100 (rice RAP-DB)
`organism`	No	Plant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxid	arabidopsis_thaliana

Output Schema

TableJSON Schema

Name	Required	Description
`found`	Yes	True if PANTHER mapped the locus; the family fields can still be null
`locus`	Yes
`pathways`	No
`accession`	No	PANTHER mapped accession
`family_id`	No	PANTHER family id, e.g. PTHR12802; null when PANTHER assigns no family
`family_name`	No
`subfamily_id`	No	e.g. PTHR12802:SF176; null when PANTHER assigns no subfamily, which is PANTHER's answer, not a failed lookup
`protein_class`	No
`subfamily_name`	No
`upstream_version`	No	PANTHER release that produced THIS response, as stated by the answer's search.product.version. null means PANTHER 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.
`go_biological_process`	No
`go_cellular_component`	No
`go_molecular_function`	No

Schema Changelog

Changes observed during successful MCP inspections.

Changed1 schema field changedv1.27.0Sep 27, 2026

changedOutput schema / properties / upstream_version / description

Previous value: -"PANTHER release that produced THIS response, — always null today: this backend states no release on its responses. null means PANTHER 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: +"PANTHER release that produced THIS response, as stated by the answer's search.product.version. null means PANTHER 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."

Changed4 schema fields changedv1.24.0Sep 26, 2026

changedOutput schema / description

Previous value: -"PANTHER protein-family classification for a locus.\n\n``found=False`` (with null/empty fields) means PANTHER could not classify the\nlocus into a family — a normal outcome, not an error."New value: +"PANTHER protein-family classification for a locus.\n\n``found=False`` (with null/empty fields) means PANTHER could not map the\nlocus — a normal outcome, not an error. A mapped locus (``found=True``) can\nstill carry null family and subfamily fields: PANTHER knows the gene and may\nannotate GO terms for it, but assigns it no family (seen live 2026-09-25 for\nan Arabidopsis mitochondrial locus)."

changedOutput schema / properties / family_id / description

Previous value: -"PANTHER family id, e.g. PTHR12802"New value: +"PANTHER family id, e.g. PTHR12802; null when PANTHER assigns no family"

changedOutput schema / properties / found / description

Previous value: -"True if PANTHER classified the locus"New value: +"True if PANTHER mapped the locus; the family fields can still be null"

changedOutput schema / properties / subfamily_id / description

Previous value: -"e.g. PTHR12802:SF176"New value: +"e.g. PTHR12802:SF176; null when PANTHER assigns no subfamily, which is PANTHER's answer, not a failed lookup"

Changed1 schema field changedv1.22.0Sep 24, 2026

addedOutput schema / properties / upstream_version

Added value: +{
+  "anyOf": [
+    {
+      "type": "string"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "description": "PANTHER release that produced THIS response, — always null today: this backend states no release on its responses. null means PANTHER 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"
+}

Addedv1.18.2Jul 24, 2026

TDQS

A4.5/5.0

Behavior5/5

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

Annotations already mark the tool read-only, idempotent, and non-destructive, so the bar for added behavior is lower. The description goes well beyond annotations by disclosing failure semantics ('found=false when PANTHER cannot map the locus'), the possibility of null family/subfamily on a mapped locus, and the external source ('pantherdb.org; free, no key'). This is valuable edge-case context for an agent.

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 front-loaded with the core action, then moves logically through return contents, edge-case behavior, tool positioning, and scope/default. It is compact, about four sentences, with no filler or redundant restatement of the schema.

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?

For a read-only lookup with two well-documented parameters and an output schema, the description covers everything operationally important: what is returned, how unmapped loci behave, organism coverage and default, authentication requirements, and relation to sibling tools. Nothing needed to invoke it correctly is missing.

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% and both parameters already carry examples and defaults, so the baseline is 3. The description adds little beyond restating the organism default ('Defaults to arabidopsis_thaliana; pass organism= for other species') and provides no new syntax or format detail for either parameter.

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 a specific verb and resource: 'Fetch the PANTHER protein-family classification for a locus', then enumerates the exact data returned (family/subfamily, GO terms, protein class, pathways). It also distinguishes itself from siblings by positioning it against gramene_homologs and consensus_homologs as an evolutionary-family view.

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?

It names the relevant alternatives and the relationship: 'Complements the sequence-homology tools (gramene_homologs / consensus_homologs) with an evolutionary-family view.' It also states scope and default behavior ('Works for all 12 organisms', 'Defaults to arabidopsis_thaliana'), but stops short of an explicit when-not-to-use rule or a direct 'use this instead of X' condition.

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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