Index / other

Plant Genomics

io-github-musharna-plant-genomics-mcp declares 58 capabilities across 58 tools, with 1 critical issue. One of them, no-revocation, is recorded for every server in the index because MCP has no field in which to declare a way to switch a tool off; a missing declaration is not evidence that the control is missing.

66/100 exposureElevated

Manifest recorded 2026-10-30 from tools/list answered by the PyPI package plant-genomics-mcp==1.30.0 (published to PyPI as plant-genomics-mcp, listed in the official MCP registry as io.github.musharna/plant-genomics-mcp 1.30.0), run in an isolated container with no network access and no credentials. The date changes only when the manifest does. Not verified by a maintainer.

Issues

These describe what this server's manifest declares. A product can provide controls that MCP has no way to express — token revocation, an admin console, audit logs — and this page cannot see them. The absence of a declaration is not evidence that a control is absent.

critical · no-revocation · All 58 tools

58 of 58 tools declare no way for the customer to switch them off once granted. This applies to every tool because MCP has no field in which to declare a revocation mechanism; the product may provide one outside MCP that a manifest cannot show.

high · no-expiry · All 58 tools

58 of 58 tools declare no expiry. This applies to every tool because MCP has no field in which to declare an expiry; the product may provide one outside MCP that a manifest cannot show.

high · no-audit-trail · All 58 tools

58 of 58 tools declare no record of their actions that the customer can read. This applies to every tool because MCP has no field in which to declare an audit requirement; the product may provide one outside MCP that a manifest cannot show.

low · uncapped-read · All 58 tools

58 tools can read data and declare no limit.

Declared capabilities

How each tool was read. declared means the server's own annotation said so — self-reported and unverified. inferred is from the tool's name. assumed means nothing indicated either way.

Tool	Read as	Basis
`ensembl_plants_lookup_locus`	`read`	declared
`get_gene_xrefs`	`read`	declared
`get_sequence`	`read`	declared
`ensembl_region_query`	`read`	declared
`phytozome_lookup_locus`	`read`	declared
`resolve_locus_to_uniprot`	`read`	declared
`uniprot_id_mapping`	`read`	declared
`maize_gene_model_translation`	`read`	declared
`locus_literature`	`read`	declared
`locus_go_annotations`	`read`	declared
`locus_plant_ontology`	`read`	declared
`go_enrichment`	`read`	declared
`gramene_homologs`	`read`	declared
`kegg_pathways`	`read`	declared
`bar_gene_summary`	`read`	declared
`bar_efp_expression`	`read`	declared
`bar_aiv_interactions`	`read`	declared
`string_interactions`	`read`	declared
`tair_locus_info`	`read`	declared
`plantcyc_locus_info`	`read`	declared
`alphafold_structure`	`read`	declared
`experimental_structures`	`read`	declared
`tf_binding_motifs`	`read`	declared
`jaspar_motif`	`read`	declared
`experimental_interactions`	`read`	declared
`locus_gene_rifs`	`read`	declared
`interpro_domains`	`read`	declared
`locus_variants`	`read`	declared
`vep_annotate`	`read`	declared
`panther_family`	`read`	declared
`entry_members`	`read`	declared
`gene_tree_members`	`read`	declared
`ensembl_plants_paralogs`	`read`	declared
`ensembl_plants_assembly`	`read`	declared
`upstream_release`	`read`	declared
`orthodb_orthologs`	`read`	declared
`aragwas_associations`	`read`	declared
`arabidopsis_natural_variation`	`read`	declared
`batch_ensembl_plants_lookup_locus`	`read`	declared
`batch_get_gene_xrefs`	`read`	declared
`batch_phytozome_lookup_locus`	`read`	declared
`batch_resolve_locus_to_uniprot`	`read`	declared
`batch_locus_literature`	`read`	declared
`blast_sequence`	`read`	declared
`batch_locus_go_annotations`	`read`	declared
`batch_gramene_homologs`	`read`	declared
`batch_kegg_pathways`	`read`	declared
`batch_bar_gene_summary`	`read`	declared
`batch_bar_aiv_interactions`	`read`	declared
`batch_string_interactions`	`read`	declared
`atted_coexpression`	`read`	declared
`batch_atted_coexpression`	`read`	declared
`analyze_locus_synth`	`read`	declared
`find_homologs_synth`	`read`	declared
`biological_context_synth`	`read`	declared
`consensus_homologs`	`read`	declared
`gene_report`	`read`	declared
`batch_locus_call`	`read`	declared

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