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  "IssueTotal": 13,
  "Held": 13,
  "Issues": [
    {
      "Title": "feat(species): cap ensembl_list_species and the species resources by default",
      "Excerpt": "### Use case\n\n`ensembl_list_species` is the discovery step most workflows start from, but neither it nor the `ensembl://species` / `ensembl://species/{division}` resources can bound their output: every unfiltered call returns the whole division. `nameContains` narrows only as well as the substring discriminates — `{ \"division\": \"EnsemblFungi\", \"nameContains\": \"saccharomyces\" }` still returns 132 species.\n\nMeasured 2026-09-23 against the default `rest.ensembl.org` endpoint, on the response a…",
      "SourceUrl": "https://github.com/cyanheads/ensembl-mcp-server/issues/3",
      "PublishedAt": "2026-06-18T10:25:04.000Z",
      "State": "open",
      "Comments": 5,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "feat(ensembl_query_region): cap high-cardinality overlap output like predict_variant/get_homology",
      "Excerpt": "### Use case\n\n`ensembl_query_region` can return very large overlap sets — a wide region with `feature: [\"variation\"]` can yield tens of thousands of entries (its own description warns a large region can return 44,000+). It emits a >1000-result warning notice but does not cap the result, so the full set still lands in both `content[]` and `structuredContent` — the same all-or-nothing cost #15 already fixed for `ensembl_predict_variant` and `ensembl_get_homology`. Measured against the live API:…",
      "SourceUrl": "https://github.com/cyanheads/ensembl-mcp-server/issues/17",
      "PublishedAt": "2026-07-10T01:01:08.000Z",
      "State": "closed",
      "Comments": 3,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(ensembl_get_sequence): region-mode rejections lack an invalid_region reason",
      "Excerpt": "### Server version\n\n0.4.4\n\n### mcp-ts-core version\n\n0.13.6\n\n### Runtime\n\nBun\n\n### Runtime version\n\n1.4.0\n\n### Transport\n\nHTTP (Streamable HTTP)\n\n### Description\n\nIn region mode, `ensembl_get_sequence` returns a reasonless `-32001` for region rejections that should be an input error. The region `.catch` recognizes only `not found|invalid|no stable id`, so these `/sequence/region` HTTP 400 messages fall through:\n\n| `id` (with `species: homo_sapiens`) | Ensembl message |\n|:--|:--|\n|…",
      "SourceUrl": "https://github.com/cyanheads/ensembl-mcp-server/issues/28",
      "PublishedAt": "2026-09-24T01:13:55.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(ensembl_query_region): out-of-bounds, reversed, and undecodable regions lack invalid_region",
      "Excerpt": "### Server version\n\n0.4.4\n\n### mcp-ts-core version\n\n0.13.6\n\n### Runtime\n\nBun\n\n### Runtime version\n\n1.4.0\n\n### Transport\n\nHTTP (Streamable HTTP)\n\n### Description\n\n`ensembl_query_region` still returns a reasonless `-32001` NotFound for three upstream region rejections that `invalid_region` should cover. Ensembl answers each with HTTP 400, and none of the messages matches the handler's `invalid_region` patterns:\n\n| `region` | Ensembl message |\n|:--|:--|\n| `1:250000000-250000100` | `Cannot request…",
      "SourceUrl": "https://github.com/cyanheads/ensembl-mcp-server/issues/27",
      "PublishedAt": "2026-09-24T00:46:50.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(ensembl_get_sequence): region mode silently ignores type and always returns genomic",
      "Excerpt": "Related: #13\n\n### Server version\n\n0.4.3\n\n### mcp-ts-core version\n\n0.13.6\n\n### Runtime\n\nBun\n\n### Runtime version\n\n1.4.0\n\n### Transport\n\nHTTP (Streamable HTTP)\n\n### Description\n\nIn region mode, `ensembl_get_sequence` never forwards `input.type` to the service. `getSequenceByRegion()` takes no type argument and hardcodes `normalizeSequence(raw, 'genomic')`, so a caller who asks for `cdna`, `cds`, or `protein` on a region receives genomic DNA labelled `type: \"genomic\"` — a wrong answer with no…",
      "SourceUrl": "https://github.com/cyanheads/ensembl-mcp-server/issues/25",
      "PublishedAt": "2026-09-19T16:11:06.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(ensembl_query_region): oversized regions return NotFound",
      "Excerpt": "### Server version\n\n0.4.3\n\n### mcp-ts-core version\n\n0.12.3\n\n### Runtime\n\nBun\n\n### Runtime version\n\nBun 1.4.0 client\n\n### Transport\n\nHTTP (Streamable HTTP)\n\n### Description\n\n`ensembl_query_region` accepts a syntactically valid region larger than Ensembl's documented 5 Mb maximum, then returns `NotFound` without its `invalid_region` reason or recovery hint. The region description recommends restricting large queries to genes but never states the hard length limit.\n\nRelated: #1.\n\n### Steps to…",
      "SourceUrl": "https://github.com/cyanheads/ensembl-mcp-server/issues/24",
      "PublishedAt": "2026-09-13T17:29:49.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "feat(ensembl_query_region): include assembly metadata",
      "Excerpt": "### Use case\n\nGenomic coordinates are assembly-specific. A region-overlap result is unsafe to carry into VEP, external annotation, or downstream interval analysis unless the response says which assembly the coordinates use.\n\n`ensembl_query_region` currently returns the submitted species and region plus feature coordinates, but no assembly name. A successful BRCA2-region query therefore cannot be handed to another system without an additional out-of-band assembly lookup.\n\n### Proposed behavior…",
      "SourceUrl": "https://github.com/cyanheads/ensembl-mcp-server/issues/23",
      "PublishedAt": "2026-08-11T12:24:23.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(validation): reject blank required identifiers",
      "Excerpt": "### Server version\n\n0.4.2\n\n### mcp-ts-core version\n\n^0.10.14\n\n### Runtime\n\nBun\n\n### Runtime version\n\n1.3.14\n\n### Transport\n\nHTTP (Streamable HTTP)\n\n### Description\n\nRequired free-form string identifiers accept blank or whitespace-only values and reach Ensembl before failing. Verified live against all five required-identifier fields — `ensembl_predict_variant.variant`, `ensembl_get_sequence.id`, `ensembl_get_xrefs.id`, `ensembl_query_region.species`/`region` — each makes a live upstream call on…",
      "SourceUrl": "https://github.com/cyanheads/ensembl-mcp-server/issues/22",
      "PublishedAt": "2026-08-11T12:24:22.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(ensembl_get_sequence): prefixed region with a digit-bearing species routes to stable-ID mode",
      "Excerpt": "### Server version\n\n0.5.0\n\n### mcp-ts-core version\n\n^0.13.6\n\n### Runtime\n\nBun\n\n### Runtime version\n\n1.4.0\n\n### Transport\n\nstdio\n\n### Description\n\n`ensembl_get_sequence` detects the prefixed region form with `/^[a-z_]+:[\\w.]+:\\d+-\\d+$/i`, so a species name containing digits never matches. Ensembl strain genomes carry digits in their internal names (`mus_musculus_129s1svimj`, from `/info/genomes`), and a valid prefixed region for one is sent to `/sequence/id` as a stable ID instead of…",
      "SourceUrl": "https://github.com/cyanheads/ensembl-mcp-server/issues/33",
      "PublishedAt": "2026-09-24T02:57:42.000Z",
      "State": "open",
      "Comments": 0,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(ensembl_get_sequence): protein ID with type cdna returns protein labelled cdna",
      "Excerpt": "### Server version\n\n0.4.4\n\n### mcp-ts-core version\n\n0.13.6\n\n### Runtime\n\nBun\n\n### Runtime version\n\n1.4.0\n\n### Transport\n\nHTTP (Streamable HTTP)\n\n### Description\n\n`ensembl_get_sequence` labels a record with the `type` the caller requested rather than the `molecule` Ensembl returned. For a protein ID requested as `cdna` or `genomic`, Ensembl returns the protein sequence (`\"molecule\":\"protein\"`). The tool reports it as `type: \"cdna\"` and renders its length in `bp`, so the caller gets a wrong…",
      "SourceUrl": "https://github.com/cyanheads/ensembl-mcp-server/issues/30",
      "PublishedAt": "2026-09-24T01:44:43.000Z",
      "State": "open",
      "Comments": 0,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(ensembl_get_sequence): unknown species, non-coding protein/cds, and malformed regions lack reasons",
      "Excerpt": "### Server version\n\n0.4.4\n\n### mcp-ts-core version\n\n0.13.6\n\n### Runtime\n\nBun\n\n### Runtime version\n\n1.4.0\n\n### Transport\n\nHTTP (Streamable HTTP)\n\n### Description\n\n`ensembl_get_sequence` still returns reasonless errors, or the wrong reason, for three input mistakes. Each case has an actionable recovery that the caller never sees:\n\n| Input | Ensembl (HTTP 400) | Tool today |\n|:--|:--|:--|\n| `{\"id\":\"1:1-100\",\"species\":\"homo_sapienz\"}` | `Can not find internal name for species 'homo_sapienz'` |…",
      "SourceUrl": "https://github.com/cyanheads/ensembl-mcp-server/issues/29",
      "PublishedAt": "2026-09-24T01:44:41.000Z",
      "State": "open",
      "Comments": 0,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "bug(ensembl_query_region): reject an empty feature list",
      "Excerpt": "### Server version\n\n0.4.2\n\n### mcp-ts-core version\n\n^0.10.14\n\n### Runtime\n\nBun\n\n### Runtime version\n\n1.3.14\n\n### Transport\n\nHTTP (Streamable HTTP)\n\n### Description\n\n`ensembl_query_region` accepts an empty `feature` array even though Ensembl requires at least one feature type. The request reaches the provider without a feature filter, and the resulting error is classified as `not_found` with `data.reason` absent entirely — not merely a generic reason, the field is missing from the error…",
      "SourceUrl": "https://github.com/cyanheads/ensembl-mcp-server/issues/21",
      "PublishedAt": "2026-08-11T12:24:19.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "feat(ensembl_get_sequence): add bounded, retrievable sequence windows",
      "Excerpt": "### Use case\n\nFull sequences already exceed useful MCP response sizes for real genes, and the two client surfaces diverge: `content[]` always renders a fixed ~300–370 character preview regardless of sequence length, while `structuredContent` carries the complete sequence. Measured live against GRCh38:\n\n| Call | seq length | `content[]` chars | `structuredContent` bytes |\n|---|---:|---:|---:|\n| TP53 genomic | 25,768 | 365 | 25,898 |\n| BRCA2 genomic | 85,183 | 366 | 85,314 |\n| BRCA2 protein |…",
      "SourceUrl": "https://github.com/cyanheads/ensembl-mcp-server/issues/19",
      "PublishedAt": "2026-08-11T12:24:15.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Maintainer",
      "Rank": "recent",
      "Extractor": "github_issue"
    }
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      "13 reported issues below",
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