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v1.9.0

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@Clare72 Clare72 released this 27 Apr 17:02
· 616 commits to main since this release

VFBquery v1.9.0

New features

RelatedTools field in get_term_info

get_term_info responses now include a top-level RelatedTools array listing
MCP tools that are useful for the entity but are dispatched outside the
run_query path. Each entry has tool, label, and default_args ready to
copy into the MCP tool call.

Currently surfaced:

  • get_hierarchy with subclass_of — for cell-type classes (Class +
    Cell).
  • get_hierarchy with part_of — for nervous-system regions (Class +
    Nervous_system, excluding cells), plus the nervous system root
    (FBbt_00005093).
  • find_stocks — for FlyBase feature IDs (FBgn, FBal, FBti, FBtp,
    FBco, FBst). Use this rather than run_query / FindStocks when you need
    the optional collection_filter parameter (Bloomington, Kyoto, VDRC, etc.).
  • find_combo_publications — for FBco split-GAL4 combinations. Use rather
    than run_query / FindComboPublications when you need full citation
    metadata (DOI, PMID, miniref, year).

Behaviour changes

PartsOf and NeuronsPartHere no longer offered for neuron classes

Both queries are now suppressed when an entity has Neuron in its SuperTypes:

  • PartsOf on a neuron class isn't a meaningful query — anatomical sub-parts
    of neuron types aren't modelled at the class level in a way that returns
    useful results.
  • NeuronsPartHere ("neurons with some part in <a neuron>") doesn't make
    sense.

Brain regions, neuropils, and other non-cell anatomy continue to receive both
queries.

Schema

Backward-compatible: RelatedTools is an optional new field; existing
consumers ignoring unknown fields are unaffected.

Motivation

Driven by analysis of a Llama-3.3-70B benchmark run against the VFB MCP, where
the model frequently failed to discover get_hierarchy and to differentiate
stock/publication tools from run_query query types. Surfacing these directly
in get_term_info removes the dependence on the model remembering the
relevant MCP tool exists.