MGI through GeneFoundry

Router invocation: mgi_get_server_capabilities()

Return the mgi-link discovery surface. detail='summary' (default) is light: identity/build/MGI release, the tool list WITH call signatures, accepted argument aliases, response modes, recommended workflows, error taxonomy, and limits. detail='full' adds vocabularies (allele types, marker types, match types) and the ortholog field catalogue. Call this first in a cold session, or read mgi://tools / mgi://capabilities. Signature: get_server_capabilities(detail=).

Router invocation: mgi_get_diagnostics()

Report the local MGI index status: whether the data is built, the loaded release, marker/allele/phenotype/ortholog/disease counts, schema version, and when it was built. Use this to confirm freshness or diagnose a data_unavailable error. Signature: get_diagnostics().

Router invocation: mgi_resolve_marker()

Resolve any mouse marker reference to its canonical MGI record. Accepts a mouse symbol (current or synonym, case-insensitive), an MGI id (MGI:98968 or 98968), OR a human gene symbol / HGNC id (resolved to the mouse ortholog). Returns {mgi_id, symbol, name, marker_type, match_type (mgi_id|current|synonym|ortholog)}. An ambiguous symbol returns an ambiguous_query error with the candidate list (not silently picked). A human symbol identical to the mouse symbol resolves as match_type=current (case collision) rather than ortholog; the marker is the same. Signature: resolve_marker(query, response_mode=).

Router invocation: mgi_get_marker()

Return the full MGI marker record, resolved from an MGI id, mouse symbol/synonym, or human ortholog. Includes name, marker/feature type, GRCm39 location, NCBI/Ensembl ids, synonyms, the human ortholog (symbol/HGNC/OMIM), and summary counts (alleles, phenotypes, phenotype references, diseases). response_mode controls verbosity. Signature: get_marker(query, response_mode=).

Router invocation: mgi_search_markers()

Free-text search over mouse marker symbols, names, and synonyms (FTS, relevance-ranked). Returns ranked {mgi_id, symbol, name, marker_type, score, match} summaries. Exact symbol/synonym hits are PINNED first (match: exact_symbol|exact_synonym|fts) so an exact gene is never buried under transgenes or lncRNAs. Returns a truncation contract {total, returned, limit, truncated}; when truncated, next_commands includes a widen step. marker_type optionally restricts to a type (e.g. 'Gene'). Nomenclature-only: no phenotype semantics — use search_phenotype_terms + find_markers_by_phenotype for phenotype-driven discovery, or resolve_marker for an exact symbol/id. Signature: search_markers(query, marker_type=, limit=, response_mode=).

Router invocation: mgi_get_marker_alleles()

Return the phenotypic alleles / mutations for a mouse marker — the gene page's 'All Mutations and Alleles' panel. Includes per-allele {allele_id, symbol, name, allele_type, attributes, pubmed_ids} and the generation-method category_counts (Targeted, Endonuclease-mediated, Radiation induced, Chemically induced, Transgenic, ...). allele_type optionally filters (accepts friendly tokens like 'knockout', 'crispr', 'targeted'). Returns a truncation contract {total, returned, limit, truncated}; when truncated, next_commands includes a widen step. Signature: get_marker_alleles(query, allele_type=, limit=, response_mode=).

Router invocation: mgi_get_marker_phenotypes()

Return the Mammalian Phenotype (MP) annotations for a mouse marker. By default (minimal/compact/standard) returns a DEDUPLICATED, support-ordered list of DISTINCT MP terms — each {mp_id, mp_term, genotype_count} (standard adds systems[]) — so the most replicated phenotypes come first and none are buried alphabetically. response_mode=full returns the per-genotype rows {mp_id, mp_term, allelic_composition, genetic_background, pubmed_id, genotype_id, ...}. Every response carries a phenotype summary and a truncation contract {total, returned, limit, truncated}; when truncated, next_commands includes a widen step. mp_system optionally restricts to one top-level system (name like 'renal/urinary system' or its MP id). SCOPE: annotations are single-locus, NON-conditional genotypes (MGI_GenePheno); conditional/Cre-driven and multi-genic genotypes are EXCLUDED (see the response 'scope'/'scope_note'), so a zero or empty result does not mean the gene lacks that phenotype in mouse — confirm on the MGI gene page. Signature: get_marker_phenotypes(query, mp_system=, limit=, response_mode=).

Router invocation: mgi_get_phenotype_overview()

Return a per-system phenotype overview grid: for each top-level MP system annotated for the marker (adipose tissue, cardiovascular system, renal/urinary system, nervous system, neoplasm, vision/eye, ...), the distinct annotated MP terms rolled up via the MP ontology. Use this for the system-level overview, then get_marker_phenotypes(mp_system=) to drill into one system. SCOPE: built from single-locus, NON-conditional genotypes (MGI_GenePheno); conditional/Cre-driven and multi-genic genotypes are EXCLUDED (see the response 'scope'/'scope_note'), so this grid is NOT a full mirror of the MGI gene page and a system may be absent here while the gene page shows it. Signature: get_phenotype_overview(query).

Router invocation: mgi_find_markers_by_phenotype()

Reverse lookup: return the mouse markers (genes) annotated with a Mammalian Phenotype term. include_descendants defaults to TRUE and changes WHICH genes are returned: it rolls up annotations to more-specific child terms via the MP ontology (e.g. MP:0005367 renal/urinary system phenotype gathers all kidney phenotypes); the flag is echoed in the response. Returns a truncation contract {total, returned, limit, truncated}; when truncated, next_commands includes a widen step. Resolve a term first with search_phenotype_terms. Signature: find_markers_by_phenotype(mp_id, include_descendants=, limit=).

Router invocation: mgi_get_marker_ortholog()

Return the mouse<->human ortholog mapping and cross-references for a marker: human symbol, HGNC id, NCBI Gene (human), Ensembl (human), OMIM gene id, and human GRCh38 coordinates. Accepts a mouse symbol/MGI id OR a human symbol/HGNC id (resolved to the mouse marker first). Signature: get_marker_ortholog(query, response_mode=).

Router invocation: mgi_get_marker_diseases()

Return the human-mouse disease models associated with a marker (Disease Ontology id + name + OMIM ids), from MGI's curated DO annotations. Accepts a mouse symbol/MGI id or a human ortholog. Signature: get_marker_diseases(query).

Router invocation: mgi_get_mp_term()

Return a Mammalian Phenotype (MP) ontology term: id, name, definition, direct parents and children (is_a edges), and the top-level system(s) it rolls up to. Use with find_markers_by_phenotype to go from a phenotype to the mouse genes that model it. Signature: get_mp_term(mp_id).

Router invocation: mgi_search_phenotype_terms()

Free-text search over Mammalian Phenotype (MP) term names and definitions (FTS, relevance-ranked). Returns {mp_id, name, definition, score} plus a truncation contract {total, returned, limit, truncated} (widen step in next_commands when truncated). Use this to resolve a phenotype description to an MP id, then find_markers_by_phenotype or get_mp_term. Signature: search_phenotype_terms(query, limit=).