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- string_proteins_for_term
Retrieve proteins annotated with a functional term or descriptive text in a single species. You can query for tissues, compartments, diseases, processes, pathways, and domains. IMPORTANT: For cross-species comparisons, run this tool separately for each species. Select relevant model organisms to search or ask user to provide the selection. The results reflect annotation depth within each category; use caution when interpreting. If no results are found, try simplifying the query. For tissue queries, follow BRENDA tissue nomenclature and omit the word "tissue" (e.g. use "skin" instead of "skin tissue"). Output fields: - category: Source database of the matched functional term (e.g. GO, KEGG, Reactome, Pfam, InterPro). - term: Exact identifier for the functional term. - description: The free text description of the term. - proteinCount: Number of proteins annotated with that term - preferredNames: Full protein-name list when `detail_for_term` is set - stringIds: STRING protein identifiers when returned - preferredNames_omitted: True when a row omits the protein-name list - stringIds_omitted: True when STRING identifiers are omitted
- string_sequence_search
Searches the STRING database using **amino acid sequences** to identify matching proteins. - Accepts a single sequence or multiple sequences in FASTA format. - Returns the most similar STRING protein(s) for the specified species, based on sequence similarity. - Use this when the protein identifier is unknown or unresolvable by `string_resolve_proteins`.
- string_query_species
Search for species or clades available in STRING by free-text query and return their NCBI taxonomy IDs. - Use this when the user asks which species or clades are present in STRING, or when you need the correct NCBI taxon ID to pass to other tools. - use this to resolve NCBI taxons IDs to their scientific names. - Accepts up to 100 taxon IDs separated by `%0d`. - The results are limited to the top 50 matches per query. - When the user asks for a species list, do not list clades. - If the requested species cannot be matched (i.e. the correct species is not present in the results), **immediately invoke the 'string_help' tool with topic='missing_species'**.
- scalix_db_search_columns
Search for columns by name or type across all tables.
- scalix_search
Search the Scalix original-source index — a curated set of original publishers (newsrooms, wires, regulators), not the open web. Returns originals only by default (syndicated copies collapsed to the source that published first), with provenance: source, published date, region, and canonical flag.
- search_food
Search Japanese foods by name (Japanese or romaji-free text). Returns candidates with nutrition per 100g, source, and disclaimer.
- get_nutrition
Get nutrition facts per 100g for a food ID returned by search_food.
- search_fish
Search fish and aquatic animal profiles in the Atlarium habitat database.
- search_plants
Search aquatic plants in the Atlarium database.
- search_products
Search public habitat products in the Atlarium database.
- search_guides
Search Atlarium habitat guides and educational content.
- search_algae
Search public algae diagnostic profiles with symptoms, causes and treatment guidance.
- search_diseases
Search public aquatic disease diagnostic profiles and advisory treatment information.