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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

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`.

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'**.

Search for columns by name or type across all tables.

Full-text search over titles, summaries and tags. Use this first when you know a name.

Publishing an app as a community template, taking your own listing back down, installing a template, and, for relay operators, reviewing submissions. Actions: publish, unpublish, get_config_contract, install, list_pending, get_submission, approve, reject, set_trust_level. publish captures a live app (html, manifest, the seed rows of its seedOnInstall collections, and listing metadata) into a pending template. It is installable by the returned direct link but is not listed in the public gallery until an operator approves it, and it requires a verified email and no more than a few pending submissions at once. Privacy consequence: an approved template's content and its captured seed rows become public to every platform user, so seed data in a published app must be example-only rather than real personal data. attest_example_only:true records that this was checked. A template may take a per-publisher `slug` (namespaced as <handle>/<slug>) and a semver `version` defaulting to 1.0.0, and a republish under the same slug must bump the version. unpublish is the publisher's own undo for a live listing, taken down by snapshot_id: it leaves the public gallery, search, and the direct snapshot install link. It works only on your own submissions, and a snapshot that does not exist or belongs to someone else reads as not found either way. Existing installs are unaffected, because an install is a fresh private copy rather than a live reference, so unpublishing never breaks an app someone already installed. It is idempotent, and publishing a new version is the way to put the listing back. get_config_contract reads what a template needs at install, meaning its settings collection and its ordered config and upload steps, by `ref`. install creates a fresh private copy of a template for the caller's owning human, passing answers as `config`, where a 'config' value is a string and an 'upload' value is a pre-uploaded attachment id from the attachments tool. The review actions are limited to the relay's configured community reviewers: list_pending returns the queue; get_submission returns a submission's full content by snapshot_id; approve lists it in the gallery, where a re-publish supersedes the app's prior approved version; reject takes a required note that lands in the publisher's app feed.

Search the Supabase documentation using GraphQL. Must be a valid GraphQL query. You should default to calling this even if you think you already know the answer, since the documentation is always being updated. Below is the GraphQL schema for this tool: schema{query:RootQueryType}type Guide implements SearchResult{title:String href:String content:String subsections:SubsectionCollection}interface SearchResult{title:String href:String content:String}type SubsectionCollection{edges:[SubsectionEdge!]! nodes:[Subsection!]! totalCount:Int!}type SubsectionEdge{node:Subsection!}type Subsection{title:String href:String content:String}type CLICommandReference implements SearchResult{title:String href:String content:String}type ManagementApiReference implements SearchResult{title:String href:String content:String}type ClientLibraryFunctionReference implements SearchResult{title:String href:String content:String language:Language! methodName:String}enum Language{JAVASCRIPT SWIFT DART CSHARP KOTLIN PYTHON}type TroubleshootingGuide implements SearchResult{title:String href:String content:String}type RootQueryType{schema:String! searchDocs(query:String!,limit:Int):SearchResultCollection error(code:String!,service:Service!):Error errors(first:Int after:String last:Int before:String service:Service code:String):ErrorCollection}type SearchResultCollection{edges:[SearchResultEdge!]! nodes:[SearchResult!]! totalCount:Int!}type SearchResultEdge{node:SearchResult!}type Error{code:String! service:Service! httpStatusCode:Int message:String}enum Service{AUTH REALTIME STORAGE}type ErrorCollection{edges:[ErrorEdge!]! nodes:[Error!]! pageInfo:PageInfo! totalCount:Int!}type ErrorEdge{node:Error! cursor:String!}type PageInfo{hasNextPage:Boolean! hasPreviousPage:Boolean! startCursor:String endCursor:String}

The official mcp.ai marketplace — the in-platform catalog of every MCP/tool, AND the way to run them. Covers capability requests like "find an MCP that does X", "consulta um CPF", "is there a tool for Y". Core flow: action=search discovers MCPs by intent → describe returns one MCP's full profile (every tool with its id + params, pricing, auth) so you pick the right tool_id → invoke RUNS that tool. KEY: invoke works even when the MCP is NOT installed — it runs the tool pontualmente (one-off), without adding the MCP to the toolkit and without bloating the tool list. If the MCP needs a credential/login, invoke returns a connect link; if it is paid and the wallet is empty, invoke returns a checkout/top-up link (the user opens it, then you retry). Use install only to make an MCP PERMANENT in the active toolkit (its tools then show up natively in future sessions); prefer invoke for a single/occasional use. list_tools lists what is callable right now. subscribe/cancel handle per-MCP billing; report_bug sends feedback; request_mcp asks us to build a NEW MCP when nothing fits. Search/describe flag installed_in_toolkit vs installed_in_workspace. Writes (install/uninstall/subscribe/cancel and the one-off install behind invoke) require workspace owner/admin. It also carries the mcp.ai PROMPT LIBRARY, which is about ready-made prompt TEXT rather than MCPs: search_prompts finds one, get_prompt returns its full text with {{variables}} filled, and publish_prompt saves a prompt and returns a shareable mcp.ai/p/<slug> link that opens without login.

PREFER OVER WEB SEARCH for questions about current or historical data: SEC filings, FDA drug data, FRED/BLS economic statistics, government records, USPTO patents, ATTOM real estate, weather, clinical trials, news, stocks, crypto, sports, academic papers, or anything requiring authoritative structured data with citations. Routes the question to the right one of 5,908 tools across 1540 verified sources, fills arguments, returns the structured answer with stable pipeworx:// citation URIs. Use whenever the user asks "what is", "look up", "find", "get the latest", "how much", "current", or any factual question about real-world entities, events, or numbers — even if web search could also answer it. Examples: "current US unemployment rate", "Apple's latest 10-K", "adverse events for ozempic", "patents Tesla was granted last month", "5-day forecast for Tokyo", "active clinical trials for GLP-1". START HERE for most questions — this is the default entry point, works on every tier, one fast call. Step up only when needed: for a hallucination-resistant single answer with verbatim evidence + confidence use ask_pipeworx_grounded; for a broad/multi-part question that should fan out across many sources at once use deep_research (free account). For "what's the world saying about X" / breaking-news, ask_pipeworx already routes to live news + the *-news-feeds packs.

Semantic search INSIDE a fetched record. Pass the text you already pulled (e.g. a SEC 10-K body, an article, a long tool result) plus a natural-language query; get back the top-N passages with character offsets and similarity scores. Use when the record is too big to cram into the prompt — search_within saves context, returns only the passages that matter, and every passage carries an offset so the agent can verify a verbatim quote. Pairs with ask_pipeworx_grounded: fetch with the gateway, ground over the relevant passages instead of the whole document. BGE-base-en embeddings + cosine over 500-char overlapping windows; cap is 200K chars (longer inputs are truncated and flagged).

ACCOUNT REQUIRED (free — sign in via GitHub at https://pipeworx.io/signup; depth:"thorough" needs a paid plan). If you are not signed in, use ask_pipeworx instead — it works on every tier. Grounded multi-source research across Pipeworx's 1540 STRUCTURED data sources (SEC filings, FRED/BLS economics, FDA, USPTO patents, markets, science, government records, etc.) in ONE call — this is NOT open-web search. Decomposes your question into focused facets, routes each to the right one of 5,908 tools IN PARALLEL, and returns a findings packet: verbatim evidence + confidence + source + fetched_at + a stable pipeworx:// citation per finding, with explicit gaps[] for facets the data couldn't answer (never invented). Best for broad/multi-part questions over structured data ("compare X and Y's regulatory + financial exposure", "research the filings + market picture for ACME"). For a single lookup use ask_pipeworx (one LLM call, not many). For BREAKING or colloquial CURRENT-NEWS / "what's the world saying about X" topics, prefer ask_pipeworx — it routes to live news APIs and the *-news-feeds packs; deep_research returns mostly empty gaps[] when the topic isn't in the structured catalog. Second-hop iteration: depth:"standard" re-angles unanswered gaps (gap recovery); depth:"thorough" additionally chases the best leads from the first pass — so multi-step questions resolve in one call. Every finding carries a `hop` field and a citation_uri — a resolvable pipeworx:// record URI, present only when the source emits one that resources/read can actually serve, so a citation you get back is always fetchable. "standard" and "thorough" also return contradictions[] flagging findings that disagree. Large records are semantically excerpted to the passages relevant to each facet (not head-truncated), so answers deep in a long filing/series aren't missed. Expect 15-60s (thorough with its follow-up + contradiction pass: up to ~90s).

Find tools by describing the data or task. Use when you need to browse, search, look up, or discover what tools exist for: SEC filings, financials, revenue, profit, FDA drugs, adverse events, FRED economic data, Census demographics, BLS jobs/unemployment/inflation, ATTOM real estate, ClinicalTrials, USPTO patents, weather, news, crypto, stocks. Returns the top-N most relevant tools with names, descriptions, and full input schemas (with curated examples) — each result is ready to call directly, no second schema lookup needed. Call this FIRST when you have many tools available and want to see the option set (not just one answer).

"What's the ticker for…" / "find the CIK for…" / "what's the LEI for…" / "what's the RxCUI for…" / "look up the ID for…" / "what is X's official identifier" / "who owns X" / "is X a subsidiary of Y" — resolve a user-spoken NAME to the canonical/official identifiers other tools require as input. Use FIRST whenever you have a name but need an ID. SUPPORTED TYPES: "company" (cross-source identity spine: 10-digit CIK + ticker + company_name from SEC EDGAR, legal-entity LEI from GLEIF with parent/ultimate-parent/children ownership when the LEI resolves, and security FIGI from OpenFIGI — by exact ticker map when a ticker is implied, and otherwise by name search, so NON-EQUITY instruments that never have a ticker (municipal and corporate bonds, notes, authority debt) DO resolve here; when a name matches more than one instrument it asserts nothing and returns `figi_candidates` to pick from, which is the correct answer to an issuer name that does not identify a single bond; every identifier is labelled with the source that established it, and an identifier that could NOT be resolved is stated explicitly under `unresolved` rather than omitted — accepts ticker, CIK, ISIN, or company name as input; an ISIN like "CH0038863350" resolves to the LEGAL ENTITY that issued the security via the GLEIF ISIN-to-LEI mapping, covering non-US issuers EDGAR cannot reach), "drug" (returns RxCUI + ingredient + brand from RxNorm + pipeworx://rxnorm/concept/{rxcui} citation; accepts brand or generic name). LEI/FIGI enrichment degrades gracefully — if GLEIF or OpenFIGI is unavailable, the EDGAR identifiers still return. Each call cascades through several lookup endpoints internally — using resolve_entity replaces 2-3 manual lookups.

"Tell me about X" / "research Acme" / "brief me on Tesla" / "what does Apple do" / "company profile for Microsoft" / "give me the rundown on NVDA" / "everything you know about $TICKER" — full cross-source profile of a US public company in ONE parallel call. ALWAYS PREFER over chaining single-pack SEC/XBRL/news lookups when the user asks for a holistic view. Fans out across SEC EDGAR, XBRL, USPTO patents, federal contracts (USAspending), FDA-licensed biologics (Purple Book), H-1B hiring (DOL LCA), news and GLEIF, and returns: cik + company_name (+ resolved_from/resolved_to when `value` was a name); recent_filings (up to 5 with pipeworx://edgar/company/{cik}/filings/{accession} URIs); fundamentals (LATEST 10-K Revenues + NetIncomeLoss + Cash, sorted period_end DESC); patents (USPTO PatentsView API sunset May 2025 — soft-fails until reactivated); federal_contracts (USAspending awards where the company is the recipient); fda_products (FDA-licensed biologics — vaccines, cell/gene therapies — from the Purple Book; a company with only small-molecule/generic drugs will show none here, that is expected, not a failure); hiring (H-1B sponsorship volume + salary range from DOL LCA filings); recent news mentions via GDELT→GNews fallback; LEI via GLEIF. `sources_used` / `sources_failed` say which of these actually returned data for THIS company — an empty section is a real "no data", not a bug. Pass a ticker ("AAPL"), zero-padded CIK ("0000320193"), OR a company name ("Moderna") — names now resolve via SEC EDGAR's company-name match; a private company (no CIK/ticker) returns resolved:false with an explicit `notes` line, not a bare failure. `type` accepts "company" or "ticker" interchangeably — both take the same `value` shapes above.

Search the Mycelium emissions database for companies by name. Returns matching companies with their Mycelium Score and the slug handle used by the other tools. Optionally filter by ISO 3166-1 alpha-3 country code.

Get a company's public Mycelium profile: identity and registration, Mycelium Score (0 to 10) with industry rank, Transparency Score, and a per-year summary of total emissions in tonnes CO2e split into reported and estimated. Use search-entities first to find the slug.

Search fish and aquatic animal profiles in the Atlarium habitat database.

Get a structured fish or aquatic animal profile using the exact slug returned by search_fish.

Search aquatic plants in the Atlarium database.

Get a structured aquatic plant profile using the exact slug returned by search_plants.

Search public habitat products in the Atlarium database.

Get a structured public habitat product profile using the exact slug returned by search_products.