Link compounds to protein targets, rank bioactivity, and look up drug mechanisms and indications.
Scored across 7 tools
Each tool has a clearly distinct role in the workflow: molecule search, target search, bioactivity retrieval, assay provenance, drug pharmacology, and staged-data inspection/querying. The descriptions explicitly explain boundaries and chaining relationships, so an agent can tell which tool to use for each step.
All tool names use a consistent snake_case convention with a uniform chembl_ prefix and predictable action/resource naming. The dataframe helper tools follow the same style and sit naturally alongside the search/get tools.
Seven tools is well scoped for this server: it covers the main ChEMBL workflows without excessive surface area. Every tool appears to earn its place, and the two dataframe helpers are justified by the staged-data analysis workflow.
The tool set covers the core discovery lifecycle: search compounds and targets, retrieve bioactivities, inspect assay provenance, get drug pharmacology, and analyze staged results. There are minor gaps, such as no independent assay search or broader document/record retrieval, but the primary bioactivity and compound-target workflows are well supported.
List the tables and columns staged on a canvas by chembl_get_bioactivities — inspect before calling chembl_dataframe_query to write correct SQL. Returns each table with its row count, kind (table | view), and column names + types. Unavailable when the server sets CANVAS_PROVIDER_TYPE=none.
| Name | Required | Description | Default |
|---|---|---|---|
| canvas_id | Yes | Canvas ID returned by chembl_get_bioactivities — non-null whenever that call staged a table. |
| Name | Required | Description |
|---|---|---|
| error | No | Present when the call failed. Absent on success. |
| tables | No | Tables and views staged on the canvas. |
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnly, idempotent and closed-world, and the description adds the operationally important availability gate (server-side CANVAS_PROVIDER_TYPE=none). It also characterizes the result shape (row count, kind table|view, column names + types), though that partially duplicates the output schema. It does not mention empty-canvas behavior, which is a minor remaining gap.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Three short sentences, front-loaded with the core action, then the routing advice, then the availability caveat. No filler or restatement of the title.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
With an output schema present, return values need not be explained, and one fully-described required parameter plus explicit annotations leave little unsaid. The availability limitation and the prerequisite relationship to chembl_get_bioactivities are both covered.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema coverage is 100% and the schema already documents canvas_id's origin and format, so the baseline is 3. The description adds a small amount by framing the parameter's lifecycle — the canvas is staged by chembl_get_bioactivities — which reinforces the call-order dependency for the agent.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
Specific verb + resource: lists tables and columns staged on a canvas, and attributes them to the sibling that created them (chembl_get_bioactivities). It also names the counterpart tool (chembl_dataframe_query), so an agent can separate inspection from querying without opening a schema.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
Explicit sequencing: "inspect before calling chembl_dataframe_query to write correct SQL" gives both the alternative and the condition that selects this tool. It additionally states an exclusion — unavailable when CANVAS_PROVIDER_TYPE=none — which no other field conveys.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Run a read-only SQL SELECT over the bioactivity rows chembl_get_bioactivities staged on a canvas — rank, group, dedupe, and aggregate across the FULL set, not the inline preview. Reference each staged table by the name chembl_get_bioactivities returned — bioactivities for its potency_ranked view, bioactivities_null_potency for null_potency; discover the staged tables and their columns with chembl_dataframe_describe. Compute honest aggregates here (e.g. SELECT molecule_chembl_id, MEDIAN(pchembl_value) AS med FROM bioactivities WHERE standard_type = 'IC50' GROUP BY 1 ORDER BY 2 DESC). Two independent bounds apply, each reported on its own field: truncated is true when the SQL result exceeded the canvas row cap, and rendered_rows says how many of the returned rows the markdown table holds once its character budget is reached (below row_count on a wide or long result). Page past either bound with SQL LIMIT/OFFSET — append e.g. LIMIT 500 OFFSET 500 and re-call; offsets reach rows beyond the canvas row cap. Unavailable when the server sets CANVAS_PROVIDER_TYPE=none.
| Name | Required | Description | Default |
|---|---|---|---|
| sql | Yes | A read-only SELECT against the staged tables. Reference tables by the names chembl_get_bioactivities returned. | |
| canvas_id | Yes | Canvas ID returned by chembl_get_bioactivities — non-null whenever that call staged a table. |
| Name | Required | Description |
|---|---|---|
| rows | No | Result rows (capped at the canvas row limit). Each row is a column→value map. |
| error | No | Present when the call failed. Absent on success. |
| row_count | No | Number of rows materialized in this response. |
| truncated | No | True when the SQL result exceeded the canvas row cap and was truncated — the engine bounding the result set itself, not the rendering. Independent of rendered_rows; page past it with LIMIT/OFFSET. |
| rendered_rows | No | How many of those rows the markdown table in content[] holds. Below row_count when the rendered table reached its character budget — a rendering bound, INDEPENDENT of truncated: a response can be truncated:false and still render fewer rows than row_count. Re-run the same SQL with LIMIT/OFFSET to read the rows past it. |
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations only cover safety (readOnly, idempotent); the description adds genuinely new behavior: two independent result bounds (truncated vs. rendered_rows relative to row_count), that offsets can reach rows beyond the canvas row cap, and an availability precondition. This is exactly the context annotations cannot convey.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Front-loaded with purpose, then scoping, then result-bound semantics, then pagination recipe — a sensible order. Density is high and a couple of clauses (the example query, the rendered_rows parenthetical) are long, but each carries actionable information rather than filler.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Output schema exists, yet the description still explains the two result-bound fields an agent would otherwise misread, plus pagination and the unavailability condition. Nothing needed to call this correctly or interpret its bounds is missing.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema coverage is 100%, so baseline is 3; the description earns more by naming the concrete staged table identifiers (bioactivities and bioactivities_null_potency views) and supplying a real SQL example, which clarifies how the `sql` parameter should reference staged names. It doesn't add anything about canvas_id beyond the schema.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
Opens with a specific verb and resource ('Run a read-only SQL SELECT over the bioactivity rows chembl_get_bioactivities staged') and immediately distinguishes itself from the inline preview and from chembl_dataframe_describe. An agent can tell exactly which of the sibling tools performs full-set aggregation.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
Explicitly states when to use it ('across the FULL set, not the inline preview'), routes table discovery to chembl_dataframe_describe, gives concrete pagination instructions with LIMIT/OFFSET syntax, and names the one condition under which the tool is unusable (CANVAS_PROVIDER_TYPE=none). No inference required.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Assay provenance behind a bioactivity row: description, type (binding / functional / ADMET / toxicity), the target it measures, organism, and ChEMBL's 1–9 confidence score (9 = direct assay on the protein target, lower = homologous or indirect). Supply assay_chembl_id from a chembl_get_bioactivities row. Call this to judge whether two measurements are comparable before ranking them together.
| Name | Required | Description | Default |
|---|---|---|---|
| assay_chembl_id | Yes | ChEMBL assay ID from a bioactivity row's assay_chembl_id, e.g. "CHEMBL674637". |
| Name | Required | Description |
|---|---|---|
| error | No | Present when the call failed. Absent on success. |
| organism | No | Organism ChEMBL records for the assay itself, not its target's organism. Null when the assay records none, even when the target is a human protein. |
| assay_type | No | Assay type code: B=binding, F=functional, A=ADMET, T=toxicity, P=physicochemical, U=unclassified. Null when absent. |
| description | No | Assay description text. Null when absent. |
| assay_chembl_id | No | The ChEMBL assay ID queried. |
| confidence_score | No | ChEMBL confidence score, 1–9 (9 = direct single-protein assay; lower = homologous/indirect). Null when unscored. |
| target_chembl_id | No | ChEMBL target ID the assay measures — chain to chembl_search_targets/chembl_get_bioactivities. Null when unassigned. |
| assay_type_description | No | Human-readable assay type, e.g. "Binding". Null when absent. |
| confidence_description | No | Human-readable confidence description, e.g. "Direct single protein target assigned". Null when absent. |
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already establish read-only, idempotent, open-world behavior, so the description does not need to restate safety traits. It adds useful domain transparency by explaining the 1–9 confidence score and what lower scores imply about directness of the assay.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is three dense sentences with no wasted text. It front-loads the returned provenance, then the confidence-score meaning, then the input source and use case.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
With annotations covering safety behavior and an output schema covering return structure, the description supplies the remaining domain context: what assay provenance includes, how to interpret confidence, and when to call it. Nothing essential for correct selection or invocation is missing.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema coverage is 100%, and the schema already says the parameter is a ChEMBL assay ID from a bioactivity row with an example. The description reinforces the source as chembl_get_bioactivities, but it does not add format or validation semantics beyond the schema.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description states a specific resource and tells the agent exactly what provenance fields are returned: description, type, target, organism, and confidence score. It also distinguishes this lookup from the sibling bioactivity tool by explaining that this is the assay-level context behind a bioactivity row.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
It gives an explicit source for the required ID (assay_chembl_id from a chembl_get_bioactivities row) and an explicit use case: call this before ranking measurements together to judge comparability. That is clear when-to-use guidance tied to the sibling tool.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
The flagship compound↔target bioactivity bridge: measurements for a molecule (target deconvolution / selectivity), a target (lead finding), or both together (how potently one compound hits one target). Supply at least one of molecule_chembl_id (from chembl_search_molecules) or target_chembl_id (from chembl_search_targets) — supplying both narrows to that compound–target pair, supplying neither is an error. A drug's measurements are often split across its salts and other alternate forms, so molecule_chembl_id reads that one form unless include_alternate_forms widens it to the whole family under its parent (a salt's ID included), every view, page, and spill reading the same family. Filter by standard_type (IC50/Ki/EC50/…), minimum potency pchembl_value_min, assay_type, organism, and variant (wild type, or one recorded mutant such as "T315I"). Each row carries its activity_comment and data_validity_comment, its assay variant, and its source document for citation. Not every measurement has a derivable pchembl_value, so potency_view picks which side of that split you get: the default "potency_ranked" returns the measurements that have one, most potent first (ChEMBL sorts the rest first otherwise, which is why they are not merged), and "null_potency" returns exactly the measurements that have none. totalCount is the honest full match count across both views either way. Mixing measurement types (IC50 vs Ki) is a scientific error — set standard_type to compare like with like. A popular target carries tens of thousands of rows: results spill to a DataCanvas table (call chembl_dataframe_describe for its columns, then chembl_dataframe_query for honest aggregates across the staged set), while an inline preview answers the immediate question. Each view stages its own table (bioactivities / bioactivities_null_potency), so running both against one canvas_id lets a UNION ALL rebuild the full set. A canvas is minted only when a view spills; pass its canvas_id back and every later non-cursor call re-stages the table of its view with its own rows, even when they fit inline or none match, so a successful call never leaves rows from an earlier query in it, and a spill that fails or is cancelled leaves the earlier table in place. The spill is bounded by a row cap (CHEMBL_MAX_SPILL_ROWS) and a time budget (CHEMBL_SPILL_DEADLINE_MS); when either stops it short of the view, truncated is true, truncated_by names the bound, and the table is a bounded slice, not the complete view. The inline rows are always capped at limit, so compare that against totalCount before treating them as the whole answer. Spilling needs the canvas, which is on unless the server sets CANVAS_PROVIDER_TYPE=none. Whenever a call stages nothing and rows remain past this page — the canvas is off, or the view fit inline with no canvas_id — nextCursor continues the view: pass it back as cursor, with the same filters and potency_view, for the next page. A cursor page is always returned inline and never staged, canvas or not.
| Name | Required | Description | Default |
|---|---|---|---|
| limit | No | Maximum rows in the inline preview or cursor page, up to 1000 — a larger value is served at 1000, with a notice saying so. Defaults to the server default (25). With the canvas enabled, a view that spills still stages in full whatever the limit; when a call stages nothing, nextCursor reaches the rows past limit. | |
| cursor | No | Opaque continuation token from a previous call's nextCursor — resumes the view where that page ended. Omit for the first page. Re-send the same molecule_chembl_id/target_chembl_id, include_alternate_forms, filters, and potency_view that minted it (only limit may change; it sets this page's size); redeeming it against different filters walks a different result set. A cursor page is returned inline and never staged, even with the canvas enabled. | |
| variant | No | Restrict to one assay variant of the target. "wild_type" keeps the measurements that record no variant. Any other value keeps those whose recorded assay_variant_mutation equals it whole, case-insensitively, with spaces beside "," or "/" ignored: a substitution ("T315I"), a deletion ("F508del"), a multi-mutant in the order ChEMBL records it ("L858R,T790M"; "T790M,L858R" matches nothing, and "L858R" alone matches only the single mutant), or "UNDEFINED MUTATION" for an unspecified mutant. Read assay_variant_mutation on unfiltered rows for the recorded strings. | |
| organism | No | Restrict to a target organism, e.g. "Homo sapiens" (case-insensitive exact match). | |
| canvas_id | No | Optional canvas ID from a prior call to reuse the same canvas. With it, the call re-stages the selected potency_view's table with this call's rows whether they spill, fit inline, or are empty, so a second query of the SAME view REPLACES (overwrites) its prior rows once it succeeds — it does not append, and a spill that fails or is cancelled leaves them — while the other view's table is left intact, which is what lets both coexist on one canvas. Omit it and a fresh canvas is minted only if the view spills. Left untouched on a cursor page, which never stages. | |
| assay_type | No | Restrict to an assay type code: "B" (binding), "F" (functional), "A" (ADMET), "T" (toxicity), "P" (physicochemical), "U" (unassigned). | |
| potency_view | No | Which side of the pchembl_value presence split to retrieve. "potency_ranked" (default) returns the measurements that have a derivable pchembl_value, most potent first. "null_potency" returns exactly the measurements that have none — the rows the ranked view excludes, otherwise unreachable. The two partition the match set and stage to separate canvas tables. | potency_ranked |
| standard_type | No | Restrict to one measurement type, e.g. "IC50", "Ki", "EC50". Matched exactly, case included — ChEMBL records distinct types that differ only by case, such as "Kd" and "KD". Set this to compare potencies validly. | |
| target_chembl_id | No | ChEMBL target ID (from chembl_search_targets), e.g. "CHEMBL203". Supply this, molecule_chembl_id, or both — both narrows to that compound–target pair. | |
| pchembl_value_min | No | Minimum pchembl_value (−log10 molar potency), e.g. 7 keeps sub-100 nM activities. Only valid on the potency_ranked view — the null_potency rows have no pchembl_value to compare against. | |
| molecule_chembl_id | No | ChEMBL molecule ID (from chembl_search_molecules), e.g. "CHEMBL941". Supply this, target_chembl_id, or both — both narrows to that compound–target pair. | |
| include_alternate_forms | No | Widen molecule_chembl_id to its whole family: the parent it belongs to and every salt and other alternate form ChEMBL files under it (a drug's measurements are often split across them). A salt's ID reaches its parent's family; each row keeps the molecule_chembl_id of the form it was measured on. Requires molecule_chembl_id; combines with target_chembl_id and every filter. Defaults to false: that one form's measurements only. |
| Name | Required | Description |
|---|---|---|
| error | No | Present when the call failed. Absent on success. |
| notice | No | Guidance when no measurements matched (naming the spelling ChEMBL records when the standard_type sent differs from it only by case), how to SQL the staged set, or which rows of the view an inline page holds and how to continue it — led by the disclosure that a limit above the maximum was served at the maximum. |
| spilled | No | True when the view exceeded the inline preview and spilled to the canvas. False when it fit inline — including an inline fit re-staged on a supplied canvas_id, which table_name and staged_row_count report. |
| canvas_id | No | Canvas ID holding the staged table — pass to chembl_dataframe_describe to list its columns, then to chembl_dataframe_query to run SQL over them. Null when nothing was staged: canvas disabled, a cursor page, or an inline fit with no canvas_id supplied. |
| truncated | No | True when a bound stopped the page walk short of the view — the CHEMBL_MAX_SPILL_ROWS row cap or the CHEMBL_SPILL_DEADLINE_MS time budget, as truncated_by says. The staged table is then a bounded slice, NOT the complete view, so aggregates over it are a sample. Narrow the filters to bring the view under the bound. |
| activities | No | Bioactivity rows for the selected potency_view — the inline preview, the cursor page, or the full view when it fit without spilling. |
| nextCursor | No | Opaque token for the next page of this view — pass it back as cursor with the same filters and potency_view. Minted only when nothing was staged and rows remain past this page: with the canvas disabled, on a cursor page, or when the view fit inline with no canvas_id supplied. Absent on the last page and whenever the call staged a table (a spill, or an inline fit re-staged on a supplied canvas_id). |
| table_name | No | Canvas table name holding the staged rowset, and the FROM target for chembl_dataframe_query SQL — "bioactivities" for potency_ranked, "bioactivities_null_potency" for null_potency. Null when nothing was staged. |
| totalCount | No | Total matching measurements upstream — the honest full count spanning BOTH potency views, before any preview cap. The staged/preview rows are the selected view of this. |
| potency_view | No | Which view these rows came from: "potency_ranked" = measurements with a derivable pchembl_value; "null_potency" = measurements with none. Re-call with the other value to reach the rest of totalCount. |
| truncated_by | No | The bound that cut the staged table short when truncated is true: "row_cap" — the CHEMBL_MAX_SPILL_ROWS cap; "time_budget" — the CHEMBL_SPILL_DEADLINE_MS budget ended the page walk, at its expiry or once what was left would not hold another page, so a re-call can stage more. Null when truncated is false. |
| appliedFilters | No | Filters as the server parsed them. |
| canvasDisabled | No | True when the server runs with the canvas off (CANVAS_PROVIDER_TYPE=none), so large sets could not spill — the inline rows are one page of the view, not the full set, and nextCursor continues it. |
| staged_row_count | No | Rows actually registered on the canvas table — 0 when a re-staged view matched nothing. Null when nothing was staged. Below the view total when truncated is true. |
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare read-only, open-world, and idempotent behavior, but the description adds substantial operational detail: canvas staging and overwrite semantics, spill row caps and time budgets, truncation flags, cursor pages never being staged, and the inline cap versus totalCount. Nothing contradicts the annotations.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description front-loads the core purpose and the at-least-one-ID constraint, which is effective. It is necessarily dense for a 12-parameter tool with canvas and cursor behavior, but several sentences are long and run together, reducing scannability.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
It covers all critical behavior for this complex tool: selection modes, filters, potency views, alternate forms, canvas staging, pagination, truncation, and totalCount versus inline rows. Return-value shape is handled by the output schema, so the description is complete enough for correct invocation.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
With 100% schema description coverage, the schema already carries most parameter meaning. The description still adds useful semantics, such as mixing IC50 and Ki being a scientific error, the rationale for potency_view partitioning, cursor filter consistency, and alternate-form family widening; it is not quite a 5 because much of the per-parameter detail is already present in the schema.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
It states a specific verb and resource: bioactivity measurements for a molecule, a target, or a molecule–target pair, and maps each mode to target deconvolution/selectivity or lead finding. It also distinguishes itself from sibling search tools by naming them as ID sources and from dataframe tools by pointing to them for staged results.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description explicitly says to supply at least one of molecule_chembl_id or target_chembl_id, that supplying both narrows to the pair, and that supplying neither is an error. It further explains when to use standard_type, potency_view, include_alternate_forms, and cursor, giving clear operational guidance.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Pharmacology for a drug (molecule): mechanism(s) of action, the molecular target(s) it acts on, action type (inhibitor / agonist / …), first-approval year, and clinical indications with the max phase reached for each. Supply molecule_chembl_id (from chembl_search_molecules) — a parent or any of its salts and other alternate forms gives the same answer: ChEMBL often records a drug's mechanisms and approved indications on a salt, so both lists cover the whole family under parent_molecule_chembl_id. Each mechanism names the form it is recorded on, and each indication is listed once per MeSH/EFO pair at the highest phase any form reached, with the forms it is recorded on, each at its own phase. Distinct from the openfda server's label/adverse-event view — this is the curated mechanism-and-indication record. A mechanism's target_chembl_id chains into chembl_get_bioactivities for compounds hitting the same target. Each list carries its own retrieval state: an empty mechanisms or indications array means the molecule has none recorded only when the matching mechanisms_status / indications_status is "complete" — "failed" means the list was not retrieved (the request ran out of time or ChEMBL answered with an error, as the matching *_failure says) and the array says nothing about the molecule, and "truncated" means the page cap fetched fewer rows than ChEMBL holds, which the matching *_total_count reports.
| Name | Required | Description | Default |
|---|---|---|---|
| molecule_chembl_id | Yes | ChEMBL molecule ID (from chembl_search_molecules), e.g. "CHEMBL939" for gefitinib, or the molecule's standard InChIKey, e.g. "XGALLCVXEZPNRQ-UHFFFAOYSA-N". A salt or other alternate form answers with its parent's family, the same as the parent. |
| Name | Required | Description |
|---|---|---|
| error | No | Present when the call failed. Absent on success. |
| notice | No | Disclosure of anything the two lists do not say for themselves: a list whose upstream fetch timed out or failed (so its emptiness means nothing), a list the page cap bounded, or — only when both lists came back complete and empty — that the molecule may be a research compound rather than a drug. |
| max_phase | No | Max clinical phase across indications: 4 = approved, 3–1 = trial phase, 0.5 = early phase 1, −1 = clinical with the phase unknown. Null when ChEMBL records no clinical development. |
| pref_name | No | Preferred drug name, e.g. "GEFITINIB". Null when unnamed. |
| mechanisms | No | Mechanisms of action. Empty is authoritative only when mechanisms_status is "complete". |
| indications | No | Clinical indications. Empty is authoritative only when indications_status is "complete". When "truncated", each indication's max_phase_for_ind and forms are lower bounds: rows past the page cap can raise a phase or add a form. |
| first_approval | No | Year of first approval, e.g. 2003. Null when unapproved or unknown. |
| mechanisms_status | No | Retrieval state of the mechanism list. "complete" = every row ChEMBL records for the molecule and its alternate forms is present, so an empty array is a fact about the molecule. "truncated" = the single-request page cap bounded the list, so the array is a prefix of mechanisms_total_count rows. "failed" = the list was not retrieved (the request ran out of time or ChEMBL answered with an error, as mechanisms_failure says), so the empty array is unknown data, NOT evidence that none exist — re-call chembl_get_drug_info to retry. |
| indications_status | No | Retrieval state of the indication list. "complete" = every row ChEMBL records for the molecule and its alternate forms is present, so an empty array is a fact about the molecule. "truncated" = the single-request page cap bounded the list, so the array holds the indications of the rows fetched (indications_rows_fetched, fewer than indications_total_count). "failed" = the list was not retrieved (the request ran out of time or ChEMBL answered with an error, as indications_failure says), so the empty array is unknown data, NOT evidence that none exist — re-call chembl_get_drug_info to retry. |
| mechanisms_failure | No | Why the mechanism list failed, when mechanisms_status is "failed": "timeout" = the request ran out of time before ChEMBL returned the list; "upstream_error" = ChEMBL answered with an error (a rate limit, a server error, a rejected request) or could not be reached. Null when the list did not fail. |
| molecule_chembl_id | No | The ChEMBL molecule ID queried, as the molecule's own record writes it. |
| indications_failure | No | Why the indication list failed, when indications_status is "failed": "timeout" = the request ran out of time before ChEMBL returned the list; "upstream_error" = ChEMBL answered with an error (a rate limit, a server error, a rejected request) or could not be reached. Null when the list did not fail. |
| mechanisms_total_count | No | Total mechanism rows ChEMBL holds for the molecule and its alternate forms. Exceeds the returned array length exactly when the status is "truncated". Null when the fetch failed — the count is unknown, never 0. |
| indications_total_count | No | When the status is "complete", the number of distinct indications — the returned array length, rows recorded on several forms counted once. When "truncated", the indication rows ChEMBL holds for the molecule and its alternate forms, an upper bound on the distinct indications. Null when the fetch failed — the count is unknown, never 0. |
| indications_rows_fetched | No | Indication rows fetched from ChEMBL for the molecule and its alternate forms, before rows recorded on several forms merge. When the status is "truncated", each row not fetched (indications_total_count minus this) can add at most one indication, so that difference bounds the indications missing. Null when the fetch failed. |
| parent_molecule_chembl_id | No | The parent of the queried molecule's family — the molecule itself when it is the parent or ChEMBL records no hierarchy for it. Both lists cover this parent and every alternate form ChEMBL files under it (salts, isotope-labelled and deuterated analogs). |
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already cover the read-only/idempotent profile, and the description goes well beyond them by explaining the retrieval-state contract: empty arrays only mean 'none recorded' when mechanisms_status/indications_status is 'complete', 'failed' means unretrieved with a *_failure reason, and 'truncated' ties to *_total_count. That is exactly the context needed to avoid misreading an empty result as a negative finding.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Front-loaded correctly: what the tool returns first, then ID sourcing, then family semantics, then status semantics. Every sentence is substantive, but the single dense paragraph packs three distinct topics (scope, ID handling, result-state semantics) into a run-on block, which slightly hurts scannability.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
An output schema exists, so return-field explanation is rightly omitted, yet the description still covers the one thing the schema cannot: how to interpret empty arrays versus failed or truncated retrievals. Nothing an agent needs to call this correctly or read its result safely is missing.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema coverage is 100% and the schema itself already documents the ID format, the InChIKey alternative and the salt-follows-parent behavior. The description restates the family behavior ('a parent or any of its salts ... gives the same answer') without adding syntax or format detail beyond what the parameter description carries, so the baseline 3 applies.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
Opens with a precise verb+resource: 'Pharmacology for a drug (molecule)' followed by an enumeration of exactly what comes back (mechanisms, targets, action type, first-approval year, indications with max phase). It also explicitly distinguishes itself from the openfda label/adverse-event view and from the sibling used to obtain the ID, so an agent can place it without opening the schema.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
Says where the ID comes from (chembl_search_molecules), states that parent and salt forms yield the same answer, and names the alternative (openfda server) plus the onward chaining path into chembl_get_bioactivities. Both when-to-use and when-to-use-something-else are spelled out.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Discovery entry point for compounds. Find by name / ChEMBL ID / InChIKey with the default search_type=name (supply query), or run a structure search with search_type exact | similarity | substructure (supply structure as a SMILES). At least one of query or structure is required, and structure is required for the three structure modes. Returns ChEMBL ID, preferred name, canonical SMILES, formula, MW, AlogP, Lipinski violations, QED, max clinical phase, and the family parent_chembl_id on every row; only search_type=similarity adds a Tanimoto similarity percent. Chain molecule_chembl_id into chembl_get_bioactivities or chembl_get_drug_info. A salt often ranks ahead of its parent and carries a small share of the family's measurements, so check parent_chembl_id before chaining. A capped result carries nextCursor — pass it back as cursor with the same filters to read the next page.
| Name | Required | Description | Default |
|---|---|---|---|
| limit | No | Maximum molecules to return, up to 100 — a larger value is served at 100, with a notice saying so. Defaults to the server default (25) when omitted. | |
| query | No | Search text for search_type=name — a drug name, ChEMBL ID, or InChIKey, e.g. "imatinib" or "CHEMBL25". | |
| cursor | No | Opaque continuation token from a previous call's nextCursor — resumes where that page ended. Omit for the first page. Re-send the same query/structure/filters that minted it (only limit may change; it sets this page's size); redeeming it against different filters walks a different result set. | |
| structure | No | SMILES string for structure search, e.g. "CC(=O)Oc1ccccc1C(=O)O". Required when search_type is exact/similarity/substructure. | |
| search_type | No | name = text lookup (query); exact = exact structure match; similarity = Tanimoto ≥ threshold; substructure = contains the structure. All structure modes need `structure`. | name |
| max_phase_min | No | For search_type=name, restrict to compounds at or above this max clinical phase (e.g. 4 for marketed drugs only). | |
| similarity_threshold | No | Minimum Tanimoto similarity percent for search_type=similarity (40–100; ChEMBL rejects below 40). Ignored for other modes. |
| Name | Required | Description |
|---|---|---|
| cap | No | The limit that was applied. |
| error | No | Present when the call failed. Absent on success. |
| shown | No | Number of molecules returned. |
| notice | No | Guidance when nothing matched — echoes the query and suggests how to broaden — the disclosure that a limit above the maximum was served at the maximum, and, when totalCountCapped is true, that the total is ChEMBL's search ceiling and how to narrow below it. |
| molecules | No | Matching compounds (up to the limit). |
| truncated | No | True when the result was capped at the limit. |
| nextCursor | No | Opaque token for the next page — pass it back as cursor with the same filters. Absent when this page is the last one. |
| totalCount | No | Total compounds matching before the limit was applied — a lower bound when totalCountCapped is true. |
| totalCountCapped | No | True when totalCount is ChEMBL's ceiling for the search — 10000 for a name search, 30000 for a substructure search: at least that many compounds match, and no page past the ceiling can be reached. Narrow the query to bring the matches under it. |
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations cover read-only/idempotent/open-world, and the description adds substantive behavior: a capped limit is silently served at 100 with a notice, nextCursor/cursor must be replayed with identical filters, and only similarity mode adds a Tanimoto percentage to the row shape. The salt/family-measurement caveat is genuinely non-obvious operational context.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Dense but front-loaded and free of filler — mode selection, constraints, return shape, chaining, and pagination each get one efficient sentence. It is slightly over-packed into a single block, which costs a point on scannability.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
For a 7-parameter search tool with an output schema, the description still names the per-row fields and the one mode-specific addition (Tanimoto), plus the pagination contract and the chaining path. An agent has everything needed to call it correctly on the first try.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema coverage is already 100%, so baseline is 3; the description earns extra credit by explaining the cross-parameter dependencies (search_type drives which of query/structure is required, cursor must be re-sent with the same filters) rather than restating field meanings. It doesn't add detail on similarity_threshold or max_phase_min beyond the schema, which keeps it off a 5.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
Opens with a specific role statement ('Discovery entry point for compounds') and enumerates the four search modes with the exact input each needs (query for name, structure for exact/similarity/substructure). This clearly distinguishes it from siblings like chembl_search_targets and chembl_get_bioactivities.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
Explicitly states the selection condition between name and structure modes, the 'at least one of query or structure' constraint, and pauses to warn about the salt-vs-parent ranking pitfall before chaining. It also names the correct next-step tools (chembl_get_bioactivities, chembl_get_drug_info), leaving nothing to inference.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Resolve a protein/gene/UniProt accession to the ChEMBL target ID that chembl_get_bioactivities needs for the target→leads workflow. Supply at least one of accession (UniProt, e.g. P00533), gene_symbol (e.g. EGFR), or query (free-text name); filter further by organism and target_type. Returns each target with its type, organism, and component UniProt accessions + gene symbols. A UniProt accession from the uniprot/protein server is the most precise input. A capped result carries nextCursor — pass it back as cursor with the same filters to read the next page.
| Name | Required | Description | Default |
|---|---|---|---|
| limit | No | Maximum targets to return, up to 100 — a larger value is served at 100, with a notice saying so. Defaults to the server default (25) when omitted. | |
| query | No | Free-text name match against the target preferred name, e.g. "kinase" or "growth factor receptor". | |
| cursor | No | Opaque continuation token from a previous call's nextCursor — resumes where that page ended. Omit for the first page. Re-send the same accession/gene_symbol/query/filters that minted it (only limit may change; it sets this page's size); redeeming it against different filters walks a different result set. | |
| organism | No | Restrict to a source organism, e.g. "Homo sapiens" (case-insensitive exact match). | |
| accession | No | UniProt accession of a target component, e.g. "P00533". The most precise resolver — from the uniprot/protein server. | |
| gene_symbol | No | Gene symbol of a target component, e.g. "EGFR" (case-insensitive exact match). | |
| target_type | No | Restrict to a target class, e.g. "SINGLE PROTEIN" or "PROTEIN COMPLEX". |
| Name | Required | Description |
|---|---|---|
| cap | No | The limit that was applied. |
| error | No | Present when the call failed. Absent on success. |
| shown | No | Number of targets returned. |
| notice | No | Guidance when no target matched — echoes the filters and suggests how to broaden — and the disclosure that a limit above the maximum was served at the maximum. |
| targets | No | Matching targets (up to the limit). |
| truncated | No | True when the result was capped at the limit. |
| nextCursor | No | Opaque token for the next page — pass it back as cursor with the same filters. Absent when this page is the last one. |
| totalCount | No | Total targets matching the filters before the limit was applied. |
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already cover the safety profile (readOnly, idempotent, open-world), so the description only needs incremental context — and it supplies the result cap and the nextCursor continuation contract. It does not mention rate limits or failure modes for unmatched accessions, which keeps it off a 5.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Front-loaded with the resolve action and its consumer, then input rules, then return shape, then pagination. Every sentence carries an actionable fact with no filler.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
For a 7-parameter read-only lookup with full schema coverage, output schema, and annotations, an agent has everything needed: which inputs to prefer, how filtering works, and how to page. Nothing material is missing.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema coverage is 100% so the schema carries most semantics, but the description adds real information the schema cannot: with zero required parameters, the constraint that at least one of accession/gene_symbol/query must be supplied, and which of those resolves most precisely. Cursor re-use guidance largely restates the schema's cursor description.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
States a specific verb+resource: resolve a protein/gene/UniProt accession to a ChEMBL target ID. It also ties that output directly to the sibling that consumes it (chembl_get_bioactivities), which lets an agent place this tool in the workflow without inspecting other definitions.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
Gives the input selection rule ('supply at least one of accession, gene_symbol, or query') and ranks them ('a UniProt accession … is the most precise input'), plus where the output is needed next. It lacks an explicit when-not-to-use-this statement vs. the other search siblings, so it falls short of a 5.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Recent tool additions, removals, and schema changes observed during successful MCP inspections.
chembl_get_assay1 field changedOutput schema / properties / organism / descriptionPrevious value: -"Assay organism. Null when unspecified."New value: +"Organism ChEMBL records for the assay itself, not its target's organism. Null when the assay records none, even when the target is a human protein."chembl_get_drug_info2 fields changedOutput schema / properties / indications / items / properties / max_phase_for_ind / descriptionPrevious value: -"Max clinical phase reached for THIS indication (1–4), the highest across the forms it is recorded on. Null when unknown."New value: +"Max clinical phase reached for THIS indication (4 = approved, 3–1 = trial phase, 0.5 = early phase 1, −1 = phase unknown), the highest across the forms it is recorded on. Null when unknown."Output schema / properties / max_phase / descriptionPrevious value: -"Max clinical phase across indications: 4 = marketed. Null when unknown."New value: +"Max clinical phase across indications: 4 = approved, 3–1 = trial phase, 0.5 = early phase 1, −1 = clinical with the phase unknown. Null when ChEMBL records no clinical development."chembl_search_molecules1 field changedOutput schema / properties / molecules / items / properties / max_phase / descriptionPrevious value: -"Max clinical phase: 4 = marketed drug, 0 = research compound. Null when unknown. The cheap druggability signal."New value: +"Max clinical phase: 4 = approved, 3–1 = clinical trial phase, 0.5 = early phase 1, −1 = clinical with the phase unknown. Null when ChEMBL records no clinical development (a preclinical or research compound). The cheap druggability signal."chembl_dataframe_describe1 field changedOutput schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `canvas_disabled`: Called while CANVAS_PROVIDER_TYPE is not duckdb, so no canvas exists. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `canvas_disabled`: The server runs with the canvas off (CANVAS_PROVIDER_TYPE=none), so no canvas exists. Other values are possible when a failure originates below the handler."chembl_dataframe_query1 field changedOutput schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `canvas_disabled`: Called while CANVAS_PROVIDER_TYPE is not duckdb, so no canvas exists. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `canvas_disabled`: The server runs with the canvas off (CANVAS_PROVIDER_TYPE=none), so no canvas exists. Other values are possible when a failure originates below the handler."chembl_get_assay2 fields changedInput schema / properties / assay_chembl_id / minLengthRemoved value: -1Input schema / properties / assay_chembl_id / patternAdded value: +"^\\s*[Cc][Hh][Ee][Mm][Bb][Ll]\\d+\\s*$"chembl_get_bioactivities23 fields changedInput schema / properties / assay_type / descriptionPrevious value: -"Restrict to an assay type code: \"B\" (binding), \"F\" (functional), \"A\" (ADMET), \"T\" (toxicity)."New value: +"Restrict to an assay type code: \"B\" (binding), \"F\" (functional), \"A\" (ADMET), \"T\" (toxicity), \"P\" (physicochemical), \"U\" (unassigned)."Input schema / properties / assay_type / patternAdded value: +"^\\s*(?:(?:[Bb]|[Bb][Ii][Nn][Dd][Ii][Nn][Gg]|[Ff]|[Ff][Uu][Nn][Cc][Tt][Ii][Oo][Nn][Aa][Ll]|[Aa]|[Aa][Dd][Mm][Ee]|[Aa][Dd][Mm][Ee][Tt]|[Tt]|[Tt][Oo][Xx][Ii][Cc][Ii][Tt][Yy]|[Pp]|[Pp][Hh][Yy][Ss][Ii][Cc][Oo][Cc][Hh][Ee][Mm][Ii][Cc][Aa][Ll]|[Uu]|[Uu][Nn][Aa][Ss][Ss][Ii][Gg][Nn][Ee][Dd]|[Uu][Nn][Cc][Ll][Aa][Ss][Ss][Ii][Ff][Ii][Ee][Dd])\\s*)?$"Input schema / properties / cursor / descriptionPrevious value: -"Opaque continuation token from a previous call's nextCursor — resumes the view where that page ended. Omit for the first page. Re-send the same molecule_chembl_id/target_chembl_id, filters, and potency_view that minted it (only limit may change; it sets this page's size); redeeming it against different filters walks a different result set. A cursor page is returned inline and never staged, even with the canvas enabled."New value: +"Opaque continuation token from a previous call's nextCursor — resumes the view where that page ended. Omit for the first page. Re-send the same molecule_chembl_id/target_chembl_id, include_alternate_forms, filters, and potency_view that minted it (only limit may change; it sets this page's size); redeeming it against different filters walks a different result set. A cursor page is returned inline and never staged, even with the canvas enabled."Input schema / properties / include_alternate_formsAdded value: +{
+ "default": false,
+ "description": "Widen molecule_chembl_id to its whole family: the parent it belongs to and every salt and other alternate form ChEMBL files under it (a drug's measurements are often split across them). A salt's ID reaches its parent's family; each row keeps the molecule_chembl_id of the form it was measured on. Requires molecule_chembl_id; combines with target_chembl_id and every filter. Defaults to false: that one form's measurements only.",
+ "type": "boolean"
+}Input schema / properties / limit / descriptionPrevious value: -"Maximum rows in the inline preview or cursor page. Defaults to the server default (25). With the canvas enabled, a call without cursor still spills the full set to the canvas; when a call stages nothing, nextCursor reaches the rows past limit."New value: +"Maximum rows in the inline preview or cursor page, up to 1000 — a larger value is served at 1000, with a notice saying so. Defaults to the server default (25). With the canvas enabled, a view that spills still stages in full whatever the limit; when a call stages nothing, nextCursor reaches the rows past limit."Input schema / properties / limit / maximumPrevious value: -1000New value: +10000Input schema / properties / standard_type / descriptionPrevious value: -"Restrict to one measurement type, e.g. \"IC50\", \"Ki\", \"EC50\". Set this to compare potencies validly."New value: +"Restrict to one measurement type, e.g. \"IC50\", \"Ki\", \"EC50\". Matched exactly, case included — ChEMBL records distinct types that differ only by case, such as \"Kd\" and \"KD\". Set this to compare potencies validly."Input schema / properties / target_chembl_id / patternAdded value: +"^\\s*(?:[Cc][Hh][Ee][Mm][Bb][Ll]\\d+\\s*)?$"Input schema / properties / variantAdded value: +{
+ "description": "Restrict to one assay variant of the target. \"wild_type\" keeps the measurements that record no variant. Any other value keeps those whose recorded assay_variant_mutation equals it whole, case-insensitively, with spaces beside \",\" or \"/\" ignored: a substitution (\"T315I\"), a deletion (\"F508del\"), a multi-mutant in the order ChEMBL records it (\"L858R,T790M\"; \"T790M,L858R\" matches nothing, and \"L858R\" alone matches only the single mutant), or \"UNDEFINED MUTATION\" for an unspecified mutant. Read assay_variant_mutation on unfiltered rows for the recorded strings.",
+ "type": "string"
+}Output schema / properties / activities / items / properties / activity_commentAdded value: +{
+ "description": "Depositor or curator comment on the result, free text such as \"Not Active\", \"Active\", or \"Inconclusive\" — often the only result when standard_value is null. Null when absent.",
+ "type": [
+ "string",
+ "null"
+ ]
+}Output schema / properties / activities / items / properties / assay_variant_accessionAdded value: +{
+ "description": "UniProt accession of the variant protein, which can differ from the target's own. Null when no variant is recorded, and for UNDEFINED MUTATION.",
+ "type": [
+ "string",
+ "null"
+ ]
+}Output schema / properties / activities / items / properties / assay_variant_mutationAdded value: +{
+ "description": "Variant of the target protein the assay measured, as ChEMBL records it: a substitution (\"T315I\"), a deletion (\"F508del\"), several joined by \",\" or \"/\" (\"L858R,T790M\"), or \"UNDEFINED MUTATION\" for an unspecified mutant. Null when no variant is recorded.",
+ "type": [
+ "string",
+ "null"
+ ]
+}Output schema / properties / activities / items / properties / data_validity_commentAdded value: +{
+ "description": "ChEMBL data-validity annotation, e.g. \"Outside typical range\", \"Potential transcription error\", \"Non standard unit for type\", or \"Manually validated\" (a value curators confirmed). Null when unannotated.",
+ "type": [
+ "string",
+ "null"
+ ]
+}Output schema / properties / activities / items / properties / document_chembl_idAdded value: +{
+ "description": "ChEMBL document ID of the publication or deposited dataset the measurement comes from — cite it. Null when absent.",
+ "type": [
+ "string",
+ "null"
+ ]
+}Output schema / properties / activities / items / properties / document_yearAdded value: +{
+ "description": "Publication year of the source document. Null when it has none, as for deposited datasets.",
+ "type": [
+ "number",
+ "null"
+ ]
+}Output schema / properties / activities / items / requiredPrevious value: -[
- "activity_id",
- "molecule_chembl_id",
- "molecule_pref_name",
- "target_chembl_id",
- "target_pref_name",
- "target_organism",
- "assay_chembl_id",
- "assay_type",
- "assay_description",
- "standard_type",
- "standard_relation",
- "standard_value",
- "standard_units",
- "pchembl_value",
- "type",
- "value",
- "units",
- "relation"
-]New value: +[
+ "activity_id",
+ "molecule_chembl_id",
+ "molecule_pref_name",
+ "target_chembl_id",
+ "target_pref_name",
+ "target_organism",
+ "assay_chembl_id",
+ "assay_type",
+ "assay_description",
+ "standard_type",
+ "standard_relation",
+ "standard_value",
+ "standard_units",
+ "pchembl_value",
+ "type",
+ "value",
+ "units",
+ "relation",
+ "activity_comment",
+ "data_validity_comment",
+ "assay_variant_mutation",
+ "assay_variant_accession",
+ "document_chembl_id",
+ "document_year"
+]Output schema / properties / appliedFilters / properties / scope / descriptionPrevious value: -"Which IDs scoped the query: the molecule, the target, or both when it narrowed to a compound–target pair."New value: +"Which IDs scoped the query: the molecule, the target, or both when it narrowed to a compound–target pair. Under include_alternate_forms the molecule side names the family parent whose forms were read."Output schema / properties / appliedFilters / properties / variantAdded value: +{
+ "description": "The variant filter applied — \"wild_type\", or the variant string matched, spaces beside separators removed — or null.",
+ "type": [
+ "string",
+ "null"
+ ]
+}Output schema / properties / appliedFilters / requiredPrevious value: -[
- "scope",
- "standard_type",
- "pchembl_value_min",
- "assay_type",
- "organism"
-]New value: +[
+ "scope",
+ "standard_type",
+ "pchembl_value_min",
+ "assay_type",
+ "organism",
+ "variant"
+]Output schema / properties / canvasDisabled / descriptionPrevious value: -"True when CANVAS_PROVIDER_TYPE is not duckdb, so large sets could not spill — the inline rows are a capped preview, not the full set."New value: +"True when the server runs with the canvas off (CANVAS_PROVIDER_TYPE=none), so large sets could not spill — the inline rows are one page of the view, not the full set, and nextCursor continues it."Output schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `not_found`: ChEMBL has no record for the requested identifier or structure. `rate_limited`: ChEMBL rate-limits the upstream request. `missing_filter`: Neither molecule_chembl_id nor target_chembl_id was supplied, so the query had nothing to scope to. `contradictory_potency_filter`: pchembl_value_min was supplied alongside potency_view \"null_potency\", whose rows have no pchembl_value for the floor to compare against — the combination can only ever match zero measurements. `canvas_capacity_exhausted`: The view spilled with no canvas_id supplied, and the tenant already holds as many canvases as CANVAS_MAX_CANVASES_PER_TENANT allows, so none could be minted to stage it. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `not_found`: ChEMBL has no record for the requested identifier or structure. `rate_limited`: ChEMBL rate-limits the upstream request. `missing_filter`: Neither molecule_chembl_id nor target_chembl_id was supplied, so the query had nothing to scope to. `not_a_chembl_id`: molecule_chembl_id is not a ChEMBL ID like CHEMBL941, so it could match no measurement. `alternate_forms_without_molecule`: include_alternate_forms was set without molecule_chembl_id, so there was no molecule whose family to read. `contradictory_potency_filter`: pchembl_value_min was supplied alongside potency_view \"null_potency\", whose rows have no pchembl_value for the floor to compare against — the combination can only ever match zero measurements. `canvas_capacity_exhausted`: The view spilled with no canvas_id supplied, and the tenant already holds as many canvases as CANVAS_MAX_CANVASES_PER_TENANT allows, so none could be minted to stage it. Other values are possible when a failure originates below the handler."Output schema / properties / error / properties / data / properties / reason / examplesPrevious value: -[
- "not_found",
- "rate_limited",
- "missing_filter",
- "contradictory_potency_filter",
- "canvas_capacity_exhausted"
-]New value: +[
+ "not_found",
+ "rate_limited",
+ "missing_filter",
+ "not_a_chembl_id",
+ "alternate_forms_without_molecule",
+ "contradictory_potency_filter",
+ "canvas_capacity_exhausted"
+]Output schema / properties / notice / descriptionPrevious value: -"Guidance when no measurements matched, how to SQL the staged set, or which rows of the view an inline page holds and how to continue it."New value: +"Guidance when no measurements matched (naming the spelling ChEMBL records when the standard_type sent differs from it only by case), how to SQL the staged set, or which rows of the view an inline page holds and how to continue it — led by the disclosure that a limit above the maximum was served at the maximum."chembl_get_drug_info21 fields changedInput schema / properties / molecule_chembl_id / descriptionPrevious value: -"ChEMBL molecule ID (from chembl_search_molecules), e.g. \"CHEMBL939\" for gefitinib."New value: +"ChEMBL molecule ID (from chembl_search_molecules), e.g. \"CHEMBL939\" for gefitinib, or the molecule's standard InChIKey, e.g. \"XGALLCVXEZPNRQ-UHFFFAOYSA-N\". A salt or other alternate form answers with its parent's family, the same as the parent."Output schema / anyOfPrevious value: -[
- {
- "not": {
- "required": [
- "error"
- ]
- },
- "required": [
- "molecule_chembl_id",
- "pref_name",
- "max_phase",
- "first_approval",
- "mechanisms",
- "mechanisms_total_count",
- "mechanisms_status",
- "indications",
- "indications_total_count",
- "indications_status"
- ]
- },
- {
- "required": [
- "error"
- ]
- }
-]New value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "molecule_chembl_id",
+ "parent_molecule_chembl_id",
+ "pref_name",
+ "max_phase",
+ "first_approval",
+ "mechanisms",
+ "mechanisms_total_count",
+ "mechanisms_status",
+ "mechanisms_failure",
+ "indications",
+ "indications_total_count",
+ "indications_rows_fetched",
+ "indications_status",
+ "indications_failure"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / indications / descriptionPrevious value: -"Clinical indications. Empty is authoritative only when indications_status is \"complete\"."New value: +"Clinical indications. Empty is authoritative only when indications_status is \"complete\". When \"truncated\", each indication's max_phase_for_ind and forms are lower bounds: rows past the page cap can raise a phase or add a form."Output schema / properties / indications / items / descriptionPrevious value: -"One clinical indication with the phase reached for it."New value: +"One clinical indication, listed once per MeSH/EFO pair across the drug and its alternate forms, with the highest phase reached for it and the phase each form reached."Output schema / properties / indications / items / properties / efo_idAdded value: +{
+ "description": "EFO ontology ID, e.g. \"EFO:0003060\". Null when absent.",
+ "type": [
+ "string",
+ "null"
+ ]
+}Output schema / properties / indications / items / properties / formsAdded value: +{
+ "description": "The forms of the drug the indication is recorded on, each with its own highest phase for it. Empty when ChEMBL names none.",
+ "items": {
+ "additionalProperties": false,
+ "description": "One form the indication is recorded on, at its own phase.",
+ "properties": {
+ "max_phase_for_ind": {
+ "description": "Max clinical phase THIS form reached for the indication — a deuterated analog can sit lower than its parent. Null when unknown.",
+ "type": [
+ "number",
+ "null"
+ ]
+ },
+ "molecule_chembl_id": {
+ "description": "A form of the drug the indication is recorded on — the parent, or one of its salts or other alternate forms.",
+ "type": "string"
+ }
+ },
+ "required": [
+ "molecule_chembl_id",
+ "max_phase_for_ind"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+}Output schema / properties / indications / items / properties / max_phase_for_ind / descriptionPrevious value: -"Max clinical phase reached for THIS indication (1–4). Null when unknown."New value: +"Max clinical phase reached for THIS indication (1–4), the highest across the forms it is recorded on. Null when unknown."Output schema / properties / indications / items / properties / mesh_idAdded value: +{
+ "description": "MeSH descriptor ID, e.g. \"D002289\". Null when absent.",
+ "type": [
+ "string",
+ "null"
+ ]
+}Output schema / properties / indications / items / requiredPrevious value: -[
- "mesh_heading",
- "efo_term",
- "max_phase_for_ind"
-]New value: +[
+ "mesh_id",
+ "mesh_heading",
+ "efo_id",
+ "efo_term",
+ "max_phase_for_ind",
+ "forms"
+]Output schema / properties / indications_failureAdded value: +{
+ "anyOf": [
+ {
+ "enum": [
+ "timeout",
+ "upstream_error"
+ ],
+ "type": "string"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "description": "Why the indication list failed, when indications_status is \"failed\": \"timeout\" = the request ran out of time before ChEMBL returned the list; \"upstream_error\" = ChEMBL answered with an error (a rate limit, a server error, a rejected request) or could not be reached. Null when the list did not fail."
+}Output schema / properties / indications_rows_fetchedAdded value: +{
+ "description": "Indication rows fetched from ChEMBL for the molecule and its alternate forms, before rows recorded on several forms merge. When the status is \"truncated\", each row not fetched (indications_total_count minus this) can add at most one indication, so that difference bounds the indications missing. Null when the fetch failed.",
+ "type": [
+ "number",
+ "null"
+ ]
+}Output schema / properties / indications_status / descriptionPrevious value: -"Retrieval state of the indication list. \"complete\" = every row ChEMBL records is present, so an empty array is a fact about the molecule. \"truncated\" = the single-request page cap bounded the list, so the array is a prefix of indications_total_count rows. \"failed\" = the upstream request was rejected, so the empty array is unknown data, NOT evidence that none exist — re-call chembl_get_drug_info to retry."New value: +"Retrieval state of the indication list. \"complete\" = every row ChEMBL records for the molecule and its alternate forms is present, so an empty array is a fact about the molecule. \"truncated\" = the single-request page cap bounded the list, so the array holds the indications of the rows fetched (indications_rows_fetched, fewer than indications_total_count). \"failed\" = the list was not retrieved (the request ran out of time or ChEMBL answered with an error, as indications_failure says), so the empty array is unknown data, NOT evidence that none exist — re-call chembl_get_drug_info to retry."Output schema / properties / indications_total_count / descriptionPrevious value: -"Total indication rows ChEMBL holds for this molecule (upstream page_meta.total_count). Exceeds the returned array length exactly when the status is \"truncated\". Null when the fetch failed — the count is unknown, never 0."New value: +"When the status is \"complete\", the number of distinct indications — the returned array length, rows recorded on several forms counted once. When \"truncated\", the indication rows ChEMBL holds for the molecule and its alternate forms, an upper bound on the distinct indications. Null when the fetch failed — the count is unknown, never 0."Output schema / properties / mechanisms / items / properties / molecule_chembl_idAdded value: +{
+ "description": "The form of the drug the mechanism is recorded on — the parent, or one of its salts or other alternate forms. Null when ChEMBL names none.",
+ "type": [
+ "string",
+ "null"
+ ]
+}Output schema / properties / mechanisms / items / requiredPrevious value: -[
- "target_chembl_id",
- "mechanism_of_action",
- "action_type"
-]New value: +[
+ "target_chembl_id",
+ "mechanism_of_action",
+ "action_type",
+ "molecule_chembl_id"
+]Output schema / properties / mechanisms_failureAdded value: +{
+ "anyOf": [
+ {
+ "enum": [
+ "timeout",
+ "upstream_error"
+ ],
+ "type": "string"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "description": "Why the mechanism list failed, when mechanisms_status is \"failed\": \"timeout\" = the request ran out of time before ChEMBL returned the list; \"upstream_error\" = ChEMBL answered with an error (a rate limit, a server error, a rejected request) or could not be reached. Null when the list did not fail."
+}Output schema / properties / mechanisms_status / descriptionPrevious value: -"Retrieval state of the mechanism list. \"complete\" = every row ChEMBL records is present, so an empty array is a fact about the molecule. \"truncated\" = the single-request page cap bounded the list, so the array is a prefix of mechanisms_total_count rows. \"failed\" = the upstream request was rejected, so the empty array is unknown data, NOT evidence that none exist — re-call chembl_get_drug_info to retry."New value: +"Retrieval state of the mechanism list. \"complete\" = every row ChEMBL records for the molecule and its alternate forms is present, so an empty array is a fact about the molecule. \"truncated\" = the single-request page cap bounded the list, so the array is a prefix of mechanisms_total_count rows. \"failed\" = the list was not retrieved (the request ran out of time or ChEMBL answered with an error, as mechanisms_failure says), so the empty array is unknown data, NOT evidence that none exist — re-call chembl_get_drug_info to retry."Output schema / properties / mechanisms_total_count / descriptionPrevious value: -"Total mechanism rows ChEMBL holds for this molecule (upstream page_meta.total_count). Exceeds the returned array length exactly when the status is \"truncated\". Null when the fetch failed — the count is unknown, never 0."New value: +"Total mechanism rows ChEMBL holds for the molecule and its alternate forms. Exceeds the returned array length exactly when the status is \"truncated\". Null when the fetch failed — the count is unknown, never 0."Output schema / properties / molecule_chembl_id / descriptionPrevious value: -"The ChEMBL molecule ID queried."New value: +"The ChEMBL molecule ID queried, as the molecule's own record writes it."Output schema / properties / notice / descriptionPrevious value: -"Disclosure of anything the two lists do not say for themselves: a list whose upstream fetch failed (so its emptiness means nothing), a list the page cap bounded, or — only when both lists came back complete and empty — that the molecule may be a research compound rather than a drug."New value: +"Disclosure of anything the two lists do not say for themselves: a list whose upstream fetch timed out or failed (so its emptiness means nothing), a list the page cap bounded, or — only when both lists came back complete and empty — that the molecule may be a research compound rather than a drug."Output schema / properties / parent_molecule_chembl_idAdded value: +{
+ "description": "The parent of the queried molecule's family — the molecule itself when it is the parent or ChEMBL records no hierarchy for it. Both lists cover this parent and every alternate form ChEMBL files under it (salts, isotope-labelled and deuterated analogs).",
+ "type": "string"
+}chembl_search_molecules10 fields changedInput schema / properties / limit / descriptionPrevious value: -"Maximum molecules to return. Defaults to the server default (25) when omitted."New value: +"Maximum molecules to return, up to 100 — a larger value is served at 100, with a notice saying so. Defaults to the server default (25) when omitted."Input schema / properties / limit / maximumPrevious value: -100New value: +10000Output schema / anyOfPrevious value: -[
- {
- "not": {
- "required": [
- "error"
- ]
- },
- "required": [
- "molecules",
- "totalCount",
- "truncated",
- "shown",
- "cap"
- ]
- },
- {
- "required": [
- "error"
- ]
- }
-]New value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "molecules",
+ "totalCount",
+ "totalCountCapped",
+ "truncated",
+ "shown",
+ "cap"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `not_found`: ChEMBL has no record for the requested identifier or structure. `rate_limited`: ChEMBL rate-limits the upstream request. `missing_input`: Neither query nor structure was supplied, or a structure search_type was chosen without a structure. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `not_found`: ChEMBL has no record for the requested identifier or structure. `rate_limited`: ChEMBL rate-limits the upstream request. `invalid_structure`: ChEMBL could not parse the SMILES of a similarity or substructure search. `missing_input`: Neither query nor structure was supplied, or a structure search_type was chosen without a structure. Other values are possible when a failure originates below the handler."Output schema / properties / error / properties / data / properties / reason / examplesPrevious value: -[
- "not_found",
- "rate_limited",
- "missing_input"
-]New value: +[
+ "not_found",
+ "rate_limited",
+ "invalid_structure",
+ "missing_input"
+]Output schema / properties / molecules / items / properties / parent_chembl_idAdded value: +{
+ "description": "The parent of the compound's family, e.g. \"CHEMBL553\" for erlotinib hydrochloride — the compound's own ID when it is the parent or ChEMBL records no hierarchy for it. A salt's measurements are a small share of its family's: pass the parent to chembl_get_drug_info, or set include_alternate_forms on chembl_get_bioactivities, to reach the whole family.",
+ "type": "string"
+}Output schema / properties / molecules / items / requiredPrevious value: -[
- "molecule_chembl_id",
- "pref_name",
- "canonical_smiles",
- "standard_inchi_key",
- "full_molformula",
- "mw_freebase",
- "alogp",
- "num_ro5_violations",
- "qed_weighted",
- "max_phase",
- "molecule_type"
-]New value: +[
+ "molecule_chembl_id",
+ "pref_name",
+ "canonical_smiles",
+ "standard_inchi_key",
+ "full_molformula",
+ "mw_freebase",
+ "alogp",
+ "num_ro5_violations",
+ "qed_weighted",
+ "max_phase",
+ "molecule_type",
+ "parent_chembl_id"
+]Output schema / properties / notice / descriptionPrevious value: -"Guidance when nothing matched — echoes the query and suggests how to broaden."New value: +"Guidance when nothing matched — echoes the query and suggests how to broaden — the disclosure that a limit above the maximum was served at the maximum, and, when totalCountCapped is true, that the total is ChEMBL's search ceiling and how to narrow below it."Output schema / properties / totalCount / descriptionPrevious value: -"Total compounds matching before the limit was applied."New value: +"Total compounds matching before the limit was applied — a lower bound when totalCountCapped is true."Output schema / properties / totalCountCappedAdded value: +{
+ "description": "True when totalCount is ChEMBL's ceiling for the search — 10000 for a name search, 30000 for a substructure search: at least that many compounds match, and no page past the ceiling can be reached. Narrow the query to bring the matches under it.",
+ "type": "boolean"
+}chembl_search_targets3 fields changedInput schema / properties / limit / descriptionPrevious value: -"Maximum targets to return. Defaults to the server default (25) when omitted."New value: +"Maximum targets to return, up to 100 — a larger value is served at 100, with a notice saying so. Defaults to the server default (25) when omitted."Input schema / properties / limit / maximumPrevious value: -100New value: +10000Output schema / properties / notice / descriptionPrevious value: -"Guidance when no target matched — echoes the filters and suggests how to broaden."New value: +"Guidance when no target matched — echoes the filters and suggests how to broaden — and the disclosure that a limit above the maximum was served at the maximum."chembl_dataframe_describe1 field changedInput schema / properties / canvas_id / descriptionPrevious value: -"Canvas ID returned by chembl_get_bioactivities (spilled: true)."New value: +"Canvas ID returned by chembl_get_bioactivities — non-null whenever that call staged a table."chembl_dataframe_query1 field changedInput schema / properties / canvas_id / descriptionPrevious value: -"Canvas ID returned by chembl_get_bioactivities (spilled: true)."New value: +"Canvas ID returned by chembl_get_bioactivities — non-null whenever that call staged a table."chembl_get_bioactivities15 fields changedInput schema / properties / canvas_id / descriptionPrevious value: -"Optional canvas ID from a prior call to reuse the same canvas. Each potency_view re-stages its own table, so a second query of the SAME view REPLACES (overwrites) its prior rows — it does not append — while the other view's table is left intact, which is what lets both coexist on one canvas. Omit to mint a fresh canvas."New value: +"Optional canvas ID from a prior call to reuse the same canvas. With it, the call re-stages the selected potency_view's table with this call's rows whether they spill, fit inline, or are empty, so a second query of the SAME view REPLACES (overwrites) its prior rows once it succeeds — it does not append, and a spill that fails or is cancelled leaves them — while the other view's table is left intact, which is what lets both coexist on one canvas. Omit it and a fresh canvas is minted only if the view spills. Left untouched on a cursor page, which never stages."Input schema / properties / cursorAdded value: +{
+ "description": "Opaque continuation token from a previous call's nextCursor — resumes the view where that page ended. Omit for the first page. Re-send the same molecule_chembl_id/target_chembl_id, filters, and potency_view that minted it (only limit may change; it sets this page's size); redeeming it against different filters walks a different result set. A cursor page is returned inline and never staged, even with the canvas enabled.",
+ "type": "string"
+}Input schema / properties / limit / descriptionPrevious value: -"Maximum rows in the inline preview. Defaults to the server default (25). The full set still spills to the canvas."New value: +"Maximum rows in the inline preview or cursor page. Defaults to the server default (25). With the canvas enabled, a call without cursor still spills the full set to the canvas; when a call stages nothing, nextCursor reaches the rows past limit."Output schema / anyOfPrevious value: -[
- {
- "not": {
- "required": [
- "error"
- ]
- },
- "required": [
- "activities",
- "totalCount",
- "potency_view",
- "spilled",
- "canvas_id",
- "table_name",
- "staged_row_count",
- "truncated",
- "canvasDisabled",
- "appliedFilters"
- ]
- },
- {
- "required": [
- "error"
- ]
- }
-]New value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "activities",
+ "totalCount",
+ "potency_view",
+ "spilled",
+ "canvas_id",
+ "table_name",
+ "staged_row_count",
+ "truncated",
+ "truncated_by",
+ "canvasDisabled",
+ "appliedFilters"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / activities / descriptionPrevious value: -"Bioactivity rows for the selected potency_view — the inline preview, or the full view when it fit without spilling."New value: +"Bioactivity rows for the selected potency_view — the inline preview, the cursor page, or the full view when it fit without spilling."Output schema / properties / canvas_id / descriptionPrevious value: -"Canvas ID holding the staged table — pass to chembl_dataframe_describe to list its columns, then to chembl_dataframe_query to run SQL over them. Null when canvas is disabled or nothing spilled."New value: +"Canvas ID holding the staged table — pass to chembl_dataframe_describe to list its columns, then to chembl_dataframe_query to run SQL over them. Null when nothing was staged: canvas disabled, a cursor page, or an inline fit with no canvas_id supplied."Output schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `not_found`: ChEMBL has no record for the requested identifier or structure. `rate_limited`: ChEMBL rate-limits the upstream request. `missing_filter`: Neither molecule_chembl_id nor target_chembl_id was supplied, so the query had nothing to scope to. `contradictory_potency_filter`: pchembl_value_min was supplied alongside potency_view \"null_potency\", whose rows have no pchembl_value for the floor to compare against — the combination can only ever match zero measurements. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `not_found`: ChEMBL has no record for the requested identifier or structure. `rate_limited`: ChEMBL rate-limits the upstream request. `missing_filter`: Neither molecule_chembl_id nor target_chembl_id was supplied, so the query had nothing to scope to. `contradictory_potency_filter`: pchembl_value_min was supplied alongside potency_view \"null_potency\", whose rows have no pchembl_value for the floor to compare against — the combination can only ever match zero measurements. `canvas_capacity_exhausted`: The view spilled with no canvas_id supplied, and the tenant already holds as many canvases as CANVAS_MAX_CANVASES_PER_TENANT allows, so none could be minted to stage it. Other values are possible when a failure originates below the handler."Output schema / properties / error / properties / data / properties / reason / examplesPrevious value: -[
- "not_found",
- "rate_limited",
- "missing_filter",
- "contradictory_potency_filter"
-]New value: +[
+ "not_found",
+ "rate_limited",
+ "missing_filter",
+ "contradictory_potency_filter",
+ "canvas_capacity_exhausted"
+]Output schema / properties / nextCursorAdded value: +{
+ "description": "Opaque token for the next page of this view — pass it back as cursor with the same filters and potency_view. Minted only when nothing was staged and rows remain past this page: with the canvas disabled, on a cursor page, or when the view fit inline with no canvas_id supplied. Absent on the last page and whenever the call staged a table (a spill, or an inline fit re-staged on a supplied canvas_id).",
+ "type": "string"
+}Output schema / properties / notice / descriptionPrevious value: -"Guidance when no measurements matched, or how to SQL the spilled set."New value: +"Guidance when no measurements matched, how to SQL the staged set, or which rows of the view an inline page holds and how to continue it."Output schema / properties / spilled / descriptionPrevious value: -"True when the view exceeded the preview and was staged on the canvas."New value: +"True when the view exceeded the inline preview and spilled to the canvas. False when it fit inline — including an inline fit re-staged on a supplied canvas_id, which table_name and staged_row_count report."Output schema / properties / staged_row_count / descriptionPrevious value: -"Rows actually registered on the canvas table. Null when nothing spilled. Below the view total when truncated is true."New value: +"Rows actually registered on the canvas table — 0 when a re-staged view matched nothing. Null when nothing was staged. Below the view total when truncated is true."Output schema / properties / table_name / descriptionPrevious value: -"Canvas table name holding the staged rowset, and the FROM target for chembl_dataframe_query SQL — \"bioactivities\" for potency_ranked, \"bioactivities_null_potency\" for null_potency. Null when not spilled."New value: +"Canvas table name holding the staged rowset, and the FROM target for chembl_dataframe_query SQL — \"bioactivities\" for potency_ranked, \"bioactivities_null_potency\" for null_potency. Null when nothing was staged."Output schema / properties / truncated / descriptionPrevious value: -"True when the CHEMBL_MAX_SPILL_ROWS cap was hit before the upstream view was exhausted — the staged table is a bounded slice, NOT the complete view, so aggregates over it are a sample. Narrow the filters to bring the view under the cap."New value: +"True when a bound stopped the page walk short of the view — the CHEMBL_MAX_SPILL_ROWS row cap or the CHEMBL_SPILL_DEADLINE_MS time budget, as truncated_by says. The staged table is then a bounded slice, NOT the complete view, so aggregates over it are a sample. Narrow the filters to bring the view under the bound."Output schema / properties / truncated_byAdded value: +{
+ "anyOf": [
+ {
+ "enum": [
+ "row_cap",
+ "time_budget"
+ ],
+ "type": "string"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "description": "The bound that cut the staged table short when truncated is true: \"row_cap\" — the CHEMBL_MAX_SPILL_ROWS cap; \"time_budget\" — the CHEMBL_SPILL_DEADLINE_MS budget ended the page walk, at its expiry or once what was left would not hold another page, so a re-call can stage more. Null when truncated is false."
+}chembl_get_assay2 fields changedOutput schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode."New value: +"Machine-readable failure mode. Declared by this tool: `not_found`: ChEMBL has no record for the requested identifier or structure. `rate_limited`: ChEMBL rate-limits the upstream request. Other values are possible when a failure originates below the handler."Output schema / properties / error / properties / data / properties / reason / examplesAdded value: +[
+ "not_found",
+ "rate_limited"
+]chembl_get_bioactivities2 fields changedOutput schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `missing_filter`: Neither molecule_chembl_id nor target_chembl_id was supplied, so the query had nothing to scope to. `contradictory_potency_filter`: pchembl_value_min was supplied alongside potency_view \"null_potency\", whose rows have no pchembl_value for the floor to compare against — the combination can only ever match zero measurements. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `not_found`: ChEMBL has no record for the requested identifier or structure. `rate_limited`: ChEMBL rate-limits the upstream request. `missing_filter`: Neither molecule_chembl_id nor target_chembl_id was supplied, so the query had nothing to scope to. `contradictory_potency_filter`: pchembl_value_min was supplied alongside potency_view \"null_potency\", whose rows have no pchembl_value for the floor to compare against — the combination can only ever match zero measurements. Other values are possible when a failure originates below the handler."Output schema / properties / error / properties / data / properties / reason / examplesPrevious value: -[
- "missing_filter",
- "contradictory_potency_filter"
-]New value: +[
+ "not_found",
+ "rate_limited",
+ "missing_filter",
+ "contradictory_potency_filter"
+]chembl_get_drug_info2 fields changedOutput schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode."New value: +"Machine-readable failure mode. Declared by this tool: `not_found`: ChEMBL has no record for the requested identifier or structure. `rate_limited`: ChEMBL rate-limits the upstream request. Other values are possible when a failure originates below the handler."Output schema / properties / error / properties / data / properties / reason / examplesAdded value: +[
+ "not_found",
+ "rate_limited"
+]chembl_search_molecules2 fields changedOutput schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `missing_input`: Neither query nor structure was supplied, or a structure search_type was chosen without a structure. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `not_found`: ChEMBL has no record for the requested identifier or structure. `rate_limited`: ChEMBL rate-limits the upstream request. `missing_input`: Neither query nor structure was supplied, or a structure search_type was chosen without a structure. Other values are possible when a failure originates below the handler."Output schema / properties / error / properties / data / properties / reason / examplesPrevious value: -[
- "missing_input"
-]New value: +[
+ "not_found",
+ "rate_limited",
+ "missing_input"
+]chembl_search_targets2 fields changedOutput schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `missing_input`: None of query, accession, or gene_symbol was supplied. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `not_found`: ChEMBL has no record for the requested identifier or structure. `rate_limited`: ChEMBL rate-limits the upstream request. `missing_input`: None of query, accession, or gene_symbol was supplied. Other values are possible when a failure originates below the handler."Output schema / properties / error / properties / data / properties / reason / examplesPrevious value: -[
- "missing_input"
-]New value: +[
+ "not_found",
+ "rate_limited",
+ "missing_input"
+]chembl_dataframe_describe1 field changedInput schema / properties / canvas_id / patternAdded value: +"^[A-Za-z0-9_-]{10}$"chembl_dataframe_query1 field changedInput schema / properties / canvas_id / patternAdded value: +"^[A-Za-z0-9_-]{10}$"chembl_get_assay14 fields changedOutput schema / properties / assay_type / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / assay_type / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / assay_type_description / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / assay_type_description / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / confidence_description / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / confidence_description / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / confidence_score / anyOfRemoved value: -[
- {
- "type": "number"
- },
- {
- "type": "null"
- }
-]Output schema / properties / confidence_score / typeAdded value: +[
+ "number",
+ "null"
+]Output schema / properties / description / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / description / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / organism / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / organism / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / target_chembl_id / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / target_chembl_id / typeAdded value: +[
+ "string",
+ "null"
+]chembl_get_bioactivities43 fields changedInput schema / properties / canvas_id / patternAdded value: +"^[A-Za-z0-9_-]{10}$"Output schema / properties / activities / items / properties / assay_description / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / activities / items / properties / assay_description / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / activities / items / properties / assay_type / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / activities / items / properties / assay_type / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / activities / items / properties / molecule_pref_name / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / activities / items / properties / molecule_pref_name / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / activities / items / properties / pchembl_value / anyOfRemoved value: -[
- {
- "type": "number"
- },
- {
- "type": "null"
- }
-]Output schema / properties / activities / items / properties / pchembl_value / typeAdded value: +[
+ "number",
+ "null"
+]Output schema / properties / activities / items / properties / relation / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / activities / items / properties / relation / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / activities / items / properties / standard_relation / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / activities / items / properties / standard_relation / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / activities / items / properties / standard_type / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / activities / items / properties / standard_type / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / activities / items / properties / standard_units / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / activities / items / properties / standard_units / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / activities / items / properties / standard_value / anyOfRemoved value: -[
- {
- "type": "number"
- },
- {
- "type": "null"
- }
-]Output schema / properties / activities / items / properties / standard_value / typeAdded value: +[
+ "number",
+ "null"
+]Output schema / properties / activities / items / properties / target_organism / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / activities / items / properties / target_organism / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / activities / items / properties / target_pref_name / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / activities / items / properties / target_pref_name / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / activities / items / properties / type / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / activities / items / properties / type / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / activities / items / properties / units / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / activities / items / properties / units / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / activities / items / properties / value / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / activities / items / properties / value / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / appliedFilters / properties / assay_type / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / appliedFilters / properties / assay_type / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / appliedFilters / properties / organism / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / appliedFilters / properties / organism / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / appliedFilters / properties / pchembl_value_min / anyOfRemoved value: -[
- {
- "type": "number"
- },
- {
- "type": "null"
- }
-]Output schema / properties / appliedFilters / properties / pchembl_value_min / typeAdded value: +[
+ "number",
+ "null"
+]Output schema / properties / appliedFilters / properties / standard_type / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / appliedFilters / properties / standard_type / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / canvas_id / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / canvas_id / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / staged_row_count / anyOfRemoved value: -[
- {
- "type": "number"
- },
- {
- "type": "null"
- }
-]Output schema / properties / staged_row_count / typeAdded value: +[
+ "number",
+ "null"
+]Output schema / properties / table_name / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / table_name / typeAdded value: +[
+ "string",
+ "null"
+]chembl_get_drug_info22 fields changedOutput schema / properties / first_approval / anyOfRemoved value: -[
- {
- "type": "number"
- },
- {
- "type": "null"
- }
-]Output schema / properties / first_approval / typeAdded value: +[
+ "number",
+ "null"
+]Output schema / properties / indications / items / properties / efo_term / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / indications / items / properties / efo_term / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / indications / items / properties / max_phase_for_ind / anyOfRemoved value: -[
- {
- "type": "number"
- },
- {
- "type": "null"
- }
-]Output schema / properties / indications / items / properties / max_phase_for_ind / typeAdded value: +[
+ "number",
+ "null"
+]Output schema / properties / indications / items / properties / mesh_heading / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / indications / items / properties / mesh_heading / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / indications_total_count / anyOfRemoved value: -[
- {
- "type": "number"
- },
- {
- "type": "null"
- }
-]Output schema / properties / indications_total_count / typeAdded value: +[
+ "number",
+ "null"
+]Output schema / properties / max_phase / anyOfRemoved value: -[
- {
- "type": "number"
- },
- {
- "type": "null"
- }
-]Output schema / properties / max_phase / typeAdded value: +[
+ "number",
+ "null"
+]Output schema / properties / mechanisms / items / properties / action_type / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / mechanisms / items / properties / action_type / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / mechanisms / items / properties / mechanism_of_action / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / mechanisms / items / properties / mechanism_of_action / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / mechanisms / items / properties / target_chembl_id / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / mechanisms / items / properties / target_chembl_id / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / mechanisms_total_count / anyOfRemoved value: -[
- {
- "type": "number"
- },
- {
- "type": "null"
- }
-]Output schema / properties / mechanisms_total_count / typeAdded value: +[
+ "number",
+ "null"
+]Output schema / properties / pref_name / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / pref_name / typeAdded value: +[
+ "string",
+ "null"
+]chembl_search_molecules22 fields changedOutput schema / properties / molecules / items / properties / alogp / anyOfRemoved value: -[
- {
- "type": "number"
- },
- {
- "type": "null"
- }
-]Output schema / properties / molecules / items / properties / alogp / typeAdded value: +[
+ "number",
+ "null"
+]Output schema / properties / molecules / items / properties / canonical_smiles / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / molecules / items / properties / canonical_smiles / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / molecules / items / properties / full_molformula / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / molecules / items / properties / full_molformula / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / molecules / items / properties / max_phase / anyOfRemoved value: -[
- {
- "type": "number"
- },
- {
- "type": "null"
- }
-]Output schema / properties / molecules / items / properties / max_phase / typeAdded value: +[
+ "number",
+ "null"
+]Output schema / properties / molecules / items / properties / molecule_type / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / molecules / items / properties / molecule_type / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / molecules / items / properties / mw_freebase / anyOfRemoved value: -[
- {
- "type": "number"
- },
- {
- "type": "null"
- }
-]Output schema / properties / molecules / items / properties / mw_freebase / typeAdded value: +[
+ "number",
+ "null"
+]Output schema / properties / molecules / items / properties / num_ro5_violations / anyOfRemoved value: -[
- {
- "type": "number"
- },
- {
- "type": "null"
- }
-]Output schema / properties / molecules / items / properties / num_ro5_violations / typeAdded value: +[
+ "number",
+ "null"
+]Output schema / properties / molecules / items / properties / pref_name / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / molecules / items / properties / pref_name / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / molecules / items / properties / qed_weighted / anyOfRemoved value: -[
- {
- "type": "number"
- },
- {
- "type": "null"
- }
-]Output schema / properties / molecules / items / properties / qed_weighted / typeAdded value: +[
+ "number",
+ "null"
+]Output schema / properties / molecules / items / properties / similarity / anyOfRemoved value: -[
- {
- "type": "number"
- },
- {
- "type": "null"
- }
-]Output schema / properties / molecules / items / properties / similarity / typeAdded value: +[
+ "number",
+ "null"
+]Output schema / properties / molecules / items / properties / standard_inchi_key / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / molecules / items / properties / standard_inchi_key / typeAdded value: +[
+ "string",
+ "null"
+]chembl_search_targets8 fields changedOutput schema / properties / targets / items / properties / components / items / properties / accession / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / targets / items / properties / components / items / properties / accession / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / targets / items / properties / organism / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / targets / items / properties / organism / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / targets / items / properties / pref_name / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / targets / items / properties / pref_name / typeAdded value: +[
+ "string",
+ "null"
+]Output schema / properties / targets / items / properties / target_type / anyOfRemoved value: -[
- {
- "type": "string"
- },
- {
- "type": "null"
- }
-]Output schema / properties / targets / items / properties / target_type / typeAdded value: +[
+ "string",
+ "null"
+]chembl_dataframe_describe6 fields changedInput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Input schema / additionalPropertiesAdded value: +falseOutput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Output schema / anyOfAdded value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "tables"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / errorAdded value: +{
+ "additionalProperties": {},
+ "description": "Present when the call failed. Absent on success.",
+ "properties": {
+ "code": {
+ "description": "JSON-RPC error code for this failure.",
+ "maximum": 9007199254740991,
+ "minimum": -9007199254740991,
+ "type": "integer"
+ },
+ "data": {
+ "additionalProperties": {},
+ "properties": {
+ "reason": {
+ "description": "Machine-readable failure mode. Declared by this tool: `canvas_disabled`: Called while CANVAS_PROVIDER_TYPE is not duckdb, so no canvas exists. Other values are possible when a failure originates below the handler.",
+ "examples": [
+ "canvas_disabled"
+ ],
+ "type": "string"
+ },
+ "recovery": {
+ "additionalProperties": {},
+ "description": "Actionable next step for the caller.",
+ "properties": {
+ "hint": {
+ "type": "string"
+ }
+ },
+ "required": [
+ "hint"
+ ],
+ "type": "object"
+ },
+ "retryable": {
+ "description": "Whether retrying may succeed.",
+ "type": "boolean"
+ }
+ },
+ "type": "object"
+ },
+ "message": {
+ "description": "Human-readable description of what went wrong.",
+ "type": "string"
+ }
+ },
+ "required": [
+ "code",
+ "message"
+ ],
+ "type": "object"
+}Output schema / requiredRemoved value: -[
- "tables"
-]chembl_dataframe_query6 fields changedInput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Input schema / additionalPropertiesAdded value: +falseOutput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Output schema / anyOfAdded value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "rows",
+ "row_count",
+ "rendered_rows",
+ "truncated"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / errorAdded value: +{
+ "additionalProperties": {},
+ "description": "Present when the call failed. Absent on success.",
+ "properties": {
+ "code": {
+ "description": "JSON-RPC error code for this failure.",
+ "maximum": 9007199254740991,
+ "minimum": -9007199254740991,
+ "type": "integer"
+ },
+ "data": {
+ "additionalProperties": {},
+ "properties": {
+ "reason": {
+ "description": "Machine-readable failure mode. Declared by this tool: `canvas_disabled`: Called while CANVAS_PROVIDER_TYPE is not duckdb, so no canvas exists. Other values are possible when a failure originates below the handler.",
+ "examples": [
+ "canvas_disabled"
+ ],
+ "type": "string"
+ },
+ "recovery": {
+ "additionalProperties": {},
+ "description": "Actionable next step for the caller.",
+ "properties": {
+ "hint": {
+ "type": "string"
+ }
+ },
+ "required": [
+ "hint"
+ ],
+ "type": "object"
+ },
+ "retryable": {
+ "description": "Whether retrying may succeed.",
+ "type": "boolean"
+ }
+ },
+ "type": "object"
+ },
+ "message": {
+ "description": "Human-readable description of what went wrong.",
+ "type": "string"
+ }
+ },
+ "required": [
+ "code",
+ "message"
+ ],
+ "type": "object"
+}Output schema / requiredRemoved value: -[
- "rows",
- "row_count",
- "rendered_rows",
- "truncated"
-]chembl_get_assay6 fields changedInput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Input schema / additionalPropertiesAdded value: +falseOutput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Output schema / anyOfAdded value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "assay_chembl_id",
+ "description",
+ "assay_type",
+ "assay_type_description",
+ "target_chembl_id",
+ "organism",
+ "confidence_score",
+ "confidence_description"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / errorAdded value: +{
+ "additionalProperties": {},
+ "description": "Present when the call failed. Absent on success.",
+ "properties": {
+ "code": {
+ "description": "JSON-RPC error code for this failure.",
+ "maximum": 9007199254740991,
+ "minimum": -9007199254740991,
+ "type": "integer"
+ },
+ "data": {
+ "additionalProperties": {},
+ "properties": {
+ "reason": {
+ "description": "Machine-readable failure mode.",
+ "type": "string"
+ },
+ "recovery": {
+ "additionalProperties": {},
+ "description": "Actionable next step for the caller.",
+ "properties": {
+ "hint": {
+ "type": "string"
+ }
+ },
+ "required": [
+ "hint"
+ ],
+ "type": "object"
+ },
+ "retryable": {
+ "description": "Whether retrying may succeed.",
+ "type": "boolean"
+ }
+ },
+ "type": "object"
+ },
+ "message": {
+ "description": "Human-readable description of what went wrong.",
+ "type": "string"
+ }
+ },
+ "required": [
+ "code",
+ "message"
+ ],
+ "type": "object"
+}Output schema / requiredRemoved value: -[
- "assay_chembl_id",
- "description",
- "assay_type",
- "assay_type_description",
- "target_chembl_id",
- "organism",
- "confidence_score",
- "confidence_description"
-]chembl_get_bioactivities6 fields changedInput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Input schema / additionalPropertiesAdded value: +falseOutput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Output schema / anyOfAdded value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "activities",
+ "totalCount",
+ "potency_view",
+ "spilled",
+ "canvas_id",
+ "table_name",
+ "staged_row_count",
+ "truncated",
+ "canvasDisabled",
+ "appliedFilters"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / errorAdded value: +{
+ "additionalProperties": {},
+ "description": "Present when the call failed. Absent on success.",
+ "properties": {
+ "code": {
+ "description": "JSON-RPC error code for this failure.",
+ "maximum": 9007199254740991,
+ "minimum": -9007199254740991,
+ "type": "integer"
+ },
+ "data": {
+ "additionalProperties": {},
+ "properties": {
+ "reason": {
+ "description": "Machine-readable failure mode. Declared by this tool: `missing_filter`: Neither molecule_chembl_id nor target_chembl_id was supplied, so the query had nothing to scope to. `contradictory_potency_filter`: pchembl_value_min was supplied alongside potency_view \"null_potency\", whose rows have no pchembl_value for the floor to compare against — the combination can only ever match zero measurements. Other values are possible when a failure originates below the handler.",
+ "examples": [
+ "missing_filter",
+ "contradictory_potency_filter"
+ ],
+ "type": "string"
+ },
+ "recovery": {
+ "additionalProperties": {},
+ "description": "Actionable next step for the caller.",
+ "properties": {
+ "hint": {
+ "type": "string"
+ }
+ },
+ "required": [
+ "hint"
+ ],
+ "type": "object"
+ },
+ "retryable": {
+ "description": "Whether retrying may succeed.",
+ "type": "boolean"
+ }
+ },
+ "type": "object"
+ },
+ "message": {
+ "description": "Human-readable description of what went wrong.",
+ "type": "string"
+ }
+ },
+ "required": [
+ "code",
+ "message"
+ ],
+ "type": "object"
+}Output schema / requiredRemoved value: -[
- "activities",
- "totalCount",
- "potency_view",
- "spilled",
- "canvas_id",
- "table_name",
- "staged_row_count",
- "truncated",
- "canvasDisabled",
- "appliedFilters"
-]chembl_get_drug_info6 fields changedInput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Input schema / additionalPropertiesAdded value: +falseOutput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Output schema / anyOfAdded value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "molecule_chembl_id",
+ "pref_name",
+ "max_phase",
+ "first_approval",
+ "mechanisms",
+ "mechanisms_total_count",
+ "mechanisms_status",
+ "indications",
+ "indications_total_count",
+ "indications_status"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / errorAdded value: +{
+ "additionalProperties": {},
+ "description": "Present when the call failed. Absent on success.",
+ "properties": {
+ "code": {
+ "description": "JSON-RPC error code for this failure.",
+ "maximum": 9007199254740991,
+ "minimum": -9007199254740991,
+ "type": "integer"
+ },
+ "data": {
+ "additionalProperties": {},
+ "properties": {
+ "reason": {
+ "description": "Machine-readable failure mode.",
+ "type": "string"
+ },
+ "recovery": {
+ "additionalProperties": {},
+ "description": "Actionable next step for the caller.",
+ "properties": {
+ "hint": {
+ "type": "string"
+ }
+ },
+ "required": [
+ "hint"
+ ],
+ "type": "object"
+ },
+ "retryable": {
+ "description": "Whether retrying may succeed.",
+ "type": "boolean"
+ }
+ },
+ "type": "object"
+ },
+ "message": {
+ "description": "Human-readable description of what went wrong.",
+ "type": "string"
+ }
+ },
+ "required": [
+ "code",
+ "message"
+ ],
+ "type": "object"
+}Output schema / requiredRemoved value: -[
- "molecule_chembl_id",
- "pref_name",
- "max_phase",
- "first_approval",
- "mechanisms",
- "mechanisms_total_count",
- "mechanisms_status",
- "indications",
- "indications_total_count",
- "indications_status"
-]chembl_search_molecules6 fields changedInput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Input schema / additionalPropertiesAdded value: +falseOutput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Output schema / anyOfAdded value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "molecules",
+ "totalCount",
+ "truncated",
+ "shown",
+ "cap"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / errorAdded value: +{
+ "additionalProperties": {},
+ "description": "Present when the call failed. Absent on success.",
+ "properties": {
+ "code": {
+ "description": "JSON-RPC error code for this failure.",
+ "maximum": 9007199254740991,
+ "minimum": -9007199254740991,
+ "type": "integer"
+ },
+ "data": {
+ "additionalProperties": {},
+ "properties": {
+ "reason": {
+ "description": "Machine-readable failure mode. Declared by this tool: `missing_input`: Neither query nor structure was supplied, or a structure search_type was chosen without a structure. Other values are possible when a failure originates below the handler.",
+ "examples": [
+ "missing_input"
+ ],
+ "type": "string"
+ },
+ "recovery": {
+ "additionalProperties": {},
+ "description": "Actionable next step for the caller.",
+ "properties": {
+ "hint": {
+ "type": "string"
+ }
+ },
+ "required": [
+ "hint"
+ ],
+ "type": "object"
+ },
+ "retryable": {
+ "description": "Whether retrying may succeed.",
+ "type": "boolean"
+ }
+ },
+ "type": "object"
+ },
+ "message": {
+ "description": "Human-readable description of what went wrong.",
+ "type": "string"
+ }
+ },
+ "required": [
+ "code",
+ "message"
+ ],
+ "type": "object"
+}Output schema / requiredRemoved value: -[
- "molecules",
- "totalCount",
- "truncated",
- "shown",
- "cap"
-]chembl_search_targets6 fields changedInput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Input schema / additionalPropertiesAdded value: +falseOutput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Output schema / anyOfAdded value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "targets",
+ "totalCount",
+ "truncated",
+ "shown",
+ "cap"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / errorAdded value: +{
+ "additionalProperties": {},
+ "description": "Present when the call failed. Absent on success.",
+ "properties": {
+ "code": {
+ "description": "JSON-RPC error code for this failure.",
+ "maximum": 9007199254740991,
+ "minimum": -9007199254740991,
+ "type": "integer"
+ },
+ "data": {
+ "additionalProperties": {},
+ "properties": {
+ "reason": {
+ "description": "Machine-readable failure mode. Declared by this tool: `missing_input`: None of query, accession, or gene_symbol was supplied. Other values are possible when a failure originates below the handler.",
+ "examples": [
+ "missing_input"
+ ],
+ "type": "string"
+ },
+ "recovery": {
+ "additionalProperties": {},
+ "description": "Actionable next step for the caller.",
+ "properties": {
+ "hint": {
+ "type": "string"
+ }
+ },
+ "required": [
+ "hint"
+ ],
+ "type": "object"
+ },
+ "retryable": {
+ "description": "Whether retrying may succeed.",
+ "type": "boolean"
+ }
+ },
+ "type": "object"
+ },
+ "message": {
+ "description": "Human-readable description of what went wrong.",
+ "type": "string"
+ }
+ },
+ "required": [
+ "code",
+ "message"
+ ],
+ "type": "object"
+}Output schema / requiredRemoved value: -[
- "targets",
- "totalCount",
- "truncated",
- "shown",
- "cap"
-]chembl_search_molecules3 fields changedInput schema / properties / cursorAdded value: +{
+ "description": "Opaque continuation token from a previous call's nextCursor — resumes where that page ended. Omit for the first page. Re-send the same query/structure/filters that minted it (only limit may change; it sets this page's size); redeeming it against different filters walks a different result set.",
+ "type": "string"
+}Output schema / properties / molecules / items / properties / similarity / descriptionPrevious value: -"Tanimoto similarity percent (0–100) to the query structure. Present only on similarity/substructure search."New value: +"Tanimoto similarity percent (0–100) to the query structure. Present only on search_type=similarity results; on every other search_type the key is absent, not null."Output schema / properties / nextCursorAdded value: +{
+ "description": "Opaque token for the next page — pass it back as cursor with the same filters. Absent when this page is the last one.",
+ "type": "string"
+}chembl_search_targets2 fields changedInput schema / properties / cursorAdded value: +{
+ "description": "Opaque continuation token from a previous call's nextCursor — resumes where that page ended. Omit for the first page. Re-send the same accession/gene_symbol/query/filters that minted it (only limit may change; it sets this page's size); redeeming it against different filters walks a different result set.",
+ "type": "string"
+}Output schema / properties / nextCursorAdded value: +{
+ "description": "Opaque token for the next page — pass it back as cursor with the same filters. Absent when this page is the last one.",
+ "type": "string"
+}chembl_dataframe_query3 fields changedOutput schema / properties / rendered_rowsAdded value: +{
+ "description": "How many of those rows the markdown table in content[] holds. Below row_count when the rendered table reached its character budget — a rendering bound, INDEPENDENT of truncated: a response can be truncated:false and still render fewer rows than row_count. Re-run the same SQL with LIMIT/OFFSET to read the rows past it.",
+ "type": "number"
+}Output schema / properties / truncated / descriptionPrevious value: -"True when the SQL result exceeded the canvas row cap and was truncated."New value: +"True when the SQL result exceeded the canvas row cap and was truncated — the engine bounding the result set itself, not the rendering. Independent of rendered_rows; page past it with LIMIT/OFFSET."Output schema / requiredPrevious value: -[
- "rows",
- "row_count",
- "truncated"
-]New value: +[
+ "rows",
+ "row_count",
+ "rendered_rows",
+ "truncated"
+]chembl_get_drug_info8 fields changedOutput schema / properties / indications / descriptionPrevious value: -"Clinical indications. Empty when none are recorded."New value: +"Clinical indications. Empty is authoritative only when indications_status is \"complete\"."Output schema / properties / indications_statusAdded value: +{
+ "description": "Retrieval state of the indication list. \"complete\" = every row ChEMBL records is present, so an empty array is a fact about the molecule. \"truncated\" = the single-request page cap bounded the list, so the array is a prefix of indications_total_count rows. \"failed\" = the upstream request was rejected, so the empty array is unknown data, NOT evidence that none exist — re-call chembl_get_drug_info to retry.",
+ "enum": [
+ "complete",
+ "truncated",
+ "failed"
+ ],
+ "type": "string"
+}Output schema / properties / indications_total_countAdded value: +{
+ "anyOf": [
+ {
+ "type": "number"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "description": "Total indication rows ChEMBL holds for this molecule (upstream page_meta.total_count). Exceeds the returned array length exactly when the status is \"truncated\". Null when the fetch failed — the count is unknown, never 0."
+}Output schema / properties / mechanisms / descriptionPrevious value: -"Mechanisms of action. Empty when none are recorded."New value: +"Mechanisms of action. Empty is authoritative only when mechanisms_status is \"complete\"."Output schema / properties / mechanisms_statusAdded value: +{
+ "description": "Retrieval state of the mechanism list. \"complete\" = every row ChEMBL records is present, so an empty array is a fact about the molecule. \"truncated\" = the single-request page cap bounded the list, so the array is a prefix of mechanisms_total_count rows. \"failed\" = the upstream request was rejected, so the empty array is unknown data, NOT evidence that none exist — re-call chembl_get_drug_info to retry.",
+ "enum": [
+ "complete",
+ "truncated",
+ "failed"
+ ],
+ "type": "string"
+}Output schema / properties / mechanisms_total_countAdded value: +{
+ "anyOf": [
+ {
+ "type": "number"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "description": "Total mechanism rows ChEMBL holds for this molecule (upstream page_meta.total_count). Exceeds the returned array length exactly when the status is \"truncated\". Null when the fetch failed — the count is unknown, never 0."
+}Output schema / properties / notice / descriptionPrevious value: -"Guidance when no pharmacology was found — the molecule may be a research compound, not a drug."New value: +"Disclosure of anything the two lists do not say for themselves: a list whose upstream fetch failed (so its emptiness means nothing), a list the page cap bounded, or — only when both lists came back complete and empty — that the molecule may be a research compound rather than a drug."Output schema / requiredPrevious value: -[
- "molecule_chembl_id",
- "pref_name",
- "max_phase",
- "first_approval",
- "mechanisms",
- "indications"
-]New value: +[
+ "molecule_chembl_id",
+ "pref_name",
+ "max_phase",
+ "first_approval",
+ "mechanisms",
+ "mechanisms_total_count",
+ "mechanisms_status",
+ "indications",
+ "indications_total_count",
+ "indications_status"
+]chembl_dataframe_describechembl_dataframe_querychembl_get_assaychembl_get_bioactivitieschembl_get_drug_infochembl_search_moleculeschembl_search_targetsBiomedical data: compounds, drug info, and molecular targets
Search PubChem compounds, properties, safety data, bioactivity, and cross-references.
MyChem.info MCP. Aggregated drug / chemical-compound annotation from the BioThings API: ChEMBL…
Pharma intelligence: source-linked drug, trial, result, patent, company and deal research.
Add one secure layer between your agents and this server.