# Molecular Identifier Resolver (`flintglade/molecular-identifier-resolver`) Actor Resolve molecular identifiers across official PubChem, ChEMBL, and ChEBI sources while preserving stereochemistry, salts, ambiguity, and provider disagreements. - **URL**: https://apify.com/flintglade/molecular-identifier-resolver.md - **Developed by:** [Flintglade](https://apify.com/flintglade) (community) - **Categories:** Automation, Developer tools, Other - **Stats:** 2 total users, 1 monthly users, 100.0% runs succeeded, 0 bookmarks - **User rating**: No ratings yet ## Pricing from $10.00 / 1,000 identifier resolutions This Actor is paid per event and usage. You are charged both the fixed price for specific events and for Apify platform usage. Learn more: https://docs.apify.com/platform/actors/running/actors-in-store#pay-per-event ## What's an Apify Actor? Actors are a software tools running on the Apify platform, for all kinds of web data extraction and automation use cases. In Batch mode, an Actor accepts a well-defined JSON input, performs an action which can take anything from a few seconds to a few hours, and optionally produces a well-defined JSON output, datasets with results, or files in key-value store. In Standby mode, an Actor provides a web server which can be used as a website, API, or an MCP server. Actors are written with capital "A". ## How to integrate an Actor? If asked about integration, you help developers integrate Actors into their projects. You adapt to their stack and deliver integrations that are safe, well-documented, and production-ready. The best way to integrate Actors is as follows. In JavaScript/TypeScript projects, use official [JavaScript/TypeScript client](https://docs.apify.com/api/client/js/docs.md): ```bash npm install apify-client ``` In Python projects, use official [Python client library](https://docs.apify.com/api/client/python/docs.md): ```bash pip install apify-client ``` In shell scripts, use [Apify CLI](https://docs.apify.com/cli/docs.md): ````bash # MacOS / Linux curl -fsSL https://apify.com/install-cli.sh | bash # Windows irm https://apify.com/install-cli.ps1 | iex ```bash In AI frameworks, you might use the [Apify MCP server](https://docs.apify.com/integrations/mcp.md). If your project is in a different language, use the [REST API](https://docs.apify.com/api/v2.md). For usage examples, see the [API](#api) section below. For more details, see Apify documentation as [Markdown index](https://docs.apify.com/llms.txt) and [Markdown full-text](https://docs.apify.com/llms-full.txt). # README ## Molecular Identifier Resolver Resolve molecular identifiers across official PubChem, ChEMBL, and ChEBI sources while keeping stereochemistry, charge, isotopes, components, salts, ambiguity, and provider disagreements visible. > This is an identifier-evidence tool, not medicinal, clinical, or drug advice. ### What this does not do - No medicinal chemistry recommendation. - No drug or clinical advice. - No target prediction or activity inference. - No name-only silent identity selection. - No stripping salts or stereochemistry without explicit separate representation. - No proprietary database scraping. ### Sources and authorization Version 0.1 queries the official public [PubChem PUG REST](https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest), [ChEMBL Data API](https://www.ebi.ac.uk/chembl/api/data/docs), and [ChEBI 2 public API](https://www.ebi.ac.uk/chebi/backend/api/docs/) endpoints. RDKit `2025.9.6` performs local parsing and reports canonical forms separately; it is never treated as an identity authority. See `SOURCE_POLICY.md` and the versioned files under `source_contracts/`. ### Input Supply 1-1,000 strict `{type, value}` entries. Supported types are `pubchemCid`, `chemblId`, `chebiId`, `inchiKey`, `inchi`, `smiles`, and `name`. `standardization` is `none` or `report_only`; raw input is always retained. Name searches return up to `maxCandidates` (1-25). Concurrency is capped at 8. ```json { "identifiers": [{"type": "pubchemCid", "value": "2519"}], "sources": ["pubchem", "chembl"], "standardization": "report_only", "maxCandidates": 5, "concurrency": 1 } ```` ### Output One result row is written per input identifier, followed by an uncharged run summary. Each result keeps raw input, local parse output, provider candidates, exact/related relations, evidence locators, source-response hashes, conflicts, comparability notes, and a canonical candidate only when a deterministic full-InChIKey rule is unique. The live-verified default resolves to this identity (timestamps and response hashes vary): ```json { "status": "exact", "canonicalCandidate": { "sourceId": "CHEMBL113", "preferredName": "CAFFEINE", "inchiKey": "RYYVLZVUVIJVGH-UHFFFAOYSA-N" }, "charge": {"event": "identifier-resolution", "chargeable": true} } ``` Optional bounded canonical JSON and SDF evidence artifacts are stored in the default key-value store only after the paid event is accepted and before the result row references them. Keys use Apify's portable character set and stay below 256 characters. A rejected charge writes no artifacts; a partial storage failure removes staged records and emits no dangling references. Every retained artifact has a content type, byte length, SHA-256, schema version, and generation rule. ### Pricing The only visible business event is `identifier-resolution` at **$0.01 per identifier resolution**. Exact resolutions, evidence-backed ambiguity reports, and definitive not-found results are chargeable. Invalid input, local parse failure, exhausted rate limits, and provider outages that prevent a terminal result are not charged. There is no per-source event. The Actor preflights the platform event budget and never launches more unique identifiers than it can admit; skipped identifiers receive explicit uncharged `charge_limit_reached` rows. Maximum event cost is the number of unique admitted identifiers multiplied by $0.01; platform start-event charges may apply separately. ### Limits and support The run timeout is 600 seconds. Memory is 512 MB minimum, 2,048 MB default, and 4,096 MB maximum. Responses are rejected while streaming as soon as they exceed 5 MB, before full-body buffering, and JSON depth is bounded to 32; each request has at most three attempts. For help, see `SUPPORT.md` or contact `support@flintglade.com`. # Actor input Schema ## `inputSchemaVersion` (type: `integer`): Version of the strict runtime input contract. ## `identifiers` (type: `array`): Raw values are preserved. Names return explicit candidates and are never silently promoted to identity. ## `sources` (type: `array`): Approved official providers only. ## `standardization` (type: `string`): Local RDKit calculations are reported separately and never overwrite provider identity. ## `maxCandidates` (type: `integer`): Maximum evidence-backed candidates returned for a name search. ## `include2DProperties` (type: `boolean`): Include provider formula, charge, and structure strings where available. ## `includeArtifacts` (type: `boolean`): Artifacts are written only after exactly one paid event is accepted. ## `concurrency` (type: `integer`): Maximum number of identifiers scheduled together; bounded at eight. ## Actor input object example ```json { "inputSchemaVersion": 1, "identifiers": [ { "type": "pubchemCid", "value": "2519" } ], "sources": [ "pubchem", "chembl" ], "standardization": "report_only", "maxCandidates": 10, "include2DProperties": true, "includeArtifacts": false, "concurrency": 4 } ``` # Actor output Schema ## `defaultDataset` (type: `string`): No description ## `artifacts` (type: `string`): No description ## `runSummary` (type: `string`): No description # API You can run this Actor programmatically using our API. Below are code examples in JavaScript, Python, and CLI, as well as the OpenAPI specification and MCP server setup. ## JavaScript example ```javascript import { ApifyClient } from 'apify-client'; // Initialize the ApifyClient with your Apify API token // Replace the '' with your token const client = new ApifyClient({ token: '', }); // Prepare Actor input const input = { "identifiers": [ { "type": "pubchemCid", "value": "2519" } ], "sources": [ "pubchem", "chembl" ] }; // Run the Actor and wait for it to finish const run = await client.actor("flintglade/molecular-identifier-resolver").call(input); // Fetch and print Actor results from the run's dataset (if any) console.log('Results from dataset'); console.log(`💾 Check your data here: https://console.apify.com/storage/datasets/${run.defaultDatasetId}`); const { items } = await client.dataset(run.defaultDatasetId).listItems(); items.forEach((item) => { console.dir(item); }); // 📚 Want to learn more 📖? Go to → https://docs.apify.com/api/client/js/docs ``` ## Python example ```python from apify_client import ApifyClient # Initialize the ApifyClient with your Apify API token # Replace '' with your token. client = ApifyClient("") # Prepare the Actor input run_input = { "identifiers": [{ "type": "pubchemCid", "value": "2519", }], "sources": [ "pubchem", "chembl", ], } # Run the Actor and wait for it to finish run = client.actor("flintglade/molecular-identifier-resolver").call(run_input=run_input) # Fetch and print Actor results from the run's dataset (if there are any) print("💾 Check your data here: https://console.apify.com/storage/datasets/" + run["defaultDatasetId"]) for item in client.dataset(run["defaultDatasetId"]).iterate_items(): print(item) # 📚 Want to learn more 📖? Go to → https://docs.apify.com/api/client/python/docs/quick-start ``` ## CLI example ```bash echo '{ "identifiers": [ { "type": "pubchemCid", "value": "2519" } ], "sources": [ "pubchem", "chembl" ] }' | apify call flintglade/molecular-identifier-resolver --silent --output-dataset ``` ## MCP server setup ```json { "mcpServers": { "apify": { "command": "npx", "args": [ "mcp-remote", "https://mcp.apify.com/?tools=flintglade/molecular-identifier-resolver", "--header", "Authorization: Bearer " ] } } } ``` ## OpenAPI specification ```json { "openapi": "3.0.1", "info": { "title": "Molecular Identifier Resolver", "description": "Resolve molecular identifiers across official PubChem, ChEMBL, and ChEBI sources while preserving stereochemistry, salts, ambiguity, and provider disagreements.", "version": "0.1", "x-build-id": "WG1Kn56ct1LXJGCWm" }, "servers": [ { "url": "https://api.apify.com/v2" } ], "paths": { "/acts/flintglade~molecular-identifier-resolver/run-sync-get-dataset-items": { "post": { "operationId": "run-sync-get-dataset-items-flintglade-molecular-identifier-resolver", "x-openai-isConsequential": false, "summary": "Executes an Actor, waits for its completion, and returns Actor's dataset items in response.", "tags": [ "Run Actor" ], "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/inputSchema" } } } }, "parameters": [ { "name": "token", "in": "query", "required": true, "schema": { "type": "string" }, "description": "Enter your Apify token here" } ], "responses": { "200": { "description": "OK" } } } }, "/acts/flintglade~molecular-identifier-resolver/runs": { "post": { "operationId": "runs-sync-flintglade-molecular-identifier-resolver", "x-openai-isConsequential": false, "summary": "Executes an Actor and returns information about the initiated run in response.", "tags": [ "Run Actor" ], "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/inputSchema" } } } }, "parameters": [ { "name": "token", "in": "query", "required": true, "schema": { "type": "string" }, "description": "Enter your Apify token here" } ], "responses": { "200": { "description": "OK", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/runsResponseSchema" } } } } } } }, "/acts/flintglade~molecular-identifier-resolver/run-sync": { "post": { "operationId": "run-sync-flintglade-molecular-identifier-resolver", "x-openai-isConsequential": false, "summary": "Executes an Actor, waits for completion, and returns the OUTPUT from Key-value store in response.", "tags": [ "Run Actor" ], "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/inputSchema" } } } }, "parameters": [ { "name": "token", "in": "query", "required": true, "schema": { "type": "string" }, "description": "Enter your Apify token here" } ], "responses": { "200": { "description": "OK" } } } } }, "components": { "schemas": { "inputSchema": { "type": "object", "required": [ "identifiers" ], "properties": { "inputSchemaVersion": { "title": "Input schema version", "minimum": 1, "maximum": 1, "type": "integer", "description": "Version of the strict runtime input contract.", "default": 1 }, "identifiers": { "title": "Molecular identifiers", "minItems": 1, "maxItems": 1000, "type": "array", "description": "Raw values are preserved. Names return explicit candidates and are never silently promoted to identity.", "items": { "type": "object", "additionalProperties": false, "properties": { "type": { "title": "Identifier type", "description": "Declares the exact syntax and provider lookup semantics for value.", "type": "string", "enum": [ "pubchemCid", "chemblId", "chebiId", "inchiKey", "inchi", "smiles", "name" ] }, "value": { "title": "Raw identifier", "description": "Exact identifier or structure string; retained without destructive standardization.", "type": "string", "minLength": 1, "maxLength": 8192 } }, "required": [ "type", "value" ] } }, "sources": { "title": "Official sources", "minItems": 1, "uniqueItems": true, "type": "array", "description": "Approved official providers only.", "items": { "type": "string", "enum": [ "pubchem", "chembl", "chebi" ] }, "default": [ "pubchem", "chembl", "chebi" ] }, "standardization": { "title": "Local standardization", "enum": [ "none", "report_only" ], "type": "string", "description": "Local RDKit calculations are reported separately and never overwrite provider identity.", "default": "report_only" }, "maxCandidates": { "title": "Maximum name candidates", "minimum": 1, "maximum": 25, "type": "integer", "description": "Maximum evidence-backed candidates returned for a name search.", "default": 10 }, "include2DProperties": { "title": "Include 2D properties", "type": "boolean", "description": "Include provider formula, charge, and structure strings where available.", "default": true }, "includeArtifacts": { "title": "Store JSON and SDF evidence artifacts", "type": "boolean", "description": "Artifacts are written only after exactly one paid event is accepted.", "default": false }, "concurrency": { "title": "Concurrency", "minimum": 1, "maximum": 8, "type": "integer", "description": "Maximum number of identifiers scheduled together; bounded at eight.", "default": 4 } } }, "runsResponseSchema": { "type": "object", "properties": { "data": { "type": "object", "properties": { "id": { "type": "string" }, "actId": { "type": "string" }, "userId": { "type": "string" }, "startedAt": { "type": "string", "format": "date-time", "example": "2025-01-08T00:00:00.000Z" }, "finishedAt": { "type": "string", "format": "date-time", "example": "2025-01-08T00:00:00.000Z" }, "status": { "type": "string", "example": "READY" }, "meta": { "type": "object", "properties": { "origin": { "type": "string", "example": "API" }, "userAgent": { "type": "string" } } }, "stats": { "type": "object", "properties": { "inputBodyLen": { "type": "integer", "example": 2000 }, "rebootCount": { "type": "integer", "example": 0 }, "restartCount": { "type": "integer", "example": 0 }, "resurrectCount": { "type": "integer", "example": 0 }, "computeUnits": { "type": "integer", "example": 0 } } }, "options": { "type": "object", "properties": { "build": { "type": "string", "example": "latest" }, "timeoutSecs": { "type": "integer", "example": 300 }, "memoryMbytes": { "type": "integer", "example": 1024 }, "diskMbytes": { "type": "integer", "example": 2048 } } }, "buildId": { "type": "string" }, "defaultKeyValueStoreId": { "type": "string" }, "defaultDatasetId": { "type": "string" }, "defaultRequestQueueId": { "type": "string" }, "buildNumber": { "type": "string", "example": "1.0.0" }, "containerUrl": { "type": "string" }, "usage": { "type": "object", "properties": { "ACTOR_COMPUTE_UNITS": { "type": "integer", "example": 0 }, "DATASET_READS": { "type": "integer", "example": 0 }, "DATASET_WRITES": { "type": "integer", "example": 0 }, "KEY_VALUE_STORE_READS": { "type": "integer", "example": 0 }, "KEY_VALUE_STORE_WRITES": { "type": "integer", "example": 1 }, "KEY_VALUE_STORE_LISTS": { "type": "integer", "example": 0 }, "REQUEST_QUEUE_READS": { "type": "integer", "example": 0 }, "REQUEST_QUEUE_WRITES": { "type": "integer", "example": 0 }, "DATA_TRANSFER_INTERNAL_GBYTES": { "type": "integer", "example": 0 }, "DATA_TRANSFER_EXTERNAL_GBYTES": { "type": "integer", "example": 0 }, "PROXY_RESIDENTIAL_TRANSFER_GBYTES": { "type": "integer", "example": 0 }, "PROXY_SERPS": { "type": "integer", "example": 0 } } }, "usageTotalUsd": { "type": "number", "example": 0.00005 }, "usageUsd": { "type": "object", "properties": { "ACTOR_COMPUTE_UNITS": { "type": "integer", "example": 0 }, "DATASET_READS": { "type": "integer", "example": 0 }, "DATASET_WRITES": { "type": "integer", "example": 0 }, "KEY_VALUE_STORE_READS": { "type": "integer", "example": 0 }, "KEY_VALUE_STORE_WRITES": { "type": "number", "example": 0.00005 }, "KEY_VALUE_STORE_LISTS": { "type": "integer", "example": 0 }, "REQUEST_QUEUE_READS": { "type": "integer", "example": 0 }, "REQUEST_QUEUE_WRITES": { "type": "integer", "example": 0 }, "DATA_TRANSFER_INTERNAL_GBYTES": { "type": "integer", "example": 0 }, "DATA_TRANSFER_EXTERNAL_GBYTES": { "type": "integer", "example": 0 }, "PROXY_RESIDENTIAL_TRANSFER_GBYTES": { "type": "integer", "example": 0 }, "PROXY_SERPS": { "type": "integer", "example": 0 } } } } } } } } } } ```