> ## Documentation Index > Fetch the complete documentation index at: https://docs.stackone.com/llms.txt > Use this file to discover all available pages before exploring further. # PubChem > How to set up the PubChem connector, plus the actions that are available. ![PubChem](https://stackone-logos.com/api/pubchem/filled/svg) Previewv0.1.0[See changelog](https://docs.stackone.com/connectors/pubchem/changelog.md) [99 actions](#actions) ยท 2 auth methods Research ## Getting Started **1. Create or Select a Project** Set up a new project or select an existing one. See [Organizations & Projects](https://docs.stackone.com/gateway/concepts/organizations-and-projects.md). **2. Configure the Connector** Enable the connector and set up a Connector Profile in your project. See [Setup Connector Profile](https://docs.stackone.com/gateway/quickstart.md#setup-connector-profile). **3. Link an Account** Link an account [from the dashboard](https://docs.stackone.com/connect/managing-connectors/linking-accounts.md#link-from-the-dashboard) (or via [StackOne Hub](https://docs.stackone.com/embed/account-linking/overview)). **4. Use Actions** Connect an AI platform to the linked account's actions. See [AI Platforms](https://docs.stackone.com/connect/ai-platforms/overview.md). Other ways to call actions are listed in [Protocols & SDKs](https://docs.stackone.com/connect/protocols-and-sdks.md). ## Actions Authentication type Select all | Clear NCBI API Key No Authentication No auth methods found 99 actions ActionDescription Search Compounds By Name`pubchem_search_compounds_by_name` Find PubChem compound IDs (CIDs) from a compound name or synonym. Get Compound By SMILES`pubchem_get_compound_by_smiles` Find the CID of a compound from a SMILES string. Get Compound By InChI`pubchem_get_compound_by_inchi` Find the CID of a compound from an InChI string. Get Compound By SDF`pubchem_get_compound_by_sdf` Find the CID of a compound from an SDF or MOL file text. Get Compound By InChIKey`pubchem_get_compound_by_inchikey` Find the CID of a compound from its InChIKey. Get Compound By Registry ID`pubchem_get_compound_by_registry_id` Find the CID of a compound from a registry number such as a CAS number. Search Compounds By Formula`pubchem_search_compounds_by_formula` Find compounds with a molecular formula. Autocomplete Terms`pubchem_autocomplete_terms` Suggest PubChem names that start with a text fragment. Get Compound Properties`pubchem_get_compound_properties` Get computed properties such as formula, weight, SMILES and InChIKey for one or more compounds. Get Compound Synonyms`pubchem_get_compound_synonyms` List every name PubChem has for a compound. Get Compound Description`pubchem_get_compound_description` Get the title and source-attributed text descriptions of a compound. Get Compound Registry IDs`pubchem_get_compound_registry_ids` List the registry identifiers PubChem holds for a compound, such as CAS, UNII and ChEBI. Get Compound Cross-References`pubchem_get_compound_xrefs` Get cross-references from a compound to other databases, such as PubMed, patents and genes. Get Related Compounds`pubchem_get_related_compounds` List compounds related to a compound by parent, stereo, isotope, connectivity or tautomer. Search Compounds By Cross-Reference`pubchem_search_compounds_by_xref` Find compounds that carry a given external cross-reference, such as a registry number or PubMed ID. Search Compounds By Mass`pubchem_search_compounds_by_mass` Find compounds by molecular weight, exact mass or monoisotopic mass, as an exact value or a range. Get Compound Record`pubchem_get_compound_record` Get the full structure record of one or more compounds: atoms, bonds, coordinates and properties. Get Compound Substance IDs`pubchem_get_compound_substance_ids` List the substance IDs (SIDs) that depositors submitted for a compound. Get Compound Assay Summary`pubchem_get_compound_assay_summary` Summarise the bioassay results recorded for a compound, one row per assay. Get Compound Conformers`pubchem_get_compound_conformers` List the 3D conformer IDs PubChem has for a compound. Get Compound Dates`pubchem_get_compound_dates` Get the date PubChem first created each compound record. Standardize Structure`pubchem_standardize_structure` Run a structure through PubChem's standardization and return the standardized record. Similarity Search`pubchem_similarity_search` Find compounds whose 2D structure is similar to a query structure. Substructure Search`pubchem_substructure_search` Find compounds that contain a query structure or SMARTS pattern. Superstructure Search`pubchem_superstructure_search` Find compounds that are contained in a query structure. Similarity Search 3D`pubchem_similarity_search_3d` Find compounds whose 3D shape and features are similar to a query structure. Identity Search`pubchem_identity_search` Find compounds that are identical to a query structure under a chosen definition of identity. Get ListKey IDs`pubchem_get_listkey_ids` Read a page of CIDs, SIDs or AIDs from a ListKey returned by an earlier search. Search Substances By Name`pubchem_search_substances_by_name` Find PubChem substance IDs (SIDs) from a substance name or synonym. Get Substances By Source ID`pubchem_get_substances_by_source_id` Find the substance IDs (SIDs) a source deposited under its own identifier. List Source Substances`pubchem_list_source_substances` List every substance ID (SID) a source has deposited. Search Substances By Cross-Reference`pubchem_search_substances_by_xref` Find substances that carry a given external cross-reference, such as a registry number or PubMed ID. Get Substance Record`pubchem_get_substance_record` Get the full depositor record for one or more substances. Get Substance Synonyms`pubchem_get_substance_synonyms` List the names a depositor gave one or more substances. Get Substance Compound IDs`pubchem_get_substance_compound_ids` Get the compound IDs (CIDs) that one or more substances were standardized into. Get Substance Assay IDs`pubchem_get_substance_assay_ids` List the bioassays (AIDs) that tested one or more substances. Get Substance Assay Summary`pubchem_get_substance_assay_summary` Get a table of every bioassay result for one or more substances. Get Substance Classification`pubchem_get_substance_classification` Get the classification hierarchies PubChem places a substance in. Get Substance Cross-References`pubchem_get_substance_xrefs` Get cross-references from one or more substances to other databases, such as registry numbers, PubMed and patents. Get Substance Dates`pubchem_get_substance_dates` Get the deposition, modification and hold dates of one or more substances. Get Compound Assay IDs`pubchem_get_compound_assay_ids` List the bioassays (AIDs) that tested a compound. Get Assay Summary`pubchem_get_assay_summary` Get a short summary of one or more bioassays: name, source, target and counts. Get Assay Description`pubchem_get_assay_description` Get the full description of a bioassay: protocol, readout, targets and result columns. Get Assay Targets`pubchem_get_assay_targets` List the protein and gene targets of one or more bioassays. Get Assay Compounds`pubchem_get_assay_compounds` List the compounds (CIDs) or substances (SIDs) tested in a bioassay, filtered by outcome. Get Assay Data`pubchem_get_assay_data` Get the result data of a bioassay, optionally for chosen substances only. Get Assay Dose Response`pubchem_get_assay_dose_response` Get the dose-response curves of chosen substances in a bioassay. Search Assays By Target`pubchem_search_assays_by_target` Find the bioassays (AIDs) that tested a protein or gene target. Get Assay Concise`pubchem_get_assay_concise` Get a table of every substance result in a bioassay, one row per substance. Get Assay Classification`pubchem_get_assay_classification` Get the classification hierarchies PubChem places a bioassay in. Get Assay Dates`pubchem_get_assay_dates` Get the deposition, modification and hold dates of one or more bioassays. List Assays By Type`pubchem_list_assays_by_type` List the bioassays (AIDs) of one type, such as dose-response or confirmatory assays. List Assays By Source`pubchem_list_assays_by_source` List the bioassays (AIDs) deposited by one source. Search Assays By Activity`pubchem_search_assays_by_activity` Find the bioassays (AIDs) that report a given activity column, such as EC50 or IC50. Get Gene Summary`pubchem_get_gene_summary` Get the summary of a gene: symbol, name, organism, description and synonyms. Get Gene Assay IDs`pubchem_get_gene_assay_ids` List the bioassays (AIDs) that tested a gene as a target. Get Gene Pathways`pubchem_get_gene_pathways` List the pathways that include a gene. Get Gene Identifiers`pubchem_get_gene_identifiers` List the external database identifiers PubChem holds for a gene. Get Protein Summary`pubchem_get_protein_summary` Get the summary of a protein: accession, name, organism and synonyms. Get Protein Assay IDs`pubchem_get_protein_assay_ids` List the bioassays (AIDs) that tested a protein as a target. Get Protein Pathways`pubchem_get_protein_pathways` List the pathways that include a protein. Get Protein Identifiers`pubchem_get_protein_identifiers` List the external database identifiers PubChem holds for a protein. Get Pathway Summary`pubchem_get_pathway_summary` Get the summary of a pathway: source, name, organism and description. Get Pathway Members`pubchem_get_pathway_members` List the compounds, genes or proteins that belong to a pathway. Get Taxonomy Summary`pubchem_get_taxonomy_summary` Get the summary of an organism: scientific name, common name, rank, lineage and synonyms. Get Taxonomy Assay IDs`pubchem_get_taxonomy_assay_ids` List the bioassays (AIDs) that involve an organism. Get Taxonomy Identifiers`pubchem_get_taxonomy_identifiers` List the external database identifiers PubChem holds for an organism. Get Cell Line Summary`pubchem_get_cell_line_summary` Get the summary of a cell line: accession, name, sex, category, source tissue and organism. Get Cell Line Assay IDs`pubchem_get_cell_line_assay_ids` List the bioassays (AIDs) that used a cell line. Get Cell Line Identifiers`pubchem_get_cell_line_identifiers` List the external database identifiers PubChem holds for a cell line. List Sources`pubchem_list_sources` List every source that has deposited substances or bioassays into PubChem. Get Source Table`pubchem_get_source_table` Get the table of depositing sources with their counts, category, organization and contact details. Get Conformer`pubchem_get_conformer` Get one computed 3D conformer of a compound, with atom coordinates. List Annotation Headings`pubchem_list_annotation_headings` List every PUG View annotation heading with the record type it applies to. List Heading Sources`pubchem_list_heading_sources` List the sources that provide annotations under one PUG View heading. List Source Annotations`pubchem_list_source_annotations` List the PUG View headings that one source provides annotations for. Get Classification Node Members`pubchem_get_classification_node_members` List the PubChem records classified under one node of a classification hierarchy. Get Periodic Table`pubchem_get_periodic_table` Get the periodic table of the elements with PubChem's properties for each element. List Identifier Types`pubchem_list_identifier_types` List the external identifier types PubChem can look up in one domain. List Compound Annotation Headings`pubchem_list_compound_annotation_headings` List the annotation headings that a compound has data for. Get Compound Annotations`pubchem_get_compound_annotations` Get the annotations PubChem holds for a compound, such as safety, toxicity, pharmacology and physical properties, with s... Get Compound Literature Links`pubchem_get_compound_literature_links` Get PubMed search links for the literature about a compound, grouped by subheading. Get Compound Protein Structures`pubchem_get_compound_protein_structures` List the protein structures from the PDB and MMDB that contain a compound. Get Patent`pubchem_get_patent` Get the PubChem record of a patent: abstract, dates, inventors, assignee and linked chemicals, genes and proteins. Get Record Annotations`pubchem_get_record_annotations` Get the annotations PubChem holds for a substance, gene, protein, pathway, taxonomy, cell line, bioassay or element. List Substance Annotation Headings`pubchem_list_substance_annotation_headings` List the annotation headings that a substance has data for. Get Annotations By Heading`pubchem_get_annotations_by_heading` Get every record's annotation values for one heading, with the source of each. Get Compound Source Categories`pubchem_get_compound_source_categories` List the sources that deposited data for a compound, grouped by category. Get Linkouts`pubchem_get_linkouts` List the external web pages that link out from a compound, substance or bioassay record. Get Compound QR Code`pubchem_get_compound_qr_code` Get a QR code, as SVG text, that links to a compound's PubChem page. Get Biologic Image`pubchem_get_biologic_image` Get the image of a biologic, such as a peptide or protein sequence, as SVG text. Get RDF Resource`pubchem_get_rdf_resource` Get the RDF triples PubChem holds for one resource, such as a compound, substance, bioassay or gene. Query RDF`pubchem_query_rdf` Query PubChem RDF with a graph name and optional filters, for example to find compounds by synonym. Get Co-occurrences`pubchem_get_cooccurrences` Get literature co-occurrence scores between a chemical, gene or disease and other entities. Get RDF Reference`pubchem_get_rdf_reference` Look up a literature reference in PubChem RDF by PubMed ID or DOI. Entrez Search`pubchem_entrez_search` Search PubChem Compound, Substance or BioAssay with an Entrez query and get the matching IDs. Entrez Summary`pubchem_entrez_summary` Get the Entrez document summaries for PubChem Compound, Substance or BioAssay IDs. Entrez Links`pubchem_entrez_links` Find the records in another Entrez database that are linked to PubChem Compound, Substance or BioAssay IDs. Entrez Database Info`pubchem_entrez_database_info` Get the searchable fields, links and record count of a PubChem Entrez database. This documentation is built and hosted on [Mintlify](https://mintlify.com), a developer documentation platform.