Retrieve UniProt accession ID from protein name and species. Returns the primary accession or None if not found.

Returns: str or None: UniProt accession ID string (e.g., 'P04637') or None if not found.

Retrieve protein information from UniProt database. Provide at least one of protein_id, protein_name, or gene_symbol.

Returns: dict: Protein information with accession, proteinDescription, genes, organism, sequence, functions, keywords, references or error message.

Query AlphaFold database using protein name. First converts protein symbol to UniProt ID, then fetches structure predictions.

Returns: dict: AlphaFold prediction data including PDB/CIF file URLs, confidence scores, and metadata or error message.

Get detailed antibody information by ID. Retrieves catalog number, vendor, clonality, epitope, applications, and more.

Returns: dict: Antibody details including abId, catalog numbers, vendor, clonality, epitope, applications, target species, isotype, citations or error message.

Search Antibody Registry for antibodies. Returns catalog numbers, vendors, clonality, applications, and metadata.

Returns: dict: Search results containing list of antibodies with catalog numbers, vendors, clonality, applications, metadata or error message.

Get detailed preprint metadata by DOI. Retrieves title, authors, abstract, date, version, category, license, and publication status.

Returns: dict: Preprint metadata including doi, title, authors, abstract, date, version, category, license, publication status or error message.

Search bioRxiv/medRxiv preprints by date range or recent count. Specify one search method: date range, days, or recent_count.

Returns: dict: Search results with server, search_params, total_returned, papers list (each with title, authors, abstract, metadata), pagination info or error message.

Find recruiting clinical trials by geographic location. Returns paginated results with summary breakdowns.

Returns: dict: Studies list with summary containing search location, total studies, study type/phase/condition breakdowns, recruiting locations or error message.

Search trials by condition with summary statistics. Returns paginated results with breakdowns by status, study type, and phase.

Returns: dict: Studies list with summary containing condition searched, total studies, status/study type/phase breakdowns or error message.

Search trials by intervention with condition and phase filters. Returns paginated results with breakdowns.

Returns: dict: Studies list with summary containing intervention searched, total studies, status/phase breakdowns, top conditions/sponsors or error message.

Get complete trial details by NCT ID. Retrieves study design, eligibility, outcomes, locations, contacts, and metadata.

Returns: dict: Study details with protocol sections including identification, status, sponsors, description, conditions, design, interventions, outcomes, eligibility, locations or error message.

Advanced search for trials with flexible multi-field filtering. Specify at least one search parameter.

Returns: dict: Paginated search results containing studies list with trial metadata or error message.

Get Ensembl gene ID from gene symbol. Returns the stable Ensembl ID (ENSG*) for the given gene symbol and species.

Returns: dict: Ensembl gene ID in format {'ensembl_id': 'ENSG...'} or error message.

Search Europe PMC articles by query, title, abstract, or author. Combine search terms with 'and'/'or' logic.

Returns: dict: Search results with resultList containing articles (title, authors, abstract, journal, PMC/DOI IDs) or error message.

Get full-text XML for a PMC ID. Returns the complete article XML for processing and analysis.

Returns: dict: Full-text XML content in format {'fulltext_xml': '...'} or error message.

Search grants.gov by keyword, agency, or other criteria. Returns opportunity listings with deadlines and eligibility.

Returns: dict: Grant opportunities list with titles, agencies, deadlines, funding amounts, eligibility criteria or error message.

Get InterPro entry details (family, domain, or functional site). Returns metadata from member databases like PFAM, PROSITE.

Returns: dict: Entry metadata including name, type, description, member databases, optionally interactions/pathways/cross-references or error message.

Get protein domain architecture and InterPro matches. Returns all InterPro domains, functional sites, and domain architecture.

Returns: dict: Protein metadata with interpro_matches array, interpro_match_count, domain_architecture, optionally structure data or error message.

Search InterPro entries by name, type, database, GO term, or species. Returns matching entries with metadata.

Returns: dict: Search results with results array (InterPro entries), count, total_available, search_criteria or error message.

Query OLS for all available ontologies with their metadata. Use this first to discover available ontologies.

Returns: dict: Ontologies list with id, name, description, prefix, homepage, number of terms, status or error message.

Search OLS for Cell Ontology (CL) terms using a controlled vocabulary for cell types.

Returns: dict: Cell ontology terms with cl_terms array containing id, label, definition, synonyms or error message.

Search OLS for ChEBI (Chemical Entities of Biological Interest) terms for a chemical or drug name.

Returns: dict: ChEBI terms with chebi_terms array containing id, label, description, synonyms or error message.

Search OLS for EFO/Mondo/HP IDs related to a disease name. Use this to get EFO IDs for Open Targets queries.

Returns: dict: EFO IDs with efo_ids array containing id, label, description or error message.

Search OLS for Gene Ontology (GO) terms related to a gene name using structured vocabularies.

Returns: dict: GO terms with go_terms array containing id, label, description, type or error message.

Get comprehensive details about a specific ontology term including definition, synonyms, hierarchical relationships.

Returns: dict: Term details with id, label, definition, synonyms, hierarchical info, num_descendants or error message.

Get hierarchical children of an ontology term from OLS. Includes subclasses and hierarchical properties.

Returns: dict: Parent term, hierarchical_children array with id/label/definition, total_children, page_info or error message.

Search for terms across multiple ontologies in OLS. Use get_available_ontologies() first to discover ontologies.

Returns: dict: Terms array, terms_by_ontology grouped results, total_results, ontologies_found list or error message.

Get available pharmacologic classes from FDA database. Call this first to see available options.

Returns: dict: Class type, field, available_classes array with term/count, total_found or error message.

Search for drugs by therapeutic or pharmacologic class. Use get_available_pharmacologic_classes() first for exact terms.

Returns: dict: FDA drug results array with application info, products, sponsor names or error message.

Find generic equivalents for a brand name drug. Searches ANDA entries with matching active ingredients.

Returns: dict: Brand drug info, generic_equivalents array, total_generics_found count or error message.

Count unique values in a field across FDA-approved drugs. Useful for statistical analysis.

Returns: dict: Results array with term and count for each unique value or error message.

Get general statistics about the FDA Drugs@FDA database. Includes top sponsors, dosage forms, routes, marketing status.

Returns: dict: Top sponsors, dosage_forms, administration_routes, marketing_statuses with counts or error message.

Get detailed information about an FDA-approved drug by application number. Format: NDA/ANDA/BLA followed by 6 digits.

Returns: dict: FDA drug results with application details, products, sponsor information or error message.

Get comprehensive drug labeling information from FDA. Includes active ingredients, dosage forms, administration routes.

Returns: dict: Drug label results with indications, warnings, dosage, active ingredients or error message.

Search FDA Drugs@FDA database for approved drug products. Supports multiple search criteria.

Returns: dict: Results array with drug products including application numbers, sponsors, products array or error message.

Retrieve the Open Targets GraphQL schema for query construction.

Returns: dict: Schema string in format {'schema': '...'} containing GraphQL type definitions or error message.

Retrieve example GraphQL queries for the Open Targets API. Examples demonstrate common use cases.

Returns: dict: Example queries mapped by category (informationForTarget, drugsForTarget, associatedDiseases, etc.) with GraphQL query strings.

Execute GraphQL queries against the Open Targets API. Use get_open_targets_query_examples() or get_open_targets_graphql_schema() first.

Returns: dict: GraphQL response with data field containing targets, diseases, drugs, variants, studies or error message.

Retrieve marker genes from PanglaoDB dataset with optional filters. Supports filtering by species, scores, organ, cell type, gene symbol.

Returns: dict: Markers array with gene symbols, cell types, organs, sensitivity/specificity scores or error message.

Retrieve available filter options for PanglaoDB marker genes. Returns unique values for organs and cell types.

Returns: dict: Lists of unique organ and cell_type values available in PanglaoDB dataset or error message.

Retrieve detailed information about a specific PRIDE mass spectrometry proteomics project. Returns metadata and experimental details.

Returns: dict: Project details with accession, title, description, organisms, instruments, publications, optionally files/similar_projects or error message.

Search PRIDE database for mass spectrometry proteomics projects using keywords and filters.

Returns: dict: Results array with project accessions, titles, descriptions, organisms, instruments, experiment types, count, search_criteria or error message.

Search for proteins identified in a specific PRIDE mass spectrometry project. Useful for finding specific proteins in proteomics datasets.

Returns: dict: Proteins list with accessions, names, genes, sequences, modifications, associated projects or error message.

Retrieve Human Protein Atlas information including expression, localization, and pathology data. Provide either gene_id or gene_symbol.

Returns: dict: Protein atlas data with tissue_expression, subcellular_location, pathology, antibodies, RNA/protein levels or error message.

Query the Reactome API identifier endpoint.

Use this endpoint to retrieve pathways associated with a given identifier. Always provide the species parameter to ensure the correct protein is returned.

Args: identifier (str): The identifier of the element to be retrieved base_url (str): Base URL for the Reactome API interactors (bool): Include interactors species (str or list): List of species to filter the result (accepts taxonomy ids, species names and dbId) page_size (int): Pathways per page page (int): Page number sort_by (str): Field to sort results by (e.g., "ENTITIES_PVALUE", "ENTITIES_FDR") order (str): Sort order ("ASC" or "DESC") resource (str): Resource to filter by (TOTAL includes all molecule types) p_value (float): P-value threshold (only pathways with p-value <= threshold will be returned) include_disease (bool): Set to False to exclude disease pathways min_entities (int): Minimum number of contained entities per pathway max_entities (int): Maximum number of contained entities per pathway importable_only (bool): Filter to only include importable resources timeout (int): Request timeout in seconds

Returns: dict: API response data or error information

Map protein identifiers (gene names, synonyms, UniProt IDs) to STRING database IDs. Using STRING IDs improves reliability.

Returns: str or dict: STRING ID string (e.g., '9606.ENSP00000269305') or dict with error message.

Retrieve protein-protein interactions for a given protein with scores above threshold. Always provide species parameter.

Returns: list or dict: Protein interactions array with stringId_A, stringId_B, preferredName_A/B, score, evidence channels or error message.

Generate protein-protein interaction network image from STRING database. Always provide species parameter.

Returns: Image or dict: Network visualization as PNG image object or error message.

Retrieve protein homology similarity scores from STRING database based on Smith-Waterman bit scores. Only scores above 50 reported.

Returns: list or dict: Similarity scores array with stringId_A, stringId_B, bitscore or error message.

Convert gene symbol to KEGG ID for use in subsequent API calls. Returns KEGG gene ID required for query_kegg().

Returns: str or dict: KEGG gene ID string (e.g., 'hsa:7157') or error dict.

Execute flexible KEGG API queries across pathways, genes, compounds, diseases, drugs. Use get_kegg_id_by_gene_symbol() first.

Returns: str or dict: Raw text response from KEGG API with requested data (pathways, genes, compounds, etc.) or error dict.

Search Google Scholar for publications with support for author search using 'author:"Name"' syntax. WARNING: Use responsibly, may block excessive queries.

Returns: dict: Publications list with title, authors, venue, year, citations, abstract, bib entry or error message.