Guide

• Search & lookup terms
  • .fields: fields of an ontology reference
  • .df(): reference table
  • .lookup(): Lookup terms and records with autocompletion
  • .search: Search a term against a field
• Access ontologies
  • Basic fields: name, ontology_id, definition, synonyms, children
  • .pronto: Pronto Ontology
  • Extra fields
  • Comparing ontology versions
• Validate, inspect & standardize identifiers
  • Inspect and mapping synonyms of gene identifiers
  • Standardize and look up unmapped CellMarker identifiers
• Ontology sources configuration
  • Display sources
  • Initialize a Bionty model
  • Public bionty sources
  • Local bionty sources
  • Format of the sources yaml file
  • Configure default ontologies and versions
• Configuration
  • Public bionty sources
  • Local bionty sources
  • Display sources
  • Format of the sources yaml file
  • Setting default ontologies and versions
• Extend Bionty
  • New terms and records
  • New ontologies
  • New entites
• Concepts
  • Entity
  • Bionty object
• Relating Bionty to other tools
  • Ontology mappers: Bionty
  • Data models: BioLink
  • Knowledge graph builders: Biocypher