Data DictionariesΒΆ

PATRIC uses several data dictionaries to support controlled vocabularies for certain biological entities and annotations, which provide consistent naming across data from heterogenous sources for more efficient search and query.

The following Collections store such data dictionaries and related information.

  • enzyme_class_ref: Information about EC numbers, enzyme names, and their hirarchical classification.

  • gene_ontology_ref: Information about Gene Ontology terms, their description, and their hirarchical classification.

  • id_ref: External database identified references, obtained from UniProt ID Mapping service.

  • model_complex_role: Relationships between molecular complexes and their functinal roles. Part of the Biochemistry Database from ModelSEED.

  • model_compound: Information about compounds associated with metabolic pathways. Part of the Biochemistry Database from ModelSEED.

  • model_reaction: Information about reactions involved in metabolic pathways. Part of the Biochemistry Database from ModelSEED.

  • model_template_biomass: Model template biomass. Part of the Biochemistry database from ModelSEED and used for metabolic modeling and FBA.

  • model_template_reaction: Model template reactions. Part of the Biochemistry database from ModelSEED and used for metabolic modeling and FBA.

  • pathway_ref: Relationship between EC numbers and metabolic pathways and their location on the pathway maps from KEGG.

  • protein_family_ref: Information about the PATRIC Global and Local Protein Families and their functauional roles.

  • sp_gene_ref: Specialty gene refernece datasets, collected and curated from external sources as described in the Data Section.

  • subsystem_ref: Information about the Subsystems, their classification, and corresponding functinal roles.

  • taxonomy: Information about taxoinomnic classification from NCBI Taxonomy database.