The ontology of data analysis and management (EDAM)

EDAM is a domain ontology that formalizes concepts, operations, and data types used in computational data analysis and data management across biological sciences and related domains. It provides structured vocabulary for describing bioinformatics analysis workflows, computational operations (alignment, clustering, prediction), data types, data formats, and the relationships between analysis steps. EDAM comprises four main sections: Topic (research domains and concepts), Operation (analysis/processing operations), Data (data types and identifiers), and Format (computational data formats and standards). The ontology is designed for usability by diverse stakeholders including bioinformaticians, tool developers, and researchers, with a relatively simple hierarchical structure to facilitate adoption. EDAM supports standardization of bioinformatics tool descriptions, workflow definitions, and dataset annotations, enabling automated tool discovery and workflow composition.

Example Usage: Annotate a bioinformatics tool or service with EDAM terms for Input data (e.g., EDAM:data_0006 for sequence alignment), Operation (e.g., EDAM:operation_0496 for pairwise sequence alignment), Output format (e.g., EDAM:format_1929 for FASTA), and research Topic (e.g., EDAM:topic_0199 for sequence analysis).

Metrics & Statistics

Graph Statistics

Total Nodes

12367

Total Edges

36215

Root Nodes

176

Leaf Nodes

8223
Knowledge Coverage Statistics

Classes

3513

Individuals

0

Properties

12
Hierarchical Metrics

Maximum Depth

10

Minimum Depth

0

Average Depth

2.75

Depth Variance

4.24
Breadth Metrics

Maximum Breadth

635

Minimum Breadth

5

Average Breadth

196.55

Breadth Variance

31795.52
LLMs4OL Dataset Statistics

Term Types

0

Taxonomic Relations

7916

Non-taxonomic Relations

1314

Average Terms per Type

0.00

Usage Example

Use the following code to import this ontology programmatically:

from ontolearner.ontology import EDAM

ontology = EDAM()
ontology.load("path/to/EDAM-ontology.owl")

# Extract datasets
data = ontology.extract()

# Access specific relations
term_types = data.term_typings
taxonomic_relations = data.type_taxonomies
non_taxonomic_relations = data.type_non_taxonomic_relations