The ontology of data analysis and management (EDAM)¶
EDAM is a domain ontology that formalizes concepts, operations, data types, identifiers, and formats used in computational data analysis and data management across bioinformatics, biological sciences, and related scientific domains [1] [2]. It provides a structured vocabulary for describing bioinformatics analysis workflows, computational operations, data types, data identifiers, data formats, and relationships between analysis steps [2].
EDAM is organized into four main sections: Topic, Operation, Data, and Format [1] [2]. Topic represents research domains and application areas; Operation represents analysis and processing functions; Data represents data types and identifiers; and Format represents computational data formats and standards [1]. This structure enables consistent semantic annotation of tools, workflows, databases, datasets, publications, and software resources in bioinformatics [2].
EDAM is designed for usability by diverse stakeholders, including bioinformaticians, tool developers, curators, and researchers [1]. Its relatively simple hierarchical organization supports standardized descriptions of bioinformatics tools and services, automated tool discovery, workflow composition, dataset annotation, and semantic integration of computational biology resources [2].
Example Usage: Annotate a bioinformatics tool or service with EDAM terms for input data, operation, output format, and research topic, such as sequence alignment data, pairwise sequence alignment, FASTA format, and sequence analysis. These annotations make the tool easier to discover, compare, integrate into workflows, and connect with related datasets or services [1] [2].
Metrics & Statistics¶
Total Nodes |
12367 |
Total Edges |
36215 |
Root Nodes |
176 |
Leaf Nodes |
8223 |
Classes |
3513 |
Individuals |
0 |
Properties |
12 |
Maximum Depth |
10 |
Minimum Depth |
0 |
Average Depth |
2.75 |
Depth Variance |
4.24 |
Maximum Breadth |
635 |
Minimum Breadth |
5 |
Average Breadth |
196.55 |
Breadth Variance |
31795.52 |
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