faldo

is a Ontology.

FALDO (Feature Annotation Location Description Ontology) is an ontology for describing sequence feature locations using RDF/OWL. It provides a standardized way to represent genomic and protein sequence positions, regions, and strands in Semantic Web formats.

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Domains

genomics, information technology

License

CC0 1.0

Homepage

faldo

Repository

GitHub

External IDs

No external IDs available

Product Summary

Products

From this Resource
ID Name URL Category Format Description
faldo.ttl FALDO Ontology (Turtle) faldo.ttl (13.3 KB) Ontology ttl FALDO ontology in Turtle/RDF format f...
faldo.rdf FALDO Ontology (RDF/XML) faldo.rdf (25.2 KB) Ontology rdfxml FALDO ontology in RDF/XML format
faldo.browser FALDO Ontology Browser faldo Documentation http Interactive ontology browser with cla...
faldo.kg-bioportal FALDO KGX graph (KG-Bioportal) FALDO.tar.gz (1.3 KB) Graph kgx KGX TSV transform of Feature Annotati...
From other Resources
ID Name URL Category Format Relation Description
ubkg.neo4j UBKG Neo4j Docker Distribution ubkg-downloads.xconsortia.org Graph neo4j had primary source Turnkey neo4j distributions that depl...
ubkg.csv UBKG Ontology CSV Files ubkg-downloads.xconsortia.org Graph csv had primary source Ontology CSV files that can be import...
jpost.rdf jPOSTdb RDF Files rdf Product ttl used Per-dataset Turtle files of the jPOST...

Details

FALDO

Overview

FALDO (Feature Annotation Location Description Ontology) is an ontology designed to describe the locations of sequence features in a Species Web-compatible manner using RDF and OWL. Created during the BioHackathon 2012 and 2013 meetings, FALDO provides a standardized vocabulary for representing genomic and protein sequence positions, regions, and their associated properties such as strand orientation.

Purpose

FALDO addresses the need for a consistent way to represent sequence feature locations across different biological databases and formats. It enables:

  • Interoperability between genomic databases using Semantic Web technologies
  • Standardized representation of sequence coordinates
  • Support for both exact and fuzzy position descriptions
  • Strand-aware position annotations
  • Integration with existing formats like GFF3, GTF, and INSDC

Key Concepts

Position Types

FALDO defines several types of positions:

  1. ExactPosition: Precisely known positions with specific coordinate values
  2. FuzzyPosition: Positions without exact data
  3. InBetweenPosition: Positions between two exact positions (e.g., restriction enzyme cut sites)
  4. InRangePosition: Positions known to be within a range
  5. OneOfPosition: Position known to be one of several specified locations

Strand Information

  • ForwardStrandPosition: Position on forward/positive (5’ to 3’) strand (‘+’ in GFF3)
  • ReverseStrandPosition: Position on reverse/complement (3’ to 5’) strand (‘-‘ in GFF3)
  • BothStrandsPosition: Feature on both strands
  • StrandedPosition: Parent class when strand is known

Regions and Collections

  • Region: Length of sequence with start and end positions representing a feature
  • CollectionOfRegions: Multiple regions (e.g., join() and order() in INSDC)
  • ListOfRegions: Ordered list of regions
  • BagOfRegions: Unordered collection of regions

Protein-Specific

  • N-TerminalPosition: Start of protein/polypeptide (free amine group)
  • C-TerminalPosition: End of protein/polypeptide (free carboxyl group)

Coordinate System

  • 1-based closed coordinates: First amino acid or nucleotide has position value 1
  • Nucleotide sequences: Count from 5’ end
  • Amino acid sequences: Count from N-terminus
  • Reference-based: Position values anchored to a reference sequence (contig, chromosome, etc.)

Properties

Core Properties

  • location: Links a feature to its position or region
  • begin: Inclusive beginning of a position (start)
  • end: Inclusive end of a position
  • reference: Resource that position value is anchored to
  • position: Offset along reference (integer ≥ 1)
  • before/after: For InBetweenPosition descriptions

Use Cases

  1. Genome Annotation: Describing gene, exon, and other feature locations
  2. Protein Annotation: Marking active sites, domains, and motifs
  3. Data Integration: Combining genomic data from multiple sources
  4. Format Conversion: Translating between GFF3, GTF, and RDF representations
  5. Semantic Queries: SPARQL queries across genomic databases
  6. Linked Data: Connecting genomic features across resources

Format Compatibility

FALDO can represent features from:

  • GFF3 (General Feature Format)
  • GTF (Gene Transfer Format)
  • INSDC feature tables
  • UniProt feature annotations

Serialization Formats

Available in multiple RDF serializations:

  • Turtle (.ttl): Human-readable RDF format
  • RDF/XML (.rdf): XML-based RDF format

Example Usage

FALDO allows expressing locations like:

  • “Gene X is located on chromosome 1 from position 1000 to 2000 on the forward strand”
  • “Cleavage site is between amino acids 42 and 43”
  • “Binding site is somewhere between positions 100 and 150”

Management

Creation: BioHackathon 2012 and 2013

Maintenance: Community-maintained through GitHub

Support: Google Groups forum for discussions

Repository: https://github.com/OBioFoundry/FALDO

Funding

FALDO development has been supported by:

  • National Bioscience Database Center (NBDC) of Japan Science and Technology Agency (JST)
  • Database Center for Life Science (DBCLS)
  • Research Organization of Information and Systems (ROIS)
  • Swiss Institute of Bioinformatics (SIB)
  • Swiss Federal Government (SERI)
  • NIH (R24OD011883)
  • U.S. Department of Energy (DE-AC02-05CH11231)
  • Scottish Government Rural and Environmental Research and Analysis Directorate
  • DNA Databank of Japan (DDBJ)

License

Licensed under Creative Commons Zero (CC0 1.0) - Public Domain Dedication

  • SPIN (SPARQL Inferencing Notation)
  • OWL (Web Ontology Language)
  • RDF (Resource Description Framework)

Community

  • Discussion Forum: https://groups.google.com/forum/#!forum/faldo
  • Documentation: https://github.com/OBF/FALDO
  • Ontology Browser: http://biohackathon.org/resource/faldo

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Created: June 04, 2025 | Last modified: September 23, 2026