Feature Annotation Location Description Ontology

Abbreviation: FALDO

General Information

The Feature Annotation Location Description Ontology (FALDO), to describe the positions of annotated features on linear and circular sequences for data resources represented in RDF and/or OWL. FALDO can be used to describe nucleotide features in sequence records, protein annotations, and glycan binding sites, among other features in coordinate systems of the aforementioned “omics” areas. Using the same data format to represent sequence positions that are independent of file formats allows us to integrate sequence data from multiple sources and data types.

Homepage http://biohackathon.org/resource/faldo

Countries that developed this resource Italy , Japan , Netherlands , Switzerland , United Kingdom , United States

Created in 2012

Taxonomic range

All

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: FALDO; Feature Annotation Location Description Ontology; DOI: https://doi.org/10.25504/FAIRsharing.haxp7g; Last edited: Feb. 4, 2020, 2:13 p.m.; Last accessed: Apr 10 2021 2:57 p.m.

Publication for citation FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation. Bolleman JT,Mungall CJ,Strozzi F,Baran J,Dumontier M,Bonnal RJ,Buels R,Hoehndorf R,Fujisawa T,Katayama T,Cock PJ; J Biomed Semantics ; 2016; 10.1186/s13326-016-0067-z;

This record is maintained by jerven

Record added: Jan. 16, 2017, 2:40 p.m.
Record updated: Feb. 4, 2020, 2:13 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.haxp7g' by 'The FAIRsharing Team' at 14:13, 04 Feb 2020 (approved):

	'organizations' has been modified:
		Before:
		After:
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains
		Added:
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains
		Removed:

	'supportLinks' has been modified:
		Before:
			help|https://groups.google.com/forum/#!forum/faldo
			online documentation|https://github.com/OBF/FALDO
		After:
			forum|https://groups.google.com/forum/#!forum/faldo
			online documentation|https://github.com/OBF/FALDO
			online documentation|https://github.com/OBF/FALDO
		Added:
			forum|https://groups.google.com/forum/#!forum/faldo
		Removed:
			help|https://groups.google.com/forum/#!forum/faldo

	'onto_disciplines' has been modified:
		Before:
			Life Science
		After:
			Genetics
		Added:
			Genetics
		Removed:
			Life Science

	'dataProcesses' has been modified:
		Before:
		After:
			AgroPortal: Browse / Download
			Browse
			Browse (AberOWL)
		Added:
			AgroPortal: Browse / Download
			Browse
			Browse (AberOWL)
		Removed:

	'related_standards' has been modified:
		Before:
			Resource Description Framework
			Web Ontology Language
		After:
			Resource Description Framework
			Web Ontology Language
			Sequence Ontology
			Uniprot Core Ontology
		Added:
			Sequence Ontology
			Uniprot Core Ontology
		Removed:

	'onto_domains' has been modified:
		Before:
			Nucleic acid sequence
			Sequence annotation
		After:
			Gene Feature
			Nucleic acid sequence
			Sequence annotation
			binding_site
			sequence_feature
		Added:
			Gene Feature
			binding_site
			sequence_feature
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.haxp7g' by 'The FAIRsharing Team' at 19:34, 08 Dec 2017 (approved):

	'type' has been modified:
		Before: model/format
		After: terminology artifact

Edits to 'https://fairsharing.org/FAIRsharing.haxp7g' by 'jerven' at 13:12, 08 Dec 2017 (approved):

	'supportLinks' has been modified:
		Before:
			https://groups.google.com/forum/#!forum/faldo
			https://github.com/JervenBolleman/FALDO
		After:
			https://groups.google.com/forum/#!forum/faldo
			https://github.com/OBF/FALDO
		Added:
			https://github.com/OBF/FALDO
		Removed:
			https://github.com/JervenBolleman/FALDO

Edits to 'https://fairsharing.org/FAIRsharing.haxp7g' by 'jerven' at 13:10, 08 Dec 2017 (approved):

	'bioportal_abbreviation' has been modified:
		Before: None
		After: FALDO

Support

General

forum	FALDO Google Group
online documentation	GitHub Issues at OBF Faldo
online documentation	GitHub Project

Additional Information

Contact

Jerven Bolleman

External Links

Bioportal

http://bioportal.bioontology.org/ontologies/FALDO

Tools

No tools defined

Schemas

No XSD schemas defined

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Creative Commons CC0 1.0 Universal (CC0 1.0) Public Domain Dedication

Data Access

AgroPortal: Browse / Download	http://agroportal.lirmm.fr/ontologies/FALDO
Browse	http://biohackathon.org/resource/faldo
Browse (AberOWL)	http://aber-owl.net/ontology/FALDO/#/

Publications

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation.

Bolleman JT,Mungall CJ,Strozzi F,Baran J,Dumontier M,Bonnal RJ,Buels R,Hoehndorf R,Fujisawa T,Katayama T,Cock PJ
J Biomed Semantics 2016

View Paper (PubMed) View Publication

FALDO Ontology Display

View in BioPortal.

Disclaimer: This widget assumes the availability of the ontology resources in the NCBO BioPortal.

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

Models and Formats

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases (2)

Ensembl
Ensembl creates, integrates and distributes reference datasets and analysis tools that enable genomics. Ensembl is a genome browser that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. Ensembl annotate genes, computes multiple alignments, predicts regulatory function and collects disease data.

UniProt Knowledgebase
The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation. In addition to capturing the core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and clear indications of the quality of annotation in the form of evidence attribution of experimental and computational data. The UniProt Knowledgebase consists of two sections: a reviewed section containing manually-annotated records with information extracted from literature and curator-evaluated computational analysis (aka "UniProtKB/Swiss-Prot"), and an unreviewed section with computationally analyzed records that await full manual annotation (aka "UniProtKB/TrEMBL").

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is maintained by jerven

Maintains

Swiss Institute of Bioinformatics (SIB), Switzerland (Research institute) Lead

Feature Annotation Location Description Ontology

We need your help!

Developed by

Contact Us

About FAIRsharing