Standards > terminology artifact > bsg-s000082


ready Experimental Factor Ontology

Abbreviation:EFO


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General Information
The Experimental Factor Ontology (EFO) is an application focused ontology modelling the experimental variables in multiple resources at the EBI and the Centre for Therapeutic Target Validation. The ontology has been developed to increase the richness of the annotations that are currently made in resources and to promote consistent annotation, to facilitate automatic annotation and to integrate external data. The ontology pulls together classes from reference ontologies such as disease, cell line, cell type and anatomy and adds axiomatisation as necessary to connect areas such as disease to phenotype.


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This record is maintained by siiraa  ORCID

Record updated: March 28, 2017, 5:36 p.m. by siiraa.


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Conditions of Use

License: Terms of Use for EMBL-EBI Services

Applies to: Data use

Data Access




Connectivity
EFO Ontology Display

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

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Models and Formats

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Implementing Databases (7)
BioSample at the European Bioinformatics Institute
The BioSamples database aggregates sample information for reference samples (e.g. Coriell Cell lines) and samples for which data exist in one of the EBI's assay databases such as ArrayExpress, the European Nucleotide Archive or PRIDE. It provides links to assays an specific samples, and accepts direct submissions of sample information.

Expression Atlas
The Expression Atlas is a free resource providing information on gene expression patterns under different biological conditions. Gene expression data is re-analysed in-house to detect genes showing interesting baseline and differential expression patterns, allowing a user to ask questions such as "what are the genes expressed in normal human liver" and "what genes are differentially expressed between water-stressed rice plants and controls with normal watering?". The resource also features a few proteomics data sets provided by collaborators for corroboration between gene- and protein-level expression results.

Stem Cell Discovery Engine
Comparison system for cancer stem cell analysis

ArrayExpress
ArrayExpress is a database of functional genomics experiments that can be queried and the data downloaded. It includes gene expression data from microarray and high throughput sequencing studies. Data is collected to MIAME and MINSEQE standards. Experiments are submitted directly to ArrayExpress or are imported from the NCBI GEO database.

Kidney and Urinary Pathway Knowledgebase
The KUPKB is a collection of omics datasets that have been extracted from scientific publications and other related renal databases. The iKUP browser provides a single point of entry for you to query and browse these datasets.

ENCODE Project
The ENCODE (Encyclopedia of DNA Elements) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active.

Open Targets
Open Targets designed and developed an integration and visualization platform that provides evidence about the association of known and potential drug targets with diseases. The platform is designed to support identification and prioritization of biological targets for follow-up. Each drug target is linked to a disease using integrated genome-wide data from a broad range of data sources. The platform provides either a target-centric workflow to identify diseases that may be associated with a specific target, or a disease-centric workflow to identify targets that may be associated with a specific disease. Users can easily transition between these target- and disease-centric workflows.

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Credit

Record Maintainer

Funds

Maintains

Grant Number(s)

  • 021902 (European Commision grants FELICS)

  • 200754 (gen2phen)

  • LSHG-CT-2006-037686 (EMERALD)


Publications

Modeling sample variables with an Experimental Factor Ontology.

Malone J,Holloway E,Adamusiak T,Kapushesky M,Zheng J,Kolesnikov N,Zhukova A,Brazma A,Parkinson H
Bioinformatics 2010

View Paper (PubMed) View Paper (DOI)