EFO

metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

Other names: EFO

The Experimental Factor Ontology provides a systematic description of many experimental variables available in EBI databases, and for external projects such as the NHGRI GWAS catalogue. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds.

Webpage:

https://www.ebi.ac.uk/ols/ontologies/efo

Licence:

Name: Apache v2.0
URL: https://www.ebi.ac.uk/ols/ontologies/efo

Publications:

Publications
More detailed information about this field from each metasource.

Modeling sample variables with an Experimental Factor Ontology
PMID: 20200009
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

metasource: Fairsharing.org
version: FAIRsharing.org: EFO; Experimental Factor Ontology; DOI: https://doi.org/10.25504/FAIRsharing.1gr4tz; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

Modeling sample variables with an Experimental Factor Ontology PubMed citations: 203.

203 articles citing: Modeling sample variables with an Experimental Factor Ontology

Empowering the discovery of novel target-disease associations via machine learning approaches in the open targets platform. PMID:35710324
Applying the FAIR principles to data in a hospital: challenges and opportunities in a pandemic. PMID:35468846
Harmonizing model organism data in the Alliance of Genome Resources. PMID:35380658
Expression Atlas update: gene and protein expression in multiple species. PMID:34850121
DISCO: a database of Deeply Integrated human Single-Cell Omics data. PMID:34791375
The IntAct database: efficient access to fine-grained molecular interaction data. PMID:34761267
Besca, a single-cell transcriptomics analysis toolkit to accelerate translational research. PMID:34761219
Priority index: database of genetic targets in immune-mediated disease. PMID:34751399
Computational workflow for functional characterization of COVID-19 through secondary data analysis. PMID:34746856
Accessing scientific data through knowledge graphs with Ontop. PMID:34693372
Experiment level curation of transcriptional regulatory interactions in neurodevelopment. PMID:34665801
Development of the International Classification of Diseases Ontology (ICDO) and its application for COVID-19 diagnostic data analysis. PMID:34663204
A proteomics sample metadata representation for multiomics integration and big data analysis. PMID:34615866
A compendium of uniformly processed human gene expression and splicing quantitative trait loci. PMID:34493866
Genetic Prioritization, Therapeutic Repositioning and Cross-Disease Comparisons Reveal Inflammatory Targets Tractable for Kidney Stone Disease. PMID:34489936
Linking common human diseases to their phenotypes; development of a resource for human phenomics. PMID:34425897
CanImmunother: a manually curated database for identification of cancer immunotherapies associating with biomarkers, targets, and clinical effects. PMID:34345532
Disease ontologies for knowledge graphs. PMID:34289807
UniBind: maps of high-confidence direct TF-DNA interactions across nine species. PMID:34174819
MetamORF: a repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses. PMID:34156446
Landscape of allele-specific transcription factor binding in the human genome. PMID:33980847
Secondary analysis of transcriptomes of SARS-CoV-2 infection models to characterize COVID-19. PMID:33842903
seqQscorer: automated quality control of next-generation sequencing data using machine learning. PMID:33673854
FOntCell: Fusion of Ontologies of Cells. PMID:33644039
Curation of over 10 000 transcriptomic studies to enable data reuse. PMID:33599246
Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome. PMID:33526779
Machine learning reveals bilateral distribution of somatic L1 insertions in human neurons and glia. PMID:33432196
MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes. PMID:33418085
Pancreatlas: Applying an Adaptable Framework to Map the Human Pancreas in Health and Disease. PMID:33294866
GTRD: an integrated view of transcription regulation. PMID:33231677
Open Targets Platform: supporting systematic drug-target identification and prioritisation. PMID:33196847
EpiGraphDB: a database and data mining platform for health data science. PMID:33165574
COVID-19 Surveillance in a Primary Care Sentinel Network: In-Pandemic Development of an Application Ontology. PMID:33112762
Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics. PMID:33045747
CMNPD: a comprehensive marine natural products database towards facilitating drug discovery from the ocean. PMID:32986829
The GTEx Consortium atlas of genetic regulatory effects across human tissues. PMID:32913098
Finding semantic patterns in omics data using concept rule learning with an ontology-based refinement operator. PMID:32905086
Cytokines mapping for tissue-specific expression, eQTLs and GWAS traits. PMID:32895400
"METAGENOTE: a simplified web platform for metadata annotation of genomic samples and streamlined submission to NCBI's sequence read archive". PMID:32883210
Responsible, practical genomic data sharing that accelerates research. PMID:32694666
The Phenotypic Consequences of Genetic Divergence between Admixed Latin American Populations: Antioquia and Chocó, Colombia. PMID:32681795
PS4DR: a multimodal workflow for identification and prioritization of drugs based on pathway signatures. PMID:32503412
Why data citation isn't working, and what to do about it. PMID:32367113
QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data. PMID:32343490
An Integrative Phenotype-Genotype Approach Using Phenotypic Characteristics from the UAE National Diabetes Study Identifies HSD17B12 as a Candidate Gene for Obesity and Type 2 Diabetes. PMID:32340285
BioHackathon 2015: Semantics of data for life sciences and reproducible research. PMID:32308977
Incorporation of a unified protein abundance dataset into the Saccharomyces genome database. PMID:32128557
ncRPheno: a comprehensive database platform for identification and validation of disease related noncoding RNAs. PMID:32122231
Common genetic substrates of alcohol and substance use disorder severity revealed by pleiotropy detection against GWAS catalog in two populations. PMID:32027075
Confounding Patient Factors Affecting the Proper Interpretation of the Periostin Level as a Biomarker in Asthma Development. PMID:32021310
Organizing genome engineering for the gigabase scale. PMID:32019919
Biobtree: A tool to search, map and visualize bioinformatics identifiers and special keywords. PMID:31984130
Combining lexical and context features for automatic ontology extension. PMID:31931870
GenoSurf: metadata driven semantic search system for integrated genomic datasets. PMID:31820804
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. PMID:31701156
MetaboLights: a resource evolving in response to the needs of its scientific community. PMID:31691833
Expression Atlas update: from tissues to single cells. PMID:31665515
Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction. PMID:31631012
GWAS Central: a comprehensive resource for the discovery and comparison of genotype and phenotype data from genome-wide association studies. PMID:31612961
SEAweb: the small RNA Expression Atlas web application. PMID:31598718
Ensembl Genomes 2020-enabling non-vertebrate genomic research. PMID:31598706
A Logical Model of Homology for Comparative Biology. PMID:31596473
Ontology based mining of pathogen-disease associations from literature. PMID:31533864
Identification of human genetic variants controlling circular RNA expression. PMID:31519742
The Cancer-Associated Genetic Variant Rs3903072 Modulates Immune Cells in the Tumor Microenvironment. PMID:31507631
The Length of the Expressed 3' UTR Is an Intermediate Molecular Phenotype Linking Genetic Variants to Complex Diseases. PMID:31475030
Prioritizing target-disease associations with novel safety and efficacy scoring methods. PMID:31285471
PhenoScanner V2: an expanded tool for searching human genotype-phenotype associations. PMID:31233103
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language. PMID:31225582
MultiPLIER: A Transfer Learning Framework for Transcriptomics Reveals Systemic Features of Rare Disease. PMID:31121115
Genetic and Real-World Clinical Data, Combined with Empirical Validation, Nominate Jak-Stat Signaling as a Target for Alzheimer's Disease Therapeutic Development. PMID:31072055
Navigating in vitro bioactivity data by investigating available resources using model compounds. PMID:31036807
Defining the genetic and evolutionary architecture of alternative splicing in response to infection. PMID:30975994
Ensembl variation resources. PMID:30576484
Exploring the genetic basis of human population differences in DNA methylation and their causal impact on immune gene regulation. PMID:30563547
The BioGRID interaction database: 2019 update. PMID:30476227
Open Targets Platform: new developments and updates two years on. PMID:30462303
The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. PMID:30445434
BioSamples database: an updated sample metadata hub. PMID:30407529
ChEMBL: towards direct deposition of bioassay data. PMID:30398643
EWAS Atlas: a curated knowledgebase of epigenome-wide association studies. PMID:30364969
FAANG, establishing metadata standards, validation and best practices for the farmed and companion animal community. PMID:30311252
Uncovering new disease indications for G-protein coupled receptors and their endogenous ligands. PMID:30285606
Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci. PMID:30139913
The impact of genome-wide association studies on biomedical research publications. PMID:30103832
Computational resources associating diseases with genotypes, phenotypes and exposures. PMID:30102366
Towards FAIRer Biological Knowledge Networks Using a Hybrid Linked Data and Graph Database Approach. PMID:30085931
Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center. PMID:29917015
Connecting genetics and gene expression data for target prioritisation and drug repositioning. PMID:29881461
Genomic atlas of the human plasma proteome. PMID:29875488
A guideline for reporting experimental protocols in life sciences. PMID:29868256
The Cellosaurus, a Cell-Line Knowledge Resource. PMID:29805321
GlobAl Distribution of GEnetic Traits (GADGET) web server: polygenic trait scores worldwide. PMID:29788182
Navigating the disease landscape: knowledge representations for contextualizing molecular signatures. PMID:29684165
Where to search top-K biomedical ontologies? PMID:29579141
Conserved and species-specific transcription factor co-binding patterns drive divergent gene regulation in human and mouse. PMID:29361190
Comparison, alignment, and synchronization of cell line information between CLO and EFO. PMID:29322915
A Case Study Application of the Aggregate Exposure Pathway (AEP) and Adverse Outcome Pathway (AOP) Frameworks to Facilitate the Integration of Human Health and Ecological End Points for Cumulative Risk Assessment (CRA). PMID:29236470
SATORI: a system for ontology-guided visual exploration of biomedical data repositories. PMID:29186292
Expression Atlas: gene and protein expression across multiple studies and organisms. PMID:29165655
Gramene 2018: unifying comparative genomics and pathway resources for plant research. PMID:29165610
Identification of Pleiotropic Cancer Susceptibility Variants from Genome-Wide Association Studies Reveals Functional Characteristics. PMID:29150481
Using semantics for representing experimental protocols. PMID:29132408
Drug target ontology to classify and integrate drug discovery data. PMID:29122012
The BioStudies database-one stop shop for all data supporting a life sciences study. PMID:29069414
Precision annotation of digital samples in NCBI's gene expression omnibus. PMID:28925997
In silico prediction of novel therapeutic targets using gene-disease association data. PMID:28851378
Whole-transcriptome analysis delineates the human placenta gene network and its associations with fetal growth. PMID:28693416
Building bridges between cellular and molecular structural biology. PMID:28682240
MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive. PMID:28535296
The anatomy of phenotype ontologies: principles, properties and applications. PMID:28387809
The landscape of genetic susceptibility correlations among diseases and traits. PMID:28371808
Genome-wide identification of splicing QTLs in the human brain and their enrichment among schizophrenia-associated loci. PMID:28240266
SPANG: a SPARQL client supporting generation and reuse of queries for distributed RDF databases. PMID:28178937
The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog). PMID:27899670
Open Targets: a platform for therapeutic target identification and validation. PMID:27899665
COSMIC: somatic cancer genetics at high-resolution. PMID:27899578
Ensembl 2017. PMID:27899575
The ChEMBL database in 2017. PMID:27899562
The BLUEPRINT Data Analysis Portal. PMID:27863955
Supporting the analysis of ontology evolution processes through the combination of static and dynamic scaling functions in OQuaRE. PMID:27751176
The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis. PMID:27627881
Ontology-based Vaccine and Drug Adverse Event Representation and Theory-guided Systematic Causal Network Analysis toward Integrative Pharmacovigilance Research. PMID:27458549
Publishing FAIR Data: An Exemplar Methodology Utilizing PHI-Base. PMID:27433158
First Proposal of Minimum Information About a Cellular Assay for Regenerative Medicine. PMID:27405781
NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease. PMID:27392431
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. PMID:27377652
Identification of Cancer Related Genes Using a Comprehensive Map of Human Gene Expression. PMID:27322383
GEE: An Informatics Tool for Gene Expression Data Explore. PMID:27200217
DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets. PMID:27084938
Extending gene ontology in the context of extracellular RNA and vesicle communication. PMID:27076901
Webulous and the Webulous Google Add-On--a web service and application for ontology building from templates. PMID:27042287
Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation. PMID:27011785
Linking MedDRA(®)-Coded Clinical Phenotypes to Biological Mechanisms by the Ontology of Adverse Events: A Pilot Study on Tyrosine Kinase Inhibitors. PMID:27003817
Principles of metadata organization at the ENCODE data coordination center. PMID:26980513
Ensembl regulation resources. PMID:26888907
Ten Simple Rules for Selecting a Bio-ontology. PMID:26867217
Value, but high costs in post-deposition data curation. PMID:26861660
Weakly supervised learning of biomedical information extraction from curated data. PMID:26817711
Emerging semantics to link phenotype and environment. PMID:26713234
An ISA-TAB-Nano based data collection framework to support data-driven modelling of nanotoxicology. PMID:26665069
GWASdb v2: an update database for human genetic variants identified by genome-wide association studies. PMID:26615194
LegumeIP 2.0--a platform for the study of gene function and genome evolution in legumes. PMID:26578557
Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants. PMID:26481351
NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases. PMID:26475471
RNASeqMetaDB: a database and web server for navigating metadata of publicly available mouse RNA-Seq datasets. PMID:26323714
Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies. PMID:26320941
Harmonising and linking biomedical and clinical data across disparate data archives to enable integrative cross-biobank research. PMID:26306643
Representing virus-host interactions and other multi-organism processes in the Gene Ontology. PMID:26215368
Activity, assay and target data curation and quality in the ChEMBL database. PMID:26201396
A large-scale crop protection bioassay data set. PMID:26175909
Development of an Ontology for Periodontitis. PMID:26140188
CLO: The cell line ontology. PMID:25852852
Ontology application and use at the ENCODE DCC. PMID:25776021
Describing the breakbone fever: IDODEN, an ontology for dengue fever. PMID:25646954
diXa: a data infrastructure for chemical safety assessment. PMID:25505093
Europe PMC: a full-text literature database for the life sciences and platform for innovation. PMID:25378340
ArrayExpress update--simplifying data submissions. PMID:25361974
Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways. PMID:25279814
Semantic Web repositories for genomics data using the eXframe platform. PMID:25093072
The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation. PMID:25068035
Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. PMID:25009735
WebProtégé: a collaborative Web-based platform for editing biomedical ontologies. PMID:24771560
Thematic series on biomedical ontologies in JBMS: challenges and new directions. PMID:24602198
Global meta-analysis of transcriptomics studies. PMID:24586684
The EBI RDF platform: linked open data for the life sciences. PMID:24413672
Ensembl 2014. PMID:24316576
CellFinder: a cell data repository. PMID:24304896
Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments. PMID:24304889
The European Bioinformatics Institute's data resources 2014. PMID:24271396
Updates to BioSamples database at European Bioinformatics Institute. PMID:24265224
A neuroinformatics of brain modeling and its implementation in the Brain Operation Database BODB. PMID:24234915
Biomarkers in autism spectrum disorder: the old and the new. PMID:24096533
Ontology based molecular signatures for immune cell types via gene expression analysis. PMID:24004649
CELDA -- an ontology for the comprehensive representation of cells in complex systems. PMID:23865855
Modeling functional Magnetic Resonance Imaging (fMRI) experimental variables in the Ontology of Experimental Variables and Values (OoEVV). PMID:23684873
Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts. PMID:23599415
The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics. PMID:23514033
Getting ready for the Human Phenome Project: the 2012 forum of the Human Variome Project. PMID:23401191
A semantic proteomics dashboard (SemPoD) for data management in translational research. PMID:23282161
Reuse of public genome-wide gene expression data. PMID:23269463
ArrayExpress update--trends in database growth and links to data analysis tools. PMID:23193272
The EBI enzyme portal. PMID:23175605
On the ontology based representation of cell lines. PMID:23144907
The Units Ontology: a tool for integrating units of measurement in science. PMID:23060432
Accessing data from the International Mouse Phenotyping Consortium: state of the art and future plans. PMID:22991088
Transcriptomine, a web resource for nuclear receptor signaling transcriptomes. PMID:22786849
MageComet--web application for harmonizing existing large-scale experiment descriptions. PMID:22474121
Populous: a tool for building OWL ontologies from templates. PMID:22373396
Uberon, an integrative multi-species anatomy ontology. PMID:22293552
A semantic problem solving environment for integrative parasite research: identification of intervention targets for Trypanosoma cruzi. PMID:22272365
AnnotCompute: annotation-based exploration and meta-analysis of genomics experiments. PMID:22190598
Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma. PMID:22106335
The BioSample Database (BioSD) at the European Bioinformatics Institute. PMID:22096232
Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments. PMID:22064864
Knowledge sharing and collaboration in translational research, and the DC-THERA Directory. PMID:21969471
Developing a kidney and urinary pathway knowledge base. PMID:21624162
Automating generation of textual class definitions from OWL to English. PMID:21624160
OntoCAT--simple ontology search and integration in Java, R and REST/JavaScript. PMID:21619703
ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments. PMID:21071405
Recent progress in automatically extracting information from the pharmacogenomic literature. PMID:21047206
The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources. PMID:21030441
Annotare--a tool for annotating high-throughput biomedical investigations and resulting data. PMID:20733062

Tags:

Tags
More detailed information about this field from each metasource.

assay
metasource: Fairsharing.org
version: FAIRsharing.org: EFO; Experimental Factor Ontology; DOI: https://doi.org/10.25504/FAIRsharing.1gr4tz; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

experimental measurement
metasource: Fairsharing.org
version: FAIRsharing.org: EFO; Experimental Factor Ontology; DOI: https://doi.org/10.25504/FAIRsharing.1gr4tz; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

genome-wide association study
metasource: Fairsharing.org
version: FAIRsharing.org: EFO; Experimental Factor Ontology; DOI: https://doi.org/10.25504/FAIRsharing.1gr4tz; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

independent variable
metasource: Fairsharing.org
version: FAIRsharing.org: EFO; Experimental Factor Ontology; DOI: https://doi.org/10.25504/FAIRsharing.1gr4tz; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

study design
metasource: Fairsharing.org
version: FAIRsharing.org: EFO; Experimental Factor Ontology; DOI: https://doi.org/10.25504/FAIRsharing.1gr4tz; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

assay experimental measurement genome-wide association study independent variable study design

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