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Samples, phenotypes and ontologies

Delivering databases and interoperability tools for mammalian models of disease, GWAS, PGS and Polygenic Scores.

The Samples, Phenotypes and Ontologies team, led by Helen Parkinson, is organised into three themes, Semantics as a Service, GWAS Catalog and PGS Catalogs (in Collaboration with Cambridge colleagues Mike Inouye and Sam Lambert) and mammalian models of disease. The team is part of the Knowledge Management Section and works closely with colleagues across EMBL-EBI including the Human Cell Atlas, the cohort integration project CINECA, and the Covid19 Portal. We also collaborate in delivery of the eQTL portal and supply content and ontologies to the industry-academia precompetitive OpenTargets project. Edit

Data resources

Bubastis

Bubastis

Bubastis is an ontology change tool which is able to analyse two ontologies (typically two versions of the same ontology) to highlight logical changes which have occurred and to present these changes in more or less detail, as required

CancerModels.Org

CancerModels.Org

CancerModels.Org is a research platform that aggregates, standardises, and integrates the complex and diverse data associated with patient-derived cancer models (PDCMs) using FAIR principles. It provides a unified point for PDCM stakeholders, from basic and clinical researchers to bioinfo…

eQTL Catalogue

eQTL Catalogue

The eQTL Catalogue aims to provide uniformly processed gene expression and splicing QTLs from all available public studies on human.

Experimental Factor Ontology

Experimental Factor Ontology

EFO is a data-driven ontology that imports parts of existing community ontologies into a single framework. It is used for annotation, curation, query and visualisation of data by the Gene Expression Atlas, NHGRI GWAS Catalog, BioSamples database, and is being mapped to Ensembl variation.

International Mouse Phenotyping Consortium Portal

International Mouse Phenotyping Consortium Portal

The International Mouse Phenotyping Consortium (IMPC) has initiated a global effort to generate and characterize a knockout mouse strain for every protein-coding gene in the mouse genome. EBI, The Wellcome Trust Sanger Institute and MRC Harwell deliver informatics as part of the MPI2 consortium acti…

NHGRI-EBI GWAS Catalog

NHGRI-EBI GWAS Catalog

  The GWAS Catalog is provided jointly by the http://www.genome.gov/&quothttp://www.genome.gov/&quot”>http://www.genome.gov/&quotNational Human Genome Research Institute (NHGRI) and the http://www.ebi.ac.uk/&quothttp://www.ebi.ac.uk/&quot”>http://www.ebi.ac.uk/&quotEuropean Bioinformatics Institute…

Ontology Lookup Service

Ontology Lookup Service

The OLS provides a web service interface to query multiple ontologies from a single location with a unified output format.The OLS can integrate any ontology available in the Open Biomedical Ontology (OBO) format.

Polygenic Score Catalog

Polygenic Score Catalog

A polygenic score (PGS) aggregates the effects of many genetic variants into a single number which predicts genetic predisposition for a phenotype. PGS are typically composed of hundreds-to-millions of genetic variants (usually SNPs) which are combined using a weighted sum of allele dosages multipli…

Webulous

Webulous

Webulous is an application suite for collaborative ontology development, designed to support authoring ontologies by populating ontology design patterns through simple user interfaces.

Zooma

Zooma

Zooma is a curator environment for discovering optimal ontology annotations based on real, manually reviewed data.

Latest jobs

HR Payroll and Pension Scheme Manager

Administrative and support in EMBL Heidelberg

We are looking for an experienced Human Resources Professional who is excited by the challenge of providing an excellent service in a stimulating international environment. The EMBL Human Resources unit is responsible for the Laboratory’s staff of approx. 1900 employees from over 80 nations working …

Closes on 2nd March. Posted 14th February 2025

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HR Talent Acquisition Administrator

Administrative and support in EMBL Heidelberg

Our Human Resources Department is responsible to deliver high quality HR services to all EMBL personnel working at EMBL Headquarters in Heidelberg and its 5 sites across Europe. We are looking for a motivated individual who is interested in gaining experience in HR administration and excited by the …

Closes on 9th March. Posted 14th February 2025

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