Welcome to Observ-OM and Observ-TAB

News

Observ-OM data model published

Observ-OM and Observ-TAB, the Universal syntax solutions for the integration, search, and exchange of phenotype and genotype information, is published in ​Human Mutation. Genetic and epidemiological resear ...

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• Posted: 13 years ago
• Author: Morris Swertz
• Categories: observ molgenis
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CHD7 mutation database published

We are proud with another ​MOLGENIS for the CHARGE syndrome using ​Observ-OM published in ​Human Mutation. CHD7 is a member of the chromodomain helicase DNA- ...

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• Posted: 13 years ago (Updated: 13 years ago)
• Author: Morris Swertz
• Categories: observ molgenis
• Comments (0)

The simple system to format and exchange observation data.

Background

Observ-OM is a model capture 'any' phenotype observation lead by ​EU-GEN2PHEN. Our mission mission: store individual and summary level observations in a uniform way to enable harmonization and interoperability of phenotypic and genotypic data across human genetics, model organisms and biobanks. Next to the object model we have an tabular exchange format Observ-TAB and user interfaces, search wizard, ​ontology links and Excel import/export.

Status: data model finished and in process of publication for community review.

Applications

View and download Observ-OM applications:

• the reference implementation which is available at ​http://www.ebi.ac.uk/microarray-srv/pheno (Adamusiak, Parkinson, GEN2PHEN, Swertz)
• the xQTL workbench which is available at ​http://www.xqtl.org (Arends, van der Velde)
• the BiobankCatalog by the ​NBIC Biobanking Task force (Antonakaki, Enckevoort), ​LifeLines (Lops) and ​BBMRI-NL (Swertz).
• the ​AnimalDB database for tracking animal observations (Roos)
• the NGS workbench for tracking all around next generation sequencing experiment by ​BBMRI-NL (Dijkstra)

Source code

The most recent sourcecode of all these projects is available from SVN at ​http://www.molgenis.org/svn/molgenis_apps/trunk

Developers

Observ-OM and Observ-TAB were developed by:

• ​UMC Groningen/GCC (Swertz),
• ​EBI Hinxton/FG (Adamusiak, Parkinson),
• ​FIMM Helsinki (Muilu) and
• ​U Leicester (Thorisson, Gollapudi, Brookes)
• ​other members of EU-GEN2PHEN.

Applications using Observ-OM are developed by:

• ​NBIC Biobanking for BiobankCatalog and SemanticSearch? (Antonakaki, van Enckevort, Marshall, Swertz),
• ​LifeLines for BiobankCatalog (Antonakaki, Lops, Swertz)
• ​BioSHARE for biobank data integration (Chao, Swertz)
• ​BBMRI-NL for BiobankCatalog and NgsWorkbench (Antonakaki, Swertz)
• ​U Groningen for ​AnimalDB (Roos, Boerema, Swertz)