| 1 | | TODO |
| | 1 | = Welcome to PhenoFlow = |
| | 2 | [[TOC()]] |
| | 3 | |
| | 4 | Phenoflow is the [http://www.molgenis.org MOLGENIS] reference implementation of the phenotype object model, Pheno-OM. Mission of this project is to ease harmonization and interoperability of phenotypic data across model organisms, human genetics and biobanks. The result of this project can be used as component or intermediate data model to harmonize phenotype representation in existing software initiatives like [http://www.mged.org/mage-tab/ MAGE-TAB], [http://www.xgap.org XGAP for gwas] and [http://www.hgvbaseg2p.org/index HGVbaseG2P]. PhenoFlow is developed by the [http://wiki.gcc.rug.nl UMC Groningen/GCC] (Swertz), [http://www.ebi.ac.uk/fg EBI Hinxton/FG] (Adamusiak, Swertz), [http://www.fimm.fi/ FIMM Helsinki] (Muilu) and [http://www.le.ac.uk/ge/pages/staff/staff_pages/brookes.html U Leicester] (Thorisson, Brookes) as part of and with other members of [http://www.gen2phen.org/content/phenotype-modellingg EU-GEN2PHEN]. Applications of the project are supported by [http://www.nbic.nl/support/task-forces/biobanking/ NBIC Biobanking], [http://www.lifelines.org LifeLines] and [http://www.bbmriwiki.nl BBMRI-NL]). |
| | 5 | |
| | 6 | == Motivation == |
| | 7 | The next stage of epidemiological and genetic research will depend critically on large collections of high quality samples and data. A wealth of panels from natural human and experimental model organism populations is readily available, but their annotation is scattered between thousands broad inter-institute panel biobanks and deep departmental boutique disease biobanks, each with their own data front-end. While standardization efforts have produced simple formats for the exchange and integration of high throughput data, such as [http://www.mged.org/mage-tab/ MAGE-TAB] for microarrays and [http://www.xgap.org XGAP] for xQTL studies an equally lightweight system for phenotypic data is still left wanted |
| | 8 | |
| | 9 | == Easy to adopt system == |
| | 10 | We here report an easy-to-adopt system for the harmonization, integration and search of phenotypic information from experimental and clinical biobanks. The first component is a community created flexible, ontology-enabled model for the uniform representation of any phenotypic data: panels/cohorts, individuals, protocols, observable features and values (Pheno-OM). Then we present a reusable implementation of this model, including a simple tab/excel based data file format (Pheno-TAB) to harmonize, load and share (meta)data on and a ‘database-in-a-box’ (Pheno-DB) for local biobank projects to quickly setup their own phenotype repository or customize it using the [http://www.molgenis.org MOLGENIS] system. As a next step we aim to demonstrate how use of ontologies and semantic methods in this system enable integrated search of vast collections of phenotypic information across investigations, species and even a federated network of PhenoDB installations. Thus we expect PhenoFlow to lower the barriers for phenotypic data flow between biobanks and enables integrated search across panels and species to find larger sample sets and data for the next generation of biomedical studies. |
| | 11 | |
| | 12 | == A growing range of applications == |
| | 13 | Currently the PhenoFlow model has been picked up to produce: |
| | 14 | * the '''reference implementation''' which is available at http://www.hgvbaseg2p.org/index |
| | 15 | * the '''BiobankCatalog''' by the [http://www.nbic.nl/support/task-forces/biobanking/ NBIC Biobanking Task force] (Antonakaki, Enckevoort), [http://www.lifelines.org LifeLines] (Lops) and [http://www.bbmriwiki.nl BBMRI-NL] (Swertz). |
| | 16 | * the '''AnimalDb''' database for tracking animal observations (Roos) |
| | 17 | * the '''NGS workbench''' for tracking all around next generation sequencing experiment by [http://www.bbmriwiki.nl BBMRI-NL] (Lundberg) |
| | 18 | The most recent sourcecode of all these projects is available from SVN at http://www.molgenis.org/svn/pheno |
