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* docs: added genetics data team page * docs: added genetics data KP page
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[**Back to Home**](https://github.com/NCATSTranslator/NCATSTranslator.github.io/wiki) | ||
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# Genetics Knowledge Provider (KP) | ||
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## General Description | ||
We developed the Genetics Knowledge Provider (KP), a knowledge-centric data provider for computation based genetic association results, | ||
as part of the NCATS Biomedical Data Translator (“Translator”). The Genetics KP aims to | ||
* integrate Genome Wide Association Studies (GWAS) data sources in an unbiased way. | ||
* provide a curated, unified framework for genetic associations to deepen our understanding of gene/disease biology. | ||
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The Genetics KP takes advantage of broad access to disease specific GWAS datasets, portals, and computational tools, | ||
to integrate information available for diseases and their associated genes, including similarity-based connections. We follow a stringent | ||
procedure to avoid expert bias, including data scouting and recording data provenance, to create a unified framework for gene/disease associations. | ||
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We bring to the Translator project computational genetics expertise, and using signal aggregating algorithms and tools to combine genetic signals across GWAS studies. | ||
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## Team Members | ||
* Jason Flannick - Principal Investigator and Team Lead | ||
* Noel Burt - Director, Operations and Development, Knowledge Portals | ||
* Marc Duby ([email protected]) - Principal Software Engineer - (_contact with questions_) | ||
* Ryan Koesterer - Senior Computational Analyst | ||
* Maria Costanzo - Manager, Knowledge Portals | ||
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## Genetics KP Translator Reasoner API | ||
* https://genetics-kp.transltr.io/genetics_provider/trapi/v1.4/ | ||
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## Description of Genetics KP’s data resources | ||
* _Genebass_ | ||
* Downloaded loss of function (LoF) gene/disease association data | ||
* https://app.genebass.org/ | ||
* _GenCC_ | ||
* Curated gene/disease association statistics | ||
* https://thegencc.org/ | ||
* _ClinVar_ | ||
* https://www.ncbi.nlm.nih.gov/clinvar/ | ||
* _ClinGen_ | ||
* https://clinicalgenome.org/ | ||
* _GWAS Dataset List_ | ||
* Downloaded and harmonized 200+ GWAS studies; data is used with Magma gene aggregation method | ||
* Studies mostly pertaining to metabolic and musculoskeletal diseases | ||
* https://hugeamp.org:8000/datasets.html | ||
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## Computational Tools | ||
* _Magma_ - for Gene/Disease variant pvalue aggregation using GWAS | ||
* https://ctg.cncr.nl/software/magma | ||
* _HuGE Calculator_ - For calculating the probability a gene is associated to a disease using common and rare variants | ||
* https://hugeamp.org:8000/hugecalculator.html | ||
* _PIGEAN_ - A framework for gene prioritization | ||
* https://www.kp4cd.org/index.php/node/1516 | ||
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## Source Code | ||
* _GeneticsKP_ https://github.com/broadinstitute/genetics-kp-dev | ||
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## External Documentation | ||
* _Additional Genetics KP documentation in GitHub_ https://github.com/broadinstitute/genetics-kp-dev | ||
* _Gene Level Meta Analysis Method_ https://hugeamp.org:8000/help.html?page=955 | ||
* _Calculating Gene/Disease Probability Method_ https://hugeamp.org:8000/help.html?page=961 | ||
* _Selecting and Processing of GWAS Datasets_ https://hugeamp.org:8000/help.html?page=935 |
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[Back to Teams](index.md) | ||
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# Team Genetics Data Services Provider | ||
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Genetics Data Services Provider is the team responsible for the | ||
["Genetics Data"](https://github.com/NCATSTranslator/Translator-All/wiki/Genetics-Knowledge-Provider) knowledge provider. | ||
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## Genetics Data Service Provider Team Members: | ||
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- Jason Flannick - Principal Investigator and Team Lead | ||
- Noel Burt - Director, Operations and Development, Knowledge Portals | ||
- Marc Duby ([email protected]) - Principal Software Engineer - (contact with questions) | ||
- Ryan Koesterer - Senior Computational Analyst | ||
- Maria Costanzo - Manager, Knowledge Portals | ||
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