From listmaster animalgenome.org Tue Jul 16 19:20:29 2019
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From: Chris Elsik <elsikcmissouri.edu>
Postmaster: submission approved by list moderator
To: Members of AnGenMap <angenmapanimalgenome.org>
Subject: New FAANGMine Data Mining Warehouse
Date: Tue, 16 Jul 2019 19:20:29 -0500
The first release of the FAANGMine Data Mining Warehouse is available at
http://faangmine.org.
FAANGMine is a new project supported by the National Science Foundation to
address the need for a high performance data mining resource that enables
fine-grained querying and integrating the heterogeneous FAANG data with
existing information, such as functions of known genes and research
datasets. The specific aims of the project are to 1) develop FAANGMine - a
high-performance data mining system that integrates genome assemblies and
currently available annotation data for FAANG species, 2) extend FAANGMine
by integrating new data generated by the FAANG Consortium, 3) create a
FAANGMine user community that consists of students and scientists working
on genetics of domesticated animal species.
The first FAANGMine release (v1.1) integrates the reference genomes of cat,
cattle, chicken, dog, goat, horse, pig, sheep and water buffalo with a
variety of external data sources, including genes (NCBI, Ensembl), proteins
(UniProt), protein families and domains (InterPro), orthologs and paralogs
(EnsemblCompara, OrthoDB, TreeFam), pathways (KEGG, Reactome), interactions
(BioGRID, IntAct), Gene Ontology, variants and variant effects (Ensembl),
QTL (AnimalQTLdb) and publications (PubMed). We regret that due to a data
integration issue, pig variants and variant effects are not available in
this release; we are working to resolve the issue. Future releases will
include gene expression levels computed based on reference RNA-seq
datasets, and analyzed FAANG datasets with metadata (e.g. computed
regulatory elements and chromatin states).
Best regards,
Chris Elsik
--
Christine Elsik
Associate Professor
Divisions of Animal and Plant Sciences
S134-D Animal Sciences Research Center
920 East Campus Drive
University of Missouri
Columbia, MO 65211
phone: 573-884-7422
fax: 573-882-6827
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