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Researcher Tools, Services and Support

The purpose of this guide is to provide resources and information to the UMass Medical School community about the Library's research and scholarly communication services.

Gene

Gene integrates information from many sources, giving results that include nomenclature, RefSeqs, maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.

The NCBI Bookshelf contains a comprehensive resource, Gene Help: Integrated Access to Genes of Genomes in the Reference Sequence Collection, by Brown et al, to help better use the database, as well as understand all of the information available in a record.

BioProject (formerly Genome Project)

A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. The BioProject Database is a searchable collection of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation, and mapping projects for a cellular organism.

The BioProject Quick Start Guide can help you begin using this resource.

ClinVar

ClinVar aggregates the names of medical conditions with a genetic basis from such sources as SNOMED CT, GeneReviews, Genetic Home Reference, Office of Rare Diseases, MeSH, and OMIM®. ClinVar also aggregates descriptions of associated traits from Human Phenotype Ontology (HPO), OMIM, and other ontologies. Each source of information is tracked, and can be used in queries.

This is a new and evolving resource from NCBI. Keep an eye on it for changes and/or to add your input into how you think it should work.

Consensus CDS Protein Set (CCDS)

The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. Collaborators include:

Genes and Disease

Genes and Disease is a collection of articles that discuss genes and the diseases that they cause. Genetic disorders are organized by the parts of the body affected. 

Other Useful Tools

Gene Expression Omnibus (GEO) Resources

The Gene Expression Omnibus (GEO) is a public repository that archives and freely distributes high-throughput gene expression data submitted by the scientific community. Three separate tools make up GEO:

  • GEO Database - A public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted. Tools are provided to help users query and download experiments and curated gene expression profiles.
  • GEO Datasets - A database of curated gene expression DataSets, as well as original Series and Platform records in the GEO repository. Search by experiments of interest. DataSet records contain additional resources including cluster tools and differential expression queries.
  • GEO Profiles - A database of individual gene expression profiles from curated DataSets in the GEO repository. Search for specific profiles of interest based on gene annotation or pre-computed profile characteristics.

An extensive list of FAQs and a handout are available to understand how to use GEO.

Genetic Testing Registry

The Genetic Testing Registry (GTR) provides a central location for voluntary submission of genetic test information by providers.

BioSystems

A biosystem, or biological system, is a group of molecules that interact in a biological system. The BioSystems Database serves as a centralized repository of data, and also connects the different biosystem records with associated literature, molecular, and chemical data throughout the NCBI system.

How to use the BiosSystems Database.

Database of Genotypes and Phonotypes

The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies investigating the interaction of genotype and phenotype. Users can obtain controlled access to data, download public data, and contribute their own results to the database. 

See the tutorial for a thorough overview of how to best use this resource.