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July 20, 2006
Genetic and Genomic Information from NLM and the Genetics Home Reference (GHR) (Omics Series, 9)
The United States government, in general, and the National Library of Medicine, in particular, have taken leading roles in providing information, tools, resources, and training for biomedical and life sciences researchers and clinicians, including omics researchers. Very few people make use of the full range of resources they provide. Today, we will survey a few of the broad omics resources available, and then spend a little more time on a specific resource that tends to have information for both dental researchers and clinicians.
This is probably a good time to again mention the forthcoming short course on campus about NCBI resources.
National Center for Biotechnology Information: Short Course, September 7,2006 (Hosted by the Program in Bioinformatics, Department of Human Genetics & Taubman Medical Library): http://www.hg.med.umich.edu/ncbi/
In this course, you will see overviews and demonstrations of how to use many of the databases listed below. NLM and NCBI provide an astonishing number of databases. From their main databases page, you can browse a list of many of their offerings in this area.
NLM: NCBI: Entrez: All Databases: http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi?itool=toolbar
Here are a few of the specific databases, just to give you an idea of what you might find.
3D Domains: domains from Entrez Structure: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Domains
BLAST (Basic Local Alignment Search Tool finds regions of local similarity between sequences): http://www.ncbi.nlm.nih.gov/BLAST/
Cancer Chromosomes: cytogenetic databases: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=CancerChromosomes
CDD: conserved protein domain database: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd
Gene: gene-centered information: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene
Genome Project: genome project information: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj
Genome: whole genome sequences: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome
GENSAT: gene expression atlas of mouse central nervous system: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gensat
GEO DataSets: experimental sets of GEO data: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gds
GEO Profiles: expression and molecular abundance profiles: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=geo
HomoloGene: eukaryotic homology groups: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene
Nucleotide: sequence database (GenBank): http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide
OMIA: online Mendelian Inheritance in Animals: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=omia
OMIM: online Mendelian Inheritance in Man: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM
PopSet: population study data sets: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PopSet
Probe: sequence-specific reagents: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=probe
Protein: sequence database: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein
PubChem BioAssay: bioactivity screens of chemical substances: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pcassay
PubChem Compound: unique small molecule chemical structures: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pccompound
PubChem Substance: deposited chemical substance records: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pcsubstance
SNP: single nucleotide polymorphism: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=snp
Structure: three-dimensional macromolecular structures: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure
Taxonomy: organisms in GenBank: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Taxonomy
UniGene: gene-oriented clusters of transcript sequences: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene
UniSTS: markers and mapping data: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unists
Another source they provide is the Human Genome. This resource contains an entirely different list of great tools and resources. I encourage you to explore the Human Genome more on your own.
Human Genome (an integrated, one-stop, genomic information infrastructure for biomedical researchers): http://www.ncbi.nlm.nih.gov/genome/guide/
Last, for today, but not least, is the Genetics Home Reference (GHR). The GHR serves as a bridge between the technical information for researchers and the consumer or general public. It includes information on the correspondence between specific genes and diseases, diagnostic signs/symptoms, an much more. Although the information is for consumers, it can still be fairly technical. It includes a handbook and glossary, which helps, and provides information at a level that can also be useful for the clinician. In addition, they include a list of resources about genetic conditions specifically for clinicians.
NLM: Genetics Home Reference: http://ghr.nlm.nih.gov/
GHR: Genetics Resources for Clinicians and Health Professionals: http://ghr.nlm.nih.gov/ghr/resource/clinicians
Among their newest topics on conditions, you'll find Dentinogenesis Imperfecta and Amelogenesis Imperfecta. Among their new pages on specific genes, you'll find amelogenin (amelogenesis imperfecta 1, X-linked), dentin sialophosphoprotein (DSPP), enamelin, and matrix metallopeptidase 20 (MMP20 or enamelysin). They have also recently added information on a number of specific genes that are associated with the Charcot Marie Tooth Disease. Here is a sampling of pages on dental-related conditions and genes.
CONDITIONS:
Condition: Achondrogenesis: http://ghr.nlm.nih.gov/condition=achondrogenesis
Condition: Amelogenesis Imperfecta: http://ghr.nlm.nih.gov/condition=amelogenesisimperfecta
Condition: Dentinogensis imperfecta: http://ghr.nlm.nih.gov/condition=dentinogenesisimperfecta
Condition: Fibrodysplasia ossificans progressiva: http://ghr.nlm.nih.gov/condition=fibrodysplasiaossificansprogressiva
Condition: Greig cephalopolysyndactyly syndrome: http://ghr.nlm.nih.gov/condition=greigcephalopolysyndactylysyndrome
Condition: Platyspondylic lethal skeletal dysplasia, Torrance type: http://ghr.nlm.nih.gov/condition=platyspondyliclethalskeletaldysplasiatorrancetype
Condition: Sotos syndrome: http://ghr.nlm.nih.gov/condition=sotossyndrome
GENES:
Gene: DNM2: dynamin 2: http://ghr.nlm.nih.gov/gene=dnm2
Gene: MMP20: matrix metallopeptidase 20 (enamelysin): http://ghr.nlm.nih.gov/gene=mmp20
Gene: SH3TC2: SH3 domain and tetratricopeptide repeats 2: http://ghr.nlm.nih.gov/gene=sh3tc2
Gene: YARS: tyrosyl-tRNA synthetase: http://ghr.nlm.nih.gov/gene=yars
Posted by pfa at July 20, 2006 02:16 PM