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The Magnesium Project

Volunteer Resources - Biology

Databases and Web Sites
IPRS, Inc.

http://www.iprsinc.org

Sites to use for search of general medical/biological research information.

 http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed

 http://www.ncbi.nlm.nih.gov/sites/entrez

 Sites to use for search of enzymes, proteins, etc.

http://www.ncbi.nlm.nih.gov/sites/entrez?db=Protein&itool=toolbar

www.expasy.com site

http://expasy.org/sprot/

 http://www.expasy.org/cgi-bin/sprot-search-de?DNA_methyltransferase

 http://www.uniprot.org

 http://spdbv.vital-it.ch/

http://spdbv.vital-it.ch/content.html

 Sites to use for Nutrition Data

USDA (United States Department of Agriculture)

http://fnic.nal.usda.gov/nal_display/index.php?info_center=4&tax_level=1&tax_subject=253

http://fnic.nal.usda.gov/nal_display/index.php?info_center=4&tax_level=1&tax_subject=257

 National Academy of Sciences and Institute of Medicine

http://www.livestrong.com/article/30837-minimum-daily-vitamin-mineral/

    Look up Daily Recommended Intakes (DRI) and Minimum Dietary Requirements (MDR)

http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed

Nutrition Resource Information
    Oregon State University - Micronutrient Information Center, posted by Jane Higdon, Ph.D. and others.

The Oregon State University Linus Pauling Micronutrient Information Center  has fact sheets about many of the vitamins and minerals here:  http://lpi.oregonstate.edu/infocenter/minerals/magnesium/

Food and Nutrition Information Center (FNIC) at the National Agricultural Library (NAL) for USDA.  Our Web site (http://fnic.nal.usda.gov ) provides many credible food and nutrition resources. 

You can find reports or lists of the foods containing magnesium on the USDA Nutrient Data Laboratory Nutrient List webpage (titled Reports by Single Nutrients):  http://www.ars.usda.gov/Services/docs.htm?docid=22114. This can also be accessed by clicking on “Food Composition” on our Web site.

You can view the reports sorted either alphabetically by food description (click on “A”) (https://www.ars.usda.gov/SP2UserFiles/Place/12354500/Data/SR24/nutrlist/sr24a304.pdf) or in descending order by nutrient content (click on “W”) (https://www.ars.usda.gov/SP2UserFiles/Place/12354500/Data/SR24/nutrlist/sr24w304.pdf) in terms of common household measures (e.g., one cup).

For more information on some of these specific nutrients, including many of the vitamins and minerals, please visit the National Institutes of Health Office of Dietary Supplements facts sheets webpage here:  http://ods.od.nih.gov/factsheets/Magnesium-HealthProfessional

To search for publications you can use AGRICOLA which is a primary source for agricultural information. From the NAL home page (http://www.nal.usda.gov/index.shtml)  click on “Search the NAL Catalog (AGRICOLA)” which is located on the right hand side of the page under “I Want To…”  Here is a direct link: http://agricola.nal.usda.gov/ .  For assistance using the database please refer to this page: http://agricola.nal.usda.gov/help/quicksearch.html .

KEGG Databases
Includes metabolic pathways, genomics, diseases, ligands, drugs, etc.
    http://www.genome.ad.jp/kegg

    http://www.genome.jp/kegg/kegg2.html - Encyclopedia - top level directory to all KEGG databases

    http://www.genome.jp/kegg/pathway.html

    KEGG – pathways for mineral metabolism – see e.g. http://www.kegg.jp/dbget-        bin/www_bget?cpd:C00305

    Biochemical pathways

Calcium Signaling
http://www.genome.jp/kegg/pathway/hsa/hsa04020.html

 MAPK Signaling (Mitogen Activated Protein Kinase) – most kinases are Mg activated 
http://www.genome.jp/kegg/pathway/hsa/hsa04010.html

 See also MAPK Pathway References:  http://www.genome.jp/kegg-bin/path_ref_list?pathway=04010

            See also Ortholog tables  http://www.genome.jp/kegg/ortholog/tab04010.html

See also: Receptor Tyrosine Kinases
See also: G Protein Coupled Receptors

     Calcium Channel Blocker Agents
        http://www.genome.jp/kegg/pathway/map/map07036.html

     Diseases
        http://www.genome.jp/kegg/pathway.html#disease

     5. Human Diseases Categories

 5.1 Neurodegenerative Disorders

 

Alzheimer's disease
Parkinson's disease
Amyotrophic lateral sclerosis (ALS)
Huntington's disease
Dentatorubropallidoluysian atrophy (DRPLA)
Prion disease

5.2 Infectious Diseases

 

Infectious diseases
Cholera
Epithelial cell signaling in Helicobacter pylori infection
Pathogenic Escherichia coli infection
New!

5.3 Metabolic Disorders

 

Type I diabetes mellitus
Type II diabetes mellitus
Maturity onset diabetes of the young

 Diabetes type I Reference List excerpt – as an example
http://www.genome.jp/kegg-bin/path_ref_list?pathway=04940

 PATHWAY Reference

ENTRY

04940

NAME

Type I diabetes mellitus

REFERENCE

PMID:9719467

AUTHORS

Rabinovitch A, Suarez-Pinzon WL.

TITLE

Cytokines and their roles in pancreatic islet beta-cell destruction and insulin-dependent diabetes mellitus.

JOURNAL

Biochem Pharmacol 55:1139-49 (1998)

REFERENCE

PMID:11507694

AUTHORS

Cox NJ, Wapelhorst B, Morrison VA, Johnson L, Pinchuk L, Spielman RS, Todd JA, Concannon P.

TITLE

Seven regions of the genome show evidence of linkage to type 1 diabetes in a consensus analysis of 767 multiplex families.

JOURNAL

Am J Hum Genet 69:820-30 (2001)

 =-=

An Example - Detailed list along with genetic and hsa pathway codes

   Pyruvate metabolism
        Lipoamide dehydrogenase deficiency

      Pyruvate metabolism [HSA:DLD] [PATH:hsa00620 hsa00020]

        /dbget-bin/www_bget?hsa+DLD
        /kegg-bin/mark_pathway_www?%40hsa00620/hsa:1738/cpd:C00256

     Pyruvate dehydrogenase deficiency
      Pyruvate metabolism [HSA:PDHA1] [PATH:hsa00620]

    Pyruvate carboxylase deficiency
      Pyruvate metabolism [HSA:PC] [PATH:hsa00620]

   Carbohydrate metabolism
    Glycogen storage disease
      Glycogen metabolism [HSA:G6PC GAA AGL GBE1 PYGL PFKM GYS2] [PATH:hsa00500 hsa00010]

    Galactosemia
      Galactose metabolism [HSA:GALT] [PATH:hsa00052]

    Fructose intolerance
      Fructose metabolism [HSA:ALDOB] [PATH:hsa00010]

   Lipid metabolism
    Gaucher disease
      Glycosphingolipid metabolism [HSA:GBA] [PATH:hsa00600]

    Tay-Sachs disease
      Globoside metabolism [HSA:HEXA] [PATH:hsa00603 hsa00604]

    Niemann-Pick disease
      Glycosphingolipid metabolism [HSA:SMPD1] [PATH:hsa00600]

    Fabry disease
      Glycolipid metabolism [HSA:GLA] [PATH:hsa00561 hsa00600 hsa00603]

 

1: Novartis Found Symp. 2002;247:91-101; discussion 101-3, 119-28, 244-52.

 

The KEGG database.
Kanehisa M.
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.

KEGG (http://www.genome.ad.jp/kegg/) is a suite of databases and associated software for understanding and simulating higher-order functional behaviours of the cell or the organism from its genome information. First, KEGG computerizes data and knowledge on protein interaction networks (PATHWAY database) and chemical reactions (LIGAND database) that are responsible for various cellular processes. Second, KEGG attempts to reconstruct protein interaction networks for all organisms whose genomes are completely sequenced (GENES and SSDB databases). Third, KEGG can be utilized as reference knowledge for functional genomics (EXPRESSION database) and proteomics (BRITE database) experiments. I will review the current status of KEGG and report on new developments in graph representation and graph computations.

Publication Types: Review

PMID: 12539951 [PubMed - indexed for MEDLINE]

 Other Databases

Pubmed – General biological/medical literature search

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed

Entrez – Literature

http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi

 Structural analysis

PDB - www.rcsb.org/pdb

MMDB at www.ncbi.nlm.nih.gov/Structure

SCOP www.scop.mrc-lmb.cam.ac.uk/scop

CATH www.biochem.ucl.ac.uk/bsm/cath_new

Swiss-Model (via ExPASy)  http://www.expasy.ch/swissmod/SWISS_MODEL.html

 Pharmaceutical Compounds / Ligands / Agonists / Antagonists, etc. –IUPHAR

            Source: www.IUPHAR-db.org/DATABASE/

 Sequencing

            BLAST and BLASTP – NIH

http://ncbi.nih.gov/Structure/MISC/linking.html

http://www.ncbi.nlm.nih.gov/BLAST/

The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

    Compare multiple sequences using 

Dotlet  at www.ch.embnet.org

Lalign   www.ch.embnet.org/software/LALIGN_form.html

 Proteomics

            PKR – Protein Kinase Resource – Univ. of California at San Diego, LaJolla

 Genomics

OMIM  Online Mendelian Inheritance in Man http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM

Welcome to OMIM, Online Mendelian Inheritance in Man. This database is a catalog of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere, and developed for the World Wide Web by NCBI, the National Center for Biotechnology Information. The database contains textual information and references. It also contains copious links to MEDLINE and sequence records in the Entrez system, and links to additional related resources at NCBI and elsewhere.

See Volunteer Resource for Modeling

Chemical Databases

American Chemical Society – have to pay to get full articles, but can get abstracts and citations and go to library to copy the full article.

http://chemport.cas.org/cgi-bin/sdcgi

    Pharmaceutical Compounds / Ligands / Agonists / Antagonists, etc. –IUPHAR

Source: www.IUPHAR-db.org/DATABASE/


 Disease Codes - ICD-9 and ICD-10 (Morbidity and Mortality)
            http://www.cdc.gov/nchs/icd.htm

 Medical/Laboratory Procedure Codes
            Some of the relevant procedure codes (HCPC) are:
 
Total calcium 82310
Magnesium 83735
Serum sodium 84295
Serum potassium 84132
Serum albumin 82040
Total protein 84155

 

Journal Resource:
Magnesium Research: Vol.23, n°1, 2010
 On-line Newsletter alert from John Libbey Eurotext. Web Version http://www.jle.com/e-docs/00/04/55/8A/liste_jle_news_mrh_html.md

   

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Revised: March 15, 2014