Author contact: Yu Lin (linikujp@gmail.com)
It is the ontology used to model the scientific investigation, especially Genome-Wide Association Study (GWAS), to find out genetic susceptibility factor to disease, such as Diabetes. It models the genetic varaints, polymorphisms, statistical measurement, populations and other elements that are essential to determine a genetic susceptibility factor in GWAS study. It must be used with other two ontologies, in the case of Diabetes, :Ontology of Geographical Region (OGR) and Ontology of Glucose Metabolism Disorder (OGMD) .
Ontology for Disease Genetic Investigation
The modeling documents including two papers: 1. Ontology of Genetic Susceptibility Factors to Diabetes Mellitus (OGSF-DM) http://www.academia.edu/213769/Ontology_of_Genetic_Susceptibility_Factors_to_Diabetes_Mellitus_OGSF-DM_ 2. Ontology driven modeling for the knowledge of genetic susceptibility to disease. http://www.ncbi.nlm.nih.gov/pubmed/19628970
ABI 3100 Avant Genetic Analyzer (Applied Biosystems)
Substances that are recognized by the immune system and induce an immune reaction.(MeSH)
P values were corrected for multiple tests using the Benjamini-Hochberg method.
The role which is taken by biological things(such as moleculars, cells) when they involed in a biological process, such as auto immune process, etc. its different with function.examples: a protein plays antigen role in an autoimmune process.
the technology used for dealing with biological things,such as molecular, virus, animals, gene,in molecular biology, immunology fields. you can say the wet experiment technologies.the objects of biological techniques are biological things, and the result from biological techniques is biological. Thus, the measurement of body, glucose tolerance test are not biological techniques.
frequncy of the observed genetic factors in different group of the studied population. REF:Association of the T-cell regulatory gene CTLA4 with susceptibility to autoimmune disease or: allele frequncy?
For example, a mutation in X gene cause the Y disease, then, they hold a causation relationship.
is the divided group of the study population;
Comments: This universal has also been called ‘endurant’.
Df: An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity, and has no temporal parts. Examples: a heart, a person, the color of a tomato, the mass of a cloud, a symphony orchestra,the disposition of blood to coagulate, the lawn and atmosphere in front of the White House.
Comments: This universal is also sometimes referred to by the name ‘property’, ‘trope’ or ‘mode’.
Df: The continuant entities that inhere in or are born by other entities. Examples: the mass of a cloud, the color of a tomato, the smell of mozzarella, the liquidity of blood, the disposition of fish to decay, the role of being a doctor, the function of the heart to pump blood. (BFO)
original paper which study the disease and gene relationship.
the instance is gene name which is written in the article.
generally Product means functional product, maybe sequence product?
It is a term used to describe the total genetic information(DNA content) in human cells.
Allele which is shared among sibs is identical by desent(idb),which means, this allele comes from the same person of parents.
Allele which is shared among sibs is identical by state, which means, the allele may comes from both of their parents.
Comments: This universal has also been called ‘substantial entity’.
Df: The continuant entities that are the bearers of qualities and realizables; entities in which other entities inhere and which themselves cannot inhere in anything. Examples: an organism, a heart, a symphony orchestra, a chair, the bottom right portion of a human torso, a leg, a person, a symphony orchestra, the lawn and atmosphere in front of the White House.
Definition: Investigative techniques used in pre-clinical and clinical research, epidemiology, chemistry, immunology, genetics, etc. They do not include techniques specifically applied to DIAGNOSIS; THERAPEUTICS; anesthesia and analgesia; SURGICAL PROCEDURES, OPERATIVE; and DENTISTRY. (MeSH)
is the locus defined by the linkage study based on LOD scores of the genetic markers
Maximum-likelihood LOD score(MLS). MLS may be interpreted, as the ratio of the probability that a given obeservational outcome would occur if the trait and marker loci were linked to the probability that it would occur if they were unlinked. (Gustavo Maroni, 2001, Molecular and Genetic Analysis of Human Traits, p46)
STR or microsatellite DNA has repeating units of 2 to 5 bases. Such as simple repetitive elements, (CA)n, (AAT)n, (GATA)n, also called simple sequence DNA, existing in thousands of loci in the human genome.
Definition: Minisatellite DNA are sequences in which repeating units occur in blocks of up to 50kb. Repeating units are between 10 and 200 bases in length.
also VNTR, Variable number tandem repeats
any role when it is not biological role; such as a SNP's role as a maker in associate study. Or, this role is not comes from the biological things function, but, is assigned by human being.
the technology used for dealing with non-biological things, such as: numbers, data,etc.
Obeserved_Relationship is the relationship between a genetic things with disease or related traits, which is observed by linkage or association study in genetic studies field. for example: related, susceptibility, association, and so on.
is the population studied in case-control, when the sample is the single individual, but not family,nor trios.nor pairs
Proband is the first affected family member who seeks medical attention for a genetic disorder.(wikipedia)
Df: an occurrent entity that exists in time by occurring or happening, has temporal parts, and always depends on some SNAP entity or entities. Examples: the life of an organism, the process of meiosis, the course of a disease, the flight of a bird, the process of cell division.
all the subclass holds the data, for example, instance of age is 40, instance of Odds_Ratio is 1.47
Definition: Relative risk index (lamda),express the degree to which a relative of a patient is more likely than a non relative to suffer a given syndrome.(Gustavo Maroni, 2001, Molecular and Genetic Analysis of Human Traits, p38 )
the localization relationship between genomic sequences. for example:a genetic marker is contained in a gene. or a haplotype is contained in a gene. (get idea from gdb)
he supporting evidence has classified group when it states the classified group with the OR(for example), sometimes the paper didn't declare the classified group with the supporting evidence, then we don't not need to list out the classified group.
According to the classification of WHO, Type 1 Diabetes A is autoimmune Diabetes type.
denaturing high-performance liquid chromatography [dHPLC]
haplotype-tag single nucleotide polymorphisms
A genome-wide search for human non-insulin-dependent (type 2) diabetes genes reveals a major susceptibility locus on chromosome 2
An Autosomal Genomic Scan for Loci Linked to Type II Diabetes Mellitus and Body-Mass Index in Pima Indians
Association of genetic variations near P2 promoter of the hepatocyte nuclear factor-4alpha gene and insulin secretion index in Thais.
Common variants of the novel type 2 diabetes genes, CDKAL1 and HHEX/IDE, are associated with decreased pancreatic {beta}-cell function
Finland-United States Investigation of NIDDM Genetics study
Genomewide Search for Type 2 Diabetes Susceptibility Genes in Four American Populations
LPIN2 is associated with type 2 diabetes, glucose metabolism and body composition
Linkage of Type 2 Diabetes Mellitus and of Age at Onset to a Genetic Location on Chromosome 10q in Mexican Americans
MODY is a clinically and genetically heterogeneous form of nonketotic diabetes that presents before age 25 years, usually in nonobese, asymptomatic, hyperglycemic individuals.
maturity-onset diabetes of the young (MODY)-1
1999 Mar
2007 Sep
1996 Jun
many loci shows in UniSTS, but GPD1L is contained by D3S2432 in Ensembl's map view
hepatocyte nuclear factor-4 alpha (HNF4 alpha),