SNP-Ontology full
type: Ontology
comment: Unconsistency checked by RacerPro .1.9.0 the 02/14/2007
version info: 16 Jan 2007 modification: for a compatibility with the Instance Store, 2 modification have been done - cardinalities on datatype in "sequence_position" concept have been removed - sufficiant condition in the "sequence_position" definition have been transformed in necessary conditions - suppression of hte definition line of codon saying that a codon hasLengt exactly 3
comment: A domain representation of genomic variations.
version info: version: full 1.3.1 release: 02/14/2007 author: Adrien Coulet contact: coulet at loria dot fr University of Nancy
imports: amino-acid.owl
version info: TODO: Take into account alternative splicing.
comment: Assertion with the Instance Store succesfully tested on v1.2 the 01/17/2007
version info: TODO: comment properties
version info: TODO: add add variation type information (substitution, insertion, deletion, indel, etc.)
version info: 09 Oct 2006 modifications: - addition of the isPositionIn object property (inverse of: presentsPosition, domain: sequence_position, range: sequence) - addition of this new property in the definition of the sequence_position concept

translation start
type: Class
comment: The first codon translated: ATG.
subclass of: codon

codon
type: Class
subclass of: transcript region
subclass of: genomic region
comment: A codon is a sequence of three nucleotides that codes for an amino acid residue in a protein depending to the genetic code.

inserm snp
type: Class
subclass of: locus specific variant db
comment: A private database owned by the INSERM embedding genomic variation (with no known effect) located on the LDLR gene (Chr19).

locus specific variant db
type: Class
subclass of: variant database
comment: There are specialized databases on genomic variations. i.e. specialized on one specific locus, on one specific disease, etc..

exon
type: Class
comment: An exon is any region of DNA within a gene, that is transcribed to the final messenger RNA (mRNA) molecule, rather than being spliced out from the transcribed RNA molecule. Exons of many eukaryotic genes interleave with segments of non-coding DNA (introns). The term "exon" was coined by Walter Gilbert in 1978. Definition from http://en.wikipedia.org/wiki/Exon
subclass of: transcript region
subclass of: genomic region

transcript region
type: Class
subclass of: Restriction
  on property: hasSequence
  all values from: nucleotide sequence
subclass of: Restriction
  all values from: transcript region
  on property: isPartOf
subclass of: Thing
comment: Is one portion of a, or an enire, transcript (unmature) or mRNA (mature).
disjoint with: protein region

genomic region
type: Class
disjoint with: protein region
subclass of: Thing
subclass of: Restriction
  all values from: nucleotide sequence
  on property: hasSequence
subclass of: Restriction
  all values from: genomic region
  on property: isPartOf
comment: Is one portion of a, or the whole, genome.

genome
type: Class
subclass of: genomic region
comment: A whole genome. Ex: The human genome The whole hereditary information of an organism that is encoded in the DNA (or, for some viruses, RNA). This includes both the genes and the non-coding sequences of the DNA. Definition from http://en.wikipedia.org/wiki/Genome

haplotype
type: Class
subclass of: Thing
subclass of: Restriction
  on property: isTaggedBy
  all values from: tag snp
subclass of: Restriction
  cardinality: 1
  on property: isTaggedBy
equivalent class: Class
  intersection of: Restriction
    all values from: haplotype member
    on property: hasHaplotypeMember
  intersection of: Restriction
    on property: isHaplotypeForPeopleOf
    all values from: population
comment: Haplotype is a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated. Source: wikipedia

variant
type: Class
disjoint with: sequence
disjoint with: database
disjoint with: sequence position
disjoint with: observed variation
equivalent class: Class
  comment: hasPosition only sequence_position AND hasVariation only observed_variation [new definition make it unecessary]
  union of: Class
    intersection of: Restriction
      on property: hasNucleotideVariation
      cardinality: 1
    intersection of: Restriction
      on property: hasPosition
      all values from: Restriction
        on property: hasSubSequence
        some values from: nucleotide sequence
  union of: Class
    intersection of: Restriction
      cardinality: 1
      on property: hasAAVariation
    intersection of: Restriction
      all values from: Restriction
        on property: hasSubSequence
        some values from: aa sequence
      on property: hasPosition
comment: A variant is a genomic variation description at the nucleotide or proteic level. It is defined by a position on a sequence. This sequence could be either a nucleotide sequence if the observed variation is a nucleotide variation, either a residue change if the observed variation is an residue variation. At the precised position is observed a variation (the observed variation) in the sequence respectively to a "reference" (or "known") sequence.

protein
type: Class
subclass of: protein region
comment: Proteins are large organic compounds made of amino acids arranged in a linear chain.

protein region
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: aa sequence
  on property: hasSequence
subclass of: Restriction
  on property: isPartOf
  all values from: protein region
comment: Is one portion of a, or an entire protein.
disjoint with: transcript region
disjoint with: genomic region

nucleotide
type: Class
comment: The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed) MESH:D.09.203.408.620
subclass of: Restriction
  on property: composes
  all values from: nucleotide sequence
subclass of: Thing

nucleotide sequence
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: isComposedOf
    all values from: nucleotide
  intersection of: sequence
comment: A sequence composed of one or several nucleotides. Ex: a chromosome, a gene, an exon, etc.
disjoint with: aa sequence

omim
type: Class
subclass of: generic variant db
comment: This database is a catalog of human genes and genetic disorders. It embeds information about allelic variations involved in this disorders. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM

generic variant db
type: Class
subclass of: variant database
comment: There are generic (not specialized) databases on genomic variations.

cds
type: Class
comment: It's the coding DNA sequence, starting from ATG (translation start) to the stop codon.
subclass of: genomic region

sequence
type: Class
comment: The sequence concept represents something that could be a organized succession of nucleotide or amino-acid and then could be divided in nucleotide sequences and amino-acid sequences. A sequence could be associated to its corresponding entry in a sequence database.
disjoint with: observed variation
disjoint with: database
disjoint with: sequence position
disjoint with: variant

aa sequence
type: Class
equivalent class: Class
  intersection of: sequence
  intersection of: Restriction
    on property: isComposedOf
    all values from: amino acid
disjoint with: nucleotide sequence
comment: A sequence composed of one or several amino-acids. Ex: a protein

ncbi nucleotide
type: Class
subclass of: sequence database
comment: Its the subdivision of GenBank embedding nucleotide sequences. Query it from NCBI web site at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide

sequence database
type: Class
comment: There are biological databases embedding data about sequences (nucleotide or proteic sequences).
subclass of: database

ucl ldlr
type: Class
subclass of: locus specific variant db
comment: A public database on mutations and polymorphisms of the LDLR gene. http://www.ucl.ac.uk/fh/

contig
type: Class
comment: In shotgun DNA sequencing projects, a contig (from contiguous) is a set of overlapping DNA segments derived from a single genetic source. A contig in this sense can be used to deduce the original DNA sequence of the source. This meaning of contig is in accordance with the original definition by Staden [1979]. Defintion from http://en.wikipedia.org/wiki/Contig
subclass of: genomic region

transcript
type: Class
subclass of: transcript region
comment: There are first products of transcription, before the splicing.

population
type: Class
comment: A group of indivdual.
subclass of: Thing
subclass of: Restriction
  all values from: haplotype
  on property: presentsHapoltype

promotor
type: Class
comment: A promoter is a DNA sequence that enables a gene to be transcribed. The promoter is recognized by RNA polymerase, which then initiates transcription. Defintion from http://en.wikipedia.org/wiki/Promotor
subclass of: genomic region

sequence position
type: Class
disjoint with: variant
disjoint with: database
disjoint with: sequence
disjoint with: observed variation
subclass of: Restriction
  all values from: sequence
  on property: isPositionIn
subclass of: Class
  union of: Restriction
    all values from: sequence
    on property: hasSubSequence
  union of: Restriction
    all values from: variant
    on property: hasVariant
subclass of: Thing
comment: It is a position on a sequence. Then it embeds a begin start position and an end. It should be describing the position of a subsequence in a larger sequence or the position of a variation in a sequence. NB: for a SNP the start and the stop position are the same. The start position is the first nucleotide (respectivly residue) after the 5' flanking sequence, and the stop position is the position before the first nucleotide of the 3' flanking sequence.

database
type: Class
comment: Databases are biological data sources publicly available or not.
disjoint with: sequence position
disjoint with: observed variation
disjoint with: sequence
disjoint with: variant

observed variation
type: Class
subclass of: Thing
subclass of: Restriction
  on property: isObservedIn
  some values from: variant
disjoint with: sequence
disjoint with: variant
disjoint with: database
disjoint with: sequence position
comment: It is the variation (of nucleotides or of residues) observed between the 2 patients (reference sequence and the alternative sequence - if it's possible to talk about a "reference") when a genomic variation is described. Ex: A>C, CT>A, Ser>Thr, etc.
equivalent class: Class
  intersection of: Class
    union of: nucleotide variation
    union of: aa variation
  intersection of: Restriction
    on property: hasVariantSequence
    cardinality: 2

intron
type: Class
subclass of: genomic region
comment: Introns are sections of DNA that will be spliced out after transcription, but before the RNA is used. Definition from http://en.wikipedia.org/wiki/Intron

variant database
type: Class
subclass of: database
comment: There are biological databases embedding data about genomic variations.

repeated segment
type: Class
comment: A repeated segment is a genome portion where the sequence displays some repeatitve patterns (repeatitive sequences as satellites, microsatellites, ALU repeats, etc.)
subclass of: genomic region

pharmgkb
type: Class
subclass of: generic variant db
comment: PharmGKB curates information that establishes knowledge about the relationships among drugs, diseases and genes, including their variations and gene products. http://www.pharmgkb.org/

inserm mut
type: Class
comment: A private database owned by the INSERM embedding mutation located on the LDLR gene (Chr19) known to be involved in familial hypercholesterolemia.
subclass of: locus specific variant db

utr 3 prime
type: Class
comment: 3'UTR transcripted untranslated region in 3' In mRNA, anything beyond this stop codon is part of the three prime untranslated region.
subclass of: transcript region
subclass of: genomic region

dna sequence
type: Class
disjoint with: rna sequence
subclass of: nucleotide sequence
comment: A DNA sequence i.e. an ACTG composed nucleotide sequence (at least one nucleotide). Ex: a chromosome, a gene, an exon, etc.

rna sequence
type: Class
subclass of: nucleotide sequence
disjoint with: dna sequence
comment: A RNA sequence i.e. an ACTU composed nucleotide sequence (at least one nucleotide). Ex: an mRNA

protein domain
type: Class
subclass of: protein region
comment: A structural domain ("domain") is an element of overall structure that is self-stabilizing and often folds independently of the rest of the protein chain. Definition from http://en.wikipedia.org/wiki/Structural_domain

utr 5 prime
type: Class
comment: 5' UTR: The five prime untranslated region (5' UTR) is a particular section of messenger RNA (mRNA). It precedes the translation initiation site of the gene, bounded on the 5' end by the start of transcription and on the 3' end by the start codon. Definition from http://en.wikipedia.org/wiki/5%27_UTR
subclass of: genomic region
subclass of: transcript region

chromosome
type: Class
subclass of: genomic region
comment: A chromosome is a large macromolecule into which DNA is normally packaged in a cell. Minimally, it is a very long, continuous piece of DNA (a single DNA molecule), which contains many genes, regulatory elements and other intervening nucleotide sequences. Defintion from http://en.wikipedia.org/wiki/Chromosome

hgvbase
type: Class
comment: A catalog of normal human gene and genome variation, useful as a research tool to help define the genetic component of human phenotypic variation. http://hgvbase.cgb.ki.se/
subclass of: generic variant db

organism
type: Class
comment: An organism. Ex: Homo spaiens, Escherischia Coli, Arabidopsis Thaliana, etc.

umd ldlr
type: Class
comment: A public database on mutations and polymorphisms of the LDLR gene. http://www.umd.be:2078/
subclass of: locus specific variant db

mature mrna
type: Class
subclass of: transcript region
comment: Messenger Ribonucleic Acid (mRNA) is RNA that encodes and carries information from DNA during transcription to sites of protein synthesis to undergo translation in order to yield a gene product. Mature messenger RNA, often abbreviated as mature mRNA is a eukaryotic RNA transcript that has been spliced and processed and is ready for translation in the course of protein synthesis. Defintions from http://en.wikipedia.org/wiki/Mrna

hapmap
type: Class
comment: A public resource that will help researchers find genes associated with human disease and response to pharmaceuticals by providing data about human haplotypes. http://www.hapmap.org/
subclass of: generic variant db

terminator
type: Class
comment: A terminator marks the end of a gene on the DNA for transcription. Defintition from http://en.wikipedia.org/wiki/Terminator
subclass of: genomic region

dbsnp
type: Class
subclass of: generic variant db
comment: dbSNP is the SNP database of the NCBI. Any individual is a particular version of dbSNP. Query it at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=snp ; also downloadable at ftp://ftp.ncbi.nih.gov/snp/

protein conserved domain
type: Class
comment: Proteins can be grouped together in families where all members have the same, or similar, function and are descended from a common ancestor. Proteins from the same family are usually composed of highly conserved sequence segments separated by regions of different lengths and little sequence similarity. These conserved sequence segments, called motifs, are typically 6-30 aa long and correspond to active sites, substrate or ligand binding sites, and structurally important segments of proteins. Defintion from Shmuel Pietrokovski
subclass of: protein region

reference variant
type: Class
subclass of: Restriction
  comment: unnecessary
  all values from: Restriction
    some values from: nucleotide sequence
    on property: hasSubSequence
  on property: hasPosition
subclass of: Restriction
  cardinality: 0
  on property: hasAAVariation
subclass of: Restriction
  cardinality: 1
  comment: unnecessary
  on property: hasPosition
subclass of: Restriction
  on property: hasNucleotideVariation
  comment: unnecessary
  cardinality: 1
subclass of: variant
subclass of: Restriction
  all values from: Restriction
    some values from: Class
      complement of: aa sequence
    on property: hasSubSequence
  on property: hasPosition
comment: Because one genomic variation could be represented in diferrent way (e.g. positionnned on different sequence, represented at the nucleotide or proteic level, etc.), several variant may refer to the same entity ; tit is interesting to have a reference variant. In our point of view, the reference variant is the one described at the genomic level on the complete chromosome sequence (of the current genome assembly). Ex: on the NC_000019.8 sequence

aa variation
type: Class
disjoint with: nucleotide variation
comment: It is the variation of residues observed between the 2 patients (reference sequence and the alternative sequence - if it's possible to talk about a "reference") when a genomic variation is described at the proteic level. Ex: Ser>Thr
subclass of: observed variation
subclass of: Restriction
  all values from: aa sequence
  on property: hasVariantSequence

nucleotide variation
type: Class
subclass of: Restriction
  on property: hasVariantSequence
  all values from: nucleotide sequence
subclass of: observed variation
comment: It is the variation of nucleotides observed between the 2 patients (reference sequence and the alternative sequence - if it's possible to talk about a "reference") when a genomic variation is described at the nucleotide level. Ex: A>C
disjoint with: aa variation

translation stop
type: Class
comment: The stop codon: UAA or UAG or UAA for the human genetic code.
subclass of: codon

strand
type: FunctionalProperty
comment: Forward (+ or from 5' to 3' ) or backward (- or from 3' to 5').
type: DatatypeProperty
domain: nucleotide variation

populationSize
type: FunctionalProperty
range: int
type: DatatypeProperty
comment: Number of person included in the population.
domain: population