SNP-Ontology full
type: Ontology
imports: amino-acid.owl
imports: SO
comment: A domain representation of genomic variations.
version info: version: full 1.6 release: 14/03/2017
creator: author: Adrien Coulet contact: adrien dot coulet at loria dot fr Loria - Inria NGE, University of Lorraine
comment: TODO: Take into account alternative splicing.
comment: Consistency checked by Pellet 2.0
comment: modifications 03/03/2017: - repair of the missing link to Sequence Ontology

isVariantIn
type: ObjectProperty
inverse of: regionHasVariant
domain: variant
range: Class
  union of: genomic region
  union of: protein region
  union of: transcript region
comment: A variant belongs to a region.

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

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

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

aa variation
type: Class
subclass of: observed variation
subclass of: Restriction
  on property: hasVariantSequence
  all values from: aa sequence
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

assembly
type: Class
subclass of: genomic region
comment: A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. Source: SO

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

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

cnvr
type: Class
subclass of: repeated segment
comment: copy number variable region Cf. Redon et al. Nature, 444, 23 Nov. 2006

coding variant
type: Class
equivalent class: Class
  intersection of: variant
  intersection of: Restriction
    on property: hasPosition
    all values from: Restriction
      on property: isPositionIn
      all values from: Restriction
        on property: isSequenceIn
        all values from: cds
disjoint with: non coding variant
comment: Their are variants located in coding sequence ie in cds. = variants located in translated codons. NB: Coding sequence can not be simplify to exons. It is exon minus 5'UTR and 3'UTR.

codon
type: Class
subclass of: genomic region
subclass of: transcript 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.

contig
type: Class
subclass of: assembly
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

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

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/

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

exon
type: Class
subclass of: genomic region
subclass of: transcript region
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

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

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

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

haplotype
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: hasHaplotypeMember
    all values from: haplotype member
  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

haplotype block
type: Class
subclass of: Thing
subclass of: Restriction
  on property: isASequenceComposedOf
  all values from: haplotype member
comment: A set of consecutive sites between which there is little or no evidence of historical recombination.

hapmap
type: Class
subclass of: generic variant db
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/

hgvbase
type: Class
subclass of: generic variant db
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/

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

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).

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

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..

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

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

nucleotide
type: Class
subclass of: Thing
subclass of: Restriction
  on property: composesSequence
  all values from: nucleotide sequence
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

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

nucleotide variation
type: Class
subclass of: observed variation
subclass of: Restriction
  on property: hasVariantSequence
  all values from: nucleotide sequence
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

observed allele
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: hasVariantAlleleSequence
    all values from: nucleotide sequence
  intersection of: Restriction
    on property: isObservedIn
    all values from: variant
comment: An allele observed in someone, or ina group for an identified variant. Used to distinguish variant definition (observed_variation) from genotyping in patient or in haplotype.

observed variation
type: Class
equivalent class: Class
  intersection of: Class
    union of: aa variation
    union of: nucleotide variation
  intersection of: Restriction
    on property: hasVariantSequence
    cardinality: 2
subclass of: Thing
subclass of: Restriction
  on property: isObservedIn
  some values from: variant
disjoint with: sequence
disjoint with: sequence position
disjoint with: variant
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.

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

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

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/

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

promotor
type: Class
subclass of: regulatory region
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

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

protein conserved domain
type: Class
subclass of: protein region
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

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

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

reference variant
type: Class
subclass of: variant
subclass of: Restriction
  on property: hasPosition
  all values from: Restriction
    on property: hasSubSequence
    some values from: nucleotide sequence
subclass of: Restriction
  on property: hasPosition
  all values from: Restriction
    on property: hasSubSequence
    some values from: Class
      complement of: aa sequence
subclass of: Restriction
  on property: hasAAVariation
  cardinality: 0
subclass of: Restriction
  on property: hasNucleotideVariation
  cardinality: 1
subclass of: Restriction
  on property: hasPosition
  cardinality: 1
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

regulatory region
type: Class
subclass of: genomic region
comment: A DNA sequence that controls the expression of a gene. Source: SO

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

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

sequence
type: Class
disjoint with: sequence position
disjoint with: variant
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.

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

sequence position
type: Class
subclass of: Thing
subclass of: Class
  union of: Restriction
    on property: hasSubSequence
    all values from: sequence
  union of: Restriction
    on property: hasVariant
    all values from: variant
subclass of: Restriction
  on property: isPositionIn
  all values from: sequence
disjoint with: variant
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.

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

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

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

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

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

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/

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

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

utr 5 prime
type: Class
subclass of: genomic region
subclass of: transcript region
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

variant
type: Class
equivalent class: Class
  union of: Class
    intersection of: Restriction
      on property: hasPosition
      all values from: Restriction
        on property: hasSubSequence
        some values from: aa sequence
    intersection of: Restriction
      on property: hasAAVariation
      cardinality: 1
  union of: Class
    intersection of: Restriction
      on property: hasPosition
      all values from: Restriction
        on property: hasSubSequence
        some values from: nucleotide sequence
    intersection of: Restriction
      on property: hasNucleotideVariation
      cardinality: 1
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.

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

comment: unnecessary

comment: hasPosition only sequence_position AND hasVariation only observed_variation [new definition make it unecessary]

comment: unnecessary

comment: unnecessary