SNP-Ontology full
type: Ontology
imports: amino-acid.owl
imports: sequence
comment: A domain representation of genomic variations.
comment: Unconsistency checked by Pellet 2.0
version info: TODO: Take into account alternative splicing.
version info: version: full 1.6 release: 01/15/2009 author: Adrien Coulet contact: adrien dot coulet at loria dot fr University of Nancy
version info: modifications 01/15/2009: - fixation of some bugs

haplotype
type: Class
comment: Haplotype is a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated. Source: wikipedia
equivalent class: SO_0001024
equivalent class: snpo resource:arc8c8db8

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

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

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

genomic region
type: Class
comment: Is one portion of a, or the whole, genome.
subclass of: Thing
subclass of: snpo resource:arc8c8db41
subclass of: snpo resource:arc8c8db42
disjoint with: protein region

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 region
type: Class
comment: Is one portion of a, or an entire protein.
subclass of: Thing
subclass of: snpo resource:arc8c8db29
subclass of: snpo resource:arc8c8db30
disjoint with: transcript region
disjoint with: genomic region

population
type: Class
comment: A group of indivdual.
subclass of: Thing
subclass of: snpo resource:arc8c8db2

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

observed allele
type: Class
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.
equivalent class: snpo resource:arc8c8db3

nucleotide sequence
type: Class
equivalent class: snpo resource:arc8c8db59
disjoint with: aa sequence
comment: A sequence composed of one or several nucleotides. Ex: a chromosome, a gene, an exon, etc.

variant
type: Class
disjoint with: sequence
disjoint with: database
disjoint with: sequence position
disjoint with: observed variation
equivalent class: snpo resource:arc8c8db13
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
comment: Proteins are large organic compounds made of amino acids arranged in a linear chain.
subclass of: protein region

assembly
type: Class
comment: A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. Source: SO
subclass of: genomic region
equivalent class: SO_0000353

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
disjoint with: dna sequence

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.

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/

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

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

sequence position
type: Class
disjoint with: variant
disjoint with: database
disjoint with: sequence
disjoint with: observed variation
subclass of: snpo resource:arc8c8db51
subclass of: snpo resource:arc8c8db52
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.

observed variation
type: Class
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.
disjoint with: sequence
disjoint with: variant
disjoint with: database
disjoint with: sequence position
subclass of: Thing
subclass of: snpo resource:arc8c8db32
equivalent class: snpo resource:arc8c8db33

snpo resource:arc8c8db13
type: Class
comment: hasPosition only sequence_position AND hasVariation only observed_variation [new definition make it unecessary]
union of: snpo resource:arc8c8db15

snpo resource:arc8c8db16
type: Restriction
on property: hasNucleotideVariation
cardinality: 1

snpo resource:arc8c8db23
type: Restriction
cardinality: 1
on property: hasAAVariation

aa sequence
type: Class
comment: A sequence composed of one or several amino-acids. Ex: a protein
equivalent class: snpo resource:arc8c8db74
disjoint with: nucleotide sequence

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

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..

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

transcript region
type: Class
disjoint with: protein region
comment: Is one portion of a, or an enire, transcript (unmature) or mRNA (mature).
equivalent class: SO_0000833
subclass of: snpo resource:arc8c8db57
subclass of: snpo resource:arc8c8db58
subclass of: Thing

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

nucleotide
type: Class
subclass of: snpo resource:arc8c8db28
subclass of: Thing
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

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

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

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

transcript
type: Class
subclass of: transcript region
equivalent class: SO_0000673
comment: There are first products of transcription, before the splicing.

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

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/

genome
type: Class
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
equivalent class: SO_0001026
subclass of: genomic region

omim
type: Class
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
subclass of: generic variant db

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

chromosome
type: Class
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
subclass of: genomic region
equivalent class: SO_0000340

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

haplotype block
type: Class
comment: A set of consecutive sites between which there is little or no evidence of historical recombination.
equivalent class: SO_0000355
subclass of: snpo resource:arc8c8db31
subclass of: Thing

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

nucleotide variation
type: Class
subclass of: snpo resource:arc8c8db63
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

aa variation
type: Class
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
disjoint with: nucleotide variation
subclass of: observed variation
subclass of: snpo resource:arc8c8db40

snpo resource:arc8c8db38
type: Restriction
on property: hasVariantSequence
cardinality: 2

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

promotor
type: Class
equivalent class: SO_0000167
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 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

terminator
type: Class
equivalent class: SO_0000141
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

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: assembly
equivalent class: SO_0000149

reference variant
type: Class
subclass of: snpo resource:arc8c8db43
subclass of: snpo resource:arc8c8db45
subclass of: snpo resource:arc8c8db46
subclass of: snpo resource:arc8c8db47
subclass of: variant
subclass of: snpo resource:arc8c8db48
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

snpo resource:arc8c8db43
type: Restriction
all values from: snpo resource:arc8c8db44
on property: hasPosition
comment: unnecessary

snpo resource:arc8c8db45
type: Restriction
on property: hasAAVariation
cardinality: 0

snpo resource:arc8c8db46
type: Restriction
comment: unnecessary
cardinality: 1
on property: hasPosition

snpo resource:arc8c8db47
type: Restriction
comment: unnecessary
cardinality: 1
on property: hasNucleotideVariation

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

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

cnvr
type: Class
comment: copy number variable region Cf. Redon et al. Nature, 444, 23 Nov. 2006
subclass of: repeated segment
equivalent class: SO_0001019

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

coding variant
type: Class
equivalent class: snpo resource:arc8c8db64
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.

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

mature mrna
type: Class
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
subclass of: transcript region

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

isVariantIn
type: ObjectProperty
domain: variant
range: snpo resource:arc8c8db93
comment: A variant belongs to a region.
inverse of: regionHasVariant

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

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