SNP-Ontology full
type: Ontology
comment: Unconsistency checked by RacerPro1.9.0 the 02/14/2007
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
version info: modifications 07/17/2007: - SNPO is the prefix for the namespace http://www.loria.fr/~coulet/ontology/snpontology/version1.5/snpontology_full.owl# - reorganisation of genomic region class - mapping with Sequence Ontology classes
imports: SO
version info: TODO: Take into account alternative splicing.
version info: TODO: comment properties
comment: Assertion with the Instance Store succesfully tested on v1.2 the 01/17/2007
version info: TODO: add add variation type information (substitution, insertion, deletion, indel, etc.)
imports: amino-acid.owl
comment: A domain representation of genomic variations.
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
version info: version: full 1.5 release: 11/08/2007 author: Adrien Coulet contact: adrien dot coulet at loria dot fr University of Nancy

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

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

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

transcript region
type: Class
subclass of: Thing
subclass of: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#1
subclass of: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#2
disjoint with: protein region
equivalent class: SO_0000833
comment: Is one portion of a, or an enire, transcript (unmature) or mRNA (mature).

genomic region
type: Class
subclass of: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#14
subclass of: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#15
subclass of: Thing
comment: Is one portion of a, or the whole, genome.
disjoint with: protein region

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

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

nucleotide sequence
type: Class
equivalent class: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#42
disjoint with: aa sequence
comment: A sequence composed of one or several nucleotides. Ex: a chromosome, a gene, an exon, etc.

protein region
type: Class
comment: Is one portion of a, or an entire protein.
disjoint with: genomic region
disjoint with: transcript region
subclass of: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#69
subclass of: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#70
subclass of: Thing

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: Thing
subclass of: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#3

composesSequence
type: ObjectProperty
sub property of: OBO REL part of
comment: Object Propoerty specially for nucleotide and residue that composes sequence of DNA or RNA.
domain: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#103
range: sequence
inverse of: isASequenceComposedOf

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

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

variant
type: Class
equivalent class: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#26
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.
disjoint with: observed variation
disjoint with: sequence position
disjoint with: database
disjoint with: sequence

haplotype
type: Class
equivalent class: SO_0001024
equivalent class: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#76
comment: Haplotype is a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated. Source: wikipedia
subclass of: Thing
subclass of: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#83
subclass of: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#84

tags haplotype block
type: ObjectProperty
sub property of: isHaplotypeMemberOf
comment: A tagSNP tags directly other variant (captured by proxy), but since it is located in a haplotype of a block it also tags the haplotype where is located.
domain: tag snp
inverse of: haplotypeTaggedBy

tags variant
type: ObjectProperty
comment: a tagSNP tags other haplotype member cpatured by proxy.
range: snp captured by proxy
inverse of: variant tagged by
domain: tag snp

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
subclass of: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#6
subclass of: observed variation
disjoint with: nucleotide variation

aa sequence
type: Class
disjoint with: nucleotide sequence
equivalent class: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#16
comment: A sequence composed of one or several amino-acids. Ex: a protein

observed variation
type: Class
subclass of: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#46
subclass of: Thing
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 position
disjoint with: database
disjoint with: variant
disjoint with: sequence
equivalent class: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#47

nucleotide variation
type: Class
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
subclass of: observed variation
subclass of: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#7
disjoint with: aa variation

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

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

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

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

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).

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

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
equivalent class: SO_0000149
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

assembly
type: Class
equivalent class: SO_0000353
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

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

sequence position
type: Class
subclass of: Thing
subclass of: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#8
subclass of: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#13
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.
disjoint with: observed variation
disjoint with: sequence
disjoint with: database
disjoint with: variant

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: variant
disjoint with: sequence position
disjoint with: database
disjoint with: observed variation

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

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: genomic region
subclass of: transcript region

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

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.)

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

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

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

isASequenceComposedOf
type: ObjectProperty
comment: Describes the composition of a sequence either in nucleotide or amino acids.
range: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#162
inverse of: composesSequence
domain: sequence

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
equivalent class: SO_0000167

chromosome
type: Class
equivalent class: SO_0000340
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

coding variant
type: Class
disjoint with: non coding variant
equivalent class: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#20
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.

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

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
equivalent class: SO_0000141
subclass of: regulatory region

ncbi nucleotide
type: Class
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
subclass of: sequence database

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

http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#26
type: Class
comment: hasPosition only sequence_position AND hasVariation only observed_variation [new definition make it unecessary]
union of: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#27

http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#30
type: Restriction
on property: hasNucleotideVariation
cardinality: 1

http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#37
type: Restriction
on property: hasAAVariation
cardinality: 1

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

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.

intron
type: Class
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
subclass of: genomic region

dbsnp
type: Class
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/
subclass of: generic variant db

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

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

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

http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#53
type: Restriction
cardinality: 2
on property: hasVariantSequence

population
type: Class
comment: A group of indivdual.
subclass of: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#54
subclass of: Thing

presents haplotype
type: ObjectProperty
comment: A population presents haplotype. That means that the related haplotype have been calculated with genotype coming form this population.
inverse of: isHaplotypeForPeopleOf
domain: population
range: haplotype

haplotype block
type: Class
subclass of: Thing
subclass of: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#55
equivalent class: SO_0000355
comment: A set of consecutive sites between which there is little or no evidence of historical recombination.

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

mature mrna
type: Class
equivalent class: SO_0000356
subclass of: transcript region
disjoint with: SO_0000835
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

reference variant
type: Class
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
subclass of: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#60
subclass of: variant
subclass of: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#63
subclass of: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#64
subclass of: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#65
subclass of: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#66

http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#63
type: Restriction
cardinality: 1
on property: hasNucleotideVariation
comment: unnecessary

http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#64
type: Restriction
on property: hasPosition
comment: unnecessary
cardinality: 1

http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#65
type: Restriction
on property: hasAAVariation
cardinality: 0

http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#66
type: Restriction
comment: unnecessary
all values from: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#67
on property: hasPosition

variant tagged by
type: ObjectProperty
inverse of: tags variant
comment: Variant captured by proxy are tagged by a tagSNP.
range: tag snp
domain: snp captured by proxy

observed allele
type: Class
equivalent class: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#71
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.

is statistically connected
type: SymmetricProperty
range: haplotype
domain: haplotype
type: ObjectProperty
comment: Between to related haplotype blocks haplotype could be connected statistically.

isAASequenceOf
type: ObjectProperty
sub property of: isSequenceIn
domain: genomic region
range: dna sequence
comment: isAASequenceOf links an amino acid sequence and its protein region. NB : We suppose that a protein region can not be resume to the 11 sequence.
inverse of: hasAASequence

isProteinVariantIn
type: ObjectProperty
range: protein region
domain: variant
inverse of: hasProteinVariant
comment: A variant belongs to a region.
sub property of: isVariantIn

isVariantIn
type: ObjectProperty
range: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#158
inverse of: regionHasVariant
comment: A variant belongs to a region.
domain: variant

hasDnaVariant
type: ObjectProperty
comment: A variant belongs to a region.
domain: genomic region
sub property of: regionHasVariant
range: variant
inverse of: isDnaVariantIn

isRnaVariantIn
type: ObjectProperty
domain: variant
comment: A variant belongs to a region.
range: transcript region
inverse of: hasRnaVariant
sub property of: isVariantIn

isRnaSequenceOf
type: ObjectProperty
range: transcript region
sub property of: isSequenceIn
domain: rna sequence
inverse of: hasRnaSequence
comment: isRnaSequenceOf links a sequence of rna and it transcript region. NB: We suppose that a rna region (or a complete rna) could not be resume to its nt sequence.

isDnaSequenceOf
type: ObjectProperty
range: genomic region
domain: dna sequence
sub property of: isSequenceIn
comment: This object propoerty is the link between a dna sequence and its genomic region. NB: we suppose that a genomic reion can not be resume to its nt sequence.
inverse of: hasDnaSequence

population name
type: DatatypeProperty
range: string
domain: population
comment: A given name of the population. Example: Afro-americans

generation algorithm
type: FunctionalProperty
domain: haplotype block
comment: The algorithm used to generates haplotype blocks. Example of algo used are D prime (Gabriel et al., Science, 2002), Four Gamete Rule (Wang et al, Am. J. Hum. Genet., 2002), Solid Spine of LD.
range: string
type: DatatypeProperty

r²
type: FunctionalProperty
comment: coefficient of determination. [0,1]. Example: 0.8
domain: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#165
type: DatatypeProperty
range: string

distance of first ignored markers
type: FunctionalProperty
domain: haplotype
comment: Describe the number of bases that is the limit for consideration of SNP in the construction of haplotypes. Example: Ignore pairewise comparaison of markers >500 kbases apart => 500
type: DatatypeProperty

estimation algorithm
type: FunctionalProperty
domain: haplotype
range: string
type: DatatypeProperty
comment: It is te algorithm used to estimate the haplotype. Example : accelerated EM algorithm (Qin et al, Am J Hum Genet,2002)

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

variantFunction
type: FunctionalProperty
domain: variant
type: DatatypeProperty
range: string
comment: A variant could have a consequances. The function describe this consequences. Example: missense, non sense.

HapMap allele frequency
type: FunctionalProperty
range: string
domain: variant
type: DatatypeProperty
comment: The ratio of first observed allele on other observed allele. Example: 0.8 => i.e. if hapMapAllele is A/C, the frequence of observation of A is 80% and C (and potential others) is 20%.

haplotype sequence
type: FunctionalProperty
version info: TODO: create a instance of the sequence class related to haplotype.
comment: The sequence of the haplotype.
type: DatatypeProperty
range: string
domain: haplotype

r² threshold
type: FunctionalProperty
range: string
type: DatatypeProperty
domain: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#168
comment: The threshold below which a marker is not associated with the tagSNP. Used during the tagging. Example: 0.75

HapMap alleles (strand +)
type: FunctionalProperty
comment: The 2 most frequent observed allele in HapMap. Allele observed on the + strand. Example: A/C
domain: variant
type: DatatypeProperty
range: string

haplotype population frequency
type: FunctionalProperty
domain: haplotype
type: DatatypeProperty
range: string
comment: It is the frequency of apparition of the concerned haplotype in the haplotype population.

Tagging algorithm
type: FunctionalProperty
comment: Algorithm used for the identification of tagSNP and captured SNP. Example: pairewise tagging only, aggressive tagging: use 2-marker haplotypes (LOD threshold=X), aggressive tagging: use 2- and 3-marker haplotypes
range: string
type: DatatypeProperty
domain: http://lodlaundromat.org/.well-known/genid/31126d1ced679f13cceb2406bb422d0e#171

block number
type: FunctionalProperty
type: DatatypeProperty
range: string
comment: The block number is the number that identifies the block in the haplotype construction. It is used fot hapoview construction.
domain: haplotype block

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

D'
type: FunctionalProperty
type: DatatypeProperty
range: string
comment: The D' value indicate the degree of relationship between an haplotype block and its next block. Example: D' of block 3 informs on the relationship between block 3 and block 4 of hte same construction. N.B.: D' of the last block of a construction is null. D' value is [0,1].
domain: haplotype block

excluded individual threshold
type: FunctionalProperty
range: string
type: DatatypeProperty
domain: haplotype
comment: The threshold (percentage of missing data) to exclude individual with to o much missing genotype data. Example: 50 => Exclude individuals with>50% missing genotype