]> CC0 [https://creativecommons.org/publicdomain/zero/1.0/]. 0.9.45 Begum Durgahee Best Practices 1.) The class hierarchy, object- and datatype-property hierarchies are modeled to match SIO's hierarchies. 2.) Every class and property has a label (rdfs:label) as well as a description (rdfs:comment). The description may contain an example of how a class/property is being applied. 3.) Classes that are directly related to either GFF3, GTF, GVF or VCF specification have a link-out to the specification's document as provenance indicator (via rdfs:isDefinedBy). 4.) Link-outs to Wikipedia are provided for classes whereever possible. 5.) Ontology terms are encoded in the URIs using camel case, i.e. letters following a white space in an ontology term are capitalized followed by the removal of the white space. Chris Mungall Erick Antezana Francesco Strozzi Genomic Feature and Variation Ontology (GFVO) Joachim Baran Joachim Baran Karen Eilbeck Michel Dumontier Raoul Bonnal Robert Hoehndorf Takatomo Fujisawa The Genomic Feature and Variation Ontology (GFVO) is modeled to represent genomic data using the Resource Description Format (RDF). It is captures the contents of data files that adhere to the Generic Feature Format Version 3 (GFF3, http://www.sequenceontology.org/resources/gff3.html), the General Transfer Format (GTF, http://mblab.wustl.edu/GTF22.html), the Genome Variation Format Version 1 (GVF, http://www.sequenceontology.org/resources/gvf.html), and the Variant Call Format (VCF, http://vcftools.sourceforge.net/specs.html). The creation of the ontology was inspired by previous work of Robert Hoehndorf on RDF2OWL (http://code.google.com/p/rdf2owl). Toshiaki Katayama https://github.com/BioInterchange/Ontologies describes Links to an entity for which supportive information is being provided. has annotation Links to additional annotations about an entity. has attribute Links out to aggregate information for an entity. has evidence References an entity or resource that provides supporting/refuting evidence. has first part Denotes the first entity of an ordered part relationship. has identifier Links out to an identifier. has input Links out to an entity that is the input of a "Process" subclass. has last part Denotes the last entity of an ordered part relationship. has member Denotes membership for "Collection", "Catalog" and "File" instances. has ordered part Denotes a compositional relationship to other entities, where the ordering of the composition of entities carries meaning. has output Links out to an entity that is the output of a "Process" subclass. has part Denotes a compositional relationship to other entities. has participant Denotes the participation of other entities in processes. has quality Links out to an entity that provides qualitative information. has source Denotes information origin. is about References an entity about which information is provided for. is affected by Denotes that an entity is affected by another entity. is after Denotes the trailing occurrence or succession of the subject in regards to the object. is attribute of Denotes that an entity is an attribute of the entity that this property links out to. is before Denotes the leading occurrence or precedence of the subject in regards to the object. is created by Denotes the process or method that created an entity. is described by Provides a description of the subject via reference to an object that provides further information on the subject. is located on Denotes the location of genomic feature on a landmark. is part of Denotes that an entity is an intrinsic component of an encapsulating entity. is participant in Denotes participation with another entity. is refuted by References an entity or resource that provides refuting evidence. is source of Denotes that an entity is the source of the entity that this property links out to. is spatiotemporally related to Denotes spatio-temporal relations to other entities. is supported by References an entity or resource that provides supporting evidence. is temporarily part of Denotes a temporarily constraint "isPartOf" relationship. The temporal restriction expresses that the relationship is not universally true. This property can be used to express "Derives_from" relations in GFF3. references References another entity or resource. refers to References an entity, where additional information is provided to augment the reference. has value Representation of any literal that is associated with a GFVO class instance. Domain restrictions might apply. For example, "Codon Sequence" entities restrict "has value" to be a non-empty string consisting of A, C, G, or T letters, and whose length is a multiple of 3. Alias http://en.wikipedia.org/wiki/Pseudonym An alias is an alternative name whose use is mostly non-primary. Allele Frequency 1.0 0.0 0.0 1.0 http://en.wikipedia.org/wiki/Allele_frequency Proportion of a particular gene allele in a gene pool. Amino Acid [A-Z] http://en.wikipedia.org/wiki/Amino_acid Ancestral Sequence Denotes an ancestral allele of a feature. May be used to denote the 'ancestral allele' of VCF formatted files. http://en.wikipedia.org/wiki/Ancestral_reconstruction Array Comparative Genomic Hybridization Feature provenance is based on array-comparative genomic hybridization. Attribute An attribute denotes characteristics of an entity. At this stage, "Quality" is the only direct subclass of "Attribute", whose subclasses denote qualitative properties such as sex ("Female", "Male", "Mermaphrodite"), zygosity ("Hemizygous", "Heterozygous", "Homozygous"), etc. The object property "hasQuality" (or subproperties thereof) should be utilized to express qualities of entities. The "hasAttribute" object property should be used to denote relationships to "Object" or "Process" instances, unless there is a better object property suitable to represent the relationship between the involved entities.. Average Coverage http://en.wikipedia.org/wiki/Shotgun_sequencing#Coverage Average coverage depth for a genomic locus (a region or single base pair), i.e. the average number of reads representing a given nucleotide in the reconstructed sequence. Biological Entity A biological entity an entity that contains genomic material or utilizes genomic material during its existance. Genomic material itself is represented as sub-classes of Chemical Entity. Biopolymer Sequencing Information about features and variants is based on biopolymer sequencing. http://en.wikipedia.org/wiki/Sequencing Breakpoint A breakpoint describes the source or destination of a zero-length sequence alteration. These alterations are typically insertions, deletions or translocations according to the GVF specification (see "Breakpoint_detail" in http://sequenceontology.org/resources/gvf.html). Catalog A catalog is a specialization of a "Collection", where all its contents are of the same type. Cell http://en.wikipedia.org/wiki/Cell_(biology) A cell is a biological unit that in itself forms a living organism or is part of a larger organism that is composed of many other cells. Chemical Entity A chemical entity is an entity related to chemistry. This class is typically not instantiated, but instead, its subclasses "Amino Acid", "Chromosome", "Peptide Sequence", etc., are used to represent specific chemical entities. Chromosome http://en.wikipedia.org/wiki/Chromosome A chromosome is an abstract representation of an unnamed chromosome to represent ploidy within a data set. A "Chromosome" instance is used for for denoting the locus of phased genotypes. For placing genomic features ("Feature" class instances) on a chromosome, contig, scaffold, etc., please see the "Landmark" class. Circular Helix A circular helix structure. Can be used to indicate a true "Is_circular" attribute in GFF3 and GVF. http://en.wikipedia.org/wiki/Circular_DNA Coding Frame Offset 0 2 http://en.wikipedia.org/wiki/Reading_frame Coding frame offset of the feature, if it is a coding sequence or feature that contributes to transcription and translation. It is referred to as "frame" in GTF, but called "phase" in GFF3 and GVF. A feature's coding frame offset can be either 0, 1, or 2. Codon Sequence ([ACGT]{3})+ http://en.wikipedia.org/wiki/Codon A codon sequence is a nucleotide sequence underlying a potential amino acid sequence. Codon sequences are three bases of length or multiples thereof. Collection A collection is a container for genomic data. A collection may contain information about genomic data including -- but not limited to -- contents of GFF3, GTF, GVF and VCF files. The latter are better represented by "File" class instances, whereas the result of unions or intersections between different "File" class instances should be captured within this format-independent "Collection" class. When importing data whose provenance is not a GFF3, GTF, GVF or VCF file, instances of "Collection" should be utilized too, or the more restrictive "Catalog" class should be used. Comment A comment is a remark about a piece of information, an observation or statement. In the context of GFF3, GVF, etc., genomic feature and variation descriptions, "isAfter" and "isBefore" relationships should be used to indicate where a comment is situated between pragma or feature statements of GFF3, GTF, GVF or VCF files. Contig http://en.wikipedia.org/wiki/Contig A contig is a contiguous DNA sequence that has been assembled from shorter overlapping DNA segments. Coverage 0.0 0.0 0 Number of nucleic acid sequence reads for a particular genomic locus (a region or single base pair). DNA Microarray Feature information is based on DNA microarray probes. http://en.wikipedia.org/wiki/DNA_microarray_experiment DNA Sequence ([ACGT])+ http://en.wikipedia.org/wiki/Dna_sequence DNA Sequencing http://en.wikipedia.org/wiki/DNA_sequencing Information about features and variants is based on DNA sequencing. Experimental Method An experimental method is a procedure that yields an experimental outcome (result). Experimental methods can be in vivo, in vitro or in silico procedures that are well described and can be referenced. External Reference A cross-reference to associate an entity to a representation in another database. Feature The feature class captures information about genomic sequence features and variations. A genomic feature can be a large object, such as a chromosome or contig, down to single base-pair reference or variant alleles. Female Denoting sex of a female individual. A female is defined as an individual producing ova. http://en.wikipedia.org/wiki/Female File A file represents the contents of a GFF3, GTF, GVF or VCF file. It can capture genomic meta-data that is specific to any of these file formats. The result of unions, intersections or other operations between "File" class instances should be capture with the generic "Collection" class, which is format independent, or the more restrictive "Catalog" class should be used. Forward Reference Sequence Frameshift Denotes a frameshift forward in the reference sequence. Fragment Read Platform Details about the fragment-read (single-end read) sequencing technology used to gather the data in a set. Functional Specification A functional specification of bioinformatics data, i.e. the specification of genomic material that potentially has biological function. Gametic Phase Denotes the presence of information that required capturing the gametic phase. For diploid organisms, that means that information is available about which chromosome of a chromosome pair contributed data. http://en.wikipedia.org/wiki/Gametic_phase Genome Representation of a genome. Genomic features that constitute the genome may be linked via one or more "Collection", "Catalog", "Contig", "Scaffold" or "File" instances. http://en.wikipedia.org/wiki/Genome Genome Analysis A genome analysis denotes the type of procedure that was carried out to derive information from a genome assembly. http://en.wikipedia.org/wiki/Genomics#Genome_analysis Genomic Ascertaining Method Provides information about the source of the data. Genotype The genotype is the genetic information captured in a particular genome. It can also refer to one or more populations, if statistical distributions are provided that assign genetic codes to groups of individuals. A genotype is denoted by a string of slash-separated list of alleles ("has value" property). The length of the list is dependent on the ploidy of the studied species as well as sequencing technique used. Example: "A/G" denotes a genotype with alleles "A" and "G". http://en.wikipedia.org/wiki/Genotype Germline Cell http://en.wikipedia.org/wiki/Germline The germline feature class captures information about genomic sequence features arising from germline cells. Helix Structure http://en.wikipedia.org/wiki/DNA_helix Helix structure denotes the physical shape of biopolymers. Hemizygous A sequence alteration with hemizygous alleles. http://en.wikipedia.org/wiki/Zygosity#Hemizygous Heritage http://en.wikipedia.org/wiki/Heredity Heritage denotes the passing of traits from parents or ancestors. Passed traits may not be visible as a phenotype, but instead, might only manifest as genetic inheritance. Hermaphrodite http://en.wikipedia.org/wiki/Hermaphrodite Denoting sex of an individual that contains both male and female gametes. Heterozygous http://en.wikipedia.org/wiki/Zygosity#Heterozygous A sequence alteration with heterozygous alleles. Homozygous http://en.wikipedia.org/wiki/Zygosity#Homozygous A sequence alteration with homozygous alleles. Identifier http://en.wikipedia.org/wiki/Identifier An identifier labels an entity with a single term that is interpreted as an accession. An accession labels entities that are part of a collection of similar type. Information Content Entity An information content entity requires background information or specific domain knowledge to be interpreted correctly. Interaction Describing interaction between features, such as the effect of a feature variant on another feature. Label A label is a term or short list of terms that name an entity for the purpose of lexicographically distinguishing the entity from entities of similar type. Landmark A landmark establishes a coordinate system for features. Landmarks can be chromosomes, contigs, scaffolds or other constructs that can harbor "Feature" class instances. For expressing ploidy within a data set, please refer to the "Chromosome" class. Likelihood Likelihood is the hypothetical probability of the occurrence of a certain event. Locus http://en.wikipedia.org/wiki/Locus_(genetics) A locus refers to a position (possibly multi-dimensional) within a genome or proteome. Male http://en.wikipedia.org/wiki/Male Denoting sex of a male individual. A male is defined as an individual producing spermatozoa. Match Denotes a match between the reference sequence and target sequence. Material Entity A material entity represents a physical object. In the context of genomic features and variations, material entities are cells, organisms, sequences, chromosomes, etc. Maternal Heritage http://en.wikipedia.org/wiki/Maternal_effect Maternal heritage is the passing of traits from a female to her ancestors. Mobile Element Sequence Variant Insertion or deletion of a mobile element. The exact modification is determined by a type of the Variation Ontology. Name A name assigns an entity a non-formal term (or multiples thereof) that can provide information about the entities identity. A note is a short textual description. Number of Reads 0 Number of reads supporting a particular feature or variant. Object An object is a concrete entity that realizes a concept and encapsulates data associated with said concept. Objects are typically representing tangible entities, such as "Chromosome", "DNA Sequence", but also objects such as "Identifier", "Average Coverage" or other computational or mathematical entities. Paired End Read Platform Details about the paired-end read sequencing technology used to gather the data in a set. Paternal Heritage Paternal heritage is the passing of traits from a male to his ancestors. http://en.wikipedia.org/wiki/Maternal_effect#Paternal_effect_genes Peptide Sequence ([A-Z])+ A peptide sequence is an ordered sequence of amino acid residues, but which may not necessarily be a protein sequence. For encoding sequences of proteins, the subclass "Protein Sequence" should be used. http://en.wikipedia.org/wiki/Peptide_sequence Phenotype http://en.wikipedia.org/wiki/Phenotype A phenotype description represents additional information about a sequenced individual's phenotype. A sequenced individual is represented by instances of the "Sequenced Individual" class. Phred Score 0.0 0.0 0 http://en.wikipedia.org/wiki/Phred_score The Phred score can be used to assign quality scores to base calls of DNA sequences. Prenatal Cell true A prenatal feature is purportedly associated with prenatal cells; the GVF specification declares this feature type under the prama directive "##genomic-source", but does not describe its semantics and the referenced Logical Observation Identifiers Names and Codes (LOINC, http://loinc.org), do not define the meaning or intended usage of the term "prenatal" either. http://en.wikipedia.org/wiki/Prenatal Process A process denotes a temporally dependent entity. It can be thought of as a function, where input data is transformed by an algorithm to produce certain output data. Protein Sequence http://en.wikipedia.org/wiki/Peptide_sequence A protein sequence is a peptide sequence which represents the primary structure of a protein. Quality Quality is a specific attribute that is strongly associated with an entity, but whose values are varying and disjunct. Qualities are finite enumerations, such as sex ("Female", "Male", "Hermaphrodite"), heritage ("Maternal", "Paternal"), but they also make use of the "hasValue" datatype property such as "Coding Frame Offset" (either "0", "1" or "2"). Quantity A property of a phenomenon, body, or substance, where the property has a magnitude that can be expressed by means of a number and a reference. This class is typically not directly instantiated, but instead, its subclasses "Allele Frequency", "Average Coverage", etc. are used. RNA Sequencing http://en.wikipedia.org/wiki/RNA-Seq Information about features and variants is based on RNA sequencing. Reference Sequence http://en.wikipedia.org/wiki/Reference_sequence Denotes the reference sequence of a feature. The reference sequence is of importance when dealing with genomic variation data, which is expressed by the "Variant" class. Reference Sequence Gap Denotes a gap in the reference sequence for an alignment. Reverse Reference Sequence Frameshift Denotes a frameshift backwards (reverse) in the reference sequence. Sample A sample is a limited quantity of a chemical entity of some sort, which is typically used (destructively/non-desctructively) in a scientific analysis or test. http://en.wikipedia.org/wiki/Sample_(material) Scaffold http://en.wikipedia.org/wiki/Contig A scaffold is the aggregation of multiple contigs to form a larger continuous sequencing region. Score http://en.wikipedia.org/wiki/Score_(statistics) A measure that permits the ranking of entities. Sequence ([ACGTUWSMKRYBDHVN\-]+|\~[0-9]*|\.|!|\^) A sequence provides information about any biopolymer sequences. Specialized subclasses are provided to denote specialized instances of sequences, such as "Codon Sequence", "Reference Sequence", "Protein Sequence", etc. Sequence Alignment http://en.wikipedia.org/wiki/Sequence_alignment A sequence alignment denotes the congruence of two sequences. In GFF3, a sequence alignment can be a nucleotide-to-nucleotide or protein-to-nucleotide alignment (see "The Gap Attribute", http://sequenceontology.org/resources/gff3.html). "Alignment Operation" class instances denote the actual steps that the constitute the sequence alignment. Sequence Alignment Operation http://en.wikipedia.org/wiki/Sequence_alignment A sequence alignment operation captures the type of alignment (see "Sequence Alignment") between a reference sequence and target sequence. Note that an "Alignment Operation" is situated in a linked list, where the order of the alignment operations is of significance. Sequence Variant http://en.wikipedia.org/wiki/Mutation Describing specific sequence alterations of a genomic feature. A variant is related to "Reference" class instances, which denote the sequence that serves as a basis for sequence alteration comparisons. Sequenced Individual Aggregated sequencing information for a particular individual. Sequencing Technology Platform http://en.wikipedia.org/wiki/Read_(Biology) Details about the sequencing/microarray technology used to gather the data in a set. Sex http://en.wikipedia.org/wiki/Sex Biological sex of an individual. Somatic Cell The somatic feature class captures information about genomic sequence features arising from somatic cells. http://en.wikipedia.org/wiki/Somatic Span 0 A span is an attribute denoting the number of nucleotides or peptides that an entity covers. This is directly used in conjunction with "Sequence Alignment Operation" subclasses, e.g. to express the number of nucleotides a sequence alignment match ranges over. Target Sequence Gap Denotes a gap in the target sequence for an alignment. Total Number of Reads Total number of reads covering a feature or variant. Variant Calling http://en.wikipedia.org/wiki/SNV_calling_from_NGS_data Denotes the technique of calling genomic feature variants in a genome assembly. Variant Filtering Denotes the technique of filtering genomic feature variants in a genome assembly which are not suitable for variant calling. http://en.wikipedia.org/wiki/SNV_calling_from_NGS_data Version A version names a release of a software, dataset, or other resource. A versioned resource is not necessarily public. http://en.wikipedia.org/wiki/Versioning Watson-Crick Helix http://en.wikipedia.org/wiki/Non-helical_models_of_DNA_structure#Proposal_of_Watson.E2.80.93Crick_helical_structure Helical structure as first proposed by Watson and Crick. Can be used to indicate a false "Is_circular" attribute in GFF3 and GVF. Zygosity Zygosity denotes the similarities of a specific allele in the genome of an organism. http://en.wikipedia.org/wiki/Zygosity