Core ontology for biological maps. Based on the work at Gramene: http://www.gramene.org/cmap Multiple maps may belong to a "map set". Whole Genome Shotgun sequences Source: Gramene: http://www.gramene.org/db/cmap/feature_type_info A pair of primers that amplify coding sequence of a gene. Often designed to specifically amplify only a particular allele. Source: Gramene: http://www.gramene.org/db/cmap/feature_type_info Bins are arbitrarily-defined segments delimited by two fixed core markers. A bin includes all loci from the leftmost or top core marker to the next core marker. Source: Gramene: http://www.gramene.org/db/cmap/map_type_info. Class to tag the type of MapCorrespondence. Expressed Sequence Tag Source: Gramene: http://www.gramene.org/db/cmap/feature_type_info Quantitative Trait Locus Source: Gramene: http://www.gramene.org/db/cmap/feature_type_info Centromere Source: Gramene: http://www.gramene.org/db/cmap/feature_type_info Generic marker type for any feature that has been genetically mapped. Used when the specific marker type (e.g., RFLP, SSR) is unknown. Source: Gramene: http://www.gramene.org/db/cmap/feature_type_info 1 The class of things that can be mapped onto a map. Top level suoer class for maps. Sequence Tagged Site Source: Gramene: http://www.gramene.org/db/cmap/feature_type_info Subclasses are based on Gramene's notion of a map type; see http://www.gramene.org/db/cmap/feature_type_info Messenger RNA Source: Gramene: http://www.gramene.org/db/cmap/feature_type_info The QTL map is a type of genetic map which indicates the approximate location of a quantitative trait locus (QTL) within an interval delineated by two or more markers on a genetic map. Source: Gramene: see http://www.gramene.org/db/cmap/map_type_info. A cytogenetic map is produced by direct observation of stained or labeled chromosomes. Map units are given in fraction of a chromosomal arm or centiMcClintocks (cMc). Source: Gramene: http://www.gramene.org/db/cmap/map_type_info. Entities formed by clustering datasets of EST and/or mRNA sequences, e.g. NCBI UniGenes, TIGR GIs Source: Gramene: http://www.gramene.org/db/cmap/feature_type_info 0 The class of things that have relations (via the map:hasMappable or map:hasPosition predicates) to mappable objects or positions. Thus maps are either a set of (mappable object) and/or a set of map positions. From Gramene; see http://www.gramene.org/db/cmap/map_type_info. banding Source: Gramene: http://www.gramene.org/db/cmap/feature_type_info The deletion-based cytogenetic map of an organism is a type of low-resolution physical map. It is constructed using a "genome deletion panel" which consists of a series (or collection) of mutant lines containing sub-chromosomal deletions and a reference wild-type line. Markers can be mapped onto the genome using this panel (by Southern hybridization or by PCR) based on the presence or absence of signal when comparing the banding pattern in the mutants lines with the pattern in the wild type. Linked markers (present in the same deleted region) share the same banding pattern (presence or absence) on the deletion panel. Source Gramene: see http://www.gramene.org/db/cmap/map_type_info. Source: Gramene: http://www.gramene.org/db/cmap/feature_type_info Amplified Fragment Length Polymorphism Source: Gramene: http://www.gramene.org/db/cmap/feature_type_info Oligonucleotide sequence used to initiate replication for PCR. Source: Gramene: http://www.gramene.org/db/cmap/feature_type_info Labeled probe used for fluorescent in situ hybridization Source: Gramene: http://www.gramene.org/db/cmap/feature_type_info Simple Sequence Repeat Source: Gramene: http://www.gramene.org/db/cmap/feature_type_info Interval between chromosomal breakpoints on a deletion (physical) map. Source: Gramene: http://www.gramene.org/db/cmap/feature_type_info Primer pair used to amplify an SSR. Source: Gramene: http://www.gramene.org/db/cmap/feature_type_info Denotes the computationally-determined location of a transcription unit in the genome. These are verified using experimental evidence provided by EST and full-length cDNA sequences. Source: Gramene: http://www.gramene.org/db/cmap/feature_type_info Genome Survey Sequences Source: Gramene: http://www.gramene.org/db/cmap/feature_type_info Pair of partially OVERlapping oliGOnucleotide primers, each of which primes the other in a labeling reaction. Source: Gramene: http://www.gramene.org/db/cmap/feature_type_info The maize genome has been divided into bins of approximately 20 cM. Each maize bin is delimited by two fixed core markers, one each end of the bin. The bin includes all loci (features) from the left- or topmost core marker to the next core marker. Source: Gramene: http://www.gramene.org/db/cmap/feature_type_info Restriction Fragment Length Polymorphism Source: Gramene: http://www.gramene.org/db/cmap/feature_type_info The genetic map is a representation of a meiotic-recombination map based on analysis of marker segregation in a population of offspring derived from a bi-parental cross. Marker polymorphism between the parents is required to monitor recombination among loci along a chromosome. Source Gramene: see http://www.gramene.org/db/cmap/map_type_info. 0 The physical map, as used in the Maps Module, is a representation of the collection of cloned DNA fragments that make up a genome, ordered with respect to a reference map (such as genetic map). A genome-sequencing project orders and assembles this collection in its different stages towards obtaining a full genome sequence. Source: Gramene: see http://www.gramene.org/db/cmap/map_type_info. FingerPrint Contig; sets of overlapping fingerprint clones used in physical mapping Source: Gramene: http://www.gramene.org/db/cmap/feature_type_info As used in the Gramene database, denotes any large-scale genomic clone including bacterial artificial chromosomes (BAC) and P1 artificial chromosomes . Source: Gramene: http://www.gramene.org/db/cmap/feature_type_info Class designating different types of Map or MapSet. Subclasses are based on Gramene's notion of a map type; see http://www.gramene.org/db/cmap/map_type_info. The sequence map is a summarized representation of the contiguous, assembled genomic sequence of an organism in a linear map format. Source: Gramene: see http://www.gramene.org/db/cmap/map_type_info. The class of things that have positional information about a subject's location on a map. 1 1 1 Relates a MapSet to the Map(s) it contains. The containsMap relation is stronger than the hasMap relation: the containsMap predicate forces the domain of MapSet on the subject. Relates a Map to its MapSet. Relates a Map to a MappableObject. Relates a Map or MapPosition to a MappableObject (a mappable element). Relates a Map or a Mappable Object to a MapPosition. See also onMap and positionOf. Relates a Map to a MapPosition. Relates a MapCorrespondence to a MappableObject. Super property of all object properties in this ontology. Useful for grouping object properties when viewing ontologies from multiple namespaces. Relates a MapPosition to a MapCorrespondence. Relates a MappableObject or a MapPosition to a MapCorresponence. Standardized predicate for any "thing" to assert a relationship a Map. Relates a MappableObject to a MapPosition. Relates a MapPosition to a Map. The onMap relation is stronger than the hasMap relation: the onMap predicate forces the domain of MapPosition on the subject. Relates a MapCorrespondence to a MappablePosition. Standardized predicate for any "thing" to assert a relationship a MapSet. Relates a MapPosition to a MappableObject. Relates a MappableObject to a Map. Relates a MappableObject to a MapCorrespondence. Super property of all datatype properties in this ontology. Useful for grouping datatype properties when viewing ontologies from multiple namespaces. A list of synonymous names for the Map or MapSet. Predicate for storing the chromosome number, such as "2" or "2A"; see also map:linkageGroup. The established end of the MapPosition range, in map:units. The established beginning of the MapPosition range, in map:units. The units for measuring a MapPosition range: band: cytogenetic bands bp: base pairs cM: centiMorgains cMc: centiMcClintocks other: other cMc other cM bp band A unique string designator for a Map or MapSet. Predicate for storing the linkage group designator; see also map:chromosomeNumber.