TDWG TaxonOccurrence LSID Ontology Roger Hyam TDWG Biodiversity Information Standards 2006-12-06 $Date: 2007-08-21 14:52:53 +0200 (Tue, 21 Aug 2007) $ Ontology describing the metadata returned for LSIDs that are used for taxon occurrence records. The motivation for this vocabulary is to represent DarwinCore type data in a simple way. A more refined vocabulary for occurrence data in general may be developed in the future under the auspices of Observation and Specimen Records interest group (http://www.tdwg.org/activities/osr/). 0.2 - [SVN $Rev: 1303 $] This ontology is designed to represent records of occurrences of taxa in the wild. Taxon Occurrence The record of the occurrence of a taxon either in the wild or in a collection. Identified To An identification for this occurrence record. Identified To String An identification for this occurrence record as a string Derived From This TaxonOccurrence has been derived from another occurrence record following some procedure that may be documented by the procedure property. Procedure The procedure followed that generated this record perhaps by derivation from another record or from the voucher or other means. Procedure Descriptor A string description of the procedure employed in generating this occurrence record. This may be interpreted in combination with and qualifying the procedure property. Higher Geography The combination of all geographic elements less specific than locality. "Like" query operations on this element will search for a substring that might be in any of the higher geography elements. Core:HigherGeography Continent The full, unabbreviated name of the continent on which the organism was collected or observed. Core:Continent Water Body The full, unabbreviated name of the body of water in or over which the organism was collected or observed. Core:WaterBody Island Group The full, unabbreviated name of the island group in which the organism was collected or observed. Core:IslandGroup Island The full, unabbreviated name of the island on which the organism was collected or observed. Core:Island Country The full, unabbreviated name of the country or major political unit in which the organism was collected or observed. Core:Country State Province The full, unabbreviated name of the state, province, or region (i.e., the next smaller political region than Country) in which the organism was collected or observed. Core:StateProvince County The full, unabbreviated name of the county, shire, or municipality (i.e., the next smaller political region than StateProvince) in which the organism was collected or observed. Core:County Locality The full, unabbreviated name of the locality where the organism was collected or observed. This element need not contain geographic information provided in other geographic elements. Core:Locality Minimum Elevation In Meters The minimum or actual elevation at which the collection or observation was made. Use negative values for locations below sea level. Examples: 75 (for an elevation of 100 +- 25 meters). 100 (for an elevation between 100m and 200m). Core:MinimumElevationInMeters Maximum Elevation In Meters The maximum or actual elevation at which the collection or observation was made. Use negative values for locations below sea level. Examples: Examples: 125 (for an elevation of 100 +- 25 meters). 200 (for an elevation between 100m and 200m). Core:MaximumElevationInMeters Minimum Depth In Meters The minimum or actual depth at which the collection or observation was made. Use positive values for locations below the surface. Examples: 0 (for a depth of up to 10m). 50 (for a depth between 50m and 100m). Core:MinimumDepthInMeters Maximum Depth In Meters The maximum or actual depth at which the collection or observation was made. Use positive values for locations below the surface. Examples: 10 (for a depth of up to 10m). 100 (for a depth between 50m and 100m). Core:MaximumDepthInMeters Valid Distribution Flag A flag ("true" or "false") that indicates whether the locality information represents a valid distribution occurrence for a specimen. Specimens taken from captivity and showing the captive location should use the value "false". Core:ValidDistributionFlag Earliest Date Collected The earliest date-time (Common Era calendar) in a date-time period during which an organism or group of organisms was collected or observed. If the event is recorded as occurring at a single date-time, populate both EarliestDateCollected and LatestDateCollected with the same value. Core:EarliestDateCollected Latest Date Collected The latest date-time (Common Era calendar) in a date-time period during which an organism or group of organisms was collected or observed. If the event is recorded as occurring at a single date-time, populate both EarliestDateCollected and LatestDateCollected with the same value. Core:LatestDateCollected Day Of Year The ordinal day of the year on which the object or observation was collected (1 for January 1, 365 for December 31, except in a leap year, in which case it is 366). If the EarliestDateCollected and LatestDateCollected do not occur on the same day, do not populate DayOfYear. Core:DayOfYear Decimal Latitude The latitude of the location from which the organism or observation was collected, expressed in decimal degrees. Positive values are North of the Equator, negative values are South of the Equator. Geospatial:DecimalLatitude Decimal Longitude The longitude of the location from which the organism or observation was collected, expressed in decimal degrees. Positive values are East of the Greenwich Meridian, negative values are West of the Greenwich Meridian. Geospatial:DecimalLongitude Geodetic Datum The geodetic datum to which the latitude and longitude refer. If not known, use "not recorded". This concept should be vocabulary-controlled. Geospatial:GeodeticDatum Coordinate Uncertainty In Meters The upper limit of the distance (in meters) from the given latitude and longitude describing a circle within which the whole of the described locality lies. Leave the value empty if the uncertainty is unknown, cannot be estimated, or is not applicable (because there are no coordinates). The value should be greater than zero. Geospatial:CoordinateUncertaintyInMeters Point Radius Spatial Fit A measure of how well the circle defined by the coordinates and uncertainty match the original spatial representation, as a ratio of the area of the circle to the area of the original spatial representation. Legal values are 0, greater than or equal to 1. A value of 1 is an exact match or 100% overlap. A value of 0 should be used if the given georeference does not completely contain the original representation. The PointRadiusSpatialFit is undefined if the original representation is a point without uncertainty and the given georeference is not that same point (without uncertainty). If both the original and the given georeference are the same point, the PointRadiusSpatialFit is 1. Detailed explanations with graphical examples can be found in the Guide to Best Practices for Georeferencing (Chapman and Wieczorek, eds. 2006) http://www.gbif.org/prog/digit/Georeferencing. Geospatial:pointRadiusSpatialFit Georeference Protocol A reference to the methods used for determining the coordinates and uncertainties. Example: "http://manisnet.org/GeorefGuide.html". Geospatial:GeoreferenceProtocol Georeference Sources A list of maps, gazetteers or other resources used to georeference the locality. The content of this concept is meant to be specific enough to allow anyone in the future to use the same resource to georeference the same locality. Example: "USGS 1:24000 Florence Montana Quad". Geospatial:GeoreferenceSources Georeference Sources A categorical description of the extent to which the georeference has been verified to represent the location where the specimen or observation was collected. This element should be vocabulary-controlled. Examples: "requires verification", "verified by collector", "verified by curator". Geospatial:GeoreferenceVerificationStatus Georeference Remarks Comments about the spatial description determination, explaining assumptions made in addition or opposition to the those formalized in the method referred to in GeoreferenceProtocol. Geospatial:GeoreferenceRemarks Well-Known Text Footprint A Well-Known Text (WKT; see http://en.wikipedia.org/wiki/Well-known_text) representation of the the shape (footprint) that defines the location of the occurrence. Example: the one-degree boundin box with opposite corners at (longitude=10, latitude=20) and (longitude=11, latitude=21) would be expressed in well-known text as POLYGON ((10 20, 11 20, 11 21, 10 21, 10 20)) Geospatial:WKTFootprint Footprint Spatial Fit A measure of how well the geometry expressed in the footprint match the original spatial representation, as a ratio of the area of the footprint given to the area of the original spatial representation. Legal values are 0, greater than or equal to 1. A value of 1 is an exact match or 100% overlap. A value of 0 should be used if the given georeference does not completely contain the original representation. The FootprintSpatialFit is undefined if the original representation is a point without uncertainty and the given georeference is not that same point (without uncertainty). If both the original and the given georeference are the same point, the FootprintSpatialFit is 1. Detailed explanations with graphical examples can be found in the Guide to Best Practices for Georeferencing (Chapman and Wieczorek, eds. 2006). http://www.gbif.org/prog/digit/Georeferencing Geospatial:FootprintSpatialFit Value An OccurrenceRecord may represent more that just the presence of an instance of a taxon in the wild. If the occurrence is the result of a survey there may well be a quantitative measure associated with the record such as a count or frequency. In the most simple case this property may contain the integer 0 indicating a lack of occurrence. If this property is present then its meaning (including units) should be interpreted in terms of the value of the procedure property. The associated valueConfidence property is provided to hold indication of error or deviation - again dependent on the procedure followed. FIXME Value Confidence This property should be interpreted in association with the value property. It provides a measure of error associated with that measurement in the context of the procedure followed in the procedure property. No equivalent Collector The name(s) of the collector(s) of the taxon occurrence. These may be normalised out in the collectorTeam property. Core:Collector Collector Team A breakdown of the collectors of the occurrence. An expansion of the information given in the collector property. Collectors Field Number The identifier issued for the occurrence by the collector at the time of collection. CuratorialExtension:CollectorNumber CollectorsFieldNumber Collector's Batch Number An identifying string applied to a set of objects or observations resulting from a single collecting event. CuratorialExtension:FieldNumber CollectorsFieldNumber basisOfRecord The kind of object this occurrence is e.g. herbarium, fossil, living, moving image, sound recording, bare observation etc. This property may be repeated, for example a specimen may be a herbarium specimen and also a moss packet. In addition to indicating the specimen kind with this flag implementers may choose to subclass Specimen. It is recommended that even if the Specimen class is subclassed and specialised kinds of specimens added to the vocabulary the same basic KindOfSpecimen terms are always included to enable naive clients to interpret the object. A graphical client may have a small number of icons to display next to well known specimen types for example. Core:BasisOfRecord BasisOfRecord and KindOfUnit basisOfRecordString This is a human readable account of the kind of taxon occurrence given by the basisOfRecord property. It allows for use of descriptive terms that may not be available from a controlled vocabulary. Wherever possible the basisOfRecord should be used as well as this property. Core:BasisOfRecord BasisOfRecord and KindOfUnit Host Collection A link to the collection that hosts this specimen. The collection will contain details of the collection code and host institution/organisation. Host Collection String A string representation of the collection hosting this specimen. May include the collection code. May be normalised in the hostCollection property. Core:CollectionCode SourceInstitutionID Institution Code The institution code for the collection. Provided mainly for compatibility with DarwinCore. Details of the institution may be held in the hostCollection/Collections/hostInstitution property. Core:InstitutionCode SourceInstitutionID Catalog Number The identifier used for this TaxonOccurrence within the scope of the collection. e.g. specimen id. This should be the preferred identifier. Alternative identifiers, such as additional barcodes, can be given using the dc:identifier property. CatalogNumber UnitID Verbatim Label Text The text as it occurs on the label of the specimen. Type Status String A list of one or more nomenclatural types (including type status and typified taxonomic name) represented by the object. Example: "holotype of Ctenomys sociabilis. Pearson O. P., and M. I. Christie. 1985. Historia Natural, 5(37):388" Curatorial::TypeStatus Type Status String The type of type specimen this specimen is. Curatorial::TypeStatus - but as a controlled vocabulary rather than a string. Type For Name A name for which this specimen is a type. Disposition The current disposition of the cataloged item. Examples: "in collection", "missing", "voucher elsewhere", "duplicates elsewhere". Curatorial::Disposition Individual Count The number of individuals present in the lot or container. Not to be used for observations - see the property. Curatorial::IndividualCount Verbatim Coordinates A text representation of the coordinate data (Latitude/ Longitude, UTM, TRS, etc.) from its original source if it cannot be separated into its component parts. Example: "470999 1234300". Geospatial:VerbatimCoordinates Verbatim Latitude A text representation of the Latitude part of the coordinate data from its original source. Example: 47d09'99"N Geospatial:VerbatimLatitude Verbatim Longitude A text representation of the Longitude part of the coordinate data from its original source. Example: -122.43254 Geospatial:VerbatimLongitude Verbatim Coordinate System The name of the system in which the verbatim geographic coordinates were recorded. Examples: "decimal degrees", "degrees minutes seconds", "degrees decimal minutes", "UTM" Geospatial:VerbatimCoordinateSystem Verbatim Collecting Date The verbatim original representation of the date (and time) information for the collecting event as recorded on the specimen or collection catalogue Example: "spring 1910" Curatorial:VerbatimCollectingDate Verbatim Elevation A text representation of the altitude in its original format as on the specimen or in the collection catalogue. Example: "1000+- meters". Curatorial:VerbatimElevation Verbatim Depth A text representation of the depth in its original format on the specimen or in the collection catalogue. Example: "100 to 200 ft below sea level". Curatorial:VerbatimDepth Field Notes The text representation of field notes associated with the specimen or a link to those field notes. Curatorial:fieldNotes Life Stage The age class or life stage of the biological individual represented by the catalogued object. Examples: "adult", "mature", "juvenile", "eft", "nymph", "seedling", "seed", "egg" Core:LifeStage Sex The sex of the biological individual represented by the catalogued object. Examples: "male", "female", "hermaphrodite", "gynandromorph", "monoecious", "dioecious", "not recorded", "indeterminate", "transitional" Core:Sex Has Interaction This TaxonOccurrence has an interaction with another TaxonOccurrence as represented by this TaxonOccurrenceInteraction object. Identification The identification or determination of the occurrence of a taxon to a specific taxon. Expert The person who made this identification. May also be represented by expertString. The 'Who' of and identification. Expert Name A string representation of the person or agent that identified this occurrence record. This may be interpreted in combination with method property - particularly if the method is automated and no human was present. occurrence The OccurrenceRecord that is identified by this identification. The 'What' of an identification. This property is usually omitted when and identification object is embedded within an OccurrenceRecord when the subject of the identification is implied. date The date and time the identification occurred. The 'When' of an identification. location The location the identification took place. The 'Where' of an identification. Method The procedure used to identify the occurrence. The 'How' of an identification. Method Descriptor A string description of the method employed in the identification. This may be interpreted in combination with and qualifying the method property. Confidence A measure of the confidence that the identification is correct. By default (in the absence of a method field) this should be interpreted as 0 = no confidence and 1 = total confidence but other interpretations may be appropriate depending on the value of the method field. No equivalent Taxon The TaxonConcept this occurrence is identified to. No equivalent Taxon Name A string representation of the TaxonConcept this occurrence is identified to. Be aware that using a Taxon Name in here without qualifying in what sense it is used is imprecise. Some indication of the taxonomic monograph or treatment followed is important when available. Populate the taxon property whenever possible. Higher Taxon A higher rank taxon concept this identification is associated with. Used to place the identification in context. May be repeated. No equivalent Verbatim Det The verbatim text of an identification. For example the text of a determination slip attached to a herbarium specimen. Basis Of Record Term The different kinds of records. An object used to represent the different types of taxon occurrence record. Preserved Specimen Preserved Specimen Specimen that has been preserved in some way and is intended to persist indefinitely. Typically a preserved specimen is also dead although this may not be the case with freeze dried mycological collections for example. Living Specimen Living Specimen The specimen is alive and can be expected to change either through growth, reproduction and/or death. Still Image Still Image The specimen is a picture of some kind. It may be on a physical medium or it may be digital. Moving Image Moving Image The specimen is a moving picture of some kind. It may be on a physical medium or it may be digital. Illustration Specimen Illustration Specimen The specimen is an image originally created by human hand e.g. a drawing, painting, etching etc. Digital Specimen Digital Specimen The specimen is a digital object not a physical object. Fossil Specimen Fossil Specimen The specimen is fossilised.