TDWG Natural Collection Description LSID Ontology Markus Döring, Constance Rinaldo TDWG Biodiversity Information Standards 2007-03-05 2007-09-24 Ontology describing the metadata returned for LSIDs that are used for natural collections records. i.e. curated groups of specimens. 0.81 - [SVN $Rev: 1399 $] The ontology is based on the NCD XML schema version 0.70 developed by TDWG, but taken forward in development, especially the controlled vocabulary. In some cases property names were changed, but in general all names have remained and were simple adapted to lowerCamelCase. Properties based on NCD element names starting with "Collection" have usually lost their Collection prefix. Cardinalities and multiple languages have not been adressed in particular. DublinCore is expected to be used for the digital record properties and at the same time also for the physical collection description. The expected DC properties are: Digital record: dc:source , dc:identifier , dct:created , dct:creator , dct:modified , dct:contributor , tdwg:notes Physical Collection: dc:title , dc:alternative_title , dc:description , dct:extent , tcom:note , dc:format , dc:medium , dc:accessRights , dc:rights , dc:provenance , dc:relation Collection A group of specimens or other objects about natural history. This class represents actual collections. For derived collections please use the DerivedCollection subclass. Derived collection A "derived" collection record. The record has been derived from a query on an item-level database e.g. all items from Australia. Collection Identifier The URI (LSID or URL) of the the collection. In RDF this will be used as URI of the collection resource. Parent Collection Identifier Identifier for the parent collection for this sub-collection. Enables a hierarchy of collections and sub collections to be built. Alternative Identifier Alternative identifier for the collection with an indication of the source e.g. ISCW. Description for Specialists Optional additional descriptive text using terms that are more suited to a specialist audience. Attribute indicates the language of the text. Extent An indication of the size or extent of the collection. Known to Contain Types Flag element to indicate that the collection is known to include type specimens. Primary Grouping Principle Picklist keyword to indicate what the collection is about. The intellectual basis for grouping the collection rather than grouping based on physical characteristics. Expected to contain an instance from the Primary Grouping Principle Type Term vocabulary. Primary purpose Picklist key word to indicate the primary reason that the collection was assembled. Expected to contain an instance of the Primary Purpose Type Term. Collection citation Preferred text for citing the collection, which may include sponsorship acknowledgements Formation Period Text description of the time period during which the collection was assembled e.g. "Victorian", or "1922 - 1932", or "c. 1750". Development Status Picklist keyword indicating potential for change to the scope of the collection. Expected to contain instances from the Development Status Type Term vocabulary. Conservation Status Picklist keyword indicating the conservation status of the collection using the McGinley scale. Link to the date of assessment and repeat to show sequence of snapshots. Expected to contain an instance from the Conservation Status Type Term vocabulary Conservation Status Date The date that the conservation status was assessed. Usage Conditions Terms and conditions under which the collection may be used. May be a URL to standard T&C. Default text for an institution may be overwritten for a particular collection if the restrictions are different. Contact Link to the contact details (such as postal address, email address and phone number) to get more information about this collection. Owner Link to the details for the institution or person that owns this collection. Physical Location Link to the contact details for the host institution, or person for a private collection. Kingdom Coverage Picklist keyword to indicate biological kingdom. Taxon Coverage Taxon or taxa in the collection at Family level or higher. Temporal Coverage Time period covered by the materials in the collection. Taxon coverage strength Taxon or taxa in the collection at Family level or higher which are considered a particular strength of the collection. Common Name Coverage Common names or group names equivalent to the taxon names, in the local language. Common name coverage strength Common names or group names which are considered a particular strength of the collection. Place Name Coverage Place names from which material in the collection originated. Geospatial coverage strength Place names and/or coordinates indicating the place(s) from which material in the collection originated, which are considered a particular strength of the collection. Geospatial Coordinates Decimal latitude(s) and longitude(s) of places of origin of the material in the collection. Living time period coverage Time period during which biological material was alive. Includes palaeontological time periods or other text phrases. Living Time Period Time period during which biological material was alive. Includes palaeontological time periods or other text phrases. Collection Type Picklist keyword to indicate the typical content or unifying characteristic of the collection. Expected to contain an instance for the Collection Type Term vocabulary. Specimen Preservation Method Picklist keyword indicating the process or technique used to prevent physical deterioration of non-living collections. Expected to contain an instance from the Specimen Preservation Method Type Term vocabulary. Expedition Name Uniform name for an expedition or voyage of discovery during which the material was collected. Collector name coverage Name(s) of collector(s) of the material within the collection. Related Collection Short descriptions of related collections, such as for other components of a large collection that has been dispersed. Item-Level Access URI of an item-level data source. This can be a Web service or a Webpage designed for humans. Development Status Term Controlled vocabulary for development status. active growth Material is being actively sought for this collection active growth Currently increasing in volume, count, number of taxa represented or other dimension due to intentional activity. passive growth Material is being added to this collection but not actively sought passive growth May increase in volume, count, number of taxa represented or other dimension due to unplanned and unpredicatable activity. available for sampling Material in this collection may be sampled available for sampling Collection may or will be decreasing in volume, count, representation or other dimension due to intentional destructive analytical activity. static The collection is neither growing nor decreasing static The collection cannot or will not increase or decrease in any manner. decreasing decreasing The collection is growing smaller as material is withrawn The collection is currently diminishing in volume, count, number of taxa represented, or other dimension due to intentional activity. closed No further objects will be added closed The collection is currently closed to acquisitions or deposits. lost Collection has been lost, for example destroyed in a fire lost The host institution has concluded that collection is permanently unavailable after appropriate efforts have been made although documentation of the collection exists. missing Collection cannot be found. missing The physical collection cannot be located although its documentation exists; the possibility of finding the collection exists. Institution Type Term Process or technique used to prevent physical deterioration of non-living collections. no treatment no treatment Absence of any deliberate preservation action. Not Applicable Not Applicable For living collections that grow and reproduce. Fluid-preserved Fluid-preserved Maintained in formalin, ethyl alcohol, or other liquid preservative. frozen frozen Held a temperatures below freezing (32 Degrees F or 0 degrees C). dried dried Treated or exposed to remove all internal fluids; may have used silica gel. dried and pressed dried and pressed Treated to remove all internal fluids; flattened, typically mounted on paper. tanned tanned Chemically treated skins and hides. freeze-dried freeze-dried Removal of internal liquids using cold, low humidity environment. glycerin glycerin Replacement of original internal fluids with glycerine. Surface Coating Surface Coating Application of protective or consolidating surface coating using organic or inorganic materials. Slide Mount Slide Mount Held on a glass slide using fixative and cover slip. Embedded Embedded Maintained in a solid matrix suitable for making thin sections. pinned pinned Treated to remove all internal fluids; held on metalic pin. Controlled Atmosphere Controlled Atmosphere Held in conditions that vary from the typical elemental mix of the atmosphere; usually implies reduced oxygen. cryopreserved cryopreserved Held at very low termperatures, typically in liquid Nitrogen. Recorded (analog) Recorded (analog) Observations, measurements, or images that capture phenomena in analog formats. Recorded (digital) Recorded (digital) Observations, measurements, or images that capture phenomena in digital formats. Refrigerated Refrigerated Maintained at cool temperatures above freezing. SEM stub SEM stub Mounted and coated for scanning electron microscopy. Skeletonized Skeletonized Removal of soft tissues including connective tissues. Stasis Stasis Collections capable of growing and reproducing that are held in a suspended state. Primary Purpose Type Term Controlled vocabulary for primary purpose types. research research Acquired for current and future study. education education Acquired to educate, inform, or convey information. exhibition exhibition Acquired to educate, inform, or convey information through display. ornamental ornamental Acquired for decorative purposes. Destructive analysis Destructive analysis Acquired and maintained for current and future analytical purposes that will consume the specimen or object. Monitoring Monitoring Acquired as a result of observation, measurement, or sampling. Personal Personal Acquired for idiosyncratic reasons. Voucher Voucher Acquired and maintained to document an organism, observance, or phenomenon. Commercial Micro-organism cultures. Commercial Biological material for sale. Primary Grouping Principle Type Term Controlled vocabulary for primary grouping principle. spatial Examples include arctic fauna, plants from Guiana. spatial Relating to a physical location or region. Ecosystems Examples include water column samples, forest plot collections. Ecosystems Collections relating to complex community of living organisms and their environment. Cultural Cultural Collections relating to a group of people. Taxonomic Examples include North American mammal collection, lichen collection and arachnid collection. Ecosystems Collections relating to a particular grouping of biological or geological specimens. Relationships Examples include parasite/host; symbiotic relationships Items of different kinds having an intimate biological relationship. expeditions expeditions Collections resulting from a journey or trip taken for a specific purpose. Environmental Examples include rainfall measurements, average temperature, specimens from hydrothermal vents. environmental The aggregate of external conditions in which organisms live or phenomena occur; may be defined components only. temporal Cenozoic mollusks, for example temporal Relating to a particular time period. Repository Specimens from US Mineral Management Service, specimens from US National Park Service, for example. repository Similar or related items that are placed in a facility for long term care as the result of a specific agreement. national national Relating to geopolitical boundaries. events Specimens collected at a disaster site, for example. events Collections that were made as a result of an event, or that document an event. stage Larva, fetus, for example. stage Relating to a specific phase in physical development. Kingdom Type Term Controlled vocabulary for taxonomic kingdom. Animalia Animalia Animal Kingdom Plantae Plantae Plant Kingdom Fungi Fungi Fungi Protista Protista Protists Eubacteria Eubacteria Eubacteria Archaebacteria Archaebacteria Archaebacteria Conservation Status Type Term The class for construction controlled vocabularies of conservation status. Terms are taken from the McGinley levels. McGinley level 1 Materials conservation:Conservation Problem McGinley level 1 Specimens deteriorating, potentially cullable, or unprepared. Collection unit in need of immediate attention; museum pests, rusting pins, crystallizing slide media, unringed Hoyer�s media, evaporated alcohol, fading labels, broken cover slip or slide, etc. Primary types missed in general collection. McGinley level 2 Specimen accessibility: Specimens Unidentified, Inaccessible McGinley level 2 Material properly prepared but not sorted or only rough-sorted; not readily available to specialists. McGinley level 3 Specimen accessibility: Specimens Unidentified, Accessible McGinley level 3 Specimens sorted to a level necessary to be efficiently accessible to research specialist for study. All specimens in soft-bottom trays, shell vials in jars or slide boxes, with appropriate levels denoting pertinent taxonomic information. Taxonomic category may vary among different taxa. McGinley level 4 Specimen accessibility: Specimens Identified but not Integrated into Collection McGinley level 4 Valuable material that has been identified to the species level but not yet put away effectively inaccessible. McGinley level 5 Physical organization: Specimens Identified but Curation Incomplete McGinley level 5 All specimens identified and integrated. However, this collection unit needs upgrading, e.g., names checked, header labels for unit trays prepared, transfer to soft-bottom trays, etc., box header labels checked against slides. Alcoholic collection with individual exposed vials, jar labels misleading or without detail, overall format heterogenous. McGinley level 6 Physical organization: Specimens Identified and Properly Curated in Accordance with Departmental Collection Standards McGinley level 6 All specimens in soft-bottom unit trays; all unit-tray header labels, drawer or box, and cabinet labels completed; space left for expansion. When a collection reaches Level 6, the name(s) or who did the curation, the date of curation and listing of catalogues or monographs on which the names are based should be entered in the Smithsonian Collection Inventory File computerized files. Vial within jar system established, labels complete and accurately typed, expansion space allocated, and alcohol levels adequate. McGinley level 7 Data Capture: Species Level Inventory McGinley level 7 Species inventory with header or box label generation completed. Alcoholic collection with taxa listed on jar labels and in database, as in Level 6 plus species-level inventory. McGinley level 8 Data Capture: Specimen Label Data Capture McGinley level 8 Label data are recorded for systematic, biogeography or natural history studies. The data elements recorded will vary by group, however, a d standard core set includes the following: a) a country/province/place/latitude-longitude; b) date of collection; c) collector(s); d) miscellaneous (for example, elevation, host). Miscellaneous voucher specimens, including types, from various studies are also ranked at this level. McGinley level 9 Data Capture: Research Data Capture McGinley level 9 Measurements, graphics, or other pertinent (descriptions) of specimens are captured in a database McGinley level 10 Scientific Voucher Material McGinley level 10 Groups of specimens included in published monographic, synthetic, or revisionary works, including primary type collection if storage is at Level 7 or higher. When groups of specimens serve to voucher published scientific collection-based studies and have undergone conservation and accession requirements of at least Level 7.