TDWG Natural Collection Description LSID Ontology
Markus Döring, Constance Rinaldo
TDWG Biodiversity Information Standards
2007-03-05
2015-07-01
Ontology describing the metadata returned for LSIDs that are used for
natural collections records. i.e. curated groups of specimens.
0.9
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
Version 0.9 removed subclass declarations to classes outside of this ontology in accordance with Recommendation 2.9 of the VoMaG Report http://www.gbif.org/resource/80862
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.