97 lines
4.8 KiB
Plaintext
97 lines
4.8 KiB
Plaintext
---+!! %TOPIC%
|
|
|
|
%META:TOPICINFO{author="GregorHagedorn" date="1110899211" format="1.0" version="1.5"}%
|
|
%META:TOPICPARENT{name="WebHome"}%
|
|
This topic is about attempting to subdivide the totality of biodiversity informatics into separate knowledge domains, for which object types may be defined. Bioidiversity data could then be expressed in a matrix (or composition) or such object types, see DataModelMatrix. Ultimately, the object should be in a - relatively flat - ontological hierarchy, so any suggestions about this are appreciated.
|
|
|
|
Below a rough first draft based on SDD/UBIF. We should work towards a rough consensus on how to delimit knowledge domains, and which labels for the object types are considered most useful and intuitive. In SDD we have:
|
|
* *<nop>DescriptiveData* (consisting of <nop>DescriptiveTerminology, <nop>CodedDescriptions, <nop>NaturalLanguageDescriptions, and (fixed) <nop>IdentificationKeys)<br />
|
|
plus inherited from UBIF (currently as external interface or "proxy" objects, to be revised as outlined in DataModelMatrix):
|
|
* *<nop>ClassNames* (= definition of vernacular or scientific names)
|
|
* *<nop>ClassHierarchies* (= taxonomic hierarchy, including synonmyization)
|
|
* *Objects* (ABCD Units, <nop>ObjectOccurrences?, <nop>TaxonOccurrences?
|
|
or Specimens? Problem: some uses need to validate that only
|
|
stored/preserved objects are adderessed (e.g. nomenclature), others
|
|
generalize stored and observed objects, some uses apply to parts
|
|
of objects)
|
|
* *Agents* (person, institution, software)
|
|
* *Publications* (references to digital/printed publications
|
|
or online-publications itself)
|
|
* *Geography* (geographical locations and areas.
|
|
Problem: objects in collection are called Location
|
|
rather than Geography again. Alternative Names:
|
|
Locations/Location
|
|
(not clear whether geographic or in book, document, etc.)
|
|
<nop>GeoLocations/<nop>GeoLocation - perhaps best choice?
|
|
* *<nop>MediaResources* (image, audio, video, formatted text like pdf, html, etc.)
|
|
* *MeasurementUnits* (scientific like m, kg, s, non-scientific like in, ft, oz)
|
|
|
|
In the species bank workshop in Amsterdam, I further proposed:
|
|
|
|
* *Uses* (biotechnological, medical, agricultural and mythological uses of plants)
|
|
* *Conservation* (in the sense of nature conservation/red list data, would be good to have better term, conservation may also be applied to dead objects to conserve against decay)
|
|
* *Ecology* - large area, no details ontology from me, except for
|
|
* *OrganismInteractions* = two organisms, an interaction type like host-pathogen, predator-prey, or pollinator, and area in which this interaction is known to occur
|
|
* *Distribution* in the sense of chorology, i.e. synthetic/summarized hypothesis about actual or potential distribution.
|
|
|
|
Additional types in the overall object concept, for which no root collections would be defined because they are only used in compositions may be *<nop>NomenclaturalOpinion*, *Identification*, and several types like character, concept, modifier used inside SDD.
|
|
|
|
Which other types (perhaps as subtypes in an ontology) should be defined for a start? Which names you simply dislike, even if you don't have a better one?
|
|
|
|
In email to tcs-lc list, Roger Hyam proposed a root collection *"Nomenclature"*. This corresponds with Geography, which also differs from the plural form of the class name itself. In general I think it desirable to stay with the "plural name for collections" pattern, but intuitive names may be even more important.
|
|
|
|
-- Main.GregorHagedorn - 09 Mar 2005
|
|
---
|
|
|
|
The ontology I use in The Taxonomicon looks like this:
|
|
* Nomenclature
|
|
* Rank (item)
|
|
* Scientific name (text)
|
|
* Common name (text)
|
|
* Epithet (text)
|
|
* Author citation (text)
|
|
* Nomenclatural attribute (item)
|
|
* Nomenclatural code (item)
|
|
* Taxonomy
|
|
* Taxon group (item)
|
|
* Taxon (taxon)
|
|
* Geography
|
|
* Biogeographic realm (item)
|
|
* Geographic region (item)
|
|
* Type locality (text)
|
|
* Presence (item)
|
|
* Geology
|
|
* Geologic time (item range)
|
|
* Geologic age (number range)
|
|
* Year of extinction (number)
|
|
* Ecology
|
|
* Habitat
|
|
* Ecologic realm (item)
|
|
* Major habitat type (item)
|
|
* Ecoregion (item)
|
|
* Habitat (item)
|
|
* Relationships
|
|
* Host (taxon)
|
|
* Host type (item)
|
|
* Type host (boolean)
|
|
* Parasite (taxon)
|
|
* Parasite type (item)
|
|
* Pathogen (boolean)
|
|
* Disease (text)
|
|
* Symbiont (taxon)
|
|
* Symbiont type (item)
|
|
* Commensal (taxon)
|
|
* Commensal type (item)
|
|
* Host dependency (item)
|
|
|
|
GBIF should provide a registry for all standardized objectID's, data source names and parameter names.
|
|
|
|
-- Sheila Brands, Universal Taxonomic Services, The Taxonomicon & Systema Naturae 2000 - 10 Mar 2005
|
|
|
|
---
|
|
|
|
(Donald Hobern and Sheila Brands propose a closely related discussion on whether an object-oriented approach is appropriate at all. Please discuss this under KeywordBasedDataExchange! -- Gregor - 15. March 2005)
|
|
|
|
---
|
|
|