Non-Biological tree experiments

Collections hosted at the Geological Museum and the Anthropology Department need a workaround to be incorporated in Symbiota. The workaround consists in creating a non-biological taxonomic tree where the “taxa” have to reflect some sort of classification used for non-biological specimens, such as rocks, fossils, minerals, and artifacts.

Geology trees

The Geological Museum’s specimens are hosted in three main collections: Vertebrates, Invertebrates, and Minerals. While the first two can be accommodated in the main Animalia tree, the Minerals need a custom tree. An analysis of the mineral specimen records returns 16 preliminary “taxa” (column OBJNAME):

Object taxonomy

To allow for a completely new category, that I’m going to call “Geological Specimen”, and that would be included in the highest level Object (comparable to level Organism for biological trees), rankid = 1, add new record in table taxonunits.

Symbiota accommodates many taxonomic levels under each Domain, from Kingdom to Form. The categories levels can have different names (defined field rankname with 15-character limit) and are ordered following their rank number (field rankid). Keeping in mind the required taxonomic fields for uploading specimens in the graphic interface (least inclusive name and Kingdom), a workaround has to include names that will work as “Genera” and “Species” as well.

I’m taking advantage of the taxonomic levels table, by defining the following categories in table taxonunits (rankid, equivalent to rank in biological tree):

	Object (1, Organism)
	-- Discipline (10, Kingdom)
	--- Category (180, Genus)
	---- Subcategory (220, Species)

The super rank Object requires that a taxon with that sciname and UnitName1 is added to table taxa, and then a relationship has to be added to table taxaenumtree between Object and itself (that is, Object is in Central Thesaurus and its parent is itself).

The following step is to add the actual “taxa” to the database via spreadsheet upload (option “Batch Upload a Taxonomic Data File” in sitemap.php), in increments (starting with the higher level taxa):

Note that compound names were initally uploaded as a single word, in an attempt to surpass the cleaning scripts that check for regular scientific names. Later, spaces were manually introduced either by editing the taxon directly in the interface, or in the database itself.

Note that same pattern of combined names submission was used here to submit the lower rank taxa, but the parentstr field contains names already edited (it works).

Last step was to upload specimen information with the now existing non-biological existing tree in Central Thesaurus.

Anthropology trees

======= A preliminary tree was similarly created for Anthropology (as a Discipline), under the Object “taxon”:

Categories (genera) and subactegories (species) tentatively are: