Property:preparationType

[mtrekels]

Label	Preparation Type
Definition	A term used to classify or describe an object that indicates the actions that have been taken upon it and/or the processes it has been put through to prepare it for scientific use or study.
Usage	A more specific classification of items in the collection than described in objectType.
Existing property
Existing class
Existing property identifier
Format	Text
Required	No
Repeatable	Yes
Constraints	Preparation Type should be set in conjunction with Object Type, as each Object Type has specific Preparation Types. E.g., if objectType = DNA: preparationType should be one of gDNA, eDNA, aDNA
Examples	Bones, Eggs, Fossils, Gemstones, Lysate, Macrofossils, eDNA, Viable cells, Pollen, Muscle, Leaf, Blood, Known - witheld
Notes	This can be the same as PreservationMethod (e.g. Bone), but is not always. This should not be used for classifying objects by taxon. The best way to do that is to use the Taxon class (formal taxonomy and vernacular names) or ObjectClassification class (informal classification). For large collections with multiple types use a pipe delimited list.

[Blerina01]

Might be named as a "taxon", which may be a species, subspecies, genera, family or class.

[qgroom]

I think the intention is for this to be the type of object, such as herbarium sheet, bottle, slide, skin, mounted skeleton, box etc. However, it really needs to be made clearer

[rondlg]

Hi Quentin, yes that was the intent for this property.

[mswoodburn]

Suggestion for definition/existing term from a comment in the index spreadsheet: https://www.dublincore.org/specifications/dublin-core/collection-description/collection-application-profile/#colclditemType

[mswoodburn]

BioCASE ObjectClassType vocabulary: https://www.biocase.org/doc/Results/WP3/Oldversions/SpyDoc_122/BioCASE_MetaProfile_1.22.shtml#complexType_ObjectClassType_Link01DEB818

[ekrimmel]

Is the Dublin Core 'item type' too broad? Since it is similar to and uses the same suggested controlled vocabulary as DC 'type' which is used in DwC to indicate at a very high level what the object is: PhysicalObject, MovingImage, etc.

Also, will this be equivalent to #82 ?

[qgroom]

This dimension is quite important for collecting metrics on aggregated collections. I think we need to constrain the users to a strict set of values, otherwise they will not aggregate cleanly

[qgroom]

I don't think we need to go to fine detail, as in DwC, because we want to describe collections in common terms.

[ekrimmel]

I can see why it's important to provide controlled vocabulary for this property and why this is a crucial property to define well in order to collate metrics across individual collections. I also think this is a tricky property to define and even trickier to provide a controlled vocabulary for that is detailed enough to differentiate object types in interesting ways, but broad enough to apply universally.

In the current definition I think "the physical type of object" and "that is curated as a single specimen" are problematic when combined. It might be useful to consider whether objectType is designed to fit cataloged objects or physical objects, which are not always equivalent, e.g. a cataloged object may have multiple physical objects that belong to different collections depending on preparation or research use. You might have a single organism, let's say a bat, for which you prepare a dry study skin (stored in a cabinet), a non-articulated skeleton (stored with the skin), and a DNA sample (stored in a freezer). Those three types of physical objects might be treated as a single cataloged object, i.e. one record in the database, one record on GBIF, citations in the literature for one biological individual that is now one specimen, etc.

Maybe this property just needs to be flexible enough for individual collections to determine their own scope re cataloged objects vs physical objects? In how I'm understanding the current CD model, either way would have implications for other classes: if you count all three bat parts separately then classes like Storage Location and Object Quantity fit more cleanly, but if you count all three bat parts as a single cataloged object then classes like Taxon Quantity and Digitization Level Assessment fit more cleanly.

Arctos has given this a considerable amount of thought. See their rationale for "what is a cataloged object" vs. "what kinds of parts make up a cataloged object" (also see their code table for controlled vocab, which isn't meant to be exhaustive but gives a view into how detailed some collections folks get about object type).

[mswoodburn]

As discussed, we've made this a bit more flexible in the definition and removed the controlled vocabulary constraint (although should be recommended to use some form of controlled vocabulary for any CD scheme where using this property as a dimension to group and report on CDs). I've also added in some examples based on NHM Join the Dots data.

[qgroom]

This should generally be used for classifying objects by taxon

Shouldn't this be...

This should not generally be used for classifying objects by taxon

[Blerina01]

Hi Everyone,

If we will include all the physical objects of the collection, either zoological or herbarium one, then i would agree with the second sentence which fit better "This should not generally be used for classifying objects by taxon".

Thank you!

Cheers, Blerina

On Thu, 28 Jan 2021, 19:10 Quentin Groom, notifications@github.com wrote:

This should generally be used for classifying objects by taxon

Shouldn't this be...

This should not generally be used for classifying objects by taxon

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[mswoodburn]

Yes, sorry - very bad word to miss out! I've fixed that in the notes.

[wouteraddink]

suggestion to change from objectType to materialAppearance or objectAppearance. See also my comments in https://github.com/tdwg/cd/issues/255.

controlled terms used in SYNTHESYS+ (the descriptions are for different disciplines so there is some repetition):

Dried assemblage | Not in fluid Dried - not assembled | Not in fluid, human remains bones, (not recent) Fluid preserved |   Microscope slides |   Cryopreserved/frozen - 80C |   Artefacts: climate controlled conditions | Air conditioning/climate controlled units/rooms Artefacts: non climate controlled conditions | Not air conditioned/climate controlled units/rooms can include mummies Pressed and dried | Herbarium specimens Dried | Fruits wood samples, not preserved in fluid. Fluid preserved | Flowers/fungi in alcohol/formalin/glycerine Microscopic slides | Microscopic slides Cryopreserved/frozen 80C | DNA/RNA, tissue Spore print | Spore print Dried | Not preserved in fluid Cryopreserved DNA/RNA | DNA/RNA, tissue Dried - assembled | Multiple animal parts or entire organism skeletons, stuffed animals Dried - not assembled | Animal part: tanned skin, egg shell, etc Fluid preserved | Animals in alcohol/formalin/glycerine Dried and pinned | Pinned insects Dried - assembled | Not pinned. Multiple animal parts of entire organism Dried - not assembled | Animal part. shell, bone, etc. Fluid preserved | Animals in alcohol/formalin/glycerine Microscope slides | Microscopic slides Cryopreserved / frozen -80C | DNA/RNA, tissue Other |   Unspecified Macrofossils (dry preserved) | Handspecimens/slabs/matrix support (i.e. surrounded by original sediment), matrix free (free from original sediment) - botanical, vertebrates, invertebrates, trace fossils etc. Mesofossils (dry preserved) | Small fossilised parts of plants such as fruits, leaves, and seeds contained in Jars, Franke cells - i.e. a paper container, the size of a preperation glass with a circular space covered by a lid-covering glass. Microfossils (dry preserved) | Dry samples, in jars, trays (i.e. not preserved in fluid) etc. Macrofossils (fluid preserved) | Preserved in a fluid in a jar, a concealed units. Messofossils (fluid preserved) | Preserved in a fluid in a jar, a concealed unit. Microfossils (fluid preserved) | Preserved in a fluid in a jar, a concealed unit Fossils preserved in Amber, natural resin | required to be kept in humidity and light controlled storage units. Microscope slides | Microscope slides of microfossils, messofossils and macrofossils for either binocular or petrographic microscopes Oversized fossils | Too large to be fit into standard storage units. Other | Sieving residue, other microscopic preperations (SEM stubs) etc. Unspecified Macro-objects | Handspecimens/hand-held objects/slabs that can be contained in standard units (draws, shelves, cabinets). E.g. rocks, minerals, gems (rough natural form) and ores. Micro-objects | Can only be handled/observed with the aid of a microscope. Contained in jars Cut/polished gemstones | High-expense/rare/precious stones that need careful handling and contained in secure units Microscope slides | Binocular or petrographic microscope slides of rocks, minerals, gems, ore, alloys etc Cores | Rocks, Ore, Sediments (soil, mud etc.) etc. Fluids | Hydrocarbons, oils etc. Oversized objects | Requires extra space because objects are too large for standard units/containers. Hazardous material/objects | Material or fluids that are hazardous to health - radioactive, toxic etc. Other | Does not fit into the above subcatagories. e.g. crushed rocks, other microscopic prepared objects (e.g. SEM stubs) etc. Macro-objects | Handspecimens/hand-held/slabs Meteorites, Moon rock etc Micro-objects | Can only be handled/observed with the aid of a microscope. contained in Jars, sample bags etc. Oversized objects | Requires extra space because objects are too large for standard units/containers. Microscope slides | Thin sections of meteorites etc.

This set is particularly helpful for collection management or image recognition services.

Note: This is NOT the same as BioCASE ObjectClassType vocabulary: https://www.biocase.org/doc/Results/WP3/Oldversions/SpyDoc_122/BioCASE_MetaProfile_1.22.shtml#complexType_ObjectClassType_Link01DEB818 which is more like Material (wood, bark, leaf, gold, ivory etc) although a bit mixed.

[wouteraddink]

Note that in Synth+ dashboard development this was called PreservationType which I think was not right, as that should be more something like http://arctos.database.museum/info/ctDocumentation.cfm?table=CTPART_PRESERVATION, see also https://github.com/tdwg/cd/issues/65 (preservationMethod)

[essvee]

Updated the property name + examples to reflect that this property/discussion focuses on a lower-level classification than objectType which has a new issue assigned: https://github.com/tdwg/cd/issues/304.