Specimen Parts

Parts are physical entities, in contrast to Cataloged Items (an abstract entity) or binary objects (such as Images).  One or many parts may comprise a Cataloged Item, and parts may be defined as the minimal units for which storage location, usage, and condition are tracked. (“Parts are things to which you can stick barcodes.”) In many collections, parts are nearly always “whole organisms” but in others, such as vertebrate paleontology, the variety of parts is huge.

Embryos and parasites may be treated parts of the host organism.  Ideally, embryos should be treated as separate cataloged items because they may have, or they may acquire, attributes distinct from those of their mothers.  Nevertheless it is often practical to consider them as parts of the mother until such time as they do acquire separate attributes.  Similarly, parasites have been recorded as parts of their hosts until such time as they might be worked into a separate parasite collection.

Specimen_Part.Part_Name
VARCHAR(70) not null
ctspecimen_part_name


Part Names: What we choose to name as a part depends on what we define as a part,  and while this is often obvious (e.g., “whole organism”), organisms become separated into parts in ways both standardized and not.  Thus, it is difficult to standardize vocabulary for every fragment worthy of preservation.

Vocabulary is controlled by a code table.  Part names should refer to specific anatomical parts or recognized groups of parts (e.g., “postcranial skeleton”).  With rare exception, parts are the singular form of a noun.  In some cases, where the parts may be a batch of indefinite size, the plural is included parenthetically (e.g., “endoparasite(s)”).

Parts, when separable, should be entered on individual lines of the parts grid as individual
collection objects. Distinct parts should be entered on separate lines, e.g., skull and postcranial skeleton.  A postcranial skeleton is considered a single part. Parts
already contained in the postcranial skeleton may be entered on separate lines for clarity.  An acceptable entry might be:

skull
postcranial skeleton (partial)
right humerus [part condition: broken]

Such an entry would designate a postcranial skeleton that has a broken
right humerus. Situations like this are typically discovered during
loans, are almost always unique, and should be dealt with on a case by
case basis.

Part name contains information once split out into part modifier, and also preservation and storage information. Preservation and storage information (eg, “reproductive tract (formalin-fixed, 70% ethanol)”) is not meant to replace container condition information (e.g., “checked-by-on-date” and fluid_preservation_history), but simply to facilitate searching.

“Traditional” (a concept which varies wildly by discipline and collection) part names are often stored without “modifiers.” A “skeleton” in a mammal collection probably consists of cleaned, dried bones stored at room temperature, for example.

The specimen part code table also contains a “is_tissue” flag. Parts flagged as “tissues” indicate a Specimen Part is a sample intended for subsampling and distribution, generally for purposes of destructive analysis, or simply a part with readily-available tissue from which DNA may be extracted. In general, these parts are soft organs, or parts thereof, preserved by freezing. Such samples commonly supply DNA for sequence analysis, and many researchers want to search for specimens from which they can readily obtain subsamples.

Coll_Object.Disposition
VARCHAR(20) not null
ctcoll_obj_disp


Disposition describes the status of parts and, as an abstract generality,
the status of cataloged items.  Typical values are:

  • in collection
  • being processed
  • on loan
  • missing
  • destroyed
Coll_Object.Condition
VARCHAR(255) not null

Condition is used for entries such as “broken” or “dissected”.

  • 5 – The best tissues. These have gone from a freshly killed animal directly into liquid nitrogen. The animal should not have been dead for more than thirty minutes.
  • 4 – These are tissues taken from animals only a few hours post mortem at cool temperatures. Such tissues should not have been previously frozen and thawed.
  • 3 – These are tissues taken from an animal that has been dead less than sixteen hours at cool temperatures, or tissues taken from an animal that was hard frozen soon after death and then thawed for preparation. Fur is not slipping.
  • 2 – These tissues may be beginning to show signs of decomposition.
  • 1 – These tissues are flaccid and thoroughly autolyzed. They probably stink.
Coll_Object.Lot_Count
NUMBER not null

A Lot Count is an integer that enumberates how many similar items comprise a part.  The value is frequently one (1), but collections of fish and invertebrates usually assign a single catalog number to all of the individual organisms of one species from one collecting event.  Thus, 86 minnows of one species from one place, collected at the same time, and stored together in one jar of alcohol would be a cataloged item with one part,and that part would have a lot count of 86 whole animals.

Catalog #
Part Name
Pres Method
Lot Cnt
123456
whole animal
alcohol
85
123456
skeleton
cleared and stained
1

Lot counts are not static; lots may be split into smaller lots by creating a separate part.  If one of those 86 minnows was prepared for skeletal study by clearing and staining, it would be necessary to create a second “part” within the catalogued item.

A cryotube of embryos or a box of ribs should have a lot count.  In contrast, three tubes of muscle from an individual will be tracked separately;  these should be entered as three collection objects, each with a lot count of one.

There must be a value of at least one (1) for each part, and the maximum is 99999. Lot counts are sometimes approximate. For example, a three-liter jar of small minnows in alcohol might be given a lot count of 400, at least until such time as someone counts the minnows.

Examples of lot count usage:

Material
Entry
Two embryos stored in the same cryotube embryo (lot count = 2)
Two liver samples stored in individual tubes liver (lot count = 1)
liver (lot count = 1)
Three tubes each containing five nematodes nematode (lot count = 5)
nematode (lot count = 5)
nematode (lot count = 5)
Ten vertebrae in a box vertebra (lot count = 10)
A jar of five salamanders of the same species from the same collecting event. whole animal (lot count = 5)
Specimen_Part.Sampled_From_Obj_Id
NUMBER null

Sampled From designates a part derived from another part. This is intended to be a subsample supplied to an investigator for destructive analysis. therefore it often applies to parts that are no longer in the collection, but if the subsamples or extracts thereof are returned, these can be tracked.