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.  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.

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 and definitions are now being incorporated.  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)
humerus (right) [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.

Some notes on the terminology of parts:

• An entry of skin is presumed to be traditional study
  skin unless specified otherwise.
• Part modifier rug mount, when applied to a skin,
  refers to a taxidermy-mounted rug mount of an animal. Distal phalanges
  (claws) are presumed to be present. Tanned should be entered
  as a preservation method if appropriate. Flat skins, as of small mammals,
  are not rug mounts.
• A skull is not presumed to be part of a skeleton.  Skeleton is not a valid part and is being phased out.  Complete skeletons should be entered as postcranial skeleton and skull.

Modifier:  Useful Part Modifiers include “right” or “distal”.  Unacceptable Part Modifiers include “various” and “crushed”.  Parts with no Part Modifier or Condition are presumed to be complete and undamaged.  Vocabulary controlled by a code table.

Preservation Method  is not necessary for parts where the method is self evident such as bones or traditionally-prepared (i.e., air dried) study skins.
Preservation Method may refer to a preservation process (e.g., “tanned”)
or a storage media (e.g., “ethanol”), but information about present storage (e.g., “70% ethanol”) is tracked by container.  Vocabulary is controlled by a code table.

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

• in collection
• being processed
• on loan
• missing
• destroyed

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.

Tissues?:  This is a flag that indicates that a Specimen Part is a sample intended
for subsampling and distribution, generally for purposes of destructive analysis. 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.

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)

Sampled From designates a part defived 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.