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.

Part Names

Specimen_Part . Part_Name VARCHAR(70) not null

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.

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:

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 environmental 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.

Tissue

Each part name may be flagged as representing “tissue.”

A tissue in Arctos is defined as a specimen part that was collected and/or preserved for molecular or chemical studies, and is intended for consumptive use.

While we have been unable to produce a functional definition, tissues are generally samples 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.

Tissues are not necessarily biological productions of the cataloged item. For example, parasites may be cataloged as parts and flagged as tissues.

Tissues are not necessarily suitable for any particular usage, and may include products such as venom.

Disposition

Coll_Object . Disposition VARCHAR(20) not null

Disposition describes the status of parts and, as an abstract generality, the status of cataloged items. Typical values are controlled by a code table and include:

Condition

Coll_Object . Condition VARCHAR(255) not null

Condition is used for entries such as “broken” or “dissected.” The following condition ratings apply specifically to parts with the “is_tissue” flag:

Lot Count

Coll_Object . Lot_Count NUMBER(22) 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.

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, e.g.:

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

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 crytube embryo (lot count = 2)
Two liver samples stored in individual tubes 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

Specimen_Part . Sampled_From_Obj_ID NUMBER(22) not 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.

Remarks

Coll_Object_Remark . Coll_Object_Remarks VARCHAR2(4000) null

Use remarks to document non-standard information pertaining to the specimen part. Do not use remarks for any information which could be recorded with more structure elsewhere, including Part Attributes.

Specimen Results

Specimen Results column “partdetail” contains “core” part information formatted as JSON (JavaScript Object Notation). JSON is a lightweight data exchange format capable of representing complex data (e.g., multiple parts each with multiple child attributes) as simple text strings. Most browsers will “pretty print” JSON data, making these data very human-readable.

The most simple data will be one part and it’s direct metadata:

[
  {
    "part_name": "skull",
    "lot_count": "1",
    "disposition": "in collection",
    "condition": "unchecked",
    "barcode": "",
    "container_path": "",
    "remark": "",
    "attributes": []
  } 
]

Many specimens will contain data for multiple parts:

[
  {
    "part_name": "skull",
    "lot_count": "1",
    "disposition": "in collection",
    "condition": "unchecked",
    "barcode": "",
    "container_path": "",
    "remark": "",
    "attributes": []
  },
  {
    "part_name": "study skin",
    "lot_count": "1",
    "disposition": "in collection",
    "condition": "unchecked",
    "barcode": "",
    "container_path": "",
    "remark": "",
    "attributes": []
  }
]

And some specimens will also contain part attribute data for one or more of the parts:

[
  {
    "part_name": "study skin",
    "lot_count": "1",
    "disposition": "in collection",
    "condition": "unchecked",
    "barcode": "",
    "container_path": "",
    "remark": "",
    "attributes": [
      {
        "attribute_type": "location",
        "attribute_value": "Cabinet 12; Drawer 5",
        "attribute_units": "",
        "determined_date": "",
        "determiner": "",
        "attribute_remark": ""
      }
    ]
  }
]