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.”)

Part Names

specimen_part . part_name VARCHAR(255) not null

Part names provide information about the physical objects associated with the catalog record. They can be subsampled, loaned, and have one or more attributes associated with them.

Part names should refer to specific anatomical parts or recognized groups of parts (e.g., “postcranial skeleton”). With rare exception, part names are the singular form of a noun. There is no requirement to include a part in a catalog record.

A part name should be entered for each distinct physical object associated with the catalog record e.g., skull and postcranial skeleton. Parts already contained in the postcranial skeleton may be entered on separate lines for clarity when necessary. An acceptable list of part names in a catalog record might be:

Such an entry would designate a postcranial skeleton that has a disarticulated right humerus. Situations like this are typically created when a subsample is removed for a loan. The addition of appropriate part condition, disposition, remark, and/or attribute are used to clarify.

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 enumerates 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 functionality may be used to create tissue subsamples for destructive analysis, split particularly valuable samples into multiple freezers to eliminate single-point failure risk, to better track a specific bone (e.g., for loan), or for any other situation which results in one part being split into multiple parts or altered into a new type of part.

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.

Preservation

NOTE: The definition of Tissue above is being deprecated, and embedded preservation information is being removed from part names. The following will become definitive as the migration is completed.

Part Preservation is controlled by a code table. Any part may have any number of preservation events, and like all Part Attributes they may include date and determiner information. “Tissueness” is an attribute of preservation.

For example, a part preserved in “90% ethanol” would be a tissue, unless it also has an additional (probably earlier) “formalin” attribute.

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 or RNA may be extracted. Typically, these parts are soft organs, or parts thereof, preserved by freezing, drying, or preservation in buffer or alcohol. However, tissue parts may include whole organisms or other body parts collected and preserved for the purpose of genetic, molecular, or chemical sampling. Such samples commonly supply DNA for sequence analysis, and flagging these parts as tissues allows researchers 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.

Parts flagged as tissues are not necessarily suitable for every usage, and may include products such as venom.

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": ""
      }
    ]
  }
]