Specimens or Skeletal Elements

Specimen are individual human remains which can be categorized. Many of the modules on the site are focused on specimens and their association details such as Biological Profile, DNA Profile, Measurements, Zones, Articulation, Pair Matching, Refits, Morphology, Pathology, Trauma, Taphonomy, etc. This section will explore navigating the specimens and their associations screen related characteristics.

• Specimen Navigation
• Creating a New Specimen
• Creating a New Specimen Group
• Specimen Search
• Specimen Details

Specimen Navigation

On the left side bar - you can access the main options for specimens. For Report Dashboard - please see the Reports documentation.

Creating Specimens

You can create a new specimen in multiple ways. For example you can create a a single specimen or multiple specimens belonging to a bone group such as Arm, Shoulder, Vertebral Column, Hand, Feet, etc. In the future we plan to include specimen creation via a Homunculus. I know I'm getting ahead of myself but that is on our dream list.

Single Specimen

To create a new specimen navigate to the Left Sidebar Menu -> Specimen -> New Specimen. You will be taken to the new specimen screen as shown below.

The screen fields are shown below. Fields in bold are required.

Attributes	Data Type	Size	Validation Rule	Required/Optional
Accession	String	32 chars	Can only contain letters, numbers, dash and space and should have min 3 chars	Required
Provenance1	String	32 chars	Can only contain letters, numbers, dash and space	Optional
Provenance2	String	32 chars	Can only contain letters, numbers, dash and space	Optional
Designator	Alphanumeric	32 chars	Can only contain letters and numbers	Required
External ID	String	32 chars	Can only contain numbers and decimals	Required
Bone	Id	id	valid bones via dropdown	Required
Side	String	8 chars	valid sides via dropdown (Left, Right, Middle, Unsided)	Required
Completeness	String	16 chars	valid completeness via dropdown (Complete, Incomplete)	Required

Once these details are filled and the user can either select 'SAVE AND EDIT' or 'SAVE AND ADD'. If the user selects 'SAVE AND EDIT', a new specimen with an appropriate id is generated and the user is navigated to the below screen. The screen is in View state.

1. Edit button enables the user to edit the specimen.
2. The Kebab menu button consists of DNA profile, Isotope Analysis, Zone Classification, Taphonomy, all specimen associations and pathology, and Review.

To edit a specimen, you can search for it using the advanced search feature under specimen menu or the search function available on the home page.

Edit a specimen via the home page search Edit specimen via Specimen→Advanced Search

The screen fields are shown below. Fields in bold are required.

Attributes	Data Type	Size	Validation Rule	Required/Optional
Accession	String	32 chars	Can only contain letters, numbers, dash and space and should have min 3 chars	Required
Provenance1	String	32 chars	Can only contain letters, numbers, dash and space	Optional
Provenance2	String	32 chars	Can only contain letters, numbers, dash and space	Optional
Designator	Alphanumeric	32 chars	Can only contain letters and numbers	Required
External ID	Alphanumeric	32 chars	Can only contain numbers and decimals	Required
Bone	Id	id	valid bones via dropdown	Required
Side	String	8 chars	valid sides via dropdown (Left, Right, Middle, Unsided)	Required
Completeness	String	16 chars	valid completeness via dropdown (Complete, Incomplete)	Required
Measured	Boolean		true/false toggle	Optional
DNA Sampled	Boolean		true/false toggle	Optional
Isotope Sampled	Boolean		true/false toggle	Optional
Inventory Completed	Boolean		true/false toggle	Optional
Reviewed	Boolean		true/false toggle	Optional
CT Scanned	Boolean		true/false toggle	Optional
X-ray Scanned	Boolean		true/false toggle	Optional
3D Scanned	Boolean		true/false toggle	Optional
Individual Number	String	32 chars	can only contain letters, numbers, dash and space	Optional
Remain Status	String	16 chars	valid sides via dropdown (In Lab, Released)	Optional

Click "Save" When you are done making changes.

A specimen can be deleted by clicking on the delete icon and then confirming the deletion in the pop-up.

Multiple via Bone Group

To create a multiple specimens via bone group - navigate to the Left Sidebar Menu -> Specimen -> New via Bone Group. You will be taken to the new specimens via bone group screen. Here you can create multiple specimens that belong to the same bone group.

Tip

This is the preferred way to create multiple specimens within a bone group as CoRA will automatically create articulation relationship amongst them. You can also apply Pathology, Trauma and Taphonomy to these specimens at the time of creation simplifying and speeding up the data entry process.

The fields to create a new bone group are:

• Bone Group
  • Grouping
  • Bones
  • Side (defaulted to 'Left')
  • Completeness (defaulted to 'Complete')
• Accession
  • Accession Number
  • Provenance 1
  • Provenance 2
  • Designator
• Pathology
  • Traumas
  • Pathologies
  • Taphonomies

The bolded fields are required. Once you have created a new bone group, you can edit the fields and click "Save" to update the bone group.

Attributes	Data Type	Size	Validation Rule	Required/Optional
Bone Group	String	64 chars	can only contain letters	Required
Bone Group Id	String	64 chars	valid UUID, auto generated	Required
Side	String	8 chars	valid sides via dropdown (Left, Right, Middle, Unsided)	Required
Completeness	String	16 chars	valid completeness via dropdown (Complete, Incomplete)	Required
Accession	String	32 chars	can only contain letters, numbers, dash and space and should have min 3 chars	Required
Provenance1	String	32 chars	can only contain letters, numbers, dash and space	Optional
Provenance2	String	32 chars	can only contain letters, numbers, dash and space	Optional
Starting Designator	Alphanumeric	32 chars	can only contain letters and numbers	Required
Bone	Id	id	valid bones via dropdown	Required

Once you have created a new bone group, you can edit the fields and click "Save" to update the bone group.

Tip

When creating specimens via bone groups, you only have to specify the starting designator and CoRA will automatically create the specimens with that starting designator and increment it for subsequent specimens within the bone group.

Multiple via Homunculus

To create a multiple specimens via homunculus - click the "New via homunculus" link on the Specimens left navigation bar. You will be taken to the new specimens via homunculus screen.

Warning

This is an experimental feature and is work in progress. We will keep you posted when this feature is available.

Specimen Actions or Details

The screenshot below shows the Actions or Details menu for the selected specimen. Here you can enter association data for the specimen. Each of the Action or Details menu option is explained in the following section.

Biological Profile

The Biological Profile is where you can record the various methods and method features for method type Age, Ancestry, Sex, and Stature. CoRA's intellisense engine will automatically provide you the available methods for each method type which are currently registered in CoRA. The user can add, edit or delete a method.

Age

Sex

Ancestry

Stature

Warning

This section needs to be documented

DNA Profile

The DNA Profile screen displays the following elements about a bone:

• DNA Sample Number
• Lab
• External Case #
• BTB Request Date
• BTB Results Date
• Disposition
• Sample Condition
• Weight Sample Remaining

On this screen, you can also view the "Mito", "auSTR", and "Y-STR" forms and navigate by clicking the form name or by clicking the Next button.

Isotope Analysis

The 'Create Isotope' section allows to create a isotope for the given bone. This section has the following elements. - Lab - External Case # - Isotope Sample Number

After you create the Isotope, you will receive the "success" message. By selecting the sample number, the Isotope screen pops up. Click on the Edit button to edit the information under each section.Click on the Save button under each section saves the information and navigates the user to the next section of information. All the updated information can be saved at once by clicking on the ‘Save All’ button.

Taphonomy

The Taphonomies section allows you to view Taphonomies for the given bone. To add Taphonomy, click the pencil icon to edit and select Taphonomies. Click the Save icon to save the changes.

Zonal Classification

The Zones pane displays various zones of the bone. For example below are the following zones about the Cervical Vertebra:

• Body
• Right Transverse Process
• Left Transverse Process
• Spinous Process

These fields are read only - to edit then click the pencil icon. Multiple zones can be selected. All the listed Zones can be selected or deselected by clicking the ‘Select all’ check box. Click the save icon to save the changes.

Measurements

The measurements pane displays various measurements of the given bone. Only the specimens associated with a bone that is measured will have measurements for that bone. Bones associated with a specimen that are not measured will not have any measurements. The measurements generally vary from one bone to another and following are the measurements for a given bone Femur:

• Fem_01 Maximum Length
• Fem_02 Bicondylar Length
• Fem_03 Epicondylar Breadth
• Fem_04 Maximum Head Diameter
• Fem_05 Medial-Lateral (Transverse) Subtrochanteric Diameter
• Fem_06 Anterior-Posterior (Sagittal) Subtrochanteric Diameter
• Fem_07 Anterior-Posterior (Sagittal) Midshaft Diameter
• Fem_08 Medial-Lateral (Transverse) Midshaft Diameter
• Fem_09 Maximum Midshaft Diameter of the Femur
• Fem_10 Minimum Midshaft Diameter of the Femur
• Fem_11 Midshaft Circumference
• Fem_12 Maximum Anterio-posterior Length of the Lateral Condyle
• Fem_13 Maximum Anterio-posterior Length of the Medial Condyle
• Fem_14 Minimum Anterior-Posterior Diameter of the Diaphysis
• Fem_15 Minimum Medial-Lateral Diameter of the Diaphysis
• Fem_16 Minimum Superior-Inferior Neck Diameter
• Fem_17 Maximum Diameter along the Linea Aspera
• Fem_18 Upper Breadth of Femur
• Fem_19 Lateral Condyle Height

These fields are read only - to edit, click the pencil icon. the minimum value, threshold limit and maximum limit are indicated to the user through the alerts. Click the save icon to save the changes or ‘Undo’ icon to undo all the changes made. The blue badge on top of the bone name indicates the number of measurements filled out of the total number of available measurements for that particular bone. The pane can be expanded or collapsed by clicking on the arrow icon.

Association

There are four types of associations. Process of adding each association is shown below. After the association is added, refresh the page to see the Details button updated. The details button opens a data table of all available associations under that specimen.

Pair Matching

Refits

Articulations

Morphology

Pathology, Anomaly & Trauma

Pathology, Trauma and Anomaly can be accessed on one screen as different tabs. The user can create a new item by clicking on the create button.

Pathology

Anomaly

Trauma

Specimen Review

The review tab is a pane which displays all other sub reports in one area. All reports are editable in the pane. For information on individual reports - see their detailed documentation.

Specimen Bulk Edit

Several specimen fields can be bulk-edited. To bulk edit, select multiple specimens by clicking in the boxes next to the specimens you want to edit, click on the Actions tab, and then select Batch Edit.

In the popup, select the changes you wish to make. When you mark a specimen as scanned, completed, or reviewed, the date for the change is auto-filled to the current date.

If the remains are marked as in the lab, there is no corresponding date.

If the remains are marked as released, there is a date field.

Specimen Search

The easiest way to search for specimens is to use the top search bar in the header. To find out more visit the search documentation

---

Last update: 2024-05-05
Created: 2023-12-22