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Osteoware: Standardized Skeletal Documentation Software

Osteoware: Standardized Skeletal Documentation Software

The Pathology Module

The Pathology Module Main Screen | Size, Shape and Bone-Specific Abnormality | Abnormal Bone Loss | Abnormal Bone Formation | Trauma | Porosity and Channel Formation | Pathological Conditions of the Vertebrae | Vertebral Anomalies | Arthritis | Literature Cited

The Pathology Module has the greatest number of data entry screens with each screen representing a category of pathological change such as bone loss, arthritis or trauma. Click on any of the data entry screen links listed above (in blue) to jump to that section of this webpage.


The initial organization of the module was based on Buikstra and Ubelaker (1994, hereafter referred to as the Standards), but the most extensive changes to the Standards protocols have been made in the Pathology Module of OsteowareTM, consisting primarily of expansions in the descriptive categories scored. This web content only provides a general overview of the changes, thus it is recommended that users download Volume II of the manual before beginning data entry. Neither the web content nor the user manual is intended to provide an in-depth review of paleopathology and the user should consult some of the excellent books available on the subject, such as Ortner (2003) and Aufderheide and Rodríguez-Martín (1998), if any of the conditions scored in Osteoware are unfamiliar.

In documenting pathological lesions, it is recommended that the text description field be utilized extensively to record more detailed descriptions, lesion measurements, and supplemental information such as differential diagnoses and supporting references. Because the description field is searchable, this will facilitate analysis and/or later identification of specific conditions recorded in your Osteoware database.

The Pathology Module Main Screen (Side/Aspect/Section)

When the Pathology Module is opened from the Osteoware Home Screen, the default page is the Pathology Module Main Screen (also called the Side/Aspect/Section data entry screen). Skeletal elements or anatomical regions, i.e., Upper Limb, are first selected from the Bone drop-down menu (blue box at the top of the screen).

The Pathology Module Home Screen

If the pathological condition affects the surfaces of multiple elements in a joint complex, data can be entered simultaneously for all surfaces by using the Joint button. Each selected bone in the joint complex will have a separate record in the database with identical pathology codes and description fields.

Side, Aspect, and Section menus are used to specify the areas of the selected bone, anatomical region, or joint complex affected by a pathological condition. After all selections have been made on the home screen, click on one of the tabs to continue data entry. Note that some of the screens are contextually driven (i.e., Vertebral Anomalies), meaning the skeletal element in the Pathology Module Main Screen must be selected in order to have all of the relevant data entry tabs available.

If the observations of the pathological condition are not appropriate for any of the pathology data entry screens, then select the Other Pathology NOT in System (describe in comments) check box and provide a detailed description.

At any point during data entry, you may press the Check button to view all pathology records entered for that catalogue number. You may also right-click on a record in the Check Entries screen to view the text version of the pathology codes.

The Check Entries data entry screen.

NOTE: You can go back and edit the text description of any pathology record at any time, but you will NOT be able to revise the selected check boxes or radio buttons once saved. To edit check boxes or radio buttons, delete the entire record by selecting it in the Check Data Entry screen and then pressing the Ctrl and Delete keys. Remember to copy the Description before deleting the record in order to paste it into the new entry.
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Size, Shape and Bone-Specific Abnormality

Anomalies affecting the size and shape of bone include conditions that are genetic, nutritional, behavioral, infectious, traumatic, or developmental. This module could be considered a “catch-all” for those abnormalities that do not fit well in more easily defined categories, such as trauma or abnormal bone loss; however, overlap with other categories is possible. For example, flaring metaphyses may be described as a shape abnormality as well as abnormal bone formation.

Data entry closely follows the Standards except:

  • Gigantism was added to Skeleton, Total.
  • Several common bone-specific anomalies such as paracondylar tubercles or processes, vastus notch/bipartite patella, and squatting facets were added.
  • Some of the anomalies in this section can be classified as non-metric traits rather than pathological conditions, but note that non-metric traits classified as being of “primary importance” in the Standards are scored under a separate module from pathological conditions (cranial) or scored in the inventory (post-cranial).

In future editions of Osteoware, a separate module for non-metric traits of the postcranium will be added and some of the entries such as vastus notch will be moved from their temporary location in pathology.

Data entry screen for shape abnormalities of a long bone.

Data entry screens in the Size/Shape/Bone-specific Abnormality module are contextually driven, meaning the menus and selections will change depending on the bone selected in the Pathology Module Main Screen. The screen shot shows the data entry screen that appears when a long bone (femur) is selected.

Case Study – Size/Shape/Bone-specific Abnormality

Uniform widening of a right ulna in anterior (bottom) and medial (top) view.

On the Pathology Module main screen, select Ulna from the bone drop-down menu, Right for the side, Circumferential for the aspect, and all of the sections listed. The Size/Shape/Bone-specific Abnormality screen for a long bone can then be opened and Uniform Widening entered by using the check box. The appropriate selections can also be made in the Abnormal Bone Formation data entry screen before saving. Two data records will be generated, one will contain the Size/Shape/Bone-specific Abnormality codes and the other will contain the Abnormal Bone Formation codes. The data entered on the Pathology Module Main Screen detailing anatomical location and the text in the description field will be copied into both data records.
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Abnormal Bone Loss

Abnormal bone loss can result from increased bone resorption and/or decreased bone formation, resulting in focal lesions (osteolysis) or diffuse bone loss (osteopenia/osteoporosis). Both kinds of bone loss can be scored in this module. This scoring system closely follows the Standards, except:

  • Lytic lesions at muscle/ligament attachment sites are scored separately under enthesial defects
  • Motheaten and permeated destruction were added following Ragsdale (1993).

Abnormal Bone Loss data entry screen.

The Location and Extent of Involvement are recorded for all lesions. For focal lesions, score the number of foci, maximum size, and characteristics of the lesion margins (Bony Response). Motheaten and permeated destruction refer to particular patterns of focal bone loss. Diffuse bone loss is scored with or without associated cortical thinning. Pathological structural collapse associated with bone loss is also recorded in this module, for example, collapse of the spine resulting from the lytic lesions of tuberculosis.

Lytic lesions at muscle attachments are recorded under Enthesial Defects. In future versions of Osteoware, we plan to provide a separate data entry page for recording entheseal changes in more detail. Abnormal bone loss data entry does not include vault and orbit changes attributed to porotic hyperostosis, the articular changes of arthritis, or porosity found on other skeletal elements, which are scored in other modules.

Case Study – Bone Loss

Multifocal, lytic lesions in a cranium (left) with the radiograph of the same individual (right).

First select Cranium from the Bone drop-down menu. The external table, diplöe, and inner table are affected, so all three locations are selected. The Extent of Involvement is <1/3 of the cranial surface. Six to ten foci are present and the size of the largest lesions is 1-5 cm. The lesions are characterized by localized destruction, circumscription, and sclerotic reaction; the sclerosis is visible on the radiograph. The description section should detail these pathological changes, including the specific locations, measurements and morphology of individual lesions whenever possible.
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Abnormal Bone Formation

The initial categorization of abnormal bone formation is by location: periosteal, endosteal, or abnormal matrix. Classification and data entry follows the Standards protocol except:

  • A compact/remodeled selection was added to the Periosteal Surface menu.
  • A new Surface Appearance menu was added to describe external cortical texture.
  • “Other” was added as a selection under ossified tissue.

Abnormal Bone Formation data entry screen.

The Productive Reaction Type and Surface Appearance menus refer specifically to Periosteal Bone. Both menus are left blank for bone formation on the Endosteal Surface and for Abnormal Matrix Formation. The most common productive reaction types are either solid or lamellated but distinguishing between these usually requires radiographs. If radiographs are not available and the reaction type cannot be determined based on external morphology, this section should be left blank. Comments can be entered into the description to indicate the possible range of reaction types for a given lesion. Selections under Ossified Tissue and Specific Structures help categorize different types of abnormal bone formation or identify structures commonly associated with abnormal bone to facilitate searches of the database. Exostoses at muscle attachments can be scored as enthesophytes. In future versions of Osteoware, we plan to provide a separate data entry page for recording entheseal changes in more detail.

Case Study – Abnormal Bone Formation

Occipital of a child with abnormal bone formation in the right cerebellar fossa.

Occipital is chosen from the bone drop-down menu and compact/remodeled is selected from the Periosteal Surface menu. Reaction Type is Solid and the Surface Appearance is described as Irregular because one type does not predominate (smooth, porosity, nodular). Details of this appearance can be entered into the description. If the entire endocranial surface of the Occipital was selected from the Side/Aspect/Section then the Extent of Involvement is <1/3 affected.
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The trauma module covers dislocations and various fracture types, including those caused by blunt force, sharp force, and projectile entry. Fractures involving the vertebral body or classified as spondylolysis should be recorded on the Vertebrae data entry screen. Classification and data entry follows the Standards protocol except:

  • “Other” has been added to the Fracture Type heading.
  • Deformation and Traumatic enthesopathy selections have been added to Trauma Complications.

Trauma data entry screen.

Fractures are first classified by type. Choose Other for sharp force and high velocity projectiles, and specify the cause by selecting all check boxes that apply under Fracture Characteristics. The timing of the injury is divided into perimortem and antemortem fractures. Postmortem breakage is documented in the Taphonomy Module. When it is unclear if a fracture is perimortem or postmortem, it is entered as trauma and Ambiguous, possibly perimortem is selected from the Perimortem Fractures menu. A detailed explanation of the ambiguous nature of fracture timing is then entered into the description. Degree of healing is selected when the fracture is clearly Antemortem. Dislocations are classified as traumatic, congenital, or ambiguous.

Case Study - Trauma

An antemortem fracture of the left femur. A surgical repair that used a wire to connect the fracture ends can be seen in the radiograph.

On the Pathology Module main screen select Femur from the bone drop-down menu, Left for Side, Circumferential for Aspect and Middle 1/3 of the diaphysis for Section. Fracture type is Simple (Transverse/Oblique) as seen in the radiograph. None of the Fracture Characteristics or Perimortem Fracture selections apply, so both sections are left blank. Select Callus formation, sclerotic reaction from the Antemortem fractures menu and Deformation from the Trauma Complications menu.
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Porosity and Channel Formation

This data entry screen covers porosity and vascular channels, the latter are only scored on the cranium and are most often seen in the orbits or on the endocranial surface. Many changes represent the expansion and reconfiguration of the porotic hyperostosis classification Standards to cover various types of porosity:

  • Scoring of channels (vascular) has been added.
  • Diploic expansion is scored separately for documentation of cranial porosity unrelated to porotic hyperostosis.
  • Porosity can be scored on any bone.
  • More detailed descriptions of porosity by pore size and density have been added along with features commonly associated with ectocranial porosity.
  • Pores are defined explicitly as narrow and deep perforations and distinguished from pits which are defined as wider and shallower indentations.

Porosity and Vascular Channels data entry screen.

Changes in scoring cranial porosity reflect current research in paleopathology indicating that the diplöic expansion associated with anemia is only one possible cause of orbital and ectocranial porosity. Scoring of porosity throughout the skeleton allows greater flexibility and eliminates data entry problems when it is unclear if the porosity results from woven bone formation or bone loss, particularly when histological analysis is not possible. However, when porosity is clearly just a feature of woven bone, it is still scored under abnormal bone formation.

Case Study – Porosity and Vascular Channels

Porosity and Vascular Channels on the superior aspect of the left orbit.

Cranium or Frontal is first selected from the Bone drop-down menu for the lesions of the left orbit. Pinpoint porosity and Between pinpoint and 0.5 mm are selected from the Pore Size menu because check boxes allow multiple selections. Density of Pores applies to the maximum density, so 25 to 50 High is selected. For Activity, both Active and Healing are selected; the Location of Porosity is Orbits; and Diploic Expansion is None. Other Features are those associated with ectocranial porosity so this menu is left blank. Increased vascular channels are present and these are first scored by their Location in the Orbits. Vascular channels in the orbits tend to be fine and shallow, but here they are distinct enough to score as Deep with Sharp Edges and Flat Interchannel Surfaces. Channel Density is scored as disrupting 25-50% of the lamina in the affected region.
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Pathological Conditions of the Vertebrae

This section includes age- and activity-related structures, specific types of vertebral fractures, as well as abnormalities associated with various diseases and congenital conditions. Note, however, that some Vertebral Anomalies are listed on a separate data entry screen. Several of the categories in Vertebral Pathologies include changes to the Standards protocol:

  • Porosity associated with vertebral osteophtyes was added.
  • The distinction between sacral clefting and spina bifida was clarified.
  • Vertebral body fractures were added.
  • Abnormal shape of the spinal column was added.

Vertebrae data entry screen.

Schmorl’s nodes and Spondylolisthesis are simply scored as present and detailed observations are recorded in the description field. Osteophytes and Syndesmophytes are scored by maximum degree of expression. The presence of endplate porosity associated with osteophytes is indicated in a separate menu. Unlike the Standards, a distinction is made between partial and complete cleft neural arch only and spina bifida, indicated by a cleft neural arch with additional evidence of neural tube defect such as an enlarged vertebral canal.

Spondylolysis is scored as partial or complete by the selections made on this screen. Unilateral and bilateral fractures should be specified in the description and Spondylolisthesis may also be checked when it is complication of neural arch fracture.

Vertebral body fractures are scored as compression fractures, end plate depressions with and without wedging, and biconcave bodies resulting from bone loss. Any vertebral fracture not included here, such as projectile entry, is entered in the Trauma data entry screen. Abnormal shape of the spinal column is recorded as kyphosis (angular or gradual) and/or scoliosis (left or right).

Case Study - Vertebrae

Vertebral syndesmophytes with fusion of T11 and T12 in ankylosing spondylitis.

Thoracic vertebrae is selected from the Bone drop-down menu. Syndesmophytes with fusion of spicules is then chosen from the Syndesmophyte menu. A more detailed description of the location of the syndesmophytes (e.g., where they occur along the vertebral rim) and a discussion of differential diagnosis should be included in the description section.
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Vertebral Anomalies

The Standards pathology coding did not include most of the conditions scored on the Vertebral Anomalies data entry screen, although some were listed as a single entry in the supplemental list of postcranial, non-metric traits. While many cases are not pathological in the strict sense of causing disease or disability, several can be associated with various syndromic conditions and some can have clinical consequences. Complete descriptions of these conditions can be found in Barnes (1994).

Vertebral Anomalies data entry screen.

Most of the anomalies scored on this data entry screen are abnormalities in vertebral segment identity, where the transition point between vertebral types is “shifted” cranially or caudally, i.e., the 12th thoracic vertebra becomes lumbardized in a cranial shift. It can be difficult to score shifting as cranial or caudal when the vertebral column is incomplete. When the direction of shifting is not clear, both the cranial and caudal shift should be selected.

Case Study – Vertebral Anomalies

Shifting at the lumbosacral border.

If only the sacrum is present, the shifting at the lumbosacral border could be sacralization of L5 or lumbarization of S1 and sacralization of caudal vertebrae. Both the cranial and caudal shifts are selected in ambiguous cases, and a complete explanation is entered into the Description field.
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Scoring for arthritis or degenerative joint disease closely follows the protocol of the Standards. The Arthritis data entry page does not cover some conditions specific to the spine, such as vertebral end plate degeneration or end-plate osteophytosis, which are recorded on the Vertebrae data entry screen. However, alterations of the diarthrodial spinal joints should be recorded under Arthritis.

Arthritis data entry screen.

The major skeletal indicators of arthritis (Surface Porosity, Lipping, Eburnation, Surface Osteophytes and Extent of Erosion) are first scored by degree of expression. Estimates of the fraction of the joint circumference or joint surface area affected are then selected for each arthritic change.

In many instances, selecting a joint from the Pathology Module Main Screen before data entry is preferable when the arthritic changes are similar over all joint surfaces. When arthritic changes are widespread, the user may choose entire appendages or even Skeleton, Total, although a loss in data detail will likely result. In cases involving selection of multiple joint surfaces using the joint button, the codes for arthritic changes and any comments entered will be copied in the database record of each individual bone.

Case Study - Arthritis

Osteoarthritic changes in a distal femur.

Surface porosity and erosion are clearly present; Lipping is sharp ridge; and Eburnation type is polish with grooves. Most of the changes are limited to the patellar and lateral condyle surfaces shown in the photograph, so the extent is scored as 1/3 to 2/3 of the joint circumference or surface.
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Literature Cited

Aufderheide AC and C Rodríguez-Martín (1998) Human Paleopathology. Cambridge University Press: Cambridge.

Barnes E (1994) Developmental Defects of the Axial Skeleton in Paleopathology. University Press of Colorado: Niwot, CO.

Buikstra JE and DH Ubelaker, eds. (1994) Standards for Data Collection from Human Skeletal Remains. Arkansas Archeological Report Research Series No. 44. Arkansas Archaeological Survey Press: Fayetteville.

Ortner DJ (2003) Identification of Pathological Conditions in Human Skeletal Remains, 2nd ed. Elsevier Science: San Diego.

Ragsdale BD (1993) Morphological analysis of skeletal lesions: Correlation