Bone inventory¶

For the (graphical) anthropological interface (#1473) the bones bone parts have to be recorded see concept

Vocabulary¶

As discussed in a meeting with FemCare Vienna there don't seem to be an established vocabulary available. This gives us more freedom to adapt it for our needs, some ideas:

Verify (ask around) if there really isn't an establish system that we can use -> in case there isn't one we should think about creating our own and publish it at e.g. Vocabs so that we can add information, reference them, offer it for use to others, ...
Make smaller categories for easier data entry, e.g. Arms and hands to 2 main categories. Hannah also offered to take a look at this.
From a data structure point of view a more consistent approach would be preferable (idea from Alex and not sure if this make sense from an anthropological point of view)
- Make all categories available for selection (change the orange ones)
- The current options "feel" strange: (undefined, 0%, 1-24%, 25-74%, 75-99%, 100%) because e.g. a wide range 25% - 75% and than just exactly 100% those are the categories used by FemCare. They represent what needs to be known for a bone: it's either in poor condition, good condition (25-75), great condition or not damaged at all. It would be possible to divide in 5 categories but there's no gain in knowledge by doing so. If we split the middle category, we have to decide how to upload the FemCare data as the only use 26-76%. Even though divide the middle section into two sections is an option, I would keep the 100% as one category as having a complete bone in "mint condition" without any damage or missing parts is rare and might indicate, that the bone was not buried in the death but was a part of a medical specimen or in a sarcophagus, etc, It also shows, that that bone might be great to use as a sample in further analyses, etc.%

Suggestions¶

We asked around about established systems, collected suggestions from our nice colleagues are listed below:

SaxFDM-Fokusprojekt (Barbara K.)
The Subdivision of skeletal system of the Foundational Model of Anatomy (Lukas P.)
Ask Digital Archeology group from ÖAI (Alex L.) -> Micheline Welte, Helmut Schwaiger: Anno
Ask Edeltraud Aspöck (Alex L., Matej D.) -> HumanOS see here
Ask @Stefan Eichert what is used at the NHM (Martina T.) -> @Stefan Eichert suggest to use Wikidata and maybe reference to THANADOS types
https://alexandriaarchive.org/linked-data/, skeletal element data were also linked using the Uber Anatomy Ontology (UBERON) vocabulary. (Martina T.)
Anthropological Notation Ontology (ANNO), see article (Martina T.)
From Freiburg: https://blog.metaphacts.com/semantic-knowledge-graphs-from-human-remains (Martina T.)
THANADOS bone inventory (@Nina Richards)
Anthropologists of the ÖAI (@Nina Richards) -> Were contacted
Foundational Model of Anatomy (FMA), Uberon Multi-Species Anatomy Ontology, Human Anatomy Ontology (HAO), Bone Dysplasia Ontology (BDO), Skeletal Anatomy Ontology (SAO) (chatGPT)

Structure¶

Structures as taken from working examples. Colors meaning:

Orange: will only be used as titles, it won't be possible to add bone preservation (e.g. 100%). But they can still be used to add a description, types, files, reference systems, ...
Blue: preservation will be recorded in numbers

Skull

Frontal
- Orbit R
- Orbit L
Parietal R
Parietal L
Temporal R
- Squama R
- Petrous R
- Mastoid R
Temporal L
- Squama L
- Petrous L
- Mastoid L
Occipital
- Pars squama
- Pars lateralis R
- Pars lateralis L
- Pars basilaris R
- Pars basilaris L
Sphenoid
- Ala major R
- Ala minor R
- Ala major L
- Ala minor L
- Sphenoid body
Maxilla R
Maxilla L
Nasal R
Nasal L
Lacrimale R
Lacrimale L
Ethmoid
Zygomatic R
Zygomatic L
Vomer
Palate R
Palate L
Inferior conchae R
Inferior conchae L
Mandible R
- Ramus R
- Condyle R
Mandible L
- Ramus L
- Condyle L
Auditory ossicles
- Stapes R
- Incus R
- Malleus R
- Stapes L
- Incus L
- Malleus L
Cricoid cartilage
Thyroid
Hyoid
TMJ R
TMJ L

Dentition

Permanent teeth
- Maxilla
  - Right side
    - I1 R (11)
    - I2 R (12)
    - C R (13)
    - PM1 R (14)
    - PM2 R (15)
    - M1 R (16)
    - M2 R (17)
    - M3 R (18)
  - Left side
    - I1 L (21)
    - I2 L (22)
    - C L (23)
    - PM1 L (24)
    - PM2 L (25)
    - M1 L (26)
    - M2 L (27)
    - M3 L (28)
- Mandible
  - Left side
    - I1 L (31)
    - I2 L (32)
    - C L (33)
    - PM1 L (34)
    - PM2 L (35)
    - M1 L (36)
    - M2 L (37)
    - M3 L (38)
  - Right side
    - I1 R (41)
    - I2 R (42)
    - C R (43)
    - PM1 R (44)
    - PM2 R (45)
    - M1 R (46)
    - M2 R (47)
    - M3 R (48)
Deciduous
- Maxilla
  - Right side
    - I1 R (51)
    - I2 R (52)
    - C R (53)
    - M1 R (54)
    - M2 R (55)
  - Left side
    - I1 L (61)
    - I2 L (62)
    - C L (63)
    - M1 L (64)
    - M2 L (65)
- Mandible
  - Left side
    - I1 L (71)
    - I2 L (72)
    - C L (73)
    - M1 L (74)
    - M2 L (75)
  - Right side
    - I1 R (81)
    - I2 R (82)
    - C R (83)
    - M1 R (84)
    - M2 R (85)

Shoulder girdle

Clavicle R
- Clavicula med. Epiphysis R
- Clavicula med. third R
- Clavicula mid. third R
- Clavicula lat. third R
- Clavicula lat. Epiphysis R
Clavicle L
- Clavicula med. Epiphysis L
- Clavicula med. third L
- Clavicula mid. third L
- Clavicula lat. third L
- Clavicula lat. Epiphysis L
Scapula R
- Body R
- Glenoid cavity R
- Acromion process R
- Coracoid process R
Scapula L
- Body L
- Glenoid cavity L
- Acromion process L
- Coracoid process L

Arms and hands

Arm R
- Humerus R
  - Humerus - proximal epiphysis R
  - Humerus - proximal third R
  - Humerus - middle third R
  - Humerus - distal third R
  - Humerus - distal epiphysis R
  - Glenohumeral R
  - Capitulum R
  - Trochlea R
- Ulna R
  - Ulna - proximal epiphysis R
  - Ulna - proximal third R
  - Ulna - middle third R
  - Ulna - distal third R
  - Ulna - distal epiphysis R
  - Trochlear notch R
  - Radial notch R
  - Ulna distal radioulnar R
- Radius R
  - Radius - proximal epiphysis R
  - Radius - proximal third R
  - Radius - middle third R
  - Radius - distal third R
  - Radius - distal epiphysis R
  - Articular fovea R
  - Circumferentia art. R
  - Radius distal Radioulnar R
  - Scaphoid lat. R
  - Lunate mes. R
Arm L
- Humerus L
  - Humerus - proximal epiphysis L
  - Humerus - proximal third L
  - Humerus - middle third L
  - Humerus - distal third L
  - Humerus - distal epiphysis L
  - Glenohumeral L
  - Capitulum L
  - Trochlea L
- Ulna L
  - Ulna - proximal epiphysis L
  - Ulna - proximal third L
  - Ulna - middle third L
  - Ulna - distal third L
  - Ulna - distal epiphysis L
  - Trochlear notch L
  - Radial notch L
  - Ulna Distal radioulnar L
- Radius L
  - Radius - proximal epiphysis L
  - Radius - proximal third L
  - Radius - middle third L
  - Radius - distal third L
  - Radius - distal epiphysis L
  - Articular fovea L
  - Circumferentia art. L
  - Radius distal Radioulnar L
  - Scaphoid lat. L
  - Lunate mes. L
Hand R
- Carpals R
  - Scaphoid R
  - Lunate R
  - Triquetrum R
  - Capitulum R
  - Hamatum R
  - Trapezoideum R
  - Trapezium R
  - Pisiforme R
- Metacarpals R
  - Metacarpal 1 R
  - Metacarpal 2 R
  - Metacarpal 3 R
  - Metacarpal 4 R
  - Metacarpal 5 R
- Phalanges R
  - Proximal phalanges R (no)
  - Medial phalanges R (no)
  - Distal phalanges R (no)
  - Sesamoid R (no)
Hand L
- Carpals L
  - Scaphoid L
  - Lunate L
  - Triquetrum L
  - Capitulum L
  - Hamatum L
  - Trapezoideum L
  - Trapezium L
  - Pisiforme L
- Metacarpals L
  - Metacarpal 1 L
  - Metacarpal 2 L
  - Metacarpal 3 L
  - Metacarpal 4 L
  - Metacarpal 5 L
- Phalanges L
  - Proximal phalanges L (no)
  - Medial phalanges L (no)
  - Distal phalanges L (no)
  - Sesamoid L (no)

Axial skeleton

Sternum
- Manubrium
- Body
- Xiphoid process
Ribs
- Right side
  - First rib R
    - First rib R head
    - First rib R mid.
    - First rib R stern.
  - Second rib R
    - Second rib R head
    - Second rib R mid.
    - Second rib R stern.
  - Third to tenth rib R
    - Third to tenth rib R head (no)
    - Third to tenth rib R mid. (no)
    - Third to tenth rib R stern. (no)
  - Eleventh rib R
    - Eleventh rib R head
    - Eleventh rib R mid.
    - Eleventh rib R stern.
  - Twelfth rib R
    - Twelfth rib R head
    - Twelfth rib R mid.
    - Twelfth rib R stern.
- Left side
  - First rib L
    - First rib L head
    - First rib L mid.
    - First rib L stern.
  - Second rib L
    - Second rib L head
    - Second rib L mid.
    - Second rib L stern.
  - Third to tenth rib L
    - Third to tenth rib L head (no)
    - Third to tenth rib L mid. (no)
    - Third to tenth rib L stern. (no)
  - Eleventh rib L
    - Eleventh rib L head
    - Eleventh rib L mid.
    - Eleventh rib L stern.
  - Twelfth rib L
    - Twelfth rib L head
    - Twelfth rib L mid.
    - Twelfth rib L stern.
Vertebral column
- Cervical vertebrae
  - C01 (Atlas)
    - C01 Body
    - C01 Arch R
    - C01 Arch L
  - C02 (Axis)
    - C02 Body
    - C02 Arch R
    - C02 Arch L
  - C03
    - C03 Body
    - C03 Arch R
    - C03 Arch L
  - C04
    - C04 Body
    - C04 Arch R
    - C04 Arch L
  - C05
    - C05 Body
    - C05 Arch R
    - C05 Arch L
  - C06
    - C06 Body
    - C06 Arch R
    - C06 Arch L
  - C07
    - C07 Body
    - C07 Arch R
    - C07 Arch L
- Thoracic vertebrae
  - Th01
    - Th01 Body
    - Th01 Arch R
    - Th01 Arch L
  - Th02
    - Th02 Body
    - Th02 Arch R
    - Th02 Arch L
  - Th03
    - Th03 Body
    - Th03 Arch R
    - Th03 Arch L
  - Th04
    - Th04 Body
    - Th04 Arch R
    - Th04 Arch L
  - Th05
    - Th05 Body
    - Th05 Arch R
    - Th05 Arch L
  - Th06
    - Th06 Body
    - Th06 Arch R
    - Th06 Arch L
  - Th07
    - Th07 Body
    - Th07 Arch R
    - Th07 Arch L
  - Th08
    - Th08 Body
    - Th08 Arch R
    - Th08 Arch L
  - Th09
    - Th09 Body
    - Th09 Arch R
    - Th09 Arch L
  - Th10
    - Th10 Body
    - Th10 Arch R
    - Th10 Arch L
  - Th11
    - Th11 Body
    - Th11 Arch R
    - Th11 Arch
  - Th12
    - Th12 Body
    - Th12 Arch R
    - Th12 Arch L
- Lumbar vertebrae
  - L01
    - L01 body
    - L01 Arch R
    - L01 Arch L
  - L02
    - L02 body
    - L02 Arch R
    - L02 Arch L
  - L03
    - L03 body
    - L03 Arch R
    - L03 Arch L
  - L04
    - L04 body
    - L04 Arch R
    - L04 Arch L
  - L05
    - L05 body
    - L05 Arch R
    - L05 Arch L
- Sacrum
  - S01
    - S01 body
    - S01 Arch R
    - S01 Arch L
  - S02
    - S02 body
    - S02 Arch R
    - S02 Arch L
  - S03
    - S03 body
    - S03 Arch R
    - S03 Arch L
  - S04
    - S04 body
    - S04 Arch R
    - S04 Arch L
  - S05
    - S05 body
    - S05 Arch R
    - S05 Arch L
- Coccyx

Pelvis

Pelvis R
- Ilium R
- Ischium R
- Pubis R
- Auricular surface R
- Acetabulum R
Pelvis L
- Ilium L
- Ischium L
- Pubis L
- Auricular surface L
- Acetabulum L

Legs and Feet

Leg R
- Femur R
  - Femur - proximal epiphysis R
  - Femur - proximal third R
  - Femur - middle third R
  - Femur - distal third R
  - Femur - distal epiphysis R
  - Femur head R
  - Femur Femoropatella R
  - Femur medial femorotibial R
  - Femur lateral femorotibial R
- Patella R
  - Patella Femoropatellar R
- Tibia R
  - Tibia - proximal epiphysis R
  - Tibia - proximal third R
  - Tibia - middle third R
  - Tibia - distal third R
  - Tibia - distal epiphysis R
  - Tibia medial femorotibial R
  - Tibia lateral femorotibial R
  - Tibia proximal tibiofibular R
  - Tibia talocrural R
- Fibula R
  - Fibula - proximal epiphysis R
  - Fibula - proximal third R
  - Fibula - middle third R
  - Fibula - distal third R
  - Fibula - distal epiphysis R
  - Fibula prox. Tibiofibular R
  - Fibula talofibular R
Leg L
- Femur L
  - Femur - proximal epiphysis L
  - Femur - proximal third L
  - Femur - middle third L
  - Femur - distal third L
  - Femur - distal epiphysis L
  - Femur head L
  - Femur Femoropatella L
  - Femur medial femorotibial L
  - Femur lateral femorotibial L
- Patella L
  - Patella Femoropatellar L
- Tibia L
  - Tibia - proximal epiphysis L
  - Tibia - proximal third L
  - Tibia - middle third L
  - Tibia - distal third L
  - Tibia - distal epiphysis L
  - Tibia medial femorotibial L
  - Tibia lateral femorotibial L
  - Tibia proximal tibiofibular L
  - Tibia talocrural L
- Fibula left
  - Fibula - proximal epiphysis L
  - Fibula - proximal third L
  - Fibula - middle third L
  - Fibula - distal third L
  - Fibula - distal epiphysis L
  - Fibula prox. Tibiofibular L
  - Fibula talofibular L
Foot R
- Tarsals R
  - Calcaneus R
  - Talus R
  - Navicular R
  - Cuboid R
  - Medial cuneiform R
  - Intermediate cuneiform R
  - Lateral cuneiform R
- Metatarsals R
  - Metatarsal 1 R
  - Metatarsal 2 R
  - Metatarsal 3 R
  - Metatarsal 4 R
  - Metatarsal 5 R
- Phalanges R
  - Prox. Phalang. R (no)
  - Mid. Phalang. R (no)
  - Distal Phalang. R (no)
  - Sesamoid R (no.)
Foot L
- Tarsals L
  - Calcaneus L
  - Talus L
  - Navicular L
  - Cuboid L
  - Medial cuneiform L
  - Intermediate cuneiform L
  - Lateral cuneiform L
- Metatarsals L
  - Metatarsal 1 L
  - Metatarsal 2 L
  - Metatarsal 3 L
  - Metatarsal 4 L
  - Metatarsal 5 L
- Phalanges L
  - Prox. Phalang. L (no)
  - Mid. Phalang. L (no)
  - Distal Phalang. L (no)
  - Sesamoid L (no.)

Bone preservation:

1 - Excellent: solid bone, no or little breakage or erosion
2 - Good: some breakage
3 - Fair: Some pieces of missing bone
4 - Poor: most elements broken with pieces missing, cracks, splintering and bone surface is rough
5 - Fragments: all bones are friable, splintered, or very fragmentary, extreme weathering, little identification possible

Cortical preservation:

1 - 0% of sound cortical surface
2 - 1-24% of sound cortical surface
3 - 25-49% of sound cortical surface
4 - 50-74% of sound cortical surface
5 - 75-99% of sound cortical surface
6 - 100% of sound cortical surface