fovt,futres

all terms are lower case

synonyms:

width is a synonym for breadth or depth
length + axis is a synonym for breadth
length + axis is a synonym for length

Create policy for documenting design decisions

Discussions of individual terms and design patterns should take place in github issues. Theses issues will also be discussed during group calls, so highlights from the calls should be added to the appropriate issue.

Once a decision has been made about a design patter that will be reused, it should be documented in a wiki page.

Need to create subclasses for Specimens

I.e., associate skeleton, single bone / bone fragment, whole organism

OBA

there is discrepancy with "size trait" and "bone trait". I opened an issue to ask which is preferred.

premolar terms

Premolar 1:

Premolar 2:

Premolar 3:

Premolar 4:

Premolar 5:

naming of teeth

the order should be:
upper/lower primary/secondary side tooth number measurement (e.g., upper secondary molar tooth 3 length)

all lowercase

line traits

For 2D measurements that are not already in OBA, create a line trait that describes the two anatomical entities that the measurement is between (using "connects" as is found in OBA) and then a 1D distance trait (e.g., length) of the line.

angle terms

For now we'll be ignoring traits that have angles in them.

Terms sheet

do not resort the spreadsheet.

non-specific traits

Create a parent trait (e.g., "hindfoot length") for general traits and add specific segments (e.g., hindfoot length with claw) as subclasses.

FOVT using some wrong/ideosyncratic PURLs

An example of a correct IRI is (no https!):
http://purl.obolibrary.org/obo/ENVO_01000549

Context:
https://github.com/orgs/OBOFoundry/projects/5

problem

#7 blah i want a circle

metatarsal bones

Metatarsal greatest length

Metatarsal II

Metatarsal II distal articular breadth
Metatarsal II distal articular depth
Metatarsal II greatest depth proximal
Metatarsal II greatest length
Metatarsal II minimal depth of diaphysis
Metatarsal II proximal maximal breadth

Metatarsal III

Metatarsal III+IV

Metatarsal V

Metatarsal V distal breadth
Metatarsal V greatest length

at the level of

Need to think hard about how to define something like this:

width of skull at canines
Point A: left lateral-most extent of rostrum at level of posteriormost extent of left canine alveolus.

Notes: measuring part of the rostrum, not the tooth socket, so something like "left and (lateral most part of some alveolus and (part of some (posterior most part of some canine))" or "left and (lateral posterior margin of some alveolus and (part of some canine))" doesn't work.

molar terms

Molar 1:

Molar 2:

Molar 3:

Molar 4:

Molar 5:

trigonid:

illustration of measurement

need a new annotation property that links to an illustration of the measurement

integration with Open Context

Perhaps it'd be useful to add an annotation referring to the von den driesch measurement as already defined in Open Context. Open Context has specified which bones the measurement "greatest length" refers to and which taxa that is measured in, for example.

tricky terms

create term range for Helena

model after uberon

forearm length

is there a reference or illustration for what this is?

tooth row terms

For new term requests, please provide the following information:

Preferred term label

(e.g., femur length)

Synonyms

(e.g., femur L)

Parts of the term

anatomical feature (e.g., femur)
points on feature or axis of measurement (e.g., proximal-distal axis of femur; medial condyle to greater trochanter)
type of measurement (e.g., length)

Textual definition

the definition should be understandable even for non-specialists. Include a doi to refer to any relevant article that provides additional information about the suggested term.

Suggested parent term

Please look in the hierarchy in a browser such as OLS

Reference

Please include the full reference and doi.

Attribution

If you would like a nanoattribution, please indicate your ORCID id

measurements with the same name but different end points

for measurements with the same name (e.g., femur length, humerus length, basifacial axis, or basicranial axis) but have different end points (e.g., on femur there are 2 measurements, humerus 2 measurements, basifacial and basicranium there are 2 different measurements [start at same point but end at different points]).
How should we nest these and how should we label them?

incisor terms

Incisor 1

Incisor 2:

Incisor 3:

Incisor 4:

Incisor 5:

Incisor 6:

Trait terms

refer to this issue about trait terms.
Please include:

term itself
a reference
an illustration of the measurement

using github

create a branch named after the issue to be addressed (e.g., issue-12).
list issues being addressed in the PR and assign a reviewer
when PR merged, close issue

canine terms

minimal breadth of choana

For new term requests, please provide the following information:

Preferred term label

minimal breadth of choana

Parts of the term

anatomical feature: posterior nasal aperture
points on feature or axis of measurement: left-right axis in posterior size of posterior nasal aperture
type of measurement: width

Textual definition

The length of the posterior portion of a posterior nasal aperture of the internal naris (choana) along left right axis.

Suggested parent term

'width' and ('inheres in' some 'in posterior side of' some 'posterior nasal aperture')

'anatomical line' and ('follows_axis' some 'left-right axis') and ('inheres in' some 'in posterior side of' some 'posterior nasal aperture')

Reference

ISBN: 9004086161, 9789004086166

Attribution

https://orcid.org/
0000-0001-8415-4848

naming of bones

side-bone-measurement (e.g., left occipital length)
bone-anatomical position-measurement (e.g., humerus lateral length)

only use length and axis; avoid "breadth", "depth", and "width" (e.g., humerus length ML)

synonym rules

it is preferred to use exact synonym over narrow, broad, or related
only use synonyms when they are otherwise not in the ontology
- e.g., forelimb length has forearm which has ulna, so ulna length or forearm length do not need to be synonyms
- e.g., girth is not in OBA, so chest girth needs to be a synonym of chest circumference

Skull Term To DO

@helenamachado will make patterns for skull measurements with vomer, palate, muzzle, snout

test choanal length

For new term requests, please provide the following information:

Preferred term label

choanal length

Synonyms

Textual definition

the definition should be understandable even for non-specialists. Include a doi to refer to any relevant article that provides additional information about the suggested term.

Suggested parent term

'length' and 'characteristic_of' some 'oropharyngeal choana'
'line' that 'follows_axis' some 'anterior-posterior axis' and ('characteristic_of' some 'oropharyngeal choana')

Reference

see here

Attribution

https://orcid.org/0000-0003-2699-3066
@helenamachado: https://orcid.org/000-0001-8415-4848

If you would like a nanoattribution, please indicate your ORCID id

metapodial terms

Metapodial depth at middle of diaphysis
Metapodial distal breadth
Metapodial distal depth
Metapodial greatest length of lateral part
Metapodial greatest length
Metapodial proximal breadth
Metapodial proximal depth
Metapodial smallest diaphysis breadth

Metapodial II

Metapodial II distal articular breadth
Metapodial II distal articular depth
Metapodial II greatest length
Metapodial II minimal depth of diaphysis
Metapodial II proximal maximal breadth
Metapodiall II greatest depth proximal

Metapodial III

Metapodial III+IV

Metapodial III+IV distal breadth
Metapodial III+IV distal depth
Metapodial III+IV greatest length
Metapodial III+IV proximal breadth
Metapodial III+IV proximal depth
Metapodial III+IV smallest diaphysis breadth

Metapodial IV

Metapodial IV breadth at middle of diaphysis
Metapodial IV distal articular breadth
Metapodial IV distal articular depth
Metapodial IV distal breadth
Metapodial IV greatest length
Metapodial IV minimal depth of diaphysis
Metapodial IV proximal breadth
Metapodial IV proximal maximal breadth
Metapodiall IV greatest depth proximal

Metapodial V

Metapodial V distal breadth
Metapodial V greatest length

uberon clean up and synonyms

fused metapodials follow two different forms
make synonym for secondary/permanent and primary/deciduous for teeth
intertragic incisure is also the notch
upper canine 1 should be upper canine tooth 1
upper molar 1 should be upper molar tooth 1

Add abbreviations for teeth

hierarchy of terms

for terms with the same name (e.g., skull length), but different ending points, make a parent term with that name and children terms with the specific points

midlines and midpoint

Asked uberon community about best practice for defining midpoints and midlines (if there are any)

humerus terms to add

humerus distal trochlear breadth

add refs

add refs for trait terms

terms already added

femur length from greater trochanter to medial condyle
femur length from caput to medial condyle
femur proximal breadth
femur trochanter breadth
femur caput depth
femur diaphysis breadth
femur diaphysis circumference
femur distal breadth
femur length from caput to lateral condyle
femur proximal depth
femur distal depth
femur trochlea breadth
femur diaphysis depth

tibia greatest length
tibia medial length
tibia diaphysis breadth
tibia diaphysis depth
tibia proximal breadth
tibia proximal depth
tibia distal breadth
tibia distal depth
tibia lateral length
tibia diaphysis circumference

humerus length from trochlea to greater tubercle
humerus length from trochlea to caput
humerus diaphysis breadth
humerus proximal breadth
humerus trochlea breadth
humerus distal depth
humerus proximal depth
humerus distal breadth
humerus diaphysis depth

talus distal articular breadth
talus medial trochlea tali length
talus trochlea breadth
talus distal articular depth

snout-vent length
body length with tail
body length without tail
ear length to notch
ear length to tragus
hindfoot length with nail
hindfoot length without nail
tooth row length

talus length
talus length lateral
talus length medial
talus breadth
talus lateral depth
talus medial depth
talus distal breadth

calcanus distal depth
calcaneus distal breadth
calcaneus greatest length
calcaneus proximal length

BSPO terms that are needed

anterior most part of
posterior most part of
medial most part of
lateral most part of

Add obofoundry topic to repo metadata

The OBO Foundry has recently created a topics page at https://github.com/topics/obofoundry. It would be great if you could add the obofoundry topic to your repository, since it's currently listed as active in the OBO Foundry. If you're not sure how to do that, follow the instructions here. The main issue for this task is at OBOFoundry/OBOFoundry.github.io#1538 in case you want some more context or to join the larger discussion.

metacarpal terms

Metacarpal greatest length

Metacarpal II

Metacarpal II distal articular breadth
Metacarpal II distal articular depth
Metacarpal II greatest depth proximal
Metacarpal II greatest length
Metacarpal II minimal depth of diaphysis
Metacarpal II proximal maximal breadth

Metacarpal III

Metacarpal III+IV

Metacarpal III+IV distal breadth
Metacarpal III+IV distal depth
Metacarpal III+IV greatest length
Metacarpal III+IV proximal breadth
Metacarpal III+IV proximal depth
Metacarpal III+IV smallest diaphysis breadth

Metacarpal IV

Metacarpal V

Metacarpal V distal breadth
Metacarpal V greatest length

fused bones

How should we logically define measurements over metapodials when sometimes they're fused but it's the same measurement (e.g., in horses a measurement on metapodial III is the same as metapodial in ungulates but metapodial III and IV are fused together).

New term for nose length

I need a new term for nose lenght, but I think noses are different in different taxa.

Proposed definintion: A length that inheres in a nose.

But, what is a nose?

@emerykf @rbernor @kmeshida @DrPronghorn Please tell me what you think a nose is?

OBA_VT terms

we need to fix the terms that have these IDs and either remove them, find synonyms, and/or re-create them.

body size terms

add:
gutted
skinned
skeletal

side measured

currently this is a data property, and would be queried over.
this should be an object property so it can be reasoned over in the future.

maximal breadth of choana

For new term requests, please provide the following information:

Preferred term label

maximal breadth of choana

Parts of the term

anatomical feature: posterior nasal aperture
points on feature or axis of measurement: left-right axis along midline of posterior nasal aperture
type of measurement: width

Textual definition

The length along the midline of a posterior nasal aperture of the internal naris (choana) along left right axis.

Suggested parent term

'width' and ('inheres in' some 'intersects midsagittal plane of' some 'posterior nasal aperture')

'anatomical line' and ('follows_axis' some 'left-right axis') and ('inheres in' some 'intersects midsagittal plane of' some 'posterior nasal aperture')

Reference

ISBN: 9004086161, 9789004086166

Attribution

https://orcid.org/
0000-0001-8415-4848

BSPO

made request for midlines and more axes for "most part of"

need references from the community on measurements

Would like to link illustrations and references to measurement definitions

futres / fovt Goto Github PK

fovt's People

Contributors

Stargazers

Watchers

Forkers

fovt's Issues

Preferred term label

Synonyms

Parts of the term

Textual definition

Suggested parent term

Reference

Attribution

Preferred term label

Parts of the term

Textual definition

Suggested parent term

Reference

Attribution

Preferred term label

Synonyms

Textual definition

Suggested parent term

Reference

Attribution

Preferred term label

Parts of the term

Textual definition

Suggested parent term

Reference

Attribution

Recommend Projects

Recommend Topics

Recommend Org