Note that this issue pertains only to primary labels. Full synonym
lists will of course be retained.

No discussion required

In all of the following, the Uberon label will be replaced by the VSAO
one. Where possible, this will be propagated to dependent ontologies.

Naming convention differences

VSAO tends to use relational adjectival form whereas Uberon uses a
mixture of more explicit FMA-style labels plus relational adjectives
depending on factors such as whether the label is reused in
compositional classes.

All of the following will be switched to the VSAO label

• UBERON_0007831 "skeleton of pectoral girdle" -vs- VSAO:0000156 "pectoral girdle skeleton"
• UBERON_0007832 "skeleton of pelvic girdle" -vs- VSAO:0000155 "pelvic girdle skeleton"
• UBERON_0006717 "skeleton of autopod" -vs- VSAO:0005019 "autopodial skeleton"
• UBERON_0010546 "metapodium skeleton" -vs- VSAO:0005025 "metapodial skeleton"
• UBERON_0009878 "mesopodium skeleton" -vs- VSAO:0005022 "mesopodial skeleton"
• UBERON_0010543 "skeleton of acropodium" -vs- VSAO:0005028 "acropodial skeleton"
• UBERON_0011582 "skeleton of limb/fin" -vs- VSAO:0000301 "limb/fin skeleton"
• UBERON_0007844 "cartilaginous element" -vs- VSAO:0000000 "cartilage element"

STATUS: DONE

See further down form limb/fin vs paired appendage.

Non-trivial differences

The Uberon label will be replaced by the VSAO label here

• UBERON_0000041 "dermal denticle" -vs- VSAO:0000079 "odontode scale"
• UBERON_0001075 "body of vertebra" -vs- VSAO:0000183 "vertebral centrum"
• UBERON_0001474 "bone" -vs- VSAO:0000057 "bone element"
• UBERON_0001994 "hyaline cartilage" -vs- VSAO:0000094 "hyaline cartilage tissue"

Additional discussion required

Girdle complexes

• UBERON_0010707 "appendage girdle complex" -vs- VSAO:0000214 "appendage/girdle complex"
• UBERON_0010708 "pectoral complex" -vs- VSAO:0000213 "pectoral appendage/girdle complex"
• UBERON_0010709 "pelvic complex" -vs- VSAO:0000215 "pelvic appendage/girdle complex"

The uberon labels were chosen on the basis of previous discussions. A
slash typically denotes "or", which would be misleading here, as the
class refers to the mereological sum. I would therefore advise keeping
the labels as-is.

Muscles

• UBERON_0000383 "musculature of body" -vs- VSAO:0000033 "muscular system"

def: "Anatomical system that consists of all the muscles of the body[VSAO, modified]." [VSAO:0000033]
property_value: external_definition "Anatomical system that consists of the muscles of the body.[VSAO]" xsd:string {ontology="VSAO", external_class="VSAO:0000033", date_retrieved="2012-08-14", source="VSAO:curator"}

This can be changed, but the name was deliberately chosen to reflect that this is the mereological sum of all muscles of the body.

Univocity requirements

Sometimes an Uberon label was chosen over a VSAO label, as VSAO was
originally designed purely with verteberate skeletal systems in mind,
whereas additional disambiguation is required when placing this in a
metazoan multi-system context.

In all 3 cases here I would recommend retaining the existing primary
label.

Note that in all cases it is possible to have a context-specific
primary label, but the default primary label must be unambiguous for
the context of the whole ontology.

• UBERON_0000982 "skeletal joint" -vs- VSAO:0000101 "joint"

Uberon follows FMA and other ontologies in including non-skeletal
joints such as gastro-splenic ligament. In a purely skeletal context "joint"
is unambiguous, but in a broader context it is necessary to include a
disambiguating prefix.

• UBERON_0004529 "anatomical projection" -vs- VSAO:0000180 "process"

"process" is ambiguous in a multi-ontology context. "anatomical
projection", whilst ugly, is unambiguous. (of course, these high level
terms would be hidden from most users by applications anyway)

• UBERON_0010912 "subdivision of skeleton" -vs- VSAO:0000042 "skeletal subdivision"

"subdivision of skeleton" is umabiguous. However, it's not clear
whether "skeletal subvision" refers to a subdivision of the skeleton
or the skeletal system (recall the latter is broader, and includes
joint).

Other

• UBERON_0005944 "axial skeleton plus cranial skeleton" -vs- VSAO:0000056 "axial skeleton"

This was based on the opinions of the phenoscape curators on the most
recent obo-anatomy call. Too complex to summarise here, see:
[https://docs.google.com/document/d/16JZOuH9sh_a8uIXA4cqg0Q1H6MV5yCj3-rhuKsZoV_U/edit](appendicular skeleton) docs

• UBERON_0008895 "splanchnocranium" -vs- VSAO:0000149 "pharyngeal arch"

I would strongly recommend we retain the existing label.

Note the VSAO class was part of "cranial skeleton". It had no defs or
synonyms or is_a parent, but was assumed to be intended to be
equivalent to what in uberon is called the splanchnocranium (the
endochondral parts of the cranial skeleton derived from pharyngeal
arches - system based on Kardong).

I strongly recommend the uberon label is retained here. In most
ontologies "pharyngeal arch" does not refer to the skeleton, but
instead to the embryological structures.

See [https://docs.google.com/document/d/1r9kNPpFYGdu0SpJDLyFAVQczBlG0wAZCBMd18gG3Ot8/edit#](cranial terms)

• UBERON_0010323 "cranial skeletal system" -vs- VSAO:0000049 "cranial skeleton"

Whilst "cranial skeletal system" is an ugly term, it is important we
retain consistent terminology. In previous version of VSAO we agreed
to follow the FMA system of using "skeletal system" for joints + other
skeletal elements and dividing this into skeleton and articular
system. This has certain consequences - for example, if sutures are
considered joints, then under this system they are part of the
articular system and its parent the skeletal system, but not skeleton.

• UBERON_0007380 "dermal scale" -vs- VSAO:0000048 "scale"

"scale" can be ambiguous outside a vertebrate skeletal
context. However, more work is required here. The current subclasses
in Uberon are I believe all dermal.

Limb/free limb and paired appendage

• UBERON_0002101 "limb" -vs- VSAO:0000121 "free limb"
• UBERON_0004381 "skeleton of limb" -vs- VSAO:0000300 "free limb skeleton"
• UBERON_0004708 "limb/fin" -vs- VSAO:0000067 "paired appendage"

We should use "free limb" as in VSAO. Uberon will be changed to
reflect this. This will not be immediate, as we are also changing the
multiple compositional terms that use this, and checking whether the
corresponding terms in other AOs refer to the free limb or complex
(this is almost done).

"paired appendage" is less clear. I would rather avoid this until the
appendage definition is finalized in CARO2. Also "paired appendage" is
ambiguous in a metazoan context. We explicitly want to include insect
legs here (these are grouped under a more generic class)

• UBERON_0005863 "cartilaginous condensation" -vs- VSAO:0000092 "chondrogenic condensation"

If we go with this change, I would like it to be synchronized across
multiple ontologies. Note that EHDAA2 uses "cartilage/inous
condensation" exclusively

• UBERON_0002091 "entire appendicular skeleton" -vs- VSAO:0000076 "appendicular skeleton"

We can change this back. The explicit naming was designed to eliminate
confusion whereby in some ontologies "appendicular skeleton" was used
as the superclass of the individual limb/fin skeletons

• UBERON_0004743 "coracoid bone" -vs- VSAO:0000158 "coracoid"

The VSAO class and the uberon class denote bones.

• UBERON_0001479 "sesamoid bone" -vs- VSAO:0000137 "sesamoid"

Should this be in fact split into two classes? Many of the existing
sesamoid subclasses in Uberon are bones and users would expect to find
them in a query for bones ("ossicle" is not a subclass of bone element
in VSAO)