We need terms to represent retainers. The codes we specifically need to account 
for are:

D6205: retainer - cast metal for resin bonded fixed prosthesis
D6210: retainer - porcelain/ceramic for resin bonded fixed prosthesis

The argument for removing them is that we want to simplify where reasonable and 
I'm not sure that the use of them would gain anything beyond using the 
superclass

'tooth restoration procedure' and ('has part' some 'dental material attachment 
process')

Direct restorations can use pins. The above definition would land up 
classifying such direct restorations as indirect because the placement and 
attachment of the pin would satisfy the condition.

I think I proposed at some time that direct restoration be characterized by 
shaping of the bulk of dental material inside the mouth, and indirect shaping 
outside the mouth. Perhaps those definitions would be more resilient. 

They need to be fixed. The billing codes are easy to see why they are 
problematic. The other ones less obvious - perhaps they are downstream 
consequences of the billing code issue.

As an aside I think I'd like to move to BFO2 soon as it has many more axioms to 
catch mistakes. 

Currently we say that a dental exam is part of a dental visit, and dental visit 
is an outpatient encounter.

I think dental visit should be defined as subclass of health care encounter, 
which would remove this restriction.

We need terms to represent:

D6253: provisional pontic
D6254: interim pontic

What steps will reproduce the problem?
1.
2.
3.

What is the expected output? What do you see instead?


Please use labels and text to provide additional information.

I'm not sure what the best strategy is here. Ideas:

1. Define subclasses of functional tooth with the analogous categories and have 
the cognate prosthetic, natural, and restored tooth as subtypes.

2. Something like: prosthetic left lower central secondary incisor tooth and 
(has_function some function that inheres_in some (left lower central secondary 
incisor tooth))

The problem is that it says that a role inheres in two things, which it doesn't 
in this case.

3. Define a new relation prosthetic_for 

I think this needs to be an instance:type relationship, since in the case of a 
missing tooth, congenital or otherwise the tooth (may) not exist, and therefore 
not the function.

Maybe:

x prosthetic_for Y if
exists(fy) FY =def function_of some Y
exists(fx) fx function_of x
fx instance of FY

We could then write 
prosthetic left lower central secondary incisor  subclassOf:  prosthetic_for  
value(left lower central secondary incisor) 
which would take advantage of punning (Y is an instance in the OWL expression).

We need terms to represent:

D6970: post and core in addition to fixed partial denture retainer, indirectly 
fabricated

We need terms to represent:

D2950 : core buildup, including any pins

Hi this is a test!

Other than using these classes to impart a fact about the patient, are there 
terms we expect to need these terms in their definitions?

Simplicity suggests removing these, or pushing upwards to OGMS at least part of 
the patient.

Current: A specific healthcare activity that is performed on a dental patient 
for diagnostic or therapeutic purposes.

"specific" doesn't add anything - remove.

Move editor note -> curator note (difference is that the former should be of 
use to a consumer of the ontology)

Does therapeutic include prophylactic? 

Is counseling a patient about brushing their teeth considered a dental 
procedure? If so add as example of usage. If not what differentiates it? If not 
then we can't have it be the sole kind of realization of the role, as certainly 
this kind of counseling is a realization also. Moreover diagnostic process and 
dental procedure , in OHD, are disjoint, and performing a dental clinical 
assessment while certainly a realization of the role, is excluded because the 
role is defined as being realized by a dental procedure.

If we have a partition of what the kinds of dental procedures are, at the level 
they are described in the definition, then we should consider making the union 
of them be the realization of the dental health care provider role.

I'm afraid that dental health care provider role and dental procedure together 
are circular. Each is defined effectively in terms of the other and little else.

I think this is a problem in OGMS - track 
https://code.google.com/p/ogms/issues/detail?id=88

Included here for when we get to these. The page had a nice set of definitions.

http://www.dentistry.utoronto.ca/dpes/diagnostic/patients/normal-anatomy-or-oral
-pathology-patient

A macule is a spot. Macules are well defined, flat, have a different color than 
the surrounding tissue and are usually less than 5 mm in diameter.
A patch is a larger spot. This is also a pigmented area that is generally 
greater than 5 mm in diameter.
A plaque is a slightly raised plateau-like area, and can be pigmented or not.
A polyp is a mass of tissue that projects outward from the surface of the 
mucous membranes.
A papule is a small slightly raised area less than 5 mm in diameter. It may be 
pigmented or may be the same color as the surrounding tissue.
A nodule is a lump larger than 5 mm. It may be visible or it may only be 
detectable by palpation.
A vesicle is a small blister less than 5 mm in diameter. It is raised, well 
defined and filled with clear fluid.
A bulla is a vesicle that is larger than 5 mm.
An ulcer is usually a depressed or crater-like area on the mucosa where there 
is a loss of the epithelium, which is the surface layer, and is often yellow 
white in colour.
An erosion is a shallow ulcer where the epithelium may only be partially 
destroyed. These often are red in color.
A petechia is a spot approximately 1 to 2 mm in diameter where blood has leaked 
into the surrounding tissue. These are often found in multiples, and are called 
petechiae.
An ecchymosis is a flat bruised area of haemorrhage larger than 2mm in diameter.
A hematoma is a localized collection of blood outside of a blood vessel that 
may appear raised.

Email from Bill

Currently we have the data properties "occurrence data" and
"birth_date" in OHD. These represent:

1. the date on which a procedure occured
2. the birth date of the patient

An alternative to having these as data properties is to represent this
information using ICEs. That is, have as a subtype of ICE something
like "patient birthday" and "procedure occurrence date".

There is an example of what these ICEs would be about. Would they be about the
patient/procedure or about the temporal region during which the birth
of the patient or the procedure occurred. For now, I think it would be
fine for them to be about the patient/procedure. Keeps of out of the
metaphysical deep water :(

Making this change feels ontologically right, but do we gain added
practical advantage? Are there queries that we can now do? One
possible advantage is that we can more cleanly represent case in which
such information changes. For example, a patient corrects an incorrect
information about his birthday. Is this enough motivation?

We need terms to represent:

D6972: prefabricated post and core in addition to fixed partial denture retainer

We need term to represent:

D1351: Sealant

We need to represent protective restorations.
This arises in regard to:

D2940: protective restoration

current: A series of steps followed in a regular, orderly, definite way, 
performed by a dentist or dental surgeon by manual operation on some part of 
the mouth.

I think it should mention incision. "A series of steps followed in a regular, 
orderly, definite way" seems nonessential (albeit good practice)

Are all tooth extraction procedures surgical procedures? Titus comments that he 
has done tooth extraction by pulling a tooth with two fingers. That doesn't 
sound like surgery.

In the labels and perhaps definitions of some existing terms.

Solution: Add 'a tooth surface to be restored role' analogous to tooth to be 
restored role. Currently you can figure out the surface by looking at the 
dental restoration material that participates in the restoration and following 
the 'is dental restoration of' property.

We can fix it in the current triple store if we want, roughly

construct 
  { :_r1 a 'a tooth surface to be restored role'. #:_r1 is a blank node that is created
    :_r1 realized in ?proc # ?proc and ?surface are bound by the where clause 
    :_r1 inheres in ?surface 
    # creating a human readable label might be problematic.
  }
where
  { ?proc a intracoronal restoration procedure. # should be: An restoration specific to a surface
    ?proc has_participant ?dental_material # get the dental restoration material
    ?dental_material is restoration of ?surface #follow the current relation 
    ?surface a surface. #in case there are other than surfaces that are the target of this relation
  }

That should create a new role instance and relate it properly

We do distinguish between active and inactive patients. Should we add an 
annotation?

In a previous version of the ontology we defined a tooth to be filled role that 
was realized during intracoronal restorations. This role is currently not in 
the ontology. I'm not sure we need it, since we have a tooth to be restored 
role that is realized by a restoration procedure. But, I wanted to bring it 
everyone's attention.

Here's a recent thread:

Caries as infection (not)
Alan Ruttenberg <[email protected]>
Dec 20 (2 days ago)

to Lindsay, Albert, Alexander, Bill 

Infection:

A part of an extended organism that itself has as part a
population of one or more infectious agents and that (1) exists
as a result of processes initiated by members of the infectious
agent population and is (2) clinically abnormal in virtue of the
presence of this infectious agent population, or (3) has a
disposition to bring clinical abnormality to immunocompetent
organisms of the same Species as the host (the organism
corresponding to the extended organism) through transmission of a
member or offspring of a member of the infectious agent
population.

Caries satisfies (1) and (2) but not (3).

The conclusion would be that caries is not an infection. That
seems not quite right.

Suggestions?


Alan Ruttenberg <[email protected]>
Dec 20 (2 days ago)
to Lindsay, Albert, Alexander, Bill 

Wouldn't the same logic apply to e.g. bacteremia in the case that
it is native commensal bacteria that are the circulating
bacteria.


Lindsay Cowell
Dec 20 (2 days ago)
to me, Albert, Alexander, Bill 

Isn't caries tooth decay?  In which case not an infection but
realization of an infectious disease.  Or secondary disorder


Alan Ruttenberg <[email protected]>
Dec 20 (2 days ago)

to Lindsay, Albert, Alexander, Bill 

On Sat, Dec 20, 2014 at 7:31 PM, Lindsay Cowell 
<[email protected]> wrote:

Isn't caries tooth decay?  In which case not an infection but
realization of an infectious disease.  Or secondary disorder

"tooth decay" interpreted as a disease course imply the existence
of some material basis for the disease. Asserting it would be an
infectious disease has the same issue I raised. There is a
disease course particular, so there is a disease particular that
has material basis an X. The question is, is X an infection then
it has to have the possibility of being transmitted.

Here's our definition:

A disorder that affects a tooth that includes both the infectious
organisms, the material they generate from the tooth, any immune
effectors that are a response to the presence of the disorder and
the physical changes to the tooth (i.e., demineralization or a
cavity) resulting from the disorder. It is the physical basis for
the disease "dental caries."

There are some papers that say it is transmissible - look like
only in certain circumstances - mother to child, among pre-tooth
children is what I found[1]. Maybe that's enough? I suppose it
might be true that scraping some from an adult cavity and
introducing it to a baby's mouth would, in some number of babies,
be enough to give them caries when their teeth erupt.

On the other hand, there's a NHS page [2] that argues that you
can't "catch" caries - that the relevant bacteria are generally
present in the mouth to start with, and provides a couple of
experiments as evidence.

I guess it would be interesting to know the answer in both
cases. In the case that it is transmissible it seems
unproblematically an infection. In the case not I'm guessing it
would be a colony and surrounding material as described in our
definition.


[1] http://medind.nic.in/icb/t09/i2/icbt09i2p191.pdf
[2] http://www.ncl.ac.uk/dental/oralbiol/oralenv/comment/caries_infection.htm

"Occlusial" should be "Occlusal" in "Occlusial surface enamel"

We need terms to represent:

D6973: core build up for retainer, including any pins

When Bill and I were trying to sort out how to defined prosthetic tooth we were 
wandering around the FMA representation of teeth. It is rather involved (lots 
of parts) and it occurred to me that we need a tooth diagram that relates parts 
to what the corresponding FMA classes are.

Currently the oral evaluations are parts of dental exams, which have the 
findings determined in the oral evaluation.  That's fine, but the evaluations 
themselves should also have these findings (they are assays, after all).

now: A target of material addition role that inheres in a tooth and is
realized when a tooth is the target of some dental material addition
process.

Question: Why is "direct or indirect" part of the definition. I think it can be 
omitted. If not, what is a counterexample - a something that is a target of 
material addition inhering in a tooth but not realized in a direct or indirect 
procedure.

Document general practices used in the development of OHD

Reminder that these elements should be included in OHD

Are there any?

For example a comprehensive oral evaluation would seem to include as parts both 
hard and soft tissue exams 
"it is a thorough evaluation and recording of the extraoral and intraoral hard 
and soft tissues."
 (and more - e.g. inspection of oral cavity). Instead it is part of some dental exam. What's the other part of the exam?

We *might* need terms to represent:

D1352: Preventive Resin Restoration

A comment asks: 
Use CHEBI:33521 'metal ion' in a complete definition. Fixure out how to say 
"mostly" first, however

The first step would be to assert
has_grain (see OBI) some metal ion

If we wanted to assert something like mostly then we might use something like 
concentration with a threshold. However I think 80% of what we want to 
accomplish would be to use has_grain.

If we want to include more material information we can add has_grain statements 
elsewhere
For porcelain we can add quartz CHEBI:46727 and feldspar CHEBI:48733
(http://www.dentallearning.org/course/Ceramics/Dental_Ceramics.pdf)
(http://www.ncbi.nlm.nih.gov/mesh/?term=dental+porcelain)

Other observations
According to the definitions, gold foil dental restoration material is_a high 
noble metal dental restoration material
predominately base metal dental restoration material UNION noble metal dental 
restoration material = metal dental restoration material
stainless steel dental restoration material is_a predominately base metal 
dental restoration material
titanium dental restoration material is_a predominately base metal dental 
restoration material
amalgam dental restoration material is_a predominately base metal dental 
restoration material  

typo matalic -> mettalic

On the logical side I think this means adding a target of examination (check if 
this is evaluate role in OBI).
Hard tissue exam realizes target of examination that inheres in teeth (or bone 
more generally, or connective tissue?) Choose from FMA

Soft tissue exam realizes target of examination that inheres in Mucosa of Mouth 
(I think this is the closest term in FMA for soft tissue). FMA:59660 Includes 
gingiva as part.

Actually I think these both count as OBI:Assays -> "A planned process with the 
objective to produce information about the material entity that is the 
evaluant, by physically examining it or its proxies."
In that case use evaluate role

Hard tissue definition currently:

A dental exam which includes a complete examination of hard tissues, 
specifically the teeth. It is performed tooth by tooth and documents aspects 
such as whether the tooth is missing or not, and its condition. 
----
Part after this is not definition of dental exam - put in editor note.

this is about teeth:
A tooth is typically considered healthy if it is in a virgin state, or has one 
or more restorations that restore it to full morphology and function. 

this is about disease and disorder:
Pathological conditions may include carious lesions, fractures, defective 
restorations, excessive wear and malpositions.

Soft tissue exam currently has no textual definition.

We need terms to represent:

D2954: prefabricated post and core in addition to crown

We need term(s) to represent:

D2952: post and core in addition to crown, indirectly fabricated

Currently, we are using long names as labels for the surfaces of teeth. For 
example:

"Distal surface enamel of tooth"
"Occlusal surface enamel of tooth"

It would be helpful to shorten these labels to their commonly used letters:

mesial -> m
occlusal -> o
distal -> d
lingual -> l
labial/facial - f

We already do something similar to this in our use of the annotation "ADA 
Universal Tooth Number". Should create a similar annotation for surface letters?

- Bill

The definition includes elements that do not contribute directly to defining, 
and which would be better captured in an editor note. In particular we don't 
include things that are true of "most" or elements that are "usually" true.

-> Is this enough? Do we have to rule out not being a dentist or assistant?

A dental health care provider role that inheres in a person who is a
licensed dental professional that specializes in preventative care.

"licensed or registered"
Are there places where registration or licensure is not required? Perhaps 
something about being regulated?
In India it looks like there are regulations about education but not 
requirements for license or registration
http://idhta.org/files/DH-Regulation-2008.pdf
Maybe something about being conferred the title 


-> this belongs in an editor note, not definition

Professional prophylaxis, radiographs, sealants, and nonsurgical
periodontal therapy are among the procedures performed by a
hygienist. Most are licensed to administer local anesthesia, depending
on applicable regulations in their area. They usually work for a
dentist in a dental office or clinic under a form of supervision. In
some locations hygienists are allowed to practice without a dentist's
supervision.

Current: A material to be added role that is borne by a portion of dental 
restoration material and is realized in a tooth restoration procecure in which 
the restoration material contributes to restoring the tooth.

Problem: Contributes is too loose. For example a drill 'contributes' to 
restoring a tooth.

Offered: A material to be added role that is borne by a portion of dental
restoration material and is realized in a tooth restoration procecure
in which the material becomes part of a restored tooth.

Included here for when we get to these. The page had a nice set of definitions.

http://www.dentistry.utoronto.ca/dpes/diagnostic/patients/normal-anatomy-or-oral
-pathology-patient

A macule is a spot. Macules are well defined, flat, have a different color than 
the surrounding tissue and are usually less than 5 mm in diameter.
A patch is a larger spot. This is also a pigmented area that is generally 
greater than 5 mm in diameter.
A plaque is a slightly raised plateau-like area, and can be pigmented or not.
A polyp is a mass of tissue that projects outward from the surface of the 
mucous membranes.
A papule is a small slightly raised area less than 5 mm in diameter. It may be 
pigmented or may be the same color as the surrounding tissue.
A nodule is a lump larger than 5 mm. It may be visible or it may only be 
detectable by palpation.
A vesicle is a small blister less than 5 mm in diameter. It is raised, well 
defined and filled with clear fluid.
A bulla is a vesicle that is larger than 5 mm.
An ulcer is usually a depressed or crater-like area on the mucosa where there 
is a loss of the epithelium, which is the surface layer, and is often yellow 
white in colour.
An erosion is a shallow ulcer where the epithelium may only be partially 
destroyed. These often are red in color.
A petechia is a spot approximately 1 to 2 mm in diameter where blood has leaked 
into the surrounding tissue. These are often found in multiples, and are called 
petechiae.
An ecchymosis is a flat bruised area of haemorrhage larger than 2mm in diameter.
A hematoma is a localized collection of blood outside of a blood vessel that 
may appear raised.

I think these are still dental procedures.
We'll need dental prophylaxis defined as dental procedure and prophylaxis 
(don't assert parents so we don't land up with multiple asserted inheritance. 
Then cleaning and fluoride treatment and sealants etc as subs of dental 
prophylaxis

In defining tooth restoration procedures, we (mostly myself) have been overly 
hung up on the intra/extra coronal procedure distinction. This distinction is 
difficult to maintain b/c some procedures, such as onlays, have both intra and 
extra coronal dimensions to them.

I suggest that we replace the term 'intracoronal restoration procedure' with 
the term 'surface restoration procedure'. The goal is to make it clear that 
some restoration procedures are aimed at restoring particular surfaces, as 
opposed to restoring the crown as a whole.

Suggested definition:
A tooth restoration procedure in which the structural, aesthetic, or functional 
integrity of the tooth is restored by inserting dental restoration material 
into a site that is located in the surface of the tooth.

direct dental material placement process
dental material attachment process

Each should be part of a tooth restoration
The two should also realize target of material addition and material to be 
added roles, and have specified outputs that are restored tooth.(unless pontics 
can also be restored, in which either restored or pontic)
Also have specified inputs that are tooth or restored tooth, or, if pontics can 
be restored, then function tooth. (currently only tooth is specified input, but 
you can further restore an already restored tooth so restored tooth needs to be 
included, at least)

Do I understand correctly that dental material fusion process happens outside 
the mouth?
Dental material fusions should have at least 2 dental materials as specified 
inputs, and (if I understand correctly) dental material as output.

What steps will reproduce the problem?
1.
2.
3.

What is the expected output? What do you see instead?


Please use labels and text to provide additional information.

We have, currently, 

tooth
restored tooth
functional prosthetic

I believe there should be a superclass of these three.

Not a great solution would be to assert an additional superclass. Perhaps we 
defined 'tooth function', say that each of these bears the function, and create 
'functional tooth' as a defined class - anything that has 'functional tooth' 
role.

Then we need to examine what we have asserted about each class and perhaps 
reassign the target:

Different nomenclatures for teeth should be attached to functional tooth, I 
think, as they are equally applicable to members of all three subclasses. 

Some disorders/finding, like fractured/broken tooth are applicable to all.
Some, like caries, are applicable to anything that has tooth as a part, i.e. 
natural and restored teeth
etc.

We need terms to represent:

D9110: Palliative treatment of dental pain (if related to a specific tooth)

This is to remember that we intend that all CDT codes be represented. I 
realized that we were only doing a subset when checking whether we had terms 
for dental imaging. We don't, CDT does.