Download ECE update spring IHTSDO business meeting

Events, conditions, episodes project
group activities
Bruce Goldberg, MD, PhD
ECE Goals – 2016 and onward
▪ Update the editorial guide to clarify the decision process for
assigning the various modeling patterns for combined
disorders
▪ Develop a rigorous testing approach to evaluate the combined
disorder model
▪ Introduce additional temporal intervals/sequences to
SNOMED CT using new roles or expanding the range of
values for existing roles with respect to combined disorders
and procedure complications
▪ Develop a plan for retrospectively remediating existing
combined disorder content
▪ Address complex combined disorders (>2 conditions)
▪ Update allergy model
▪ Review model for allergic condition (due to allergic reaction)
▪ Add allergic condition and autoimmune disorder under 414029004
|Disorder of immune function (disorder)|
▪ Add new classes of adverse sensitivity and intolerance
Current discussions
▪ Guidelines for modeling combined disorder patterns
▪ Addition of during, during AND/OR after to associated
with role hierarchy
▪ Application of ECE guidance retrospectively maintenance of existing descriptions that may be
ambiguous
▪ Syndromes in which constituent conditions are variably
present
Guidelines for modeling
combined disorder patterns
▪ Current model for combined disorders is based on time
intervals (co-occurrence, following) and causality
▪ Interpretation of causality and time interval between two
related disorders proving to be difficult even using a very
liberal definition of causality (indirect as well as direct),
leading to violation of the reproducibility rule
Test of reproducibility of assigning causal
relationship between two disorders
Concept
709471005 |Periodontitis co-occurrent with leukemia (disorder)|
Causation BG Causation EC Role BG
Role EC
Indirect
Indirect
Co-occurrent and due to Co-occurrent and due to
41931000119102 |Sinusitis co-occurrent with nasal polyps (disorder)|
367171000119100 |Hematuria co-occurrent and due to cystitis (disorder)|
709147009 |Gingivitis co-occurrent with diabetes mellitus (disorder)|
366961000119106 |Albinism co-occurrent with hematologic disorder (disorder)|
706913006 |Varicose veins of lower limb co-occurrent with edema (disorder)|
714203003 |Acute bronchitis co-occurrent with bronchiectasis (disorder)|
None
Direct
Indirect
None
Indirect
None
Indirect
Indirect
Indirect
None
None
Indirect
Co-occurrent
Co-occurrent and due to
Co-occurrent and due to
Co-occurrent
Co-occurrent and due to
Co-occurrent
Co-occurrent and due to
Co-occurrent and due to
Co-occurrent and due to
Co-occurrent
Co-occurrent
Co-occurrent and due to
708030004 |Pulmonary emphysema co-occurrent with fibrosis of lung (disorder)|
125011000119100 |Mild persistent asthma co-occurrent with allergic rhinitis (disorder)|
None
None
None
None
Co-occurrent
Co-occurrent
Co-occurrent
Co-occurrent
285821000119105 |Major laceration of heart co-occurrent with hemopericardium (disorder)|
713844000 |Dementia co-occurrent with human immunodeficiency virus infection (disorder)|
19448008 |Optic atrophy associated with retinal dystrophy (disorder)|
420543008 |Anemia associated with acquired immunodeficiency syndrome (disorder)|
281004 |Dementia associated with alcoholism (disorder)|
68241007 |Glaucoma associated with ocular trauma (disorder)|
Direct
Indirect
Direct
Indirect
Indirect
Direct
Direct
Indirect
None
Indirect
Indirect
Indirect
due to
Co-occurrent and due to
Co-occurrent and due to
Co-occurrent and due to
Co-occurrent and due to
due to
Co-occurrent and due to
Co-occurrent and due to
Co-occurrent
Co-occurrent and due to
Co-occurrent and due to
after
43742007 |Pericarditis associated with severe chronic anemia (disorder)|
230685009 |Myasthenia gravis associated with thymoma (disorder)|
422183001 |Skin ulcer associated with diabetes mellitus (disorder)|
421132004 |Platelet dysfunction associated with uremia (disorder)|
425390006 |Dementia associated with Parkinson's Disease (disorder)|
791000119109 |Angina associated with type II diabetes mellitus (disorder)|
230571009 |Neuropathy associated with endocrine disorder (disorder)|
403560008 |Port-wine stain associated with spinal dysraphism (disorder)|
Indirect
Indirect
Indirect
Indirect
Direct
Indirect
Unknown
None
Indirect
Indirect
Indirect
Indirect
None
None
Indirect
None
Co-occurrent and due to
Co-occurrent and due to
Co-occurrent and due to
Co-occurrent and due to
Co-occurrent and due to
Co-occurrent and due to
N/A
Co-occurrent
Co-occurrent and due to
due to
Co-occurrent and due to
Co-occurrent and due to
Co-occurrent
Co-occurrent
due to
Co-occurrent
Proposed approach to achieving
reproducibility for modeling combined
disorders
▪ Suggested resolution to the aforementioned issue is to
assign causality and time interval based on consensus,
to combined disorder concepts associated with specific
domains and provide guidelines for modeling these
domains in the editorial guide
▪ Domains would initially represent high impact, high
usage areas
▪ Examples
▪ Infections
▪ Diabetic complications
▪ AIDs related disorders
▪ Additional domains to be considered based on authors
input
Infections, co-occurrence, causation, sites
and morphology
“Covert co-occurrence”
•
•
Review of NHS GP/FP refset reveals that many concepts due to the way they are
modeled with role groups, may inherit more than parent and thus be interpreted as
consisting of more than one CLP which may not be apparent from the FSN
Example: Infective uveitis (may be recast as Uveitis co-occurrent and due to eye
infection)
Stated view
Inferred view
Infective (infectious) vs infected
▪ Difference between infections directly resulting in a
morphologically abnormal structure ( e.g. inflammation)
and infections of a morphologically abnormal structure
due to another cause (e.g. infected blister) and infections
of a previously inflamed site (infected eczema).
▪ If infections cause and occur at the same time as
inflammation they should be modeled as inflammation
co-occurrent and due to infection Y
▪ Alternatively, if inflammation is considered to be the
inevitable outcome of infections, then inflammation cooccurrent with infection Y would suffice
Standard modelling patterns (with preferred role group
combinations) required for several infectious disease
variants (which are currently inconsistently applied)
▪
▪
▪
▪
▪
▪
infection (including asymptomatic carrier states)
Infection at site
Infection by organism
Infection by organism at site
Infection by organism causing morphologic abnormality
Infection by organism causing morphologic abnormality at site (e.g.
tuberculous ascites, infective corneal ulcer)
▪ Infection by organism in morphologic abnormality
▪ Infection by organism in morphologic abnormality at site (e.g. infected
ascites, infected varicose ulcer)
▪ Infection by organism in morphologic abnormality, causing other
morphologic abnormality, at site
Diabetic complications
▪ FSN Patterns
▪
▪
▪
▪
▪
▪
X in diabetes
X of diabetes
X due to diabetes
Diabetic X
X associated with diabetes
X complication of diabetes
▪ Possible modeling patterns
▪ X due to diabetes
▪ X co-occurrent and due to diabetes
▪ Modeling pattern might be dependent upon nature of X
▪ X = coma (coma co-occurrent and due to diabetes)
▪ X = disorder of retina (disorder of retina due to diabetes)
▪ Allows for possibility of persistence of retinal disorder after treatment of diabetes with
islet cell transplant
▪ Alternate approach – apply single modeling pattern (e.g. x co-occurrent and due
to diabetes) to all diabetic complications
▪ In the majority of cases by the time long term complications appear diabetes is chronic and
incurable and will thus be necessarily present during the entire course of the complication
▪ Advantage of capturing diabetes as a second parent and thus potentially increasing the
documentation and reported prevalence of diabetes
Workplan
▪ Identify domains
▪ Based on frequency data of SNOMED from NHS GP/FP refset
and KP CMT
▪ Input from modelers (authors)
▪ Develop modeling guidelines for each
domain/subdomain
▪ Evaluate agreed upon model in test environment
▪ Update editorial guide
Addition of during, during AND/OR
after to associated with role
hierarchy
▪ Original goal of project was to develop model for
intraoperative complications
▪ Model for post operative complications exists
▪ Model to be extended to include not only intraoperative and
postoperative complications but also perioperative complications
▪ Although perioperative commonly refers to the period of time prior
to, during and after surgery, in terms of perioperative complications,
we considered perioperative as occurring during surgery, after
surgery or a time interval beginning during surgery and continuing in
the post operative period.
▪ Thus intraoperative and postoperative complications would be
considered subtypes of perioperative complications.
▪ The preoperative period was not considered for this exercise as a
complication (consequence) of surgery would not be expected to
occur prior to the surgery.
Surgical complications
▪ Proposed model for intraoperative complications is to
approve use of 371881003 |During (attribute)|with a
range limited to procedures
▪ Concern expressed that extending range of during to include
clinical findings/disorders would overlap with the co-occurrence
model for combined disorders
▪ Proposed model for perioperative complication is to
create a new role, during AND/OR after as a descendant
of associated with and an ancestor of both during and of
after
▪ Above models applicable to other procedure related
complications
Revised associated with role hierarchy
Intraoperative complication
• Intraoperative X or X during surgery
• Model
Defined
concept
≡
X
Complicatio
n
During
Surgical
Procedure
Intraoperative complication
Injury to nerve during surgery
Injury to viscus/spleen during surgery
Intraoperative fracture
Intraoperative hemorrhage
Intraoperative complication hierarchy
Perioperative complications
Remaining issues
▪ We did not consider approval of 288556008 |Before
(attribute)| at this time.
▪ It is appreciated that additional mechanisms for
representation of temporal intervals in SNOMED CT
such as the use of occurrence or another role with
307158003 |Temporal periods relating to physiological
functions (qualifier value)| may be required in addition to
before, during, during and/or after and after in order to
capture other temporal relationships such as perinatal,
perimenopausal and pregnancy-associated
Syndromes in which constituent conditions
are variably present
▪ An agreement with INSERM to add Orphanet rare diseases to
the International release of SNOMED CT.
▪ 1700 rare conditions that are variably named for the primary
clinical manifestations and the eponymous name of the
people who identified the condition.
▪ E.g. Hydrocephalus-agyria-retinal dysplasia syndrome
Walker-Warburg syndrome
▪ The issue with these terms is that the clinical manifestations
in the name of these diseases are variably present and often
not co-occurrent. Therefore, they cannot be modeled as
always and necessarily being true as having those
conditions.
▪ Questions
▪ Which term should be the FSN (eponym or clinical term) ?
▪ If the latter, what is the proper structure of the FSN? Currently
Orphanet uses dashes to separate the different clinical
manifestations
FSN Naming
▪ Current editorial favors expansions but ”…allow[ing
exceptions] when the full description is exceptionally long and
unwieldy..".
▪ Follow the current guidance to use expanded forms but
accepting that there is room for judgment.
▪ Use eponym when commonly associated with usage
▪ E.g. Tetralogy of Fallot as opposed to RVH, VSD, pulmonary
artery stenosis and overriding aorta
▪ On the actual form of the expanded term, don’t use the
full 'co-occurrent with' connective between various
components.
▪ Preference is to use a comma separated list, a final 'and' and
a closing 'syndrome’
▪ Eg. Hydrocephalus, agyria and retinal dysplasia syndrome' rather
than 'Hydrocephalus-agyria-retinal dysplasia syndrome' simply
▪ Might make parsing & word tokenization more predictable.
General modelling
▪ Building on the established genetic/congenital approach
(www.snomed.org/eg?t=findings_disorder_types_conge
nital_genet_devel_acq ) many of the new additions will
need modelling judgments on how they are added:
▪ Hereditary/genetic disorders
▪ Add as primitively asserted subtypes of 32895009 |
Hereditary disease (disorder)
▪ Congenital disorders
▪ Model with occurrence=congenital
Chromosomal abnormalities
▪ Model using the most suitable finding site=chromosome
structure refinement and associated morphology value.
▪ Example Ring chromosome 20 syndrome
▪ Finding site = 25610001 |Chromosome pair 20 (cell
structure)|
▪ Associated morphology = 23345003 |Ring chromosome
(morphologic abnormality)|
▪ Observable model required for representing specific
mutations (see e.g. artf227316 Malignant neoplasm with
gene mutation)
Specific modelling
▪ The preferred approach is to identify from the experts/literature the
essential/cardinal features of each named syndrome.
▪ Ideally each of these can be included as a role grouped 'condition'
(and thus acquires the appropriate supertype by classification), but
where this is not feasible essential features can only be included by
directly asserting as supertypes.
▪ Variant features (e.g. encephalocele for Walker-Warburg) would
not be included in the formal definition, but if important then variants
that 'include' another feature can be added as subtypes of the base
concept.
▪ Naming convention
▪ X syndrome with Y (Walker-Warburg syndrome with encephalocele)
▪ For those syndromes where only a handful of
'essential/cardinal' features are included in the definition, consider
an FSN of the type “X syndrome including phenotypic variants” to
indicate there may well be other features but they are not included
here.
Application of ECE guidance retrospectively maintenance of existing descriptions that
may be ambiguous
▪ Presentation at Montevideo meeting outlined plan for
remediating existing combined disorder content based
on identifying concepts modeled with associated with
and its descendants and attempting to reconcile the
model with the FSN
▪ Based on the current approach to providing guidelines
for modeling combined disorder concepts as outlined on
slide 6, we will initially concentrate on remediating
content for specific high frequency, high impact domains
such as infectious disease, diabetic complications, AIDS
related disorders
Revised work plan
▪ Identify relevant domains
▪ Usage analysis of NHS GP/FP refset and KP CMT donation
▪ Feedback from authors/modeling team
▪ Identify naming patterns and models within each domain
▪ Search for inferred parents that might indicate “covert” cooccurrence
▪ Determine temporal sequence and causation
▪ Apply correct model and/or FSN if required based on
domain-specific guidelines to be developed