Snomed CT Challenge - Lite

Meaning-based retrieval is a key benefit of SNOMED CT. See www.ihtsdo.org/benefits.pdf

Since January 2002, SNOMED CT International Edition has been released regularly every six months (31 January and 31 July each year). The schedule will continue until further notice. Some National Extensions of SNOMED CT are updated more frequently. At some point more frequent releases of the International Edition may also be considered.

SNOMED CT has a very broad scope of coverage because it includes not only clinical concepts but also other types of concept used to define clinical concepts. It does include geographical regions but it does not include astronomical bodies such as planets.

A preferred term is a synonym marked as "preferred" in the reference set for a language or dialect. There can be many different preferred terms - one for each language or dialect. In some cases a preferred term in one dialect may be an acceptable synonymous term in another dialect.

The three components of SNOMED CT are "concepts" each of which represents a clinical meaning, "descriptions" which associate human-readable term or phrase with a "concept" and "relationships" which link concept to one another based on the semantic relationships between them.

The | clinical course | attribute is used to represent both the onset and course of a disease.

IHTSDO (International Health Terminology Standards Development Organization) owns, maintains, licenses and distributes SNOMED Clinical Terms (SNOMED CT). It is a not-for-profit association governed by all its National Members through the General Assembly.

SNOMED CT release files are tab-delimited UTF-8 encoded text files. The standard latin alphabet, numbers and common grammatical symbol have the same values in UTF-8 and ASCII. However, UTF-8 supports the full Unicode character set by permitting multibyte encoding of characters where necessary.

Members or Affiliate Licensees can create SNOMED CT Extensions. However, in order to do this they must request, receive and use a namespace identifier. The namespace identifier distinguishes the content of Extensions created by different originators and ensures that the same SNOMED CT cannot be legitimately issued by more than one organization.

"Diabetes mellitus type 2" is a disease and thus appears as a subtype in the "Disorder" hierarchy. However, is a type of "Diabetes mellitus type 2" is also a subtype of "Clinical finding" because "Disorders" are types of "Clinical findings".

SNOMED CT maps are represented as Reference sets. The ICD-10 map in the international release includes rules that help determine maps when a clinical concept represented in SNOMED CT has several possible maps to ICD-10 categories that depending on co-existing conditions, age and sex of the patient or other factors. The maps to ICD-10 are used as basis for further mapping work to link to ICD-10-CM categories and these maps are developed in the US by NLM.

Appendectomy is defined as the excision of the appendix. While a laparoscope may be used it is not a defining attribute of appendectomy (it is a defining attribute of Laparoscopic appendectomy). Although appendectomy is a treatment for appendicitis this is not a defining attribute - it is possible to remove the appendix even when the patient does not have appendicitis.

The broad coverage of SNOMED CT enables more consistency of clinical recording across different clinical specialties. The SNOMED CT concept model uses Description Logic to enable alternative representations of similar meanings to be recognized and this enables effective meaning based retrieval of processable clinical information. SNOMED CT does not itself include decision support or interaction checking but meaning-based retrieval from records that use SNOMED CT enables decision support tools to reduce costly errors in treatment and unnecessary duplication of investigations.

All procedures are subtype descendants of the concept "procedure" (i.e. every procedure is defined as being a type of procedure). The subtype relationships in SNOMED CT are called "is a" relationships and by traversing a chain of "is a" relationships from a procedure concept eventually the "procedure" concept will be reached. Based on an editing convention, the fully specified name for a procedure concept will end with the work "procedure" in brackets. While the bracketed "hierarchy tag" a useful human-readable indication, it is not recommended as a good general way to determine whether one concept is subtype of another.

Subsets were a release file in the old release format (RF1) this was replaced in early 2012 by Release Format 2 (RF2) which includes a more flexible mechanism call "Reference sets" which can be used to represent a wide range of different types of additional information, including subsets.

Family history of a disorder is not type of that disorder. It is a type of family history of disorder. The link between family history and the disorder is referred to as | associated finding | and the | subject relationship context | indicates that the person who has (or had) the disorder is a family member.

The definition of a postcoordinated expression is an expression containing more than one concept identifier. Some of the concept identifiers may contribute contextual information such as indicating that a disorder is past history or family history rather than applying to the subject of the record at the present time. It is possible for a postcoordinated expression to represent the same meaning as an existing concept - although many postcoordinated expressions will not be matched by single concepts. The inclusion of terms in a SNOMED CT expression is optional.

The SNOMED CT hierarchy is a polyhierarchy because concepts in the hierarchy can have multiple parents. The hierarchy is based on subtype "is a" relationships. The end result of the building the hierarchy is Directed Acyclic Graph (DAG). Directed because the relationship is not reverseable (if "A is a B" then it is not possible that "B is a A") and acyclic because cyclical subtype relationships would clearly be illogical (is "A is a B" and "B is a C" it is not possible that "C is a A"). Strictly speaking the hierarchy is not multi-axial hierarchy because it has a single root concept ("SNOMED CT Concept") and all other concepts are a subtype of this concept. However, rather misleadingly the top-level hierarchies are sometimes referred to axes. The SNOMED CT hierarchy is represented by relationships - not by a sequence of characters.



Historical Note: Before 2001 now-obsolete versions of SNOMED (including SNOMED 3) were multi-axial, the axes of SNOMED 3 were defined by the initial character of the code and codes from different axes needed to be combined to represent a concept. In 2002 with the release of SNOMED CT this approach changed.

IHTSDO Membership is open to all countries and the fees payable for membership are based on the relative wealth of the country according World Bank GNI metrics. One representative of each Member country sits on the IHTSDO General Assembly. IHTSDO Members are permitted (but not required) to create National SNOMED CT Extensions and they are permitted to translate SNOMED CT concept into their national language(s) or dialects. Members are not responsible for collecting fees for use in their country because there are no fees for use of SNOMED CT in Member countries.

The meaning of a SNOMED CT concept should never be changed to meet a local requirement (concept permanence is key feature of SNOMED CT). Use of a postcoordinated expression is a useful way to represent more detailed meanings. However, if this is not supportable or does not provide sufficient specificity other approaches can be followed: It is reasonable to use a more general concept and add qualifying text where the required more specific meaning is not frequently required or as a stopgap while pursuing other approaches. If the organization maintains its own Extension then the concept can be added locally. However, if the same requirement is likely to be shared nationally or internationally then a request for addition should be raised with the National Member or IHTSDO.

The data in a FULL release goes back to the very first release of SNOMED CT in January 2002 and shows all changes since that date. Rows once added to the a release remain unchanged in all subsequent FULL releases of that file and changes are made by adding the revised version of a component as a new row with a more recent effectiveTime.

The definition of a precoordinated expression is an expression containing only one concept identifier. The meaning of a precoordinated expression matches the meaning of the concept to which it refers. Surrounding information in a record may add contextual information that refines or modifies the interpretation of an expression (e.g. a procedure has a different interpretation if it appears in record sections such as "surgical history", "plan" or "operation notes"). The inclusion of terms in a SNOMED CT expression is optional.

Subtype relationships have a relationship type that is represented by the concept | is a |. They directly relate concepts to one or more less specific concepts and these direct supertypes are referred to as parents of the concept. Subtype relationships indirectly relate clinical concepts to broad clinical categories such as "clinical finding", "procedure" and "observable entity".

The Affiliate License Agreement issued by the IHTSDO and permit use of the SNOMED CT International Release. Some IHTSDO Members act as licensing agents for the IHTSDO but the license is still issued by IHTSDO as the licensor. IHTSDO Members are permitted to license their own National Extensions to IHTSDO Affiliates. Affiliates are required to report use in non-Member Territories and to pay fees for those uses. Affiliates are not permitted to translate SNOMED CT content. IHTSDO Members are permitted to translate SNOMED CT into their national language(s) and dialect(s).

The DELTA release only includes rows that have been added or changed since the last release. Therefore, the rows in the DELTA release include all rows in the FULL release for the same date that have an effectiveTime greater than the date of the previous release. The changes since the last release represent the most recent status of the concept so the rows in the DELTA release will also appear in the SNAPSHOT release. Where a concept has been made inactive since the last release these inactive rows will be in the DELTA release.

An SCTID is a number (a 64 bit integer) and the number itself says nothing about the meaning of the component that it identifies (the meaning of a concept is represented by relationships between concepts). The SCTID does contain some additional information: (a) a partitionId which indicates which type of component it represents (concept, description or relationship) and whether the component was originated in an Extension, (b) a check-digit and (c) in the case of components that are part of an Extensions a namespace identifier which indicates which Extension it was originated in. The namespace identifier is not present in components that originated in the SNOMED CT International Release.

SNOMED CT does not have semantic identifiers instead it uses relationships between concepts to represent formal definitions of concepts. These formal definitions are used to compute a subtype hierarchy - a polyhierarchy in which a concept may have more than one parent supertypes. Concepts (and other SNOMED CT components) are permanent and identifiers are never reused for a different purpose. However, SNOMED CT is able to evolve gracefully using a formal approach to changes and additions, all of which are version tracked.

The SNAPSHOT view of a SNOMED CT release can be generated from a FULL release - by taking only the row with the highest effectiveTime for each distinct id. The SNAPSHOT view of a SNOMED CT release can also be generated from the previous SNAPSHOT and the most recent DELTA release. In this case the two files are merged. Rows in the DELTA file are added to the new SNAPSHOT view if the id is unique, where a DELTA release row has the same id as a previous SNAPSHOT row, the row from the DELTA release replaces the row in the previous SNAPSHOT.

This is valid close to user expression and it represents "open fracture of the shaft of the left femur". It is not a normal form expression because in the normal form laterality is nested under the body structure to which it applies (in this case it would be nested under "shaft of femur"). The expression representation without terms is also valid because the expression grammar allows terms to be optionally added to assist human-readability.

In both RF1 and RF2 "Fully specified name" and "Synonym" are description types. However, in RF2 the preferred term is description of type "Synonym" which is marked as "Preferred". Also in RF2, the text definitions of some concept are included in an additional Descriptions file and they have the description type "Definition".

The correct option all resolve to the same normal form in which excision of gall bladder and exploration of bile duct are represented by separate relationship groups. The incorrect options fail to unambiguously associate excision with the gall bladder while separately associating exploration with the bile duct.

The "Stated Relationship" release file contains all the relationships that have been authored and passed quality assurance review. It does not include any inferred relationships.

The "Relationship" release file contains non-redundant relationships inferred from the relationships authored by the SNOMED CT editors. The inferred view is generated by using a description logic classifier which ensure the consistency of defining relationships. Additional relationships are inferred by the classifier are included in the "Relationship" file. Some relationships that are authored turn out to be redundant after classification and are not included in the "Relationship" file.

A SNAPSHOT release contains the most recent row for each component at the time of the release. The SNAPSHOT is generated by filtering the FULL release so that where there may be several rows with the same id in the FULL release, the SNAPSHOT only includes one row for each distinct id (i.e. the row highest effectiveTime). Therefore, every row in the SNAPSHOP is identical to a row in the FULL release. In the case of inactive concepts, the most recent row is a row representing the fact that the concept is inactive - so these inactive concept are represented in the SNAPSHOT.

The "appendix" is a body structure whereas "appendicitis" is a disorder, which is a type of clinical finding. "Finding site" is an attribute rather than a procedure or body structure. This attribute is used to define clinical finding based on their site ("appendicitis (disorder)" has "finding site (attribute)" "appendix (body structure)"). Procedures include anything that is (or can be) done so this includes "physiotherapy". "Color of iris" is an "observable entity"; it is not a "clinical finding" because it does not specify the observed value "Blue iris" is a "clinical finding" because it includes the value.

The standard SNOMED CT release format since 2012 (RF2) includes three distinct release types. The "FULL" release type includes all versions of all SNOMED CT components ever release (i.e. a complete history since the first SNOMED CT release in January 2002). The "SNAPSHOT" release type also includes all components ever released but omits the history only showing the most recent state of the component at the time of the release. The "DELTA" release type only contains the components added or changed since the previous release. The result of combining the the previous "FULL" release with the current "DELTA" is the current "FULL" release.

SNOMED CT concept represent clinical idea and descriptions associate these concept with human-readable term. Relationship represent associations between concepts. Reference sets can be used to represent additional non-defining information about concepts. A simple reference set represents a subset of concepts (or description) - the non-defining information that it add is simply that the concept is in the identified subset.

SNOMED CT is concept orientated because it concepts represent an idea rather a particular term or phrase. Concepts are permanent and once created they remain in every release with the same identifier and meaning but they can be marked as inactive if they are no longer considered appropriate for use. SNOMED CT identifiers are integers and the sequence of characters in the identifier does not convey any meaning.

The GA is the highest governance body. It elects the MB, which is responsible for directing the work of the organization. The GA also elects people to serve on Standing Committees, which are advisory groups providing input issues relevant to their scope. Special Interest Groups are open to anyone who accepts the terms of the Participation Conditions (www.ihtsdo.org/participation_conditions.pdf). They provide provide opportunities for sharing ideas and contributing the work of the IHTSDO in clinical specialty domains and functional areas (including Implementation, Education, Mapping and Translation).