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Extracts

Many extracted substances in SNOMED CT are not specific to either the part of the plant (root, seed, leaf, etc.) or the form (powder, dry or soft extract, etc.). The specific part of the plant should be known and documented when using these substances in modeling medicinal products. The less specific descriptions may find use in hierarchies besides Pharmaceutical / biologic product (product), such as the need to record an adverse reaction to a substance where the full details are unknown. While the most specific information is encouraged, all levels of specificity can be represented in SNOMED CT.

Naming pattern:

FSN: [Scientific name of source organism] <part of plant> extract (substance)

PT: [Common name of organism] <part of plant> extract

SYN: [Scientific name of source organism] <part of plant> extract

Note: Extraction method (via alcohol, water, CO2) is not required as it obscures the distinction between the substance and product hierarchies. While the method of extraction is clinically important, types of solvents used in production are not required due to the need for less precise use cases.

Extracts that include form

For extracts that include form (such as dry), the form should follow the source in the FSN and the corresponding SYN. The PT can have the form either in front of or following the source, whichever is prevailing in the literature.

  • For example,

    • FSN: Betula dry extract (substance)

    • PT: Dry birch extract

Preferred references for plant scientific and common names include the following:

  • Integrated Taxonomic Information System

  • Catalogue of Life

Thermo Fisher Scientific may be consulted for allergens.

The Global Substance Registration System (GSRS) is a good resource for substance names (INN, chemical names) but not necessarily the best for synonyms.

Some requests are for extracts of which the genus is too broad, while the requirement for the species is too specific. In these cases, the common name can be used; a scientific name is not used.

  • For example,

    • If the requested concept is for blueberry extract, there is no single genus and species that identifies the blueberry plant. The Vaccinium genus includes cranberry, ligonberry, and other berry plants in addition to blueberry. There are multiple blueberry species. Therefore, the concept can be created for blueberry extract without a scientific name. The common name has a case sensitivity indicator of ci.

See related section at

Though an extract is derived from a substance, it is not a type of that substance.

  • For example,

  • |Ginkgo biloba extract (substance)| would not have a parent of |Ginkgo biloba (substance)|.

SYN: Betula dry extract

Naming references

Level of specificity

Extract is not a type of the plant

General Naming Conventions | Specifications SNOMED CT Editorial Guide | SNOMED International Documents

Deoxyribonucleic acid and ribonucleic acid

Ribonucleic acid of X organism

Modeling

Parent concept

Most distal appropriate descendant of 118248003 |Microbial ribonucleic acid (substance)|

Semantic tag

(substance)

Definition status

Primitive

Pattern:

  • Ribonucleic acid of X organism (substance)

For example,

  • Ribonucleic acid of Norovirus genogroup I (substance)


Preferred Term (US/GB) with initial letter case sensitive:

Pattern:

  • X organism RNA

For example,

  • Norovirus genogroup I


Pattern: A synonym that matches FSN

For example,

  • Ribonucleic acid of Norovirus genogroup I

Additional synonyms (when a legitimate synonym exists for Organism name) are applicable.

The following illustrates the stated and inferred view:

Pattern:

  • Ribosomal ribonucleic acid of X organism (substance)

For example,

  • Ribosomal ribonucleic acid of Candida (substance)


Preferred Term, with Initial letter case sensitive.

Pattern:

  • X organism rRNA

For example,

  • Candida rRNA


Pattern:

  • A synonym that matches FSN

For example,

  • Ribosomal ribonucleic acid of Candida

Additional synonyms (when a legitimate synonym exists for Organism name) are applicable.

The following illustrates the stated and inferred view:

Pattern: Messenger ribonucleic acid of X organism (substance)

For example,

  • Messenger ribonucleic acid of Severe acute respiratory syndrome coronavirus 2 (substance)


Preferred Term, with Initial letter case sensitive.

Pattern: X organism mRNA

For example,

  • SARS-CoV-2 mRNA


Pattern: A synonym that matches FSN

For example,

  • Messenger ribonucleic acid of Severe acute respiratory syndrome coronavirus 2

Additional synonyms (when a legitimate synonym exists for Organism name) are applicable.

Stated and inferred view of 1119343008 |Messenger ribonucleic acid of severe acute respiratory syndrome coronavirus 2 (substance)|:

Pattern: Messenger ribonucleic acid of X organism encoding for protein Y (substance)

For example,

  • Messenger ribonucleic acid of Severe acute respiratory syndrome coronavirus 2 encoding spike protein (substance)


Preferred Term, with Initial letter case sensitive.

Pattern: X organism mRNA encoding for protein Y

For example,

  • SARS-CoV-2 mRNA encoding spike protein


Pattern: A synonym that matches FSN

For example,

  • Messenger ribonucleic acid of Severe acute respiratory syndrome coronavirus 2 encoding spike protein (substance)

Additional synonyms (when a legitimate synonym exists for Organism name) are applicable.

Stated and inferred view of 1155866009 |Messenger ribonucleic acid of severe acute respiratory syndrome coronavirus 2 encoding spike protein (substance)|:

Pattern: Deoxyribonucleic acid of X organism (substance)

For example,

  • Deoxyribonucleic acid of Aspergillus terreus (substance)


Preferred Term (US/GB), with Initial letter case sensitive:

Pattern: X organism DNA

For example,

  • Aspergillus terreus DNA


Pattern: A synonym that matches FSN

For example,

  • Deoxyribonucleic acid of Aspergillus terreus

Additional synonyms (when a legitimate synonym exists for Organism name) are applicable.

The following illustrates the stated and inferred view:

Antivenom

Attribute:

Has disposition

Range: < 726711005 |Disposition (disposition)|

  • While the allowed range is broader, substance concepts should only use <726711005 |Disposition (disposition)| as the attribute value.

Cardinality: 0..*

Attribute:

Has disposition

Range: <726711005|Disposition (disposition)

  • While the allowed range is broader, substance concepts should only use <726711005 |Disposition (disposition)| as the attribute value.

Cardinality: 0..*

Attribute:

Has disposition

Range: <726711005 |Disposition (disposition)|

  • While the allowed range is broader, substance concepts should only use <726711005 |Disposition (disposition)| as the attribute value.

Cardinality: 0..*

Attribute:

Has disposition

Range: <726711005 |Disposition (disposition)

  • While the allowed range is broader, substance concepts should only use <726711005 |Disposition (disposition)| as the attribute value.

Cardinality: 0..*

Attribute:

Is modification of

Range <105590001 |Substance (substance)|

Cardinality: 0..*

One relationship to be created to represent each modified component of the substance

Attribute:

Has disposition

Range: <726711005 |Disposition (disposition)|

  • While the allowed range is broader, substance concepts should only use <726711005 |Disposition (disposition)| as the attribute value.

Cardinality: 0..*

Parent concept

Most distal appropriate descendant of 118251005 | Microbial ribosomal ribonucleic acid (substance)|

Semantic tag

(substance)

Definition status

Primitive

Attribute:

Is Modification of

Range <105590001 |Substance (substance)|

Cardinality: 0..*

One relationship to be created to represent each modified component of the substance

Parent concept

Most distal appropriate descendant of 69908008 |Messenger ribonucleic acid (substance)|

Semantic tag

(substance)

Definition status

Primitive

Attribute:

Is modification of

Range <105590001 |Substance (substance)|

Cardinality: 0..*

One relationship to be created to represent each modified component of the substance

Parent concept

Most distal appropriate descendant of 69908008 |Messenger ribonucleic acid (substance)|

Semantic tag

(substance)

Definition status

Primitive

Attribute:

Is modification of

Range <105590001 |Substance (substance)|

Cardinality: 0..*

One relationship to be created to represent each modified component of the substance

Parent concept

Most distal appropriate descendant of 118249006 |Microbial deoxyribonucleic acid (substance)|

Semantic tag

(substance)

Definition status

Primitive

Attribute:

Is modification of

Range <105590001 |Substance (substance)|

Cardinality: 0..*

One relationship to be created to represent each modified component of the substance

Naming

FSN

Preferred Term

Synonyms

Exemplar

Ribosomal ribonucleic acid of X organism

Modeling

Naming

FSN

Preferred Term

Synonyms

Exemplar

Messenger ribonucleic acid of X organism

Modeling

Naming

FSN

Preferred Term

Synonyms

Exemplar

Messenger ribonucleic acid of X organism encoding for specific protein

Modeling

Naming

FSN

Preferred Term

Synonyms

Exemplar

Deoxyribonucleic acid of X organism

Modeling

Naming

FSN

Preferred Term

Synonyms

Exemplar

Provide Feedback

|Has disposition| = 763291003 |Antivenom (disposition)|

  • Use antivenom, not antivenin, for FSNs and Preferred Terms. Synonyms containing antivenin are not created routinely but may be created upon request.

  • FSNs should be based on the scientific name if there is a one-to-one correspondence. Naming conventions for polyvalent antivenoms (effective against multiple organisms) will not comply with this naming convention and will be evaluated on a case-by-case basis. Preferred Terms are based on the common name.

  • Synonyms based on the scientific name should be created in most cases.

Useful reference: Current version of WHO Guidelines for the Production, Control and Regulation of Snake Antivenom Immunoglobulins

Pattern:

  • X antivenom (substance), where X = scientific name of organism

For example,

  • Chironex fleckeri antivenom (substance)


Pattern:

  • Y antivenom, where Y = Common name of organism

For example,

  • Australian box jellyfish antivenom

Exception

  • When there is no common name for the organism, the PT will match the FSN


Pattern:

  • A synonym that matches FSN (If not used Preferred term; see notes above)

For example,

  • Chironex fleckeri antivenom

Additional synonyms (e.g., when other legitimate synonyms exist for Organism name) are applicable and are evaluated on a case-by-case basis

For example,

  • Deadly sea wasp antivenom

The following illustrates the stated view of 699514008 |Chironex fleckeri antivenom (substance)|:

Provide Feedback

Parent concept

Most distal appropriate descendant of 115668003 |Biological substance (substance)|

Semantic tag

(substance)

Definition status

Primitive

Modeling

Attribute

Naming

FSN

Preferred Term

Synonyms

Exemplar

Edible substances

Overview

Substance concepts should, where possible, be modeled with either a structural parent or one that denotes source or origin.

Modeling

Parent concept

Most distal appropriate descendant of 762766007 |Edible substance (substance)|

Additional parent concepts may be modeled to denote origin or structural characteristics.

Semantic tag

(substance)

Definition status

FSN, PT or Synonym should not contain "- dietary" context in descriptions

FSN, PT or Synonym should not contain brand or trade names.

Culinary name should be used for the FSN and PT when referring to meat products and food, e.g., Beef dripping (substance), Pork sausage (substance).

If there are additional adjectives such as baked, boiled, fried, lean, minced, low-fat, roast, or stewed, these adjectives should proceed the name of source organism, e.g., Fried beef steak (substance), Tinned fish (substance).

Pattern:

  • X (substance)

For example,

  • Betel nut (substance)

  • Wheat dextrin (substance)

  • Tinned fish (substance)


Pattern:

  • X

For example,

  • Betel nut

  • Wheat dextrin

  • Tinned fish


Pattern: scientific name if appropriate

For example,

  • Areca catechu

The following illustrates the stated and inferred view.

The following illustrates the stated and inferred view.

Substances specifying physical state or physical form

Overview

Concepts specifying a particular physical state (e.g. liquid, solid, fumes, vapor, crystal, foam) of a substance should be represented as the sibling for the unspecified substance and also have a parent concept that relates to the structure of the substance.

Concepts specifying a particular physical form (e.g. micronized, macrocrystal, microsphere) should have a parent concept that relates to the structure of the substance and also an Is modification of (attribute) relationship to the unspecified substance concept.

Modeling - Micronized substance

Parent concept

Most distal appropriate descendant of 105590001 |Substance (substance)|

An additional parent concept to be allocated to denote physical form as appropriate

Semantic tag

Fumes should be expressed in the plural (i.e. fumes as opposed to fume).

Fumes and vapor are different and so should not be used as synonyms on the same concept.

Pattern:

  • X fumes (substance)

  • X micronized (substance)

For example,

  • Bauxite fumes (substance)

  • Fenofibrate micronized (substance)


Pattern:

  • X fumes

  • X micronized

For example,

  • Bauxite fumes

  • Fenofibrate micronized


Pattern: X form to represent EN-GB language variants where appropriate

For example,

  • Fenofibrate micronised

View of both stated and inferred form of 278945005 |Iron fumes (substance)|:

Stated view of 414246008 |Fenofibrate micronized (substance)|:

Primitive

Naming

FSN

Preferred Term

Synonyms

Exemplars

Provide Feedback

(substance)

Definition status

Primitive

Attributes

738774007 |Is modification of (attribute)| relationship to the unspecified substance

726542003 |Has disposition (attribute)| as appropriate

Naming

FSN

Preferred Term

Synonyms

Exemplar

https://www.commerce.wa.gov.au/worksafe/gases-vapours-smoke-and-fumes
Provide Feedback

Flap substances

Overview

This section includes concepts that represent flap substances used in flap surgery. The concepts in this subhierarchy are used to define:

Flap composition

  • For example,

    • bone, skin, muscle, myocutanous, osteocutaneous

Flap blood supply

  • For example,

    • Free flap: A completely detached flap transferred with its own blood supply intact is known as a free flap. A free flap is re-attached at the recipient site, which is a highly skilled technique, often involving microsurgical anastomosis of the blood vessels

    • Pedicle flap: A pedicle flap is transferred still attached to its original blood supply (the pedicle)

Flap substances exist for free flaps and pedicle flaps (<<261238005 |Free flap (substance)| and << 261235008 |Pedicle flap (substance)|) and reflect the fact that whether a flap is free or pedicle is also a function of its blood supply (i.e. completely unattached from its original blood supply, or still attached via a vascular pedicle).

Flap substances comprising composite multiple flap tissues are siblings (and not subtypes) of the various single tissue flap substances from which they are composed.

Flap substances should not include the procedure method, such as whether a flap is local or distant, or if a flap is rotated or advanced.

The concepts in this subhierarchy must not be conflated with either the donor procedure site or the site that the procedure acts upon.

For substances representing skin flaps, the FSN and PT contains ‘skin flap’ with an acceptable synonym of ‘cutaneous flap’.

For osteocutaneous flaps, terming for FSN and PT is ‘osteocutaneous flap’ with an acceptable synonym of ‘osseocutaneous flap’.

Substances specifying bound

Creation of substance concepts that contain “bound” is limited to the measurement of biological substances (Observable entities, evaluation procedures, LOINC collaboration project) or to report their level (clinical findings).

Where the substance is "bound" the molecule to which the substance is bound to may be specified in the term.

Parent concept

Most distal appropriate descendant of 256683004 |Flap (substance)|

Semantic tag

(substance)

Definition status

Primitive

Modeling

Naming

Exceptions

Flaps that include the named specific muscle site are to remain as a refinement in the flap substances; for example, 840353005 |Transverse rectus abdominis myocutaneous flap (substance)|.

Provide Feedback

Definition status

Primitive

Attribute

726542003 |Has disposition (attribute)|

Pattern: Bound X (substance)

For example,

  • Bound insulin (substance)

  • Protein bound iodine (substance)

  • Albumin bound thyroxine (substance)


Pattern: Bound X (substance)

For example,

  • Bound insulin

  • Protein bound iodine (substance)

  • Albumin bound thyroxine (substance)

The following illustrates the stated and inferred view:

Provide Feedback

Parent concept

Most distal appropriate descendant of 115668003 |Biological substance (substance)|

Semantic tag

(substance)

Bound substances Overview

Modeling

Terming

FSN

Preferred Term

Exemplar

Metabolites

Overview

A metabolite is a substance created or utilized during metabolism, the process by which the body breaks down food, drugs, chemicals, or its own tissues (e.g., fat, muscle). Metabolites are differentiated from derivatives, that are compounds synthesized by modifying precursor compounds and are important in discovery of new drugs (e.g., molecules with improved efficacy, reduced toxicity, or enhanced pharmacokinetic profiles), materials science (e.g., polymers with altered properties), and agrochemicals (e.g., potent pesticide).

Concepts representing Metabolites of X will be considered for inclusion based upon project requirements.

Modeling

Parent concept

767279008 |Metabolite (substance)|

Pattern: X metabolite (substance)

For example,

  • Cocaine metabolite (substance)


Pattern: X metabolite

For example,

  • Cocaine metabolite

The following illustrates the stated and inferred view:

Semantic tag

(substance)

Definition status

Primitive

Attribute

None

Naming

FSN

Preferred Term

Exemplar

Provide Feedback

Substance Specific Guidelines

This section of the document provides guidance for specific types of substances.

  • Antibodies and antigens

  • Antivenom

  • Autoantibody

Conjugate acids, bases and salts
Deoxyribonucleic acid and ribonucleic acid
Edible substances
Extracts
Flap substances
Fractionated and unfractionated substances
Hydrates and anhydrous substances
Ions and electrolyte substances
Isomers
Metabolites
Radioactive substances
Saturated or unsaturated substances
Substances specifying a source or origin
Substances specifying bound
Substances specifying free or unbound or unconjugated
Substances specifying intact, fragment or subunit
Substances specifying physical state or physical form
Provide Feedback

Substances specifying free or unbound or unconjugated

Overview

Creation of substance concepts that contain terms such as “free” (or "unbound" or "unconjugated") is limited to the measurement of biological substances (Observable entities, evaluation procedures, LOINC collaboration project) or to report their level (clinical findings). These concepts are created as siblings of the base concepts with a "substance X and X derivatives" or "X and X compound" as common supertype.

Modeling

Parent concept

Most distal appropriate descendant of 105590001 |Substance (substance)|

Semantic tag

(substance)

Pattern: Free X (substance)

For example,

  • Free iodine (substance)


Pattern: Free X

For example,

  • Free iodine


Optional pattern: Unbound x

For example,

  • Unbound iodine

The following illustrates both the stated and inferred view:

The following illustrates the hierarchy view:

Definition status

Primitive

Attribute

726542003 |Has disposition (attribute)|

Naming

FSN

Preferred Term

Synonyms

Exemplar

Provide Feedback

Substances specifying a source or origin

Overview

A recombinant (A new entity e.g., gene, protein, cell, or individual that results from genetic recombination) or synthetic/semi-synthetic substance (of, relating to, or produced by chemical or biochemical synthesis; especially: produced artificially) is similar in structure (but not identical to the naturally occurring substance). It should be created as a sibling of the naturally occurring substance.

A substance that is part of (e.g. dander) or is derived from (e.g. Insulin) an organism (human or non-human) is identical and should be created as a child of the naturally occurring substance.

Modeling

Parent concept

Most distal appropriate descendant of 105590001 |Substance (substance)|

“Recombinant”, “Synthetic”, or “Semi-synthetic” should precede the name of the substance

The source organism name should precede the name of the substance

  • An exception to this rule is the naming of DNA, RNA, rRNA, antibody, Immunoglobulin, and antigen of organisms, which should follow the guideline specified for antibodies and antigens

  • For some non-human sources, there are different ways of referring to the source organism:

    • The common name of the organism e.g. pig, cow, horse, mouse, sheep

Additional adjectives (such as labeled, Iodinated) should proceed the name of source organism

  • For example,

    • Lente human insulin (substance)

    • Iodinated (125-I) human serum albumin (substance)

If a concept includes “recombinant” or “synthetic” as well as a source organism, “recombinant” or “synthetic” should precede the source organism name

  • For example,

    • Recombinant bovine growth hormone (substance)

Pattern:

  • [Source organism] X (substance)

  • Recombinant X (substance)

  • Synthetic X (substance)

For example,

  • Human antithrombin III (substance)

  • Recombinant thrombin (substance)

  • Synthetic steroid (substance)


Pattern:

  • [Source organism] X

  • Recombinant X

  • Synthetic X

For example,

  • Human antithrombin III

  • Recombinant thrombin

  • Synthetic steroid


The naming of DNA, RNA, rRNA, antibody, Immunoglobulin, and antigen of organisms should follow the specific guideline for this type of substances.

Stated view of 411973001 |Bovine thrombin (substance)|

The common name of an organism is used when referring to a part of the organism or to non-meat products

  • E.g. Pig epithelium, Cow milk

  • An adjective referring to the organism, e.g. porcine, bovine, equine, murine, ovine

    • The adjective is usually used when referring to a substance extracted from the organism

      • E.g. Bovine growth hormone (substance), Porcine calcitonin (substance)

  • The adjective is commonly used in referring to the organism hosting a virus, but there are exceptions. In general, proper name of organism such as virus name should be preserved as it is (including the case sensitivity):

    • Ribonucleic acid of Bovine leukemia virus (substance)

    • Immunoglobulin G antibody to Eastern equine encephalitis virus (substance)

    • Antigen of Nairobi sheep disease virus (substance)

  • Semantic tag

    (substance)

    Definition status

    Primitive

    Attribute

    738774007 |Is modification of (attribute)| as applicable

    726542003 |Has disposition (attribute)| as appropriate

    Naming

    FSN

    Preferred Term

    Exception

    Exemplar

    Provide Feedback

    Conjugate acids, bases and salts

    Overview

    Acids substance concepts should be modeled with a structural parent concept.

    Salts should be modeled with a conjugate base as parent (if one exists, otherwise they are modeled with a structural parent). Salts may have an Is modification of (attribute) relationship to the conjugate acid where a specific use case is identified. See examples of such use cases at Concepts Representing a Substance or its Modifications.

    Conjugate base concepts (e.g., valproate, pamidronate, etidronate) should only be created where a specific use case is identified, for example, when required to support the definition of other concepts in the terminology.

    Conjugate bases should be created as separate concepts - not added as synonyms to the corresponding acid concept.

    New instances of substance concepts containing the word salt will not be added. The existing concepts will be reviewed, and if possible, will be replaced by equivalent compounds.

    Modeling

    Where INN names exist, these should be used for the FSN and PT.

    Pattern:

    • X sulfate (substance)

    • X pamidronate (substance)

    For example,

    • Copper sulfate (substance)

    • Disodium pamidronate (substance)

    • Etidronate (substance)

    Exception:

    • Valproate sodium (substance)


    Pattern:

    • X sulfate

    • X pamidronate

    For example,

    • Copper sulfate

    • Pamidronate monosodium

    • Etidronate

    Exception:

    • Valproate sodium


    Pattern: Pamidronate X

    For example,

    • Pamidronate monosodium

    • Valproate sodium

    Stated view of 387080000 |Valproic acid (substance)|:

    Stated and inferred view of 387481005 |Sodium valproate (substance)|:

    Hierarchy view of 264325000 |Valproate (substance)| subtypes:

    The following illustrates the stated and inferred views.

    Parent concept

    Most distal appropriate descendant of 312413002 |Substance categorized structurally (substance)|

    Semantic tag

    (substance)

    Definition status

    Primitive

    Attribute:

    Is Modification of

    Range <105590001 |Substance (substance)|

    Cardinality: 0..1

    Used to identify the conjugate acid

    Attribute:

    Has disposition

    Naming

    FSN

    Preferred Term

    Synonyms

    Exemplar

    Provide Feedback

    Range: <726711005 |Disposition (disposition)|

    • While the allowed range is broader, substance concepts should only use <726711005 |Disposition (disposition)| as the attribute value.

    Cardinality: 0..1

    Hydrates and anhydrous substances

    Modeling

    Parent concept

    Most distal appropriate descendant of 105590001 |Substance (substance)|

    Semantic tag

    (substance)

    Definition status

    Primitive

    Hydates are modeled with an 738774007 | Is modification of (attribute)| relationship to the substance with unspecified hydration.

    For example,

    • Ferrous oxalate dihydrate (substance) is modification of → Ferrous oxalate

    • Caffeine hydrate (substance) is modification of → Caffeine

    • Zinc sulfate heptahydrate (substance) is modification of → Zinc sulfate

    Pattern:

    • X hydrate (substance)

    • X dihydrate (substance)

    • X monohydrate (substance)

    For example,

    • Copper sulfate pentahydrate (substance)


    Pattern:

    • X hydrate

    • X dihydrate

    • X monohydrate

    For example,

    • Copper sulfate pentahydrate

    The following illustrates the inferred view.

    Caffeine hydrate (substance) IS MODIFICATION OF Caffeine (substance)

    Anhydrous compounds have an 738774007 | Is modification of (attribute)| relationship to the unspecified substance, i.e., where the level hydration is not specified.

    For example,

    • Sodium carbonate anhydrous (substance) is modification of → Sodium carbonate

    • Theophylline anhydrous (substance) is modification of → Theophylline

    Pattern:

    • X anhydrous (substance)

    For example,

    • Theophylline anhydrous (substance)


    Pattern:

    • X anhydrous

    For example,

    • Theophylline anhydrous


    Anhydrous X

    The following illustrates the inferred view.

    |Theophylline anhydrous (substance)| IS MODIFICATION OF |Theophylline (substance)|

    Saturated or unsaturated substances

    Modeling

    Parent concept

    Most distal appropriate descendant of 115668003 |Biological substance (substance)|

    Semantic tag

    (substance)

    Definition status

    Primitive

    Saturated X (substance)

    Unsaturated X (substance)

    For example,

    • Unsaturated adipate (substance)


    Saturated X

    Unsaturated X

    For example,

    • Unsaturated adipate


    X Saturated or X Unsaturated

    For example,

    • Adipate unsaturated

    The following illustrates the stated and inferred view:

    Substances specifying intact, fragment or subunit

    Fragments are created as siblings of the intact/whole/entire substance.

    “Intact” should not be included when referring to the "entire substance" or "whole substance"; it is implied.

    Alpha and beta sub-units should be the children of the entire substance, where "nicked" substances and fragments should be the siblings.

    INN should be used for the Preferred Term where they exist.

    Attribute

    738774007 |Is modification of (attribute)| relationship to the substance with unspecified hydration

    726542003 |Has disposition (attribute)|, as appropriate

    Hydrates

    Naming

    FSN

    Preferred Term

    Exemplar

    Anhydrous compounds

    Naming Guidelines

    FSN

    Preferred Term

    Synonyms

    Exemplar

    Provide Feedback

    Semantic tag

    (substance)

    Definition status

    Primitive

    Attribute

    |Has disposition| as appropriate

    Pattern:

    • X fragment (substance)

    • X subunit (substance)

    For example,

    • Corticotropin, big fragment (substance)|

    • Thyrotropin beta subunit (substance)


    Pattern:

    • X fragment

    For example,

    • Corticotropin, big fragment

    • Thyrotropin beta subunit

    Provide Feedback

    Parent concept

    Overview

    Modeling

    Most distal appropriate descendant of 115668003 |Biological substance (substance)|

    Naming

    FSN

    Preferred Term

    Attribute

    None

    Naming

    FSN

    Preferred Term

    Synonyms

    Exemplar

    Provide Feedback

    Autoantibody

    Modeling

    Parent concept

    Most distal appropriate descendant of 30621004 |Autoantibody (substance)|

    Semantic tag

    (substance)

    Definition status

    Primitive

    Pattern: "Antibody to" + Antibody target

    Note: An antibody target can be an antigen or another antibody.

    For example,

    • Antibody to nuclear antigen (substance)

    • Antibody to thyroglobulin immunoglobulin G (substance)


    Pattern: Antibody target + "antibody"

    For example,

    • Nuclear antibody or Thyroglobulin immunoglobulin G antibody


    Pattern: A synonym that matches FSN

    For example,

    • Antibody to nuclear antigen

    • Antibody to thyroglobulin immunoglobulin G

    Pattern: Antibody target + "Ab"

    For example,

    • Nuclear Ab

    • Thyroglobulin IgG Ab

    Additional synonyms:

    • Add a description containing antibody target + "autoantibody"

      • Nuclear autoantibody

      • Thyroglobulin IgG autoantibody

    Ions and electrolyte substances

    Previously, SNOMED CT represented ions and electrolytes as separate concepts. Although the two terms are subtly different, there is considerable overlap in their definitions, and they seem to be used interchangeably in medicine. The Substances Redesign Project Group considered this issue and determined the following:

    • Ions should be modeled as child concepts of the substance.

    • A second parent (in addition to X (substance)), that indicates the concept is an ionized substance, should be modeled.

    In general, anti X antibody or anti X autoantibody is redundant and should be avoided. However, description(s) that are commonly used are considered for addition on a case by case basis, for example:
    • ANA - anti-nuclear antibody

    Attribute

    None

    Naming

    FSN

    Preferred Term

    Synonyms

    Provide Feedback

    Use a descendant of 86355000 |Electrolyte (substance)| as the additional parent. (<<86355000 |Electrolyte (substance)| are used in LOINC term expression associations.)

  • Non-Ionized/Non-Ionised substances should not be created.

  • Parent concepts

    Most distal appropriate descendant of 86355000 | Electrolyte (substance)|

    Most distal appropriate descendant of 312413002 |Substance categorized structurally (substance)|

    Semantic tag

    (substance)

    Definition status

    Primitive

    Attribute

    None

    Pattern:

    • X ion (substance)

    For example,

    • Ferric ion (substance)


    Pattern:

    • X ion

    For example,

    • Ferric ion


    Pattern: "Ionized X" and "X electrolyte" Add "Ionised X" as GB synonym.

    For example,

    • Ionised fluorine

    • Ionized fluorine

    • Fluoride electrolyte

    Where an element can exist with more than one level of oxidation, for example, iron can exist in either the ferric (Fe3+) or ferrous (Fe 2+) ionization states, the synonyms "Ionised X" and "Ionized X" should not be added since they are ambiguous.

    The following illustrates the Stated andInferred view:

    The following illustrates the hierarchy view:

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    Overview

    Modeling

    Naming

    FSN

    Preferred Term

    Synonyms

    Exemplar

    Fractionated and unfractionated substances

    Overview

    Substance concepts that contain terms such as “fractionated” or “unfractionated” are not created in the Substance hierarchy. "Unfractinated" should not be included when referring to the "entire substance" or "whole substance"; it is implied. "Fractionated" usually refers to a separation technique or process.

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    Antibodies and antigens

    Overview

    This section includes concepts that represent

    • Antigen of organism

    • Antibody to organism

    • Immunoglobulin G, M, A, E, D antibody to organism

    Organism above includes substances derived from an organism, for example, feather or protein.

    When referring to an organism name, while the Linnean taxon ranks (such as genus) are not included, the subspecies variants (such as biotype and serotype) are included in the naming. This avoids ambiguity when the same number or letter is used to refer to different organism variants.

    • For example,

      • Without mentioning the specific variant (serogroup vs. serotype) and the nomenclature system (Danish vs. American), Streptococcus pneumoniae 48 can refer to the following:

        • Streptococcus pneumoniae Danish serotype 48 (which is equivalent to Streptococcus pneumoniae American serotype 82)

    The antigen name is usually derived from the biological name of the organism as opposed to the disease or infection that the organism may cause and/or that the vaccine may provide immunization for.

    Pattern:

    • Antigen of X organism (substance)

    For example,

    • Antigen of Filaria (substance)

    • Antigen of Alternaria alternata protein (substance)


    Pattern:

    • X organism antigen

    For example,

    • Filaria antigen

    • Alternaria alternata protein antigen

    Exception:

    • Preferred term for |Antigen of live attenuated Mycobacterium bovis| is |Bacillus Calmette-Guerin antigen|


    1. Pattern: A synonym that matches FSN

      1. For example,

        1. Antigen of Filaria

    There is a requirement for the inclusion of characteristic technologies that are essential for distinguishing between different antigen variants that are used in manufacturing vaccine products, e.g., live attenuated, inactivated, or subunit antigens. Antigen variants are evaluated for:

    • References such as WHO, CDC, UpToDate, vaccine package inserts

    • Inclusion in the international release vs. national extensions

    • Hierarchy they belong to: Substance or Product

    To prevent the creation of transient or short-lived viral strain content, the International Release will not create specific viral variant strains or their corresponding antigen substance concepts when those variants have only brief or limited existence. For the purpose of defining clinical drugs or vaccine products in the International Release, stable higher-level parent virus or antigen concepts should be used instead. National Release Centers (NRCs) that require representation of specific viral variants for local regulatory or clinical use cases may create such concepts within their extensions.

    "Antigen of X" is in scope for the international release and is modeled in the Substance hierarchy. It is a generic grouper concept and subsumes all instances of antigen variants related to Organism X.

    • X refers to a bacteria, virus, fungus, or parasite except when antigen refers to the organism “toxin/toxoid”, where it can only apply to a bacteria.

    “Antigen of live attenuated X” is in scope for the international release and is modeled in the Substance hierarchy as a direct child of |Antigen of X|.

    • It refers to attenuated whole cell bacteria or whole virus where the strains are made less virulent so infection is usually inapparent or very mild. It may be used in the creation of vaccine products for certain patient groups, and hence, is of clinical significance.

    • The following subtypes are also in scope for the international release and are modeled in the Substance hierarchy as direct children of |Antigen of live attenuated X|. In the following examples, human and bovine refer to source organisms which are differentiated from the organism producing antigen, i.e., Rotavirus.

      • “Live attenuated human X”, e.g., Antigen of live attenuated human Rotavirus serotype G1P[8]

    “Antigen of inactivated whole X” is in scope for the international release and is modeled in the Substance hierarchy as a direct child of Antigen of X.

    • It refers to the killed version of the organism that causes a disease.

    • As of the July 2020 release, the word "whole" is added to all new and existing concepts referring to "Antigen of inactivated X" to further clarify the differentiation between "Antigen of inactivated whole organism" (referring to a killed organism as a whole) and "Antigen of organism [subunit]" (referring to subparts of an organism).

    “Antigen of acellular X” is in scope for the international release and is modeled in the Substance hierarchy as the direct child of "Antigen of X".

    • "Antigen of acellular X", when it exists, can only apply to a bacteria.

    “Antigen of X [subunit]” is in scope for the international release and is modeled in the Substance hierarchy as the direct child of “Antigen of X”.

    • Subunit antigens differ from inactivated whole-cell antigens by referring only to the antigenic parts of the pathogen. These parts are necessary to elicit a protective immune response. The word “inactivated” does not need to be part of the name unless it is referring to a whole cell or a whole virus, i.e., for descriptions referring to a subunit, the word inactivated will be omitted as redundant.

    • [Subunit] refers to a sub-part of an organism i.e. a specific, isolated protein of the pathogen, a recombinant protein (made by recombinant DNA techniques), an inactivated toxin (toxoid), or a capsular polysaccharide/oligosaccharide coating of an encapsulated bacterium:

      • "Antigen of X [protein/recombinant protein]" is in scope for the international release and is modeled in the Substance hierarchy.

    When referring to Organism parts/subunits:

    • Referring to more than one subunit (e.g., combined protein such as Bordetella pertussis FIM 2 and FIM 3 antigen) would not be acceptable for the Substance hierarchy; the combined protein needs to be modeled at the product level with more than one active ingredient.

    • Abbreviated organism subunit names such as "Corynebacterium diphtheriae CRM197 protein", are not allowed in a fully specified name (and similar synonym). The FSN and similar synonym should only include the spelled-out terms, i.e., "Corynebacterium diphtheriae cross-reacting material 197 protein".

    • Abbreviated organism part names are allowed in a preferred term (and other synonyms). The abbreviations do not need to be accompanied by the fully expanded term, which is an exception to the general naming guidelines on abbreviations and acronyms in the SNOMED CT Editorial Guide.

    Inclusion of vaccine manufacturing techniques and/or residuals in antigen names is generally out of scope for the international release. However, exceptions can be made for applicable use cases.

    • "Antigen of X grown in nervous tissue" or "Antigen of X grown in cellular line" is acceptable for inactivated Rabies antigens grown in brain tissue or cell lines and is included in the international release, considering the difference in the adverse reactions that they cause. If and when created:

      • "Antigen of X grown in cellular line" will be a grouper and other subgroups will be added as needed, e.g., "grown in Human diploid cell".

      • "Antigen of X grown in nervous tissue" should indicate the specific type of nervous tissue, e.g., brain.

    • Antigen of X

      • Antigen of live attenuated X

      • Antigen of inactivated whole X

    The following illustrates the stated and inferred view:

    Pattern:

    • Antibody to X organism (substance)

    For example,

    • Antibody to Bebaru virus (substance)


    Pattern:

    • X organism antibody

    For example,

    • Bebaru virus antibody


    1. Pattern: A synonym that matches FSN

      1. For example,

        1. Antibody to Bebaru virus

    Additional synonyms (e.g., when a legitimate synonym exists for Organism name, such as common names) are applicable.

    The following illustrates the stated and inferred view:

    Pattern:

    • Immunoglobulin G, M, A, E, D antibody to X organism (substance)

    For example,

    • Immunoglobulin M antibody to Clostridium difficile (substance)

    • Immunoglobulin G antibody to Juglans (substance)


    Pattern:

    • X organism IgG, M, A, E, D

    For example,

    • Clostridium difficile IgM

    • Walnut IgG

      • Walnut is the common name for Juglans.


    1. Pattern: A synonym that matches FSN

      1. For example,

        1. Immunoglobulin M antibody to Clostridium difficile

    Additional synonyms (e.g., when a legitimate synonym exists for Organism name, such as common names) are applicable.

    • For example,

      • Juglans IgG

        • Juglans is the scientific name for walnut.

    The following illustrates the stated and inferred view:

    Streptococcus pneumoniae American serotype 48 (which is equivalent to Streptococcus pneumoniae Danish serotype 7B)

  • Streptococcus pneumoniae serogroup 48

  • Antigen of Alternaria alternata protein
  • Pattern: X organism Ag

    1. For example,

      1. Filaria Ag

      2. Alternaria alternata protein Ag

  • Other

    1. |X organism inactivated toxin| for concepts referring to |X organism toxoid (substance)|

    2. Additional synonyms (e.g., when a legitimate synonym exists for Organism name, such as common names) are applicable and are evaluated on a case-by-case basis.

  • “Live attenuated human-bovine reassortant X”, e.g., Antigen of live attenuated human-bovine reassortant Rotavirus serotype G1

    • It represents a specific, isolated protein of the pathogen or a recombinant protein.

    • When both "Antigen of X [protein]" and "Antigen of X [recombinant protein]" exist for X organism, they are modeled as siblings.

  • “Antigen of X capsular polysaccharide/oligosaccharide" is in scope for the international release and is modeled in the Substance hierarchy.

    • It represents a polysaccharide/oligosaccharide antigen and acts as a grouper for the following:

      • "Antigen of X capsular polysaccharide/oligosaccharide unconjugated”, which represents a polysaccharide/oligosaccharide antigen without conjugation to any carrier protein or toxoid

      • “Antigen of X capsular polysaccharide/oligosaccharide conjugated”, represents a grouper concept and will be created in the international release and in the Substance hierarchy per request and (based on current ED guidelines) only if it has more than one child concept.

        • Exception can apply if there is a use case that support retaining/creating these conjugate groupers:

          • Recording the history of a conjugated vaccine when the type of conjugated protein is not known

      • “Antigen of X capsular polysaccharide/oligosaccharide conjugated to Y”, which represents an oligosaccharide or polysaccharide antigen attached to a protein Y, where “Y” refers to a carrier protein to increase efficacy and immunogenicity e.g. Corynebacterium diphtheriae cross-reacting material 197 protein.

        • It is the direct child of single parent |Antigen of X capsular polysaccharide/oligosaccharide conjugated|. There are no clinical use case that requires association to the conjugated part of antigen as an additional parent. This classification is in line with all other similar concepts (modifications such as pegylated substances).

  • “Antigen of X toxoid” is in scope for the international release and is modeled in the Substance hierarchy.

    • Like other subunit antigens, “Antigen of X toxoid” is classified under "Antigen of X". While the toxin is not an intrinsic part of the organism, it is a product of the organism that would not exist in the absence of that organism. In other words, there is always a direct association between the substance and the source organism. There are other antigenic proteins that are generated by the organism (e.g. surface protein) and they are classified as children of "Antigen X organism". The only difference, in comparison to toxoids, is that they are not being excreted by the organism.

    • Toxoid antigens are based on the toxin produced by certain bacteria (e.g., tetanus or diphtheria), which has been chemically processed so that it is still immunogenic. Once the toxin has been inactivated, it is called a toxoid.

    • A toxoid can be an antigen in its own right, or it can be conjugated to another antigen.

    • For example, the following PT includes CRM which is the abbreviated form for cross-reacting material.

      • Streptococcus pneumoniae Danish serotype 1 capsular polysaccharide antigen conjugated to Corynebacterium diphtheriae CRM197 protein

    "Split virion" and "surface subunit" is acceptable when the proposed granular antigen is used in a real Clinical Drug, e.g., Influenza antigens.

    • For influenza strains, the candidate vaccine virus (CVV) is not included in the antigen name in the international release. The justification is that each pharmaceutical company may use a different CVV to manufacture their product, or they may omit that level of detail in their product information. However, each of the recommended "parent strain + CVV" are antigenically like the parent virus.

  • "Antigen of X adsorbed" is in scope for the international release and is modeled in the Substance hierarchy. It is not required to specify details regarding what is adsorbed with as there is no known use-case at this point.

  • With the exception of conjugated proteins/toxoids that are in scope for the international release, inclusion of other adjuvants as well as delivery mechanisms (e.g., aluminum salts, oil-in-water emulsions, virosomes) is currently on hold and will be considered if and when associated requests and uses cases are presented.

  • "Purified" will not be included in antigen names as the clinical value of stating "purified antigen" is not clear. In addition, in some cases, it is implied that an antigen is purified based on the preparation technique. This inconsistency in naming (stated vs. implied) can lead to misclassification. If needed, it can be accomplished by using groupers or other modeling considerations in future. But for now, adding a maintenance burden with very limited benefit does not seem valuable.

  • Inclusion of non-antigenic vaccine ingredients, such as preservatives and stabilizers, is out of scope for the international release.

  • For “Antigen of inactivated whole X”, the inactivation technique (e.g., heat inactivated, formalin inactivated) is out of scope for antigens in the International Release.

  • Antigen of acellular X
  • Antigen of X [protein/recombinant protein]

  • Antigen of X toxoid

  • Antigen of X polysaccharide/oligosaccharide

    • Antigen of X polysaccharide/oligosaccharide unconjugated

    • Antigen of X polysaccharide/oligosaccharide conjugated

      • Antigen of X polysaccharide/oligosaccharide antigen conjugated to Y

  • Pattern: X organism Ab
    1. For example,

      1. Bebaru virus Ab

    Immunoglobulin G antibody to Juglans
  • Pattern: Anti-X organism IgM

    1. For example,

      1. Anti-Clostridium difficile IgM

      2. Anti-Juglans IgG

  • Parent concept

    Most distal appropriate descendant of 116633006 |Microbial antigen (substance)|

    Semantic tag

    (substance)

    Definition status

    Primitive

    Attribute

    N/A

    Parent concept

    Most distal appropriate descendant of |116642004 |Antimicrobial antibody (substance)|

    Semantic tag

    (substance)

    Definition status

    Primitive

    Attribute

    None

    Parent concept

    Most distal appropriate descendant of 70095009 |Immunoglobulin isotype (substance)| and |Antibody to X organism (substance)| if present in SNOMED CT

    Semantic tag

    (substance)

    Definition status

    Primitive

    Attribute

    None

    Modeling - Antigen of X organism

    Naming - Antigen of X organism

    FSN

    Preferred Term

    Synonyms

    Antigen variants

    Variants reviewed to date

    The classification of the antigen variants in the Substance hierarchy:

    Exemplar

    Modeling - Antibody to X organism

    Naming - Antibody to X organism

    FSN

    Preferred Term

    Synonyms

    Exemplar

    Modeling - Immunoglobulin G, M, A, E, D antibody to X organism

    Naming - Immunoglobulin G, M, A, E, D antibody to X organism

    FSN

    Preferred Term

    Synonyms

    Exemplar

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    Aggregating data for forecasting
  • The existing grouper concepts with just one child will not be deprecated at this time. However, requests for addition of these concepts will be rejected.

  • Radioactive substances

    Representation of radioactive isotopes

    Modeling

    Parent concept

    Most distal appropriate descendant of 89457008 |Radioactive isotope (substance)|

    Most distal appropriate descendant of 33638001 |Isotope (substance)|

    Semantic tag

    (substance)

    Definition status

    Primitive

    Pattern:

    • [name of isotope]-[atomic number] (substance)

    For example,

    • Gallium-67 (substance)


    Pattern:

    [name of isotope]-[atomic number]

    For example,

    • Gallium-67


    Pattern:

    • [atomic number]-[chemical symbol]

    For example,

    • 67-Ga

    The following illustrates the hierarchy view:

    The following illustrates the stated and inferred view:

    Superscripts should not be used in either Fully Specified Name, Preferred Term, or synonyms.

    Parentheses should be used to delineate the atomic number and chemical symbol from the rest of the terming; this aligns with INN.

    Pattern: [name of isotope] ([atomic number]-[chemical symbol]) [salt] (substance)

    For example,

    • Gallium (67-Ga) citrate (substance


    Pattern: [name of isotope] ([atomic number]-[chemical symbol]) [salt]

    For example,

    • Gallium (67-Ga) citrate

    The following illustrates the stated and inferred view:

    Superscripts should not be used in either Fully Specified Name, Preferred Term, or synonyms.

    The Fully Specified Name should explicitly state that a component was “labeled” by a radioisotope in the FSN. Do not use “with”, “and”, or “tagged”.

    Omit the word “labeled” from the PT; keep a synonym to match the FSN.

    The following illustrates both the stated and inferred view:

    Attribute:

    Has disposition

    • Range: <726711005 |Disposition (disposition) |

      • NOTE: While the allowed range is broader, substance concepts should only use <726711005 |Disposition (disposition)| as the attribute value.

    • Cardinality: 0..1

    Attribute:

    Has disposition

    Range: <726711005 |Disposition (disposition) |

    • While the allowed range is broader, substance concepts should only use <726711005 |Disposition (disposition)| as the attribute value.

    Cardinality: 0..1

    Attribute:

    Is modification of

    • Range <105590001 |Substance (substance)|

    • Cardinality: 0..*

    • One relationship to be created to represent each modified component of the substance

    Attribute:

    Has disposition

    • Range: <726711005 |Disposition (disposition)|

      • NOTE: While the allowed range is broader, substance concepts should only use descendants of the concept 726711005 |Disposition (disposition)| as the attribute value.

    • Cardinality: 0..1

    Parent concept

    Most distal appropriate descendant of 89457008 |Radioactive isotope (substance)|

    Semantic tag

    (substance)

    Definition status

    Primitive

    Attribute:

    Is modification of

    • Range <105590001 |Substance (substance)|

    • Cardinality: 0..*

    • One relationship to be created to represent each modified component of the substance

    Parent concept

    Most distal appropriate descendant of 89457008 |Radioactive isotope (substance)| and a second parent identifying the labeled component

    Semantic tag

    (substance)

    Definition status

    Primitive

    Attribute:

    Is modification of

    Range <105590001 |Substance (substance)|

    Cardinality: 0..*

    One relationship to be created to represent each modified component of the substance

    Naming

    Superscripts should not be used in either Fully Specified Name, Preferred Term, or synonyms.

    FSN

    Preferred Term

    Synonyms

    Exemplar

    Representation of radioisotope with salt

    Modeling

    Naming

    FSN

    Preferred Term

    Exemplar - radioisotope with salt

    Representation of combined radioisotope substances

    Modeling

    Naming

    Exemplar - combined radioisotope substances

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    Isomers

    Overview

    Within the substances hierarchy in SNOMED CT there are a number of substances where that is either a mix of isomers of a single chemical, a racemic mix or a single isomer.

    • Omeprazole and Esomeprazole

    • Cetirizine and Levocetirizine

    • Loratadine and Desloratadine

    Each of these substances will all need to be represented in SNOMED CT as separate concepts to support the representation of active ingredients in SNOMED CT and should be represented as sibling concepts without any SNOMED CT relationship created between the two substances.

    The following illustrates the hierarchy view for Omeprazole and Esomeprazole:

    Exemplar

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