SNOMED CT Editorial Guide

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Fully Specified Name

The fully specified name (FSN) of organism concepts, names classes that are officially recognized Linnaean taxonomic classes (other than species), and include a designation of rank. They include, but are not limited to Phylum, Order, Suborder, Class, Family, Genus, and subspecies. 

Properly constructed FSNs contain terms indicating the taxonomic rank + the recognized name of that rank + semantic tag.

For example,

Rank

The naming convention is not applied to concepts that only refer to a subgroup of a rank.

For example,

    • Vancomycin resistant Enterococcus (organism) is correct in capitalizing Enterococcus. It refers to a subclass of the genus, Enterococcus species that are resistant. Enterococcus is a scientific name of an organism class; therefore, the first letter is capitalized. 
    • Vancomycin resistant Genus Enterococcus is incorrect. It refers to the rank only, Genus Enterococcus.

Official names of organisms may include abbreviations such as “subsp.” and  “subgen.” (Domain Bacteria and Kingdom Plantae). Official names of organisms may also include parentheses e.g. “Cypraea (Cypraea) tigris” (Kingdom Animalia) and “Bacillus (subgen. Bacillus Cohn 1872, 174) subtilis” (Domain Bacteria). 

  • The FSN of organisms should include the expanded word for rank i.e. “subgenus” or “subspecies” and not an abbreviation of same. 
  • The FSN should not include parentheses.

For example,

    • Genus Pleione subgenus Scopulorum (organism)
    • Genus Cypraea subgenus Cypraea tigris (organism)
    • Staphylococcus succinus subspecies casei (organism)

Exception

When the same Scientific Name is used in two different hierarchies (two different kinds of organisms), use the authority of the scientific name in the FSN to distinguish the concepts. The name authority is typically found in the authoritative source for the organism name.

For example, 

    • Genus Edwardsiella Andres, 1883 (organism)
    • Genus Edwardsiella Ewing and McWhorter, 1965 (organism)

Preferred Term

The Preferred Term is the official scientific name. It may include abbreviations and/or parentheses. The preferred term usually does not include the taxonomic rank designation except for the following cases:

  • Official names of organisms may include abbreviated taxonomic rank such as “subg.“ "subgen." or “subsp.”.
  • In rare cases, two Linnaean taxon ranks in the same hierarchy may have the same name. For example, in Kingdom Bacteria, "Thermodesulfobacteria" is an applicable term at both Phylum and Class levels. In this case, the taxon rank is included in the preferred term to prevent any ambiguity.

For example,

    • Cypraea (Cypraea) tigris
    • Pleione subg. Scopulorum
    • Bacillus (subgen. Bacillus Cohn 1872, 174) subtilis
    • Staphylococcus succinus subsp. casei

Exceptions

  • If a common name exists for an organism in primary references, then it could be used as the Preferred Term for the organism.

For example,

388618001 |Family Felidae (organism)|, PT: cats

388626009 |Genus Felis (organism)|, PT: small cats

  • If a common name is shared between more than one organism, the preferred term should adhere to the following format: Scientific Name with annotated common name to prevent confusion. A dash may be used to separate the two names.

For example,

1697006 |Genus Megapodius (organism)| and 107060000 |Family Megapodiidae (organism)| share the common name “Megapodes”. The Preferred term for the two concepts is as follows:

1697006 |Genus Megapodius (organism)| PT: Megapodius - megapodes

107060000 |Family Megapodiidae (organism)| PT: Megapodiidae - megapodes

  • An organism's common name might be the same as the scientific name for another organism.  Example: Gorilla is the scientific name for 389217005 |Genus Gorilla (organism)|, but it is the common name for 8807009 |Gorilla gorilla (organism)|. In these cases, the latter concept's preferred term should be the scientific name with annotated common name to prevent confusion, Example: For 8807009 |Gorilla gorilla (organism)|, the preferred term is “Gorilla gorilla - gorilla"

  • When the same Scientific Name is used in two different hierarchies (two different kinds of organisms), use the Scientific Name with annotated common name as PT to prevent confusion. A dash may be used to separate the two names. Use the common name from the authoritative source. If a common name is not listed in the authoritative source, use the NCBI BLAST name as common name in the PT. If a common name is not in either the authoritative source or in the NCBI BLAST names, consult the literature or other resources for a distinguishing name to use in the PT. 


For example,

The genus of bacteria Edwardsiella does not have a common name listed in the authoritative source. Therefore, use the NCBI BLAST name "enterobacteria" in the PT.  For the genus of animals Edwardsiella, use the common name "sea anemones" from the authoritative source.

Genus Edwardsiella - Enterobacteria
Genus Edwardsiella - sea anemones

  • Occasionally we may need to add a word to the common name specified in the resources to make the common name more explicit. Example: Loxosceles reclusa has a common name of brown recluse in ITIS, which is one of the SNOMED primary references. To make the naming more explicit, the word spider has been added to the preferred term:

FSN: 23312003 |Loxosceles reclusus (organism)|

PT: Brown recluse spider

  • When there are multiple names listed as common name for an organism in primary references, additional references should be consulted to locate the most commonly used term.
  • High level taxonomic terms often refer to groups of organisms. The preferred terms need to reflect that grouping. 

For example,

"Order Columbiformes" represent all Genera of Doves and pigeons, so the preferred term for 107097005 |Order Columbiformes (organism)| is: Doves and pigeons.

Qualifiers in organism names

When modeling organisms with qualifiers, the qualifier should be placed in front of the organism name.

Organism class variants

The description of organism classes that are subspecies subtypes and variants may include terms such as serogroup, serotype, biotype, variant, biovar, serovar, and pathovar.

For example,

The subspecies types and variants should be included in the FSN, PT and other descriptions as per terming in authoritative resource where one exists (example: see sub-sections for Salmonella serotype nomenclature as well as Streptococcus pneumoniae below). In the absence of such resources, associated scientific literature is consulted for the most common and accurate representation. Inclusion of the subspecies types and variants accurately is to avoid 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 equvalent to Streptococcus pneumoniae American serotype 82)
    • Streptococcus pneumoniae American serotype 48 (which is equivalent to Streptococcus pneumoniae Danish serotype 7B)
    • Streptococcus pneumoniae serogroup 48

Abbreviations (var, var., sv, sv., bv, bv., pv, pv.) must not be used in the FSN.

Capitalization of organism names and binomial format

Official scientific names for organisms should be capitalized. The designation of rank does not require capitalization. 

For example,

There is an exception to the above guidelines where the binomial format for an organism species includes capitalization of the first word, i.e., the genus name, but the species name begins with a lower-case letter.

For example,

If the species name includes any other word, they are not capitalized unless they are proper nouns, or parts of proper nouns.

For example,

    • 31989009 |Murray Valley encephalitis virus (organism)|

Salmonella serotype nomenclature

Salmonella serotypes have a quadrinomial format of Genus species subspecies Serotype where the serotype name is capitalized.

For example,

Additional descriptions, without the species and subspecies names, are in common usage for Salmonella serotypes.

For example,

In SNOMED CT, the serotype name in the description should be capitalized.

Salmonella Serotypes

Salmonella serotypes, without the species and subspecies names, should not be confused with binomial species names of other organisms.

Streptococcus pneumoniae

Streptococcus pneumoniae is a human pathogen whose virulence is based on its protective polysaccharide capsule. Study of the polysaccharide capsule has identified multiple serogroups and serotypes. Serotypes are defined by the chemical structure and immunologic properties of their polysaccharide; each serogroup contains one or more serotypes that elicit the same antibody response.

There are two serotype naming systems, one in the U.S. and one in Denmark. The Danish system is nearly universally accepted and preferred. For details, please refer to See Geno K A, Gilbert G L, Song J Y, Skovsted I C, Klugman K P, Jones C, Konradsen H B, Nahm M H. Pneumococcal capsules and their types: past, present, and future. Clinical Microbiology Reviews 2015; 28(3):871-899. [PMID: 26085553]).

Streptococcus pneumoniae concepts

A review of Streptococcus pneumoniae serotypes in SNOMED CT showed lack of specificity, as well as inconsistency, in the naming of Streptococcus pneumoniae serotypes. Guidelines for creating concepts containing Streptococcus pneumoniae serotypes were formulated. They are as follows:

FSN and preferred term (PT) descriptions should follow the Danish naming system. When an American synonym exists, it should be added. A synonym (SYN) that matches the FSN, but does not contain the naming system can also be added. 

For example,

698149000 | Streptococcus pneumoniae serotype 48 (organism)|  is renamed as follows:

      • FSN: Streptococcus pneumoniae Danish serotype 48 (organism)
      • PT: Streptococcus pneumoniae Danish serotype 48
      • SYN: Streptococcus pneumoniae American serotype 82
      • SYN: Streptococcus pneumoniae serotype 48

The guidelines for creating new concepts containing Streptococcus pneumoniae serotypes also apply to concepts in other SNOMED CT hierarchies, such substances and procedures.

For example,

120683007 | Streptococcus pneumoniae serotype 7F antibody (substance)|  is renamed as follows:

      • FSN: Antibody to Streptococcus pneumoniae Danish serotype 7F (substance)
      • PT: Streptococcus pneumoniae Danish serotype 7F Ab
      • SYN: Antibody to Streptococcus pneumoniae Danish serotype 7F
      • SYN: Anti-Streptococcus pneumoniae Danish serotype 7F antibody
      • SYN: Streptococcus pneumoniae Danish serotype 7F antibody
      • SYN: Antibody to Streptococcus pneumoniae American serotype 51

Legacy Streptococcus pneumoniae concepts

FSNs that adhered to one of the naming systems were kept, but changes were made to the descriptions, based on the above guidelines. Any resulting duplicates were deprecated.

FSNs that did not adhere to one of the naming system were inactivated as ambiguous. They were replaced with newly created concepts, based on the above guidelines.

Missing serotype concepts were added.

Influenza virus nomenclature

Follow the latest names for genus and species according to the taxonomy authority.  Although the genus and species names for influenza viruses are similar, they each follow a distinct pattern, which should be used in SNOMED CT. Also, the name of the virus should always be capitalized.

For species, the word virus is included as a separate word and follows the letter designation.

For example,

For genus, virus is included in the genus name and is not a separate word.

For example, 

The disorder influenza need not be capitalized. 

US/GB spelling variants for taxonomic concepts 

Taxonomic resources (e.g. Integrated Taxonomic Information System or ITIS, List of Prokaryotic names with Standing in Nomenclature or LPSN) use the official scientific name for organisms. Similarly, in SNOMED CT, the official scientific name should be used in FSNs and PTs. For descriptions representing common names, if the spelling in a country or region is different, the preferred spelling should be added in the language RefSet extension as a synonym.


Use of X species

In the context of the Linnaean organism hierarchy, there is no difference between Salmonella species and simply Salmonella, the genus. Terms with X species, such as Salmonella species, are routinely used in laboratory reporting. They may provide additional information, other than the place of the organism in the Linnaean hierarchy. However, the intended connotation may vary from lab to lab and from organism to organism.


Since the organism concept represents a class of organisms, it cannot also represent what was, was not, or what will be done to identify the organism. Neither can it represent other information about the result. If there is additional information to report, it should be in a separate statement or comment (e.g. further species identification pending or sent to reference laboratory for further identification or further identification to be done if clinically indicated).

X species

Addition of X species as a description to genus X is allowed and is done per request.

Microorganism name changes

Microorganism taxonomic names may change, often due to scientific advances. This may result in:

  • Finding an organism in a particular taxonomic group (e.g. Genus) that is unrelated, on a molecular basis, to other members of the group.
  • Reassessing the taxonomic group originally established, based on phenotypic characteristics.
  • Proposing to reassign the organism to a different existing or new taxonomic group.

On a case by case basis, requests for name changes are based on the following use cases:

The name of an organism changes. This scenario is also applicable when an organism name changes on multiple occasions over time.

    • Change the FSN for affected concepts, but not the concept ID, by creating a new FSN and description.  Inactivate the old FSN with an inactivation value of Outdated. 
    • Retain the old name as a synonym.

A single species is reclassified as multiple species. This scenario is applicable if the change in classification happens at a single point in time and is reflected as such in the authoritative resources.

    • Create the new concepts. 
    • Inactivate the original concept as ambiguous. 
    • Set a possibly equivalent to relationship between the old concept and the new concepts.

Multiple species are reclassified as one. This scenario is applicable if the change in classification happens at a single point in time and is reflected as such in the authoritative resources.

    • Create a new concept.
    • Inactivate the existing concepts as outdated with replaced by relationships to the new concept.

Organism life stages

Concepts in the organism hierarchy represent fully realized organisms. An organism's life cycle stage is a characteristic of a given taxon. It represents different stages of life e.g. egg, larva, and adult.

 Organism stages themselves are characteristics common to members of a given taxon.

SNOMED CT allows for the representation of an organism in a specific life cycle stage. 

For example,


  • Similarly,
    • An egg of a particular nematode, e.g. 42625000 | Strongyloides stercoralis (organism)|  is an organism. It is alive and can pass through other stages appropriate to its species. 

      However, the egg stage of Strongyloides stercoralis is not an organism. Many diagnostic test results, identify organisms ‘participating’ in particular life cycle stages.

For example, the results of a 83033005 | Fecal analysis (procedure)|  may identify the presence of 609326000 | Larva of Strongyloides stercoralis (organism)|  and  699572004 | Egg of Strongyloides stercoralis (organism)| .

Organism concepts

Concepts in the organism hierarchy should not represent organism structures (e.g. fungal hyphae). In addition, the word "stage" should be excluded from concepts representing life cycle of an organism (e.g. larval stage of a nematode parasite). This does not preclude representations of organisms ‘participating’ in a specific stage of life e.g. 609061000 |Larva of genus Ascaris (organism)|.

Naming patterns

FSN pattern: (Life cycle stage) of (Taxon including rank, if required) (organism)

For example, 

The name of the rank is included with the first letter lower case, except at the species and subspecies levels, where the Linnaean binomial and trinomial are specified.

PT pattern: (Taxon including rank, if required) (life cycle stage)

For example, 

    • Phylum Nemata adult
    • Strongyloides stercoralis egg

Cestode larvae

A number of cestode larvae have historically been referred to using Linnaean binomial names that are completely different from corresponding adult (or egg) names.

For example,

PT pattern: Linnaean binomial of larva OR (Taxon including rank if required) (life cycle stage)

For example,

    • Cysticercus bovis
    • Cysticercus cellulosae
    • Class Cestoda larva

    Although rare, a subtype of cestode larva may appear to be a Linnaean trinomial name. This, then, is the PT:
    • Diphyllobothrium latum sparganum

Other acceptable synonyms

Some organisms and stages are referred to in an adjectival form (e.g. Ascarid egg) or by common name (e.g. adult nematode).  When used (especially when described as part of a request), these terms may be included as additional synonyms.

Homotypic and heterotypic synonyms

Homotypic synonyms (also referred to as objective or nomenclatural or obligate synonyms), sometimes indicated by a triple bar , are based on the exact same type specimen. These synonyms are published in the scientific literature following the formal nomenclatural rules (that is, they are declared through a nomenclatural act).

Heterotypic synonyms (also referred to as subjective or taxonomic synonyms), sometimes indicated by “=“, are based on different type specimens. These synonyms rely on the opinions of taxonomists rather than on the formal nomenclatural rules.

In SNOMED CT, homotypic synonyms can be added as descriptions on concepts as per primary references and the various International Codes of Nomenclature.  Additional synonyms are expected to be referenced in current literature.  Heterotypic synonyms can be added to aid search and analysis; they would only be considered for addition if requested and are supported by a primary resource, e.g. LPSN.  They should not be added if adding them would generate confusion. 

Dual nomenclature of pleomorphic fungi

According to the International Code of Nomenclature for algae, fungi, and plants (IAPT), as of 1 January 2013, the historical system of permitting separate names for anamorphs and telemorphs of fungi with a pleomorphic lifecycle was ended, and one fungus can only have one name. All legitimate names proposed for a species, regardless of what stage they are typified by, can serve as the correct name for that species. It has been recognized that there could be many names that might merit formal retention or rejection, and the problem of choosing one name among many remains to be examined for many species. Therefore, latest updates in the credible resources and/or scientific articles should be consulted for the most current name.

Resources for organism naming

SNOMED International utilizes various resources when reviewing changes to the organism hierarchy. They include:
 

Bacteria

  • List of Prokaryotic names with Standing in Nomenclature (LPSN)
  • International Committee on Systematics of Prokaryotes (ICSP)
  • International Journal of Systematic and Evolutionary Microbiology
  • DSMZ-Prokaryotic Nomenclature Up-to-date

Fungi

  • MycoBank Database
  • Index Fungorum

Viruses

  • International Committee on Taxonomy of Viruses (ICTV)

Parasites

  • National Center for Biotechnology Information (NCBI) Taxonomy.  Although not an authoritative source, NCBI Taxonomy provides useful links to other sources; it is used by Unified Medical Language System (UMLS) as a QA source.

General

  • Catalogue of Life (https://www.catalogueoflife.org/). This is the result of cooperation between ITIS (https://www.itis.gov) and Species 2000 (https://www.sp2000.org/).  Please note, Catalogue of Life may not be up to date for all areas.  For bacteria, fungus, and virus, consult resources noted above as primary references.

  • International Code of Zoological Nomenclature (ICZN)
  • International Code of Nomenclature for algae, fungi, and plants (IAPT)


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