Organism Naming Conventions

This Editorial Guide is used for Education Purposes Only. It is used in the Authoring Courses and Certifications. It is based on the January 2026 Editorial Guide.

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,

  • 106544002 | Family Enterobacteriaceae (organism)|

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)

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,

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

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,

  • 698206009 | Brucella suis biovar 4 (organism)|

Serovar and serotype are generally synonymous, with a preference for serovar in the FSN and PT unless there is an authoritative source for the organism that uses serotype.

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)

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

Official scientific names for organisms should be capitalized. The designation of rank does not require capitalization. This guideline is applicable to the organism current name as well as older names and synonyms.

• For example,

  • 426813007 | Order Acidobacteriales (organism) | has case significance of Initial character case insensitive.

  • 72646003 | Streptococcus equinus (organism) | contains a heterotypic synonym of "Streptococcus bovis". Both of these descriptions are scientific names of the organism, and therefore, both have a case sensitivity indicator of Entire term case sensitive (CS).

Capitalization is applicable to the organism scientific name, e.g., Hepatitis B virus, Buffalopox virus, Cowpox virus, Dengue virus, Herpes simplex virus 1, Herpes simplex virus 2, Herpes simplex virus 3, Human immunodeficiency virus 1 , Influenza virus A, Influenza virus B, Influenza virus C, Measles morbillivirus and Measles virus, Orf virus, Rabies virus, Rubella virus, Salmonella enterica subspecies enterica serovar Typhi, Vaccinia virus, Vesicular stomatitis Indiana virus, Yellow fever virus, Human papillomavirus x (where x is number representing the serotype).

The name of the associated disease does not require capitalization, e.g., hepatitis, buffalopox, cowpox, dengue, herpes, influenza, measles, orf, rabies, rubella, typhoid, smallpox, vesicular stomatitis, yellow fever.

Non-taxonomic groupers, such as human herpes simplex virus , herpes simplex virus , influenza virus , human immunodeficiency virus , and human papillomavirus are recorded with a case sensitivity indicator of Entire term case insensitive (ci).

There are cases where the authoritative resources do not have an entry for the official name of an organism. For these concepts, the associated literature is referenced for naming and case sensitivity assignments.

• For example,

  • Severe acute respiratory syndrome coronavirus 2 is below species level and does not have an entry in the authoritative resource, International Committee on Taxonomy of Viruses (ICTV). Therefore, it is recorded with a case sensitivity indicator of Entire term case insensitive (ci), since the majority of references do not capitalize “severe”.

Common names usually have case sensitivity indicator of Entire term case insensitive (ci).

• For example,

  • Domestic cat, common name of 448169003 |Felis catus (organism)|, has case sensitivity indicator of Entire term case insensitive (ci).

If the common name includes any proper nouns, or parts of proper nouns, they need to capitalized.

• For example,

  • 598003 |Vespa crabro (organism)| has the preferred /common name of European hornet with the case sensitivity indicator of Entire term case sensitive (CS)

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

• For example,

  • A synonym for 114683003 | Salmonella Doel (organism) | is Salmonella enterica subsp. enterica ser. Doel

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

• For example,

  • 656008 | Salmonella Os (organism) |

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

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. []).

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 as follows:

    • FSN: Streptococcus pneumoniae Danish serotype 48 (organism)

    • PT: Streptococcus pneumoniae Danish serotype 48

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

• For example,

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

    • FSN: Antibody to Streptococcus pneumoniae Danish serotype 7F (substance)

    • PT: Streptococcus pneumoniae Danish serotype 7F Ab

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 taxonomic 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,

  • 407482004 | Influenza C virus (organism)|

  • 710661004 | Immunoglobulin M antibody to Influenza B virus (substance)|

  • 10674911000119108 | Otitis media caused by Influenza A virus (disorder)|

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

• For example,

  • 407481006 | Genus Gammainfluenzavirus (organism)|

  • 407477006 | Genus Alphainfluenzavirus (organism)|

The disorder influenza need not be capitalized.

• For example,

  • 408687004 | Healthcare associated influenza disease (disorder)|

  • 230188005 | Post-influenza encephalitis (disorder)|

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.

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).

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.

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,

  • 337915000 | Homo sapiens (organism) | are organisms. Homo sapiens include humans, in general, as well as children.

  • Childhood is a life cycle stage, however it is not an organism.

• Similarly,

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) |.

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

• For example,

  • 609043009 | Adult of phylum Nemata (organism)|

  • 699572004 | Egg of Strongyloides stercoralis (organism)|

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

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,

  • 47399003 | Larva of Taenia saginata (organism) |, a human tapeworm, is usually called Cysticercus bovis.

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:

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 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.

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.

There is currently no standard approach in authoritative sources for naming rough bacterial strains. Multiple representations of rough organisms exist in the literature; however, in the absence of a formal standard, SNOMED International has adopted the notation “O rough” for the fully specified name and preferred term of new content.

• For example,

  • 720764004 | Yersinia enterocolitica serogroup O rough (organism)

Alternative representations, such as O-rough, rough, or Orough, may be included as synonyms when use case requires.

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

• 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

• MycoBank Database

• Index Fungorum

• International Committee on Taxonomy of Viruses (ICTV)

• Integrated Taxonomic Information System (ITIS)

• 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.

• Catalogue of Life (). This is the result of cooperation between ITIS and Species 2000. 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)