1. (existing FSN – hierarchy designator omitted) (proposed term)
Organism class
(existing FSN – hierarchy designator omitted)
(proposed term)
Life cycle stage
(defining class)
Instance |
Ascaris lumbricoides
Any / all / not specified
The A lumbricoides parasitizing Fred. |
Ascaris lumbricoides egg
Egg stage of Ascaris lumbricoides
An A. lumbricoides egg retrieved from Fred, sitting on a microscope slide. |
Ascaris lumbricoides larval form
Ascaris lumbricoides larva
Larval stage of Ascaris lumbricoides
An A. lumbricoides larva in Fred’s lung biopsy. |
Ascaris lumbricoides worm
Ascaris lumbricoides adult
Adult stage of Ascaris lumbricoides
An adult A. lumbricoides living in Fred’s intestine.
| Ascaris
Genus Ascaris
The organisms parasitizing a particular patient.
First let me say that if I were the king of terminology, SNOMED CT would not carry descendants of organisms that represent the organism in a particular life-cycle stage. I do not have a rule written down that explains my truncation in any logical fashion. It is not a class/instance boundary. However, they already exist and they are the subject of (nearly all) the requests for content in this area.
The first column are existing organism classes in SNOMED CT. The second column are my suggested revisions to FSN and PT. The third column are NOT to be in the organism hierarchy but rather placed appropriately among the qualifier values. The instances are meant to be free-living organisms not uses of the concepts in/on a laboratory report.
I do not agree with carrying the taxon rank (e.g. “Genus”) in the FSN. I believe we’re stuck with it.

2. (existing FSN – hierarchy designator omitted) Definition Use case
Organism class
(existing FSN – hierarchy designator omitted)
Definition
Use case
Ascaris lumbricoides
Class that includes all organisms in any stage of their life cycle that bear an A. lumbricoides genome.
Value for “causative agent” role in logical definition of | Infection by Ascaris lumbricoides (disorder).
Ascaris lumbricoides egg
An egg of A. lumbricoides
Value recorded in/on a diagnostic report
Egg stage of Ascaris lumbricoides
A life cycle stage of A. lumbricoides. The eggs of this organism are produced in the GI tract of human beings. A. lumbricoides embryos develop during this stage. Eggs are ingested by the host (human being) and hatch to become A. lumbricoides larvae.
Value for “participates in” role in logical definition of | Ascaris lumbricoides egg
Ascaris lumbricoides larva
A larva of A. lumbricoides
Larval stage of Ascaris lumbricoides
A life cycle stage of A. lumbricoides. The larvae of this organism first migrate to the lungs where they molt, are coughed up and swallowed. These larvae mature in the GI tract of human beings. A. lumbricoides embryos develop during this stage.
Value for “participates in” role in logical definition of | Ascaris lumbricoides larva
Concept classes in red do not currently exist.

3. (existing FSN – hierarchy designator omitted) Definition Use case
Organism class
(existing FSN – hierarchy designator omitted)
Definition
Use case
Ascaris lumbricoides adult
An adult of the species A. lumbricoides
Value recorded in/on a diagnostic report
Adult stage of Ascaris lumbricoides
A life cycle stage of A. lumbricoides. The adults of this organism live in the GI tract of human beings and reproduce sexually. The female lays eggs in the GI tract of human beings. This is the (human) parasitic stage.
Value for “participates in” role in logical definition of | Ascaris lumbricoides adult
| Ascaris
Value in causative agent role for | Ascariasis (disorder)
Concept classes in red do not currently exist and are not needed in the short term.

4. OBO v SNOMED CT organism class
Reference: **imported from "
*The Parasite Life Cycle ontology was developed as part of the NIH-funded
"Semantics and Services enabled Problem Solving Environment for Tcruzi"
project (Grant#1R01HL A1). The Kno.e.sis center, Computer Science
and Engineering Department, Wright State University, Center for Bioinformatics,
Department of Genetics, University of Pennsylvania School of Medicine, USA and
the Tarleton Lab, Center for Tropical and Emerging Global Diseases (CTEGD),
University of Georgia, USA collaborated to create this ontology.
Resource page:

5. OBO v SNOMED CT Life-cycle stage class
The nearest existing equivalent to life-cycle stage is | Life-cycle form (organism). We have already agreed that “form” is ambiguous (at least) and that we really mean “stage” in this context. Is there a use case for the life-cycle stages (how valuable is the model).

6. The OPL is currently populated (only) with a limited list of protozoa
The OPL is currently populated (only) with a limited list of protozoa. Focus on the last “row” of the diagram. It represents modeling and terming I would like to recommend.
I do not believe that the two SNOMED CT concept classes on this slide are equivalent to the Uberon and OPL concept classes to which they are connected.
The two classes in orange aren’t sustainable in either ontology I think.
I do not believe that “Epimastigote stage” is equivalent to “epimastigote form of protozoa.” I believe that |Epimastigote form of protozoa (organism) is really “Protozoal epimastigote” or “Epimastigote of a protozoa” NB… terming rules get real messy here. Adjectival form of organism class? Noun form? Prepositional phrase? I’m actually pretty sure that “epimastigotes” are only protozal.
I believe that Life-cycle form should be retired and Life-cycle stage take it’s place (IF definitions are required at all).

7. SNOMED CT version of the model
I do not know of a use case for any of the life-cycle stages in clinical medicine. May serve an aggregation function? Would facilitate cross walk to OBO/OPL?
“Participates in” role does not currently exist in SNOMED CT. I’m not convinced that these require modeling. Leave all content primitive for the near term?
In order to avoid mass retirement, I believe we should leave the egg, larva and adult with their SCTID intact create a new description, assign FSN to new description. Status of former FSN to synonym.
I do not think that the life-cycle stages (qualifier values) are required at this time.