(existing FSN – hierarchy designator omitted) (proposed term) Organism class (existing FSN – hierarchy designator omitted) (proposed term) Life cycle stage (defining class) Instance 19061001 | Ascaris lumbricoides Any / all / not specified The A lumbricoides parasitizing Fred. 699574003 | Ascaris lumbricoides egg Egg stage of Ascaris lumbricoides An A. lumbricoides egg retrieved from Fred, sitting on a microscope slide. 609064008 | Ascaris lumbricoides larval form Ascaris lumbricoides larva Larval stage of Ascaris lumbricoides An A. lumbricoides larva in Fred’s lung biopsy. 609046001 | Ascaris lumbricoides worm Ascaris lumbricoides adult Adult stage of Ascaris lumbricoides An adult A. lumbricoides living in Fred’s intestine. 66953006 | 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.

(existing FSN – hierarchy designator omitted) Definition Use case Organism class (existing FSN – hierarchy designator omitted) Definition Use case 19061001 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 50982003 | Infection by Ascaris lumbricoides (disorder). 699574003 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 699574003 | Ascaris lumbricoides egg 609064008 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 609064008 | Ascaris lumbricoides larva Concept classes in red do not currently exist.

(existing FSN – hierarchy designator omitted) Definition Use case Organism class (existing FSN – hierarchy designator omitted) Definition Use case 609046001 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 609064008 | Ascaris lumbricoides adult 66953006 | Ascaris Value in causative agent role for 2435008 | Ascariasis (disorder) Concept classes in red do not currently exist and are not needed in the short term.

OBO v SNOMED CT organism class Reference: **imported from "http://purl.obolibrary.org/obo/uberon.owl" *The Parasite Life Cycle ontology was developed as part of the NIH-funded "Semantics and Services enabled Problem Solving Environment for Tcruzi" project (Grant#1R01HL087795-01A1). 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: http://knoesis.wright.edu/trykipedia

OBO v SNOMED CT Life-cycle stage class The nearest existing equivalent to life-cycle stage is 278306005 | 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).

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 103549002|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).

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.