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1/28/2018 IHTSDO-455 (artf7628) Organism Cycles - previously Taxon specific life cycle forms - IHTSDO Content - SNOMED Confluence Pages / … / Content Project Tracker Documents IHTSDO­455 (artf7628) Organism Life Cycles ­ previously Taxon specific life cycle forms

Created by Cathy Richardson, last modified by Jeff Wilcke on 2018­Jan­24

The word versions of the inception and elaboration phases of content development were used as the basis when this page was first developed. The content here will be modified and added to over time as the project progresses.

Links:

 IHTSDO­455 ­ jiraissues.unexpected.error Jira issues is not available

Document review: JIRA IHTSDO­455 Organism Life Cycles Documentation Review (Please note this page does not have public access) Approvals

Phase Date Approved by Comments

Inception 20171027 James T. Case None

Elaboration 20171027 James T. Case Approved once agreement on FSN naming achieved. 20171130 James T. Case Approved.

Testing

Construction

Advisory Group Sign off required

Note draft guidance (to be clarified): Approval should be sort at the end of the Elaboration/Testing phase where required

Group Approval Required?

Editorial Yes

Modelling Yes

Content Managers

SNOMED CT Content Improvement Project Inception phase

Project ID: Topic:

Date

Version 0.01

Amendment History

Version Date Editor Comments

0.9 20150414 Jeff R. First draft for comments Wilcke

0.91 20170223 Jeff R. Respond to reviewer comments Wilcke

1.0 2017091 Jeff R. Remove model as part of solutions. Previous Wilcke comments and responses need to be cleaned up (reviewed, resolved and deleted?).

Review Timetable

Review date Responsible owner Comments

20171027 James T. Case ­ Head of Terminology No comments https://confluence.ihtsdotools.org/display/IHTSDO1/IHTSDO-455+%28artf7628%29+Organism+Life+Cycles+-+previously+Taxon+specific+life+cycle+forms 1/14 1/28/2018 IHTSDO-455 (artf7628) Organism Life Cycles - previously Taxon specific life cycle forms - IHTSDO Content - SNOMED Confluence

© International Health Terminology Standards Development Organisation 2012. All rights reserved. SNOMED CT® was originally created by the College of American Pathologists. This document forms part of the International Release of SNOMED CT® distributed by the International Health Terminology Standards Development Organisation (IHTSDO), and is subject to the IHTSDO’s SNOMED CT® Affiliate Licence. Details of the SNOMED CT® Affiliate Licence may be found at http://www.ihtsdo.org/our­standards/licensing/. No part of this document may be reproduced or transmitted in any form or by any means, or stored in any kind of retrieval system, except by an Affiliate of the IHTSDO in accordance with the SNOMED CT® Affiliate Licence. Any modification of this document (including without limitation the removal or modification of this notice) is prohibited without the express written permission of the IHTSDO. Any copy of this document that is not obtained directly from the IHTSDO [or a Member of the IHTSDO] is not controlled by the IHTSDO, and may have been modified and may be out of date. Any recipient of this document who has received it by other means is encouraged to obtain a copy directly from the IHTSDO [or a Member of the IHTSDO. Details of the Members of the IHTSDO may be found at http://www.ihtsdo.org/members/].

Links: Advisory Group Sign off required 1 Glossary 1.1 Terms 2 Introduction 2.1 Purpose 2.2 Audience 2.2.1 Identification of stakeholders 2.2.2 Input from stakeholders 2.2.3 Degree of consensus on the statement of problem 3 Statement of the problem or need 3.1 Background 3.2 Summary of problem or need, as reported 3.3 Summary of requested solution 3.4 Statement of problem as understood 3.5 Detailed analysis of reported problem, including background 3.6 Subsidiary and interrelated problems 3.6.1 includes definitive reference to “form” 3.6.2 Latin binomial surrogates for life cycle stages 3.6.2.1 Cestode larvae 3.6.2.2 Dimorphic fungi 3.6.3 Common organism names and forms 4 Risks / Benefits 4.1.1 Risks of not addressing the problem 4.1.2 Risks of addressing the problem 5 Requirements: criteria for success and completion 5.1 Criteria for success/completion 5.2 Strategic and/or specific operational use cases 5.2.1 Use case 1 5.2.1.1 Fit with IHTSDO strategy 5.2.2 Use case 2 6 Outline Possible Technical Approaches and Concept Model 6.1 Indicative Solutions 6.1.1 Approach One 6.1.1.1 End user Impact of approach one 6.1.2 Approach Two 6.1.2.1 End user Impact of approach two 7 Indicative Project Plan 7.1 Scope of elaboration phase 7.2 Projection of overall project size and resource requirements 7.2.1 Expected project resource requirement 7.2.2 Expected project impact and benefit 7.2.3 Indicative resource estimates for elaboration, construction, transition and maintenance: 8 Appendices 8.1 Appendix One : Related user requests 9 Works Cited Elaboration phase 2 Introduction 2.1 Purpose 2.2 Audience and stakeholder domain 2.2.1 Input from stakeholders 3 Solution Development 3.1 Initial Design 3.1.1 Outline of initial design 3.1.2 Significant design or implementation decisions / compromises 3.1.2.1 Exceptions and Problems 3.1.2.2 Design Strengths 3.1.2.3 Design Weakness 3.1.2.4 Design Risks 4 Recommendation 4.1.1 Detailed design final specification 4.1.2 Iteration plan 5 Quality program criteria 5.1 Quality metrics 5.1.1 Quality metric 1 5.1.2 Quality metric 2 5.2 Use case scenarios 5.2.1 Scenario One 5.2.1.1 Expected Setting 5.2.1.2 Data capture requirement 5.2.1.3 Data retrieval requirement 5.3 Test cases 6 Updated Project Resource Estimates 6.1 Projection of remaining overall project resource requirements 6.1.1 Expected project resource requirement category 6.1.2 Expected project impact and benefit 6.1.3 Indicative resource estimates for construction, transition and maintenance: https://confluence.ihtsdotools.org/display/IHTSDO1/IHTSDO-455+%28artf7628%29+Organism+Life+Cycles+-+previously+Taxon+specific+life+cycle+forms 2/14 1/28/2018 IHTSDO-455 (artf7628) Organism Life Cycles - previously Taxon specific life cycle forms - IHTSDO Content - SNOMED Confluence 1 Glossary 1.1 Domain Terms

Taxon In , a taxon (plural taxa; back­formation from ) is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit.

Organism An individual form of life, such as a , an , a bacterium, a protist, or a ; a body made up of organs, organelles, or other parts that work together to carry on the various processes of life. organism. Dictionary.com. The American Heritage® Stedman's Medical Dictionary. Houghton Mifflin Company. http://dictionary.reference.com/browse/organism (accessed: March 23, 2015).

(Organism) In SNOMED, the concept classes in the organism hierarchy are taken to represent members of biological taxa not the taxa themselves. Taxa are assumed to be qualifier values not organisms. This by convention and referencing work by Stefan Schulz (Organism Ontology ­ OBO).

Life cycle A series of stages and transitions between stages that an organism undergoes, returning to the starting state. Some stages represent particular morphologies and life functions of an individual (e.g., larva), other stages represent genetic duplication of an original organism (e.g., egg). Life cycle schemes include asexual reproduction, sexual reproduction or both depending on the organism. "The concept is closely related to those of the life history, development and ontogeny, but differs from them in stressing renewal." (1)

Life cycle A particular point in an organism life cycle characterized by a specific morphologic form, particular biological functions and particular environmental and host stage requirements. For example, the epimastigote stage of trypanosomes multiplies in the salivary gland of mosquitos while the trypomastigote stage multiplies in the host.

2 Introduction 2.1 Purpose

The general purpose of this project is to consider the appropriate representation of organisms and organism life cycle stages (aka life cycle forms). The specific purpose of this project is distinguish between organisms and organism life cycle changes, to edit the existing hierarchy to reflect the differences and to develop editorial guidance for incorporating organism hierarchy content used as values for laboratory reporting in parasitology.

2.2 Audience

The audience for this document includes all standards terminology leaders, implementers and users but is especially targeted at those stakeholders from the diagnostic laboratory domain.

2.2.1 Identification of stakeholders

Diagnostic laboratories have self­identified as stakeholders in this problem.

2.2.2 Input from stakeholders

This document is being provided to members of the Organisms and Infectious Disease Project Group.

2.2.3 Degree of consensus on the statement of problem

No consensus exists as of this version of this document.

3 Statement of the problem or need 3.1 Background

Laboratories report the identity of parasites using names that identify the taxon of the organism (i.e., , , etc.). Life cycle stage name (i.e., egg, larva, adult) of the organism that is/was present in the diagnostic sample or test preparation. Related concept classes (e.g., 699574003 | Ascaris lumbricoides egg) are part of the SNOMED CT organism hierarchy. There is no official editorial guidance for this content.

3.2 Summary of problem or need, as reported

Requests for terms related to parasites and life cycles, though infrequent, are ongoing. Terms suggested by users have generated questions among IHTSDO editors concerning the meaning, terming principles and hierarchy placement. Terming and hierarchical placement of , helminths and in SNOMED can be made more consistent and clear if guidelines and terming principles are specified. The specific request is to develop guidelines for editing organism content related to life cycles.

3.3 Summary of requested solution

The requested solution is for presentation of a model and terming rules to facilitate editing and selection of appropriate concept classes for particular purposes.

3.4 Statement of problem as understood

When parasitism in a patient is confirmed by a laboratory, the laboratory observation is of an organism living through a particular stage of its life (cycle). It is identified by its , reproductive status, biochemistry etc. and the observation is independent of host range (e.g., definitive host) or location in the host (e.g. small intestine). On the other hand, when the life cycle of a parasite is described, it is demarcated into stages described by the host range , host location, morphologic form (e.g., egg), of stages, etc. A life cycle stage is directly related to an organism , but it is not an organism. Placement of the life cycle classes in the organism hierarchy is not appropriate. In SNOMED CT, single concept classes (e.g., 609064008 | Ascaris lumbricoides larval form) are subtypes of both organism classes (19061001 | Ascaris lumbricoides) and classes that represent life cycle stages (284720001 | Helminthic life cycle form). As a result of the ambiguity created by the hierarchy, previous editors created terms such as 609069003 | “Filariform larval form of Genus Strongyloides (organism)” for these concept classes. Terms such as these are not used by either diagnostic laboratories or biologists who study parasites. In the end, neither the hierarchy nor these terms clearly distinguish between a stage in the life cycle of the organism and the organism itself. Users are uncertain as to the meaning and selection of organism content required for laboratory reporting in diagnostic parasitology and SNOMED CT editors are uncertain as to placement and terming rules when new content requests are submitted.

3.5 Detailed analysis of reported problem, including background https://confluence.ihtsdotools.org/display/IHTSDO1/IHTSDO-455+%28artf7628%29+Organism+Life+Cycles+-+previously+Taxon+specific+life+cycle+forms 3/14 1/28/2018 IHTSDO-455 (artf7628) Organism Life Cycles - previously Taxon specific life cycle forms - IHTSDO Content - SNOMED Confluence Background It is the intrinsic nature of organisms that they progress through various life stages and produce future generations. Adults reproduce, eggs are fertilized and mature, children grow and mature and so forth. At specific points in time, an organism that has the genetic material of a particular biological taxon will display characteristics of a particular stage in the life cycle natural to that taxon. Once born, a human being its life as infant then child then juvenile then adult (other demarcations are reasonable, these serve to illustrate the point). Similarly, a egg hatches, a larva emerges, the larva matures to become an adult and the adult lays eggs. In contrast to the organism itself, a life cycle stage is characterized not only by its relationship to a particular taxon but also by the conditions required for its existence. Some stages occur in the definitive host, some do not. Some stages are infective, some are not. In the clinical laboratory, the thing that has been identified is an instance of an organism (class) that is existing in a specific life cycle stage of that organism. A nematode larva is a nematode as a human child is a human being. A laboratory does not identify a life cycle stage, it notes the existence of an organism that was presented for identification in a particular stage. DPDx is a website developed and maintained by CDC’s Division of Parasitic Diseases and Malaria (DPDM). DPDx includes concise reviews of parasite biology including illustrations of life cycles. Each life cycle illustration labels the infective stage or stages and the diagnostic stage or stages for the referenced parasite while the legends for these illustrations describe the circumstances of the organism as it passes through each stage. While the image and the legend take different perspective, the terms that describe the parasite are the nearly the same for both. The “diagnostic stage” of Ascaris lumbricoides is “Fertilized egg” in the image while the legend states that “Fertile eggs embryonate and become infective.” So it is that the language of parasite life cycles does not provide differentiation between organism and life cycle classes. The Ontology for Parasite LifeCycle (OPL) is an Open Biomedical Ontology (OBO) candidate ontology (2). OPL aligns itself with the Basic Formal Ontology (3) (BFO). OPL places organisms under the top level class “Continuant” and places life cycle stages under the top level class “Occurant.” In OPL and as shown in Figure 1, Trypanasoma cruzi epimastigote is created as a descendant of continuant and organism. Trypanasoma cruzi epimastigote stage is created as a descendant of Occurrant and the Uberon class “Life­cycle stage.” Epimastigote and epimastigote stage are related through a relationship “participates­in.”

Figure 3.1. Distinct representation and modeling of Trypanosoma cruzi epimastigote (T. curzi epimastigote) and T. cruzi epimastigote (life cycle) stage in the Ontology for Parasite LifeCycle (OPL).

The Parasite Life Cycle ontology was developed as part of the NIH­funded "Semantics and Services enabled Problem Solving Environment for Tcurzi" project (Grant #1R)1HL087795­01A1. Resource page http://knoesis.wright.edu/node/1883.

Parasitology references refer to life cycle stages when describing life cycles and may refer to the organisms themselves as “forms.” The same literature may also use “life cycle stage” and “life form” interchangeably and the need to maintain any distinction is not obvious. It is not unusual to see adult, adult form, adult worm, and worm used interchangeable for the adult stage of Ascarids. The actual but subtle difference between generic names for stages (e.g., adult) and more specific names for forms (e.g., worm) has contributed to misunderstandings and mistakes by editors. The organism content in SNOMED CT includes concept classes that refer to organism classes identified only by taxon. The obvious taxonomic information begins with major taxonomic divisions such as 417396000 | Kingdom Protozoa (organism) and 421727006 | Phylum Nemata (organism) and leads to species classes such as 88274000 | Trypanosoma cruzi (organism). Distal to the Latin binomials (species) and trinomials () there is a desire on the part of SNOMED CT users to record the organism as it was observed (participating IN some life cycle stage). For example, Chagas disease is confirmed in the laboratory by either the presence of Trypanasoma cruzi trypomastigotes in blood samples or the presence of Trypanasoma cruzi amastigotes in tissue (4). In SNOMED CT concept classes that represent organism identification appear to be ambiguous and that impression is created both by certain terming patterns (e.g. Strongyloides stercoralis larval form) as well as hierarchy placement. Most recent editions of SNOMED CT follow naming patterns and hierarchy placement suggested by an informal guidance document “Organism Life Cycle Form Requests” (Collabnet doc9241). Although this document was created as a report to IHTSDO from SNOMED Terminology Solutions (CAP) staff, it has stood for quite some time as a substitute for a formal editorial guideline. This document calls for placement of organism life cycle concepts as descendants of both the related organism class and a life cycle class. Further, it suggests creating a terming style that does not comport with names found in the literature or textbooks. This has created a few specific interrelated problems in this portion of the hierarchy. Many of the terms are rendered in an unnatural and inconsistent naming style. Among the , the naming pattern that has emerged for subtypes in life cycles is shown in Figure 2, Panel A. For species subtypes the patterns for eggs (Genus species egg),” larvae (Genus species larval form) and adults (Genus species worm) are different. An egg is simply “egg” while larva are given a non­standard term “larval form”. The substitution of “worm” for “adult” in these organisms is questionable as the worm morphology applies to the larval forms. One of the content requests that highlighted this problem was for “Strongyloides stercoralis adult form” and was made by a user who did not recognize the meaning of the existing term “Strongyloides stercoralis worm.” Panel B of Figure 2 shows that the pattern changed again when subtypes of a life cycle term were created. The first level is Ascaris lumbricoides egg and the fertile and infertile subtypes have the word “form” appended. At the Genus rank, the word “form” is included and the word order reversed as is the case for 609061000 | Larval form of Genus Ascaris (organism). This pattern is reversed again for taxonomic ranks above Genus such as 284722009 | Nematode larva (organism).

Figure 3.2. Examples of life cycle terming patterns present in the organism hierarchy. In the left panel, the subtypes of Strongyloides stercoralis each represent the organism "participating" (existing) in a life cycle stage. The egg is rendered in a natural style, the larva includes the word "form," while the adult is termed using the word "worm." In the right hand panel, Ascaris lumbricoides egg is rendered in natural style while fertile and infertile eggs have the word "form" added. The right hand panel also demonstrates the dual inheritance of concepts that specify a particular form of the organism.

The existing hierarchy specifies that “organism X in Y life cycle form” and “life cycle form Y of X organism” are represented in single concept classes. As there is no logical model for the organism hierarchy, previous editors created supertypes in place of defining attribute value relationships. Most leaf nodes in this area are appropriately placed for the supertype that represents the species identity of the organism (directly or via transitive closure). The meaning of the other inheritance path is not clear but as these are ultimately subtypes of life cycle form via transitive closure, their co­assignment with the would seem inappropriate. A concept class should not simultaneously be a class of organisms that (at the time https://confluence.ihtsdotools.org/display/IHTSDO1/IHTSDO-455+%28artf7628%29+Organism+Life+Cycles+-+previously+Taxon+specific+life+cycle+forms 4/14 1/28/2018 IHTSDO-455 (artf7628) Organism Life Cycles - previously Taxon specific life cycle forms - IHTSDO Content - SNOMED Confluence some observation is performed) exhibits the form correct for some life cycle stage and a class representing a life cycle form. It is not clear whether this is the source or the result of representing life cycle forms/stages in the names of the diagnostic organism concept classes, but it has resulted in a lack of clarity for users and editors alike.

3.6 Subsidiary and interrelated problems

Similar Life cycle stage issues exist for other organisms including protozoa, fungi, viruses and insects. Specific solutions and certain content errors are specific to the particular organism classes.

3.6.1 Common name includes definitive reference to “form”

Common names generally only represent one life cycle stage but the specific stage represented is not consistent across the hierarchy. The concept class 22085009 | Tenebrio molitor (organism) with a common name = “Mealworm.” The concept class is represented by the correct Latin binomial name for Tenebrio molitor in any life cycle stage (egg, larva, pupa, adult) but the common name “Mealworm” is a reference to the most often recognized pest form of the organism, its larva. Editors also created questionable supertypes to accommodate the error. Tenebrio molitor is a concept class that represents all organisms that possess the genetic material to manifest the characteristics of the class in any stage of its life. The existing ancestor relationships of this concept, 284715001 | larva (organism) and 106771004 | Beetle AND/OR beetle larva (organism) would seem to be logically incompatible and neither is correct as supertypes for an organism class that includes eggs and pupae as well.

Figure 3.3. Incorrect modeling of the species Tenebrio molitor. Marked in red, the concept classes 106771004 | Beetle AND/OR beetle larva (organism) and 284715001 Insect larva (organism) are incorrect supertypes for this species (organism) class. The concept class 106771004 | Beetle AND/OR beetle larva (organism) duplicates the meaning of 106765005 | Order Coleoptera (organism), the order of insects that are beetles.

3.6.2 Latin binomial surrogates for life cycle stages

3.6.2.1 Cestode larvae

Cestode larvae were originally given taxonomic standing and their own Latin binomial names independent of the relationship between adult and larval stages. The species class 61085008 | Taenia saginata (organism) is valid. The larva class 47399003 | Cysticercus bovis (organism) is deprecated within the formal taxonomy but maintained as a valid "generic" name for the larval form of Taenia saginata. SNOMED CT has a concept class 703757009 | Taenia saginata larval form (organism) that should probably be considered a for Cystecercus bovis. Finally the adult tapeworm concept class is represented as 703758004 | Taenia saginata worm (organism). Panel A of Figure 4 shows the relationships among these concept classes in the January 1, 2015 version of SNOMED CT. Figure 5 is a graphical representation of the hierarchy for the two terms and shows the redundancy created in this portion.

Figure 3.4. The left panel demonstrates a variation at the Genus level where "worm form" is used in place of "worm" (as with its parent "Cestode worm"). The right hand panel demonstrates a varation unique to tapeworm species. Cystecercus bovis is the larval form of Taenia saginata. An editor unfamiliar with life cycle naming among the cestodes created the cuplicate concept Tainia saginata larval form.

Figure 3.5. Concept duplication and subtype inconsistencies related to the larva of Taeina saginata. Red bidirectional arrows identify duplication(s).

https://confluence.ihtsdotools.org/display/IHTSDO1/IHTSDO-455+%28artf7628%29+Organism+Life+Cycles+-+previously+Taxon+specific+life+cycle+forms 5/14 1/28/2018 IHTSDO-455 (artf7628) Organism Life Cycles - previously Taxon specific life cycle forms - IHTSDO Content - SNOMED Confluence 3.6.2.2 Dimorphic fungi

Like the cestodes, fungi naming occasionally includes different names for different life cycle stages of the same organism. The Ajellomyces are a genus of fungi in the phylum, in the Ajellomycetaceae family.[2] The genus contains three species, which have a widespread distribution, especially in tropical areas.[3] The species Ajellomyces capsulatus is significant to human health as the causative agent of histoplasmosis.[4] However, this species is more usually referred to as Histoplasma capsulatum, with the designation Ajellomyces capsulatus referring to the vegetative (ascomycetous perfect) stage.[5] Similar situations exist for other dimorphic fungi.

3.6.3 Common organism names and forms

Three concept classes appear to represent “yeast” in SNOMED CT namely 62093005 | Yeast (organism), 285290002 | Yeast form (organism) and 10541008 | True yeast (organism). Table three describes difficulties associated with usability and reproducibility of each.

Table 1. SNOMED CT organism classes for “yeast.”

Concept class General Descendants supertype (via transitive closure)

285290002 | 278306005 | Life­ Concept classes that represent yeast “morphologies” (only). It does not appear that this class is part of the transitive closure path of any actual Yeast form cycle form proper Linnaean organism class.

10541008 | 410607006 | None. References indicate that this is a common name for organisms belonging to 426013006 | Order Saccharomycetales. There are several True yeast Organism proper Linnaean organism classes that should be descendants.

62093005 | 278306005 | Life­ Proper Linnaean organism­only classes with no reference to life­cycle form. Yeast cycle form 410607006 | Organism

4 Risks / Benefits

4.1.1 Risks of not addressing the problem

Editors and users will continue to have difficulty with decisions related to selection or creation of organism classes that make reference to particular life cycle stages. Most of the content, especially content related to parasitism.

4.1.2 Risks of addressing the problem

There will be little disruption related to “re­terming” of the affected organism classes, mostly because the terms will be in a more familiar and consistent style. Any (as yet unidentified) uses of the current life­cycle form subhierarchy could be affected. Any application of queries designed to aggregate based on the subtypes of “Life­cycle form” would have to be converted to gather on the basis of attribute­value pairs.

5 Requirements: criteria for success and completion 5.1 Criteria for success/completion 5.2 Strategic and/or specific operational use cases

Outline fit with IHTSDO strategic goals;

5.2.1 Use case 1

The primary use of the affected concept classes is for result reporting of organism names and incorporation into laboratory information systems.

5.2.1.1 Fit with IHTSDO strategy

The primary use case, result reporting, is listed as Priority 1E in the 2010 Product Development Plan. Certain organisms would also be necessary for Public health surveillance and reporting (Priority 1F).

5.2.2 Use case 2

It is not clear that a use case exists for the life cycle stages other than application in an eventual logical model for the organism content in this area.

6 Outline Possible Technical Approaches and Concept Model 6.1 Indicative Solutions

6.1.1 Approach One

Develop a simpler and more consistent terming scheme for the organism content. Organisms in particular life cycle stages. Where possible life cycle names should be general (i.e., egg, larva, adult, etc.) rather than based on the morphology of the life cycle stage (i.e., worm, beetle, etc.). Develop a logical model for life cycle specific organism content. This model should be based on the clear separation between organism classes (BFO: Continuant) and life cycle stages (BFO: Occurant) classes. The logical model need not be deployed to solve the existing problems, but should serve to guide actual model implementation.

6.1.1.1 End user Impact of approach one https://confluence.ihtsdotools.org/display/IHTSDO1/IHTSDO-455+%28artf7628%29+Organism+Life+Cycles+-+previously+Taxon+specific+life+cycle+forms 6/14 1/28/2018 IHTSDO-455 (artf7628) Organism Life Cycles - previously Taxon specific life cycle forms - IHTSDO Content - SNOMED Confluence A successful approach should leave end users with a better understanding of the content in this area, should help editors produce more consistent terms for these organisms and should assist in evaluating user content requests while helping users make the requests more cogent.

6.1.2 Approach Two

In addition to the steps proposed in Approach One, a more comprehensive solution to the problem would Create life cycle stage concept classes, required for the model, as descendants of 362981000 | Qualifier value (qualifier value). Create an attribute appropriate for linking organism classes to life cycle stages (that will no longer be organisms). Evaluate and model affected concept classes. Retire existing life cycle form subtypes that do NOT have supertypes in the proper Linnaean hierarchy above some arbitrary level. Nearly all the first generation descendants of 278306005 | Life­cycle form (organism) have a Linnaean supertype. However, the utility of concepts such as 115989009 | Fungal morphologic state (organism) for any particular SNOMED CT user group is likely to be very low. Decisions to retire or retain this content should be based on some perception of the utility of the affected classes. One notable exception to this is the class 446975004 | Arachnid egg (organism). In this case the term refers to Arachnid but the class is a subtype of Life­cycle form but NOT a subtype of 76222001 | Class Arachnida (organism) when it probably should be.

6.1.2.1 End user Impact of approach two

If the organism and life cycle stage concept classes are separated, there may be some users who will lose functionality related to selection and aggregation based on life­cycle stage. That functionality can be restored via the defining attribute value classes of a properly rendered model.

7 Indicative Project Plan 7.1 Scope of elaboration phase

The elaboration phase should be completed by an individual with experience using and or managing the organism content of SNOMED CT and specifically by an individual knowledgeable about the range of organisms likely to be affected by these changes. The solution is likely to affect approximately 325 existing organism concept classes and may involve the creation of some number of quality values and at least one model attribute. Knowledge and understanding of SNOMED CT modeling and the ongoing work being done by the Organism and Infectious Disease Project Group are also required. The problem should not recur providing attention is paid to all the organism classes involved. This problem was first presented primarily as a request for guidance for the naming of nematodes related to life cycle stages. The range of the problem spans organism classes including, but perhaps not limited to helminths, insects, protozoa, and perhaps others.

7.2 Projection of overall project size and resource requirements

7.2.1 Expected project resource requirement

e.g. The project resource requirement is classed as SMALL – less than 1 person year

7.2.2 Expected project impact and benefit

e.g. The project impact is SMALL – significant improvement to a minority but potentially high profile use case

7.2.3 Indicative resource estimates for elaboration, construction, transition and maintenance:

Elaboration phase: 1 person month effort, 3­6 months elapsed time Construction and transition phase: 325 concepts to be reviewed, approximately ½ will need new terms (descriptions) authored and many will require adjustments to existing modeling. Creation of some number of values (20 – 50) to support the model.

Maintenance phase: 10 ­ 30 new ‘frequent usage’ concept requests in 1st 3 years

8 Appendices 8.1 Appendix One : Related user requests

9 Works Cited

1. The architecture of the life cycle in small organisms. Koufopanou, Graham Bell and Vassiliki. 1991, Philosophical Transactions: Biological Sciences, Vol. 332 (1262), pp. 81–89. 2. Parasite Life Cycle Ontology. [Online] April 9, 2015. http://purl.obolibrary.org/obo/uberon.owl. 3. Institute for Formal Ontology and Medical Information Science (IFOMIS). BFO Basic Formal Ontology Home page. BFO Basic Formal Ontology. [Online] 4 13, 2015. http://ifomis.uni­saarland.de/bfo/. 4. Centers for Disease Control. DPDx ­ Laboratory Identification of Parasitic Diseases of Public Health Concern. Centers for Disease Control. [Online] March 12, 2015. http://www.cdc.gov/dpdx/trypanosomiasisAmerican/. 5. Gene Ontology Consortium home page. Gene Ontology Consortium. [Online] April 9, 2015. http://geneontology.org. 6. Centers for Disease Control. DPDx ­ Laboratory Identification of Parasitic Disease of Public Health Concern. CDC Centers for Disease Control and Prevention. [Online] 4 9, 2015. http://www.cdc.gov/dpdx/. 7. Houghton Mifflin Company. organism. The American Heritage® Stedman's Medical Dictionary. [Online] March 23, 2015. http://dictionary.reference.com/browse/organism.

Elaboration phase

SNOMED CT Content Improvement Project Elaboration phase https://confluence.ihtsdotools.org/display/IHTSDO1/IHTSDO-455+%28artf7628%29+Organism+Life+Cycles+-+previously+Taxon+specific+life+cycle+forms 7/14 1/28/2018 IHTSDO-455 (artf7628) Organism Life Cycles - previously Taxon specific life cycle forms - IHTSDO Content - SNOMED Confluence Project ID: Topic:

Date

Version 1

Amendment History

Version Date Editor Comments

1 20150704 Jeff R. First draft for comments Wilcke

1.1 20170829 Jeff R. Remove references to organism "model" which will not be executed. Wilcke Provide detailed editing guidance in the form of expected (resulting) primitive hierarchies. Terming principles need to be reviewed and agreed to by Project Group.

1.2 20171108 Jeff R. Strengthened "naming" issues section. Wilcke Updated figures of organism content for clarification. Figures describe all name changes in the organism content. Provided a list of concepts that will be retired during first phase of construction (separating organism from life­cycle content).

Review Timetable

Review date Responsible owner Comments

20151207 James T. Case See inserted comments.

20171027 James T. Case See inserted comments.

© International Health Terminology Standards Development Organisation 2012. All rights reserved. SNOMED CT® was originally created by the College of American Pathologists. This document forms part of the International Release of SNOMED CT® distributed by the International Health Terminology Standards Development Organisation (IHTSDO), and is subject to the IHTSDO’s SNOMED CT® Affiliate Licence. Details of the SNOMED CT® Affiliate Licence may be found at http://www.ihtsdo.org/our­standards/licensing/. No part of this document may be reproduced or transmitted in any form or by any means, or stored in any kind of retrieval system, except by an Affiliate of the IHTSDO in accordance with the SNOMED CT® Affiliate Licence. Any modification of this document (including without limitation the removal or modification of this notice) is prohibited without the express written permission of the IHTSDO. Any copy of this document that is not obtained directly from the IHTSDO [or a Member of the IHTSDO] is not controlled by the IHTSDO, and may have been modified and may be out of date. Any recipient of this document who has received it by other means is encouraged to obtain a copy directly from the IHTSDO [or a Member of the IHTSDO. Details of the Members of the IHTSDO may be found at http://www.ihtsdo.org/members/]. Glossary was duplicated and therefore removed.

2 Introduction 2.1 Purpose

The general purpose of this project is to consider the appropriate text representations and hierarchy placement of organisms and organism life cycle stages (aka life cycle forms). A secondary purpose of this project is to provide develop editorial guidance for incorporating organism hierarchy content used as values for laboratory reporting in parasitology.

2.2 Audience and stakeholder domain

The audience for this document includes all standards terminology leaders, implementers and users but is especially targeted at those stakeholders from the diagnostic laboratory domain. A further significant audience is the community of SNOMED authors that may be requested to implement the recommended specification.

2.2.1 Input from stakeholders

No new input or specific requests has come from stakeholders since approval of the inception document. Members of the Organism and Infectious Disease Model Project Group have reviewed a draft document that describes details of a draft solution.

3 Solution Development 3.1 Initial Design

3.1.1 Outline of initial design

The solution for this particular problem will be executed in stages. Stages 1 and 2 are intended to separate organism concept classes from those that do not represent whole organisms and to improve the consistency of organism descriptions while aligning the descriptions with SNOMED CT editorial guidance. A review of descendants of 278306005 | Life­cycle form indicates that there are 335 descendant (subtype) classes. Of these, 81 have no subtype connections to recognizable Linnaean taxons. As they are disconnected logically from the SNOMED classes that represent extant organisms, it is difficult to be certain of the meaning(s) and use(s) of these 81 classes, but they appear to fall into several distinct concept types as listed in Table 3.1 The remaining 254 subtypes appear to have correct relationships to existing Linnaean concepts. Many will require extensive description editing described in Stage 2. Stage 1. Inactivate concept class that are not organisms. 1a. Inactivate concept classes that are navigation­only as they clearly refer to life cycle forms (stages or states). Table 3.1 Column 1. 1b. Inactivate concept classes that are ambiguous or do not refer to any particular organism taxon or list of taxons. Table 3.1 Column 2. 1c. Inactivate concept classes that refer to organism structures, but do NOT represent intact organisms. Table 3.1 Column 3. https://confluence.ihtsdotools.org/display/IHTSDO1/IHTSDO-455+%28artf7628%29+Organism+Life+Cycles+-+previously+Taxon+specific+life+cycle+forms 8/14 1/28/2018 IHTSDO-455 (artf7628) Organism Life Cycles - previously Taxon specific life cycle forms - IHTSDO Content - SNOMED Confluence 1d. Inactivate concept classes that refer directly to (and only to) an organism state, stage or form. Table 3.1 Column 4. 1e. Determine disposition of classes that appear to represent "finding" morphologies (e.g. 260236001 | Ectothrix describes a dermatophyte infection where fungal hyphae are on the outside of hair shafts). Table 3.1 Column 5. 1e. Inactivate concept classes that duplicate living organism classes. Table 3.1 Column 6.

Table 3.1. Descendants of 278306005 | Life­cycle form (organism) that will either be retired or attached to appropriate points in the organism hierarchy. Most represent organism content but are not extant organisms. Relationships of these concept classes to Linnaean organism classes can sometimes be inferred but but may not be subtype (Is a). Others clearly seem to be organisms but are not appropriately assigned to an extant organism subhierarchy. Table headings represent the issue that requires editing attention.

(1) Organizing (2) Ambiguous (3) Organism (4) Concept classes (5) Concept classes (6) Duplicates (7) Subtype (is a) (navigational) concept concept classes, structures ­ these making literal that should be existing relationships can be classes. Only Kingdom could qualify as classes do not reference to states, SNOMED­CT Linnaean created to proper Protozoa is subtype of organisms yet represent whole stages or forms. morphologies concept class. Linnaean class. Retain its associated available organisms. COULD be created as these as candidate Linnaean class, the information organisms of the form organism classes. rest only connect to inadequate to link "Anamorph of Life­cycle form a direct to any particular Fungus." Suggest descendant of the Linnaean class. waiting for user organism root. request.

278306005 | Life­cycle 103567009 | Worm 284688000 | Fungal 41809005 | Anamorph 260236001 | 86802003 | 446975004 | Arachnid form larvae hyphae state Ectothrix Caterpillar egg 409973005 | Arachnid 103565001 | Worm 264289006 | Branching 63054009 | Holomorph (Defining feature for (Duplicates 285297004 | Bacterial life­cycle form eggs hyphae certain dermatophyte 125068003 | Larva cell 48490002 | infections = "mycelia of Order 409976002 | Tick life­ 103566000 | 263694005 | Broad Synanamorph outside hair shafts") Lepidoptera) 46994008 | Bacterial cycle form Infective worm eggs irregular hyphae 72678006 | Teleomorph 260237005 | 106771004 | 284718004 | Bacterial 103567009 | Worm 263817002 | Narrow state Endothrix Beetle AND/OR 413627006 | Bacterial life­cycle form larvae hyphae beetle larva Stalk Cell (Defining feature for 115989009 | Fungal 103570008 | 264877004 | Non­ certain dermatophyte (Duplicates 264397001 | Budding morphologic state Encysted larvae branching hyphae infections = "mycelia 106765005 | yeast 67764007 | Fungal 103569007 | 82052005 | inside hair shafts") Order Coleoptera) 285300009 | Dividing reproductive state Infective filariform Pseudohypha bacterial cell larvae 284687005 | Fungal life­ 284689008 | Fungal 264404001 | cycle form 263883009 | Spore mycelium Encapsulated yeast 284720001 | Helminthic 103570008 | 39417006 | Ascoma 285291003 | Fungal life­cycle form Encysted larvae unicell 88501005 | Ascus 284714002 | Insect life­ 103566000 | (fungus) 284716000 | Insect egg cycle form Infective worm eggs 285292005 | Fungal 285298009 | Insect 284692007 | Protozoal 48458007 | Parasite fruiting body imago life­cycle form larvae 285292005 | Fungal 284715001 | Insect (descendant of both Life­ 263883009 | Spore fruiting body larva cycle form and Kingdom Protozoa) 285299001 | Insect nymph 103535006 | Life form of parasite 284717009 | Insect pupa 115988001 | Fungal structural elements 110376008 | Intracellular elementary (NOT a descendant of bodies life­cycle form) 284727003 | Louse egg 8181006 | Maggot 415934008 | Monascus 415935009 | Monascus ruber 285288003 | Multiple budding yeast 125072004 | anemone larvae 285296008 | Virion 62093005 | Yeast 5020009 | Annelloconidium 58988000 | Arthroconidium 285287008 | Arthrospore 52471008 | Ascospore 33818004 | Asexual fungal spore 15596004 | Ballistoconidium 9488003 | Ballistospore 35376000 | Blastoconidium 42128004 | Chlamydoconidium https://confluence.ihtsdotools.org/display/IHTSDO1/IHTSDO-455+%28artf7628%29+Organism+Life+Cycles+-+previously+Taxon+specific+life+cycle+forms 9/14 1/28/2018 IHTSDO-455 (artf7628) Organism Life Cycles - previously Taxon specific life cycle forms - IHTSDO Content - SNOMED Confluence 14127004 | Conidium 46901008 | Fungal spore 260105003 | Hormodendrum spore 40949007 | Macroconidium 65180005 | Microconidium 89983006 | Phialoconidium 2870003 | Sexual fungal spore 588009 | Sporangium 79541003 | Yeast spore

Stage 2. Edit organisms (originally descendants of 278306005 | Life­cycle form) l that remain after stage 1. 2a. Establish or correct subtype relationships between candidate organism content (remaining after stage 1) and proper Linnaean classes. Table 3.1 Column 7. a. Organisms (no reference to forms or stages) ­ Genus Monascus, Monascus ruber, Yeast b. Class Insecta identified in life­cycle stages (egg, larva, nymph, pupa, adult) c. Class Arachnida eggs d. Fungal and bacterial cell forms e. Fungal 2b. Correct descriptions of organism contents where required. Figure 3.1 shows the specific corrections that will be made to concept classes between Phylum Nemata and Strongyloides stercoralis. Terming rules for organisms identified associated with life­cycle stages will be a direct extension of the existing SNOMED CT editorial guidance for the organism hierarchy (7.1.2 Naming conventions for the organism hierarchy). FSNs for these concept classes will begin with the life­cycle stage qualifier and end with a proper rendering of the FSN of it's immediate supertype.

Table 3.2. Example descriptions for life­cycle concept classes based on the FSN of the immediate supertype. These examples serve to illustrate the approach that is being recommended for various kinds of organisms but is certainly not all­inclusive either in regards to the organism sub­hierarchy to which they belong nor does it attempt to capture the entire list of life­cycle stages that are being referenced.

Stage FSN Other terms

Egg Species: Egg of Strongyloides stercoralis (organism) PT: Strongyloides stercoralis egg Genus and above: Egg of Genus Strongyloides PT: Strongyloides egg

Larva Species: Larva of Strongyloides stercoralis PT: Strongyloides stercoralis larva Genus and above: Larva of Genus Strongyloides PT: Strongyloides larva

Cestode larva Species: Larva of Taenia saginata PT: Taenia saginata larva Synonym: Cysticercus bovis Genus: Larva of Genus Taenia (organism) PT: Taenia larva Synonym: Cysticercus Species: Larva of Dipylidium caninum PT: Dipylidium caninum larva Synonym: Diplydium caninum cysticercoid Genus: Larva of Genus Echinococcus PT: Echinococcus larva Synonym: Hydatid Cyst

Rhabditiform larva Species: Rhabditiform larva of Strongyloides stercoralis (organism) Strongyloides stercoralis rhabditiform larva Genus and above: Rhabditiform larva of Genus Strongyloides (organism) Strongyloides rhabditiform larva

Insect larva Class: Larva of Class Insecta (organism) PT: Class Insecta larva Synonym: Insect larva Order: Larva of Order Diptera (organism) PT: Order Diptera larva Synonym: Maggott Order: Larva of Order Coleoptera (organism) PT: Order Coleoptera larva Synonym: Beetle larva Order: Larva of Order Lepidoptera (organism) PT: Order Lepidoptera larva Synonym: Caterpillar

Insect Adult Class: Adult of Class Insecta (organism) PT: Class Insecta adult Synonym: Insect imago

Adult Species: Adult of Strongyloides stercoralis (organism) PT: Strongyloides stercoralis adult Genus and above: Adult of Genus Strongyloides PT: Strongyloides adult

Spore Kingdom: Spore of Kingdom fungi (organism) PT: Kingdom Fungi spore Synonym: Fungal spore

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Figure 3.1 Graphic representation of the edited concept class descriptions between Phylum Nemata and the rhabditiform larval form of Strongyloides stercoralis. The concept "Helminthic life­cycle form" will be inactivated in the organism hierarchy.

3.1.2 Significant design or implementation decisions / compromises

Organism Hierarchy Seventy­five percent of classes descendant from 278306005 | Life­cycle form are already subtypes of other (proper) organism classes. For example all of the nematode concept classes that refer in some way to a particular life stage of a nematode (e.g., Ascaris lumbricoides adult, larva and egg) appear to be placed correctly in the organism hierarchy. Other organism subhierarchies (cestodes, fungi, protozoa, insects, etc.) may require significant revision as various misalignments and incorrect taxonomic assignments exist among these concept classes. These revisions will not be completed during this project. Going forward, no restrictions are suggested for addition of organisms “in a particular life cycle stage.” As subtypes of the correct organism class (i.e., family, genus, or species) such concepts classes should be created at taxonomic level required to support stakeholder use cases. For example, no particular attempts should be made to restrict inclusion of concept classes such as “Ascarid egg” which can be accommodated in addition to "Ascaris lumbricoides egg". For this project, the aim will be to conserve existing content and no attempt will be made to "complete" the organism hierarchy through systematic addition of similar content. That said, minimal or no restrictions should be placed on concept requests in this sub­hierarchy Life Stages The life­cycle content in SNOMED CT was created before the Ontology for Parasite LifeCycle (OPL) was created. The OPL establishes a clear dicotomy between a conceptual "stage in a life­cycle" and an example of an organism participating in a given life­cycle stage. The SNOMED CT life­cyle content in table 3.1 appears to create hierarchical relationships in order to define life­cycle based subtypes of organisms and distinguish them from their taxon classes. Unfortunately this approach placed content that was clearly not an organism subtype in the organism hierarchy. To follow the ontologically correct approach taken by OPL, content that defines an organism should be represented as one or more types of qualifier value. Utility of such a list of qualifier values is based on a well­defined model for organism definitions which does not exist and is not being pursued at this time. In the absence of an organism model, it is not clear that there is a viable use case for creating qualifier value (sub)hierarchies. While this project and the not­organism content identified herein may serve as a partial basis for development of a related qualifier value hierarchy, it is incomplete and not particularly logical. In future, it may be reasonable to incorporate this content in SNOMED CT, but it should be based on defined goals and a logical model for organism definitions. Neither exists at this time.

3.1.2.1 Exceptions and Problems

The existing sub­hierarchy under 278306005 | Life­cycle form (organism) is intercalated among subhierarchies representing widely disparate kinds of organisms. At the present time logical and lexical errors that exist at the intersections between these hierarchies change based on the kind of organism (helminths, fungi, arachnids, insects etc.). The original issue raised by editors concerning life­cycle stages came from requests for additional content in the “nematode subhierarchy” (descendants of 421727006 | Phylum Nemata) where the problem is almost entirely lexical. Separation of life­cycle stages from organisms in this area, as shown in Figures 2 and 3 only slightly alters the organism hierarchy. Reorganizing the fungi (especially dimorphic fungi) will require editorial decisions concerning fungal classes that were part of a dual naming system that has recently been deprecated by recognized authorities[JTC5] . Many fungal descendants of life­cycle form are more properly thought of as “states” than “stages[JTC7] ” (e.g., fungal anamorph) as from one form to another does not necessarily occur. There have been recent significant revisions to fungal taxonomy independent of the life­cycle problem. General revisions to the fungi are almost certainly more numerous than revisions based on life­cycle state though the two problems are inter­related. Correct placement of fungi will require a separate project. A very small number of insects and arachnids are incorrectly classified from a taxonomic point of view. As detailed in the inception document for this problem, some of the errors are related to life­cycle stages and some are not. Finally, the protozoa will likely require only minimal editing. There are very few concept classes representing protozoa participating in a particular life­ cycle stage. On the other hand there exists a parallel hierarchy of parasitic life­cycle stages that is almost a complete duplication of the parasite life­cycle stage subtypes. The grouper concept class 103535006 | Life stage of parasite should be retired.[JTC8]

3.1.2.2 Design Strengths

Design simplifies the hierarchies and makes the meaning of the classes explicit. Terms required for laboratory reporting will be in a more natural style and therefore more easily recognized by stakeholders.

3.1.2.3 Design Weakness

Any users who base aggregation queries on (current) subtypes of life­cycle stages presently in the organism hierarchy will need to change queries to a text­matching approach (e.g. Descendants of Nematode + containint "egg"). While not a trivial change, consistent terming should make this a functional approach.

3.1.2.4 Design Risks

Description of risk Importance Mitigation plan

Queries to extract value sets based on the existing primitive hierarchies will produce different results. As the specific needs of Low to med Prepare for requests to increase such users have not been described (detailed use case examples do not exist at this time), adjustments to the values granularity of the value hierarchies and hierarchy may be necessary following initial introduction of this content. to modify specificity of the model to meet user needs.

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4.1.1 Detailed design final specification

The design specification will be implemented as follows: 1. Review and identify existing concept classes that represent organisms identified (in part) by their existence particular life­cycle stages and morphological states. a. Inactivate (retire) life­cycle (only) concept classes. b. Retain existing (correct) relationships to bona fide organism concept classes intact. c. Correct terms according to proposed principles. 2. Incorporate terming rules into SNOMED CT Editorial Guideline. 3. Retain history of inactivated content to inform future work.

4.1.2 Iteration plan

Input will be solicited from the Organisms and Infectious Disease Project Group members. Refinements will be based on the presence of organism content required for laboratory reporting and life­cycle content required for recall and aggregation.

5 Quality program criteria 5.1 Quality metrics

5.1.1 Quality metric 1

Component Characteristic and Description Metric Target Result

Organism Char: Adherence to terming guidelines ­ Proportion of 100% classes that are life­cycle subtypes life­cycle stage of taxonomic (or state) classes properly subtypes. Descr: The fully specified names should be rendered in a style consistent with the SNOMED CT Editorial Guidline named as specified in section 3.1.1 above. The preferred terms (US and GB English) for each concept class should be rendered in a clear and natural style. Terms in the organism hierarchy should not include “stage” “state” ­ Numerator = or “form” so that they can be easily identified as organism classes. total of properly termed classes ­ Denominator = total of applicable classes

5.1.2 Quality metric 2

Component Characteristic and Description Metric Target Result

Life­cycle stage (or state) value classes. Char: Granularity Correct auto­ 100% NB. It is not clear whether the organism classification of classes will ever be modeled in this way. Descr: Granularity of value hierarchy should be sufficient to produce proper defined classes is Proposal creates the capability to do so. classification of organism classes when used in definitions. Granularity supported. beyond minimum sufficiency should be supported by practical/valid use cases.

5.2 Use case scenarios

5.2.1 Scenario One

5.2.1.1 Expected Setting

Laboratory reporting of findings related to the presence of organisms in diagnostic samples submitted to confirm parasitism.

5.2.1.2 Data capture requirement

Concept classes should conform to the nature of the test result being reported. Example: The standard method for diagnosing ascariasis is by identification of Ascaris eggs (e.g. 699566004 | Egg form of Genus Ascaris / Ascaris egg) in a stool sample using a microscope. When multiple life stages of a particular organism may be the object of a report, all stages must be represented in the organism hierarchy. While the standard diagnosis may be microscopic detection of eggs, ascariasis may also be diagnosed on autopsy based on the presence of adult ascarids in the gastrointestinal tract.

5.2.1.3 Data retrieval requirement

Users should be able to recall organism identities recorded by laboratories and aggregate them by taxonomic class and by life­cycle stage or state.

5.3 Test cases

6 Updated Project Resource Estimates

This project should require one to perhaps two person months to complete. It will be necessary to create editorial guidance related to new terming approach. In addition to familiarity with SNOMED CT editorial policies in general, editor should be familiar with principles of zoology/taxonomy. Specific knowledge related to nematode, cestode and trematode parasites, protozoa and fungi would be desirable but the editor will likely need to seek input and guidance from outside experts.

6.1 Projection of remaining overall project resource requirements https://confluence.ihtsdotools.org/display/IHTSDO1/IHTSDO-455+%28artf7628%29+Organism+Life+Cycles+-+previously+Taxon+specific+life+cycle+forms 12/14 1/28/2018 IHTSDO-455 (artf7628) Organism Life Cycles - previously Taxon specific life cycle forms - IHTSDO Content - SNOMED Confluence 6.1.1 Expected project resource requirement category

The project can be handled as a fast track. Project management beyond consultation concerning correct placement of classes in the organism taxonomy should not be required.

6.1.2 Expected project impact and benefit

Impact of these changes will be small. Mainly successful completion of this project will remove certain obstacles to accepting new content in this area.

6.1.3 Indicative resource estimates for construction, transition and maintenance:

Construction and transition phase: 325 concepts to be reviewed, approximately ½ will need new terms (descriptions) authored and many will require adjustments to existing modeling. Creation of some number of values (20 – 50) to support the model.

Maintenance phase: 10 ­ 30 new ‘frequent usage’ concept requests in 1st 3 years. Fewer thereafter.

[JTC1]Where in the qualifier hierarchy would you propose to locate this?

@ Jeff Wilcke ­ I think it's first valid to ask, in the absence of an organism model, whether this content is actually needed and if so whether a logical hierarchy serves a purpose (the alternative is a list) . The most conservative approach is to retain the content but move it to an appropriate place. There is no obvious home for this qualifier hierarchy. I’m not sure what principles guide placement of qualifiers. I can imagine a “family” of “organism qualifiers” (life cycle stages, organism shapes, etc.) and I would place these directly under 362981000 | Qualifier value (qualifier value). I considered placing them as “descriptors” as some of that content seems similar, but I am not entirely comfortable that these are genuinely “descriptors” and not something much more specific.

[JTC2]It sounds from this that before we do any rearrangement or retirement that we need to create at least the basic qualifier hierarchy to avoid rework, no?

@ Jeff Wilcke ­ I certainly agree that this could or should be a first step. That said, I'm not sure it would actually avoid re­work. To discover all the qualifiers needed, one would first have to identify all the organism concepts that need qualifiers. Chicken v egg? We would then need this reviewed by the user community.

@ Jeff Wilcke ­ That's above my level of responsibility but I understand. Challenging thing will be to find a user community with either sufficient interest or sufficient terminology experience. Does it also assume that we will actually attempt to execute an organism model (something I'm not sure we can/should pursue at this point)?

[JTC3]Not sure I understand the inclusion of “adult” in these non­adult stages.

@ Jeff Wilcke ­ TYPO! Cut and paste error. Just wrong.

[JTC4]What would be the full hierarchy here so editors would know where to put this sub­hierarchy?

@ Jeff Wilcke ­ I’m not sure exactly what you mean. Organism life­cycle stage is the root. After that, the content depends entirely on what organisms need life­cycle stages. Somewhere in this document, there’s a comment about the qualifier values could be a list (a one­level hierarchy) or something more elegant. Not sure of the need. See JTC2 comment above.

[JTC5]Please provide a reference.

@ Jeff Wilcke ­ International Code of for , fungi, and (Melbourne Code) adopted by the Eighteenth International Botanical Congress Melbourne, Australia, July 2011. Unfortunately "Histoplasma" persists in Index Fungorum because, like the List of Prokaryotic Names with Standing, it is not considered to be a taxonomic reference. Outdated names are not retired. Index Fungorum does not provide a taxonomic and does not include “previous name” references. In the specific case of Histoplasma capsulatum the correct supertype is Ajellomyces (genus). The Histoplasma (genus) is a genus member of 106569002 | Form family Moniliaceae (organism). The so­called "Form" taxons account for (among other things) the dimorphic fungi. Each "form" of Ajellomyces capsulatum () got its own genus designation before it became clear that they were the same fungus. I suspect this triggered the creation of 289924001 | Fungal microorganism (organism) distinct from 414561005 | Kingdom Fungi (organism) as the "forms" (Form family, Form Class) are not listed in Index Fungorum. Although Form taxons appear in older taxonomic references, they've never actually been recognized taxonomic categories (in Index Fungorum).

[JTC6]This opens the door to a discussion of a sub­hierarchy of “organism structures” rather than place these in the qualifier hierarchy as they are not really qualifiers, but are structural. Most people would not be supportive of including these under the existing top­level hierarchy of “Body structure”, which leads to a separate top­level hierarchy of “non­human organism structure” or some similar name.

@ Jeff Wilcke ­ It does. There are at least two issues here. 1) I would agree that these are not “Body structures” (either proper or improper). I would concede that placing them in the qualifier hierarchy is stop­gap at best. However, I would also challenge any assertion that the effect on classification (of anything in SNOMED) would be altered by either choice. Needs to be debated. 2) the real use of "Mycelium" is more likely as microscopic findings as in "I saw mycelium in this microscopic field."

[JTC7]Participates­in requires a life­stage, but the stage is represented by a structure. Do we need both?

@ Jeff Wilcke ­ I think concepts like "spore" actually represent two things. First, like mycelium one can see "spores" on a slide ­ they are structures. But they also represent a functional state of bacteria (they are not merely structural). That said I would suggest that as there is little likelihood that we will be creating a functional organism model in the near term, references to “modeling” (in this document) could (perhaps should) be removed. This ends up creating questions about retaining those concepts that are “states only” (apply generally to multiple organisms). Qualifier hierarchy becomes a sort of “graveyard” for these if the model is never developed. We can lean towards SNOMED’s “concept retention” preferences or simply retire as having no particular value. I would argue that an incremental step is to move them, not delete them and NOT turn them into a robust hierarchy until such time as an organism model is proposed, accepted and can be practically managed (authored).

[JTC8]Strongly agree.

@ Jeff Wilcke ­ !

[JTC9]Need a recommendation all the way up to the top to guide the editors.

@ Jeff Wilcke ­ See previous comments. I think the first decision is between a simple list and a full hierarchy. If full hierarchy, I would infer from your comment that every project proposal in a primitive hierarchy would require (nearly) full construction to proceed. That seems to (to me) to place construction activities in the elaboration process. I think examples should be created and the content placed in the hands of sensible knowledgeable authors?

[JTC10]I am assuming you mean to retire only those that are extant in the Organism hierarchy, correct?

@ Jeff Wilcke ­ Not completely understanding the question. I think the answer is correct. I'm not sure what to retire that does not exist? I'm probably misreading your comment.

[JTC11]Where would we place this subhierarchy in the qualifier value top level hierarchy?

@ Jeff Wilcke ­ I see no obvious organization to the top level of the qualifier values. The main question is whether these belong at the top or in a sub­hierarchy. Try as I might, I’ve not found a sub­hierarchy that I would recommend. https://confluence.ihtsdotools.org/display/IHTSDO1/IHTSDO-455+%28artf7628%29+Organism+Life+Cycles+-+previously+Taxon+specific+life+cycle+forms 13/14 1/28/2018 IHTSDO-455 (artf7628) Organism Life Cycles - previously Taxon specific life cycle forms - IHTSDO Content - SNOMED Confluence

[JTC12]Does this one attribute suffice for all three of the value types above “life­cycle stage”, “morphologic state” and “structural element”?

@ Jeff Wilcke ­ Participates in (attribute) would suffice for life­cycle stage and morphologic state I think. See previous comment JTC7. Bacteria in spore form are just “in” a state of suspended animation (the spore). There is no sound argument I can think of for AVOIDING a separate attribute when the structure is considered defining for the organism (not the organism in a life­cycle stage or state) or if there's a reason to (generically) report the presence of a structure. I’m not certain it would serve a classification purpose. I don’t THINK there are organisms that in a given life­cycle state that are in multiple morphologic states. In fact the life­cycle stages are identified (almost?) mostly by morphology (I’m not thinking of a counter example). This requires a concept model change and should be reviewed by the Modeling Advisory Group

@ Jeff Wilcke ­ Yes, though it looks more and more as if model goes beyond what's needed (or actually going to happen) here. To my thinking, a model is more of a justification for retaining the qualifier list than anything.

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