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: 

https://projects.jira.snomed.org/browse/IHTSDO-455

Document review: JIRA IHTSDO-455 Organism Life Cycles Documentation Review (Please note this page does not have public access)

Approvals 

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Note draft guidance (to be clarified): Approval should be sort at the end of the Elaboration/Testing phase where required

Amendment History

Review Timetable

© 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/our-standards/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from the IHTSDO [or a Member of the IHTSDO] is not controlled by the IHTSDO, and may have been modified and may be out of date.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/].

1 Glossary

1.1 Domain Terms

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 self-identified 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., genus, species, 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 protozoa, helminths and insects 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 morphology, 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), order of stages, etc.   A life cycle stage is directly related to an organism class, 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 hybrid 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

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 lives its life as infant then child then juvenile then adult (other demarcations are reasonable, these serve to illustrate the point).   Similarly, a nematode 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 “Life-cycle stage.”   Epimastigote and epimastigote stage are related through a relationship “participates-in.” 

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).

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).
Open
The Parasite Life Cycle ontology was developed as part of the NIH-funded "Semantics and Services enabled Problem Solving Environment for Tcurzi" project (Grant #1R)1HL087795-01A1. 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 (subspecies) 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” ().  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 nematodes, 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 non-standard 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.

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.

Open

Open

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 co-assignment with the species concept would seem inappropriate.  A concept class should not simultaneously be a class of organisms that (at the time 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 | Insect 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.

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.

Open

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 synonym 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 3.4. 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.

Open

Open

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

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

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 Ascomycota 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. 

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 “re-terming” 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 life-cycle form subhierarchy could be affected.  Any application of queries designed to aggregate based on the subtypes of “Life-cycle form” would have to be converted to gather on the basis of attribute-value 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

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 | Life-cycle 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 Life-cycle 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 life-cycle 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, 3-6 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 1^st 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.uni-saarland.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

Amendment History

Review Timetable

© 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/our-standards/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 | Life-cycle 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.