JIRA Issue: https://projects.jira.snomed.org/browse/IHTSDO-1003 

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Amendment History

Review Timetable

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Table of Contents
1 Glossary
1.1 Domain Terms
2 Introduction
2.1 Purpose
2.2 Audience and stakeholder domain
2.2.1 Input from stakeholders
2.2.2 Degree of consensus on the statement of problem
3 Statement of the problem or need
3.1 Summary of problem or need, as reported
3.2 Summary of requested solution
3.3 Statement of problem as understood
3.4 Detailed analysis of reported problem, including background
3.5 Subsidiary and interrelated problems
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
5.2.2 Use case 2…
6 Solution Development
6.1 Initial Design
6.1.1 Outline of initial design
6.1.2 Significant design or implementation decisions / compromises
6.1.3 Evaluation of Design
6.2 Iteration One
6.2.1 Outline of revised design
6.2.2 Significant design or implementation changes
6.2.3 Evaluation of Revised Design
6.3 Iteration Two ..
7 Recommendation
7.1.1 Detailed design final specification
7.1.2 Iteration plan
8 Quality program criteria
8.1 Quality metrics
8.1.1 Quality metric 1
8.1.2 Quality metric 2
8.2 Use case scenarios
8.2.1 Scenario One
8.2.2 Scenario Two
8.2.3 Scenario …
8.3 Test cases
9 Project Resource Estimates
9.1 Scope of construction phase
9.2 Projection of remaining overall project resource requirements
9.2.1 Expected project resource requirement category
9.2.2 Expected project impact and benefit
9.2.3 Indicative resource estimates for construction, transition and maintenance:

Glossary

Domain Terms

Introduction

Purpose

The purpose of this project is to consider steps to improve the accuracy and utility of the upper 2 or 3 levels of the SNOMED-CT Organism hierarchy.  At present, the affected content includes correct and incorrect (outdated, inaccurate, duplicative) concepts and concept descriptions.  As the organism hierarchy is all primitive and is likely to remain so in the near term, correction of the upper organism hierarchy levels is seen as a necessary precursor to creating a subtype hierarchy that supports accurate concept retrieval, aggregation and analysis.

… very general outline of problem being considered
SNOMED CT projects transition from Inception Phase  Elaboration Phase  Construction Phase  Transition Phase. This document combines the documentation of the Inception and Elaboration Phases.
The Inception Phase focuses on understanding the problem and its scope, identifying stakeholders and their requirements, and identifying risks.
The purpose of the Elaboration Phase is to develop, document and test one (or more) possible technical solutions, and to reach a recommendation and provide a detailed specification of a preferred solution to be taken forward to the construction phase.

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 infectious disease and laboratory medicine, including public health and laboratory data collection and reporting.  A further significant audience is the community of SNOMED authors that may be requested to implement the recommended specification.

Input from stakeholders

No direct input has been received from stakeholders.  This project primarily affects the efforts of editors and authors of SNOMED content that uses organisms as values for etiologic agents and test components.  

Degree of consensus on the statement of problem

The SNOMED-CT Organism hierarchy is primarily used to provide values for laboratory reports of etiologic agents.   Concept classes required for this activity are predominately from the genus, species and various subspecies (e.g. serotype) levels of the SCT organism hierarchy.  Often, these concepts are provided to diagnostic laboratories in the form of subsets extracted for this purpose such as the PHIN VADS file "List of all microorganism concepts from SNOMED CT - July 31st 2010 version"  LINK: Microorganism SNOMED Value Set.  For these reasons laboratory users need not be familiar with or even aware of the top levels of the SCT Organism hierarchy.  Editors and authors with knowledge of organism content in SNOMED CT generally and consistently recognize several problems with the upper levels of that hierarchy.

Statement of the problem or need

Summary of problem or need, as reported

Most "reports" related to the upper levels of the SCT Organism hierarchy take the form of inquiries about or comments concerning errors and inconsistencies. 

Summary of requested solution

Correct and clarify the first 2 - 5 levels of the SCT organism hierarchy to provide a reliable foundation for adding and editing SCT organism concept classes required for laboratory reporting.

Statement of problem as understood

The top 2 - 5 levels of the SCT Organism hierarchy include numerous factual, naming and logic errors.  If these upper level concept classes are to serve as a foundation for the rest of the organism content and especially if they are to correctly facilitate organism class selection, aggregation, and analysis, these errors should be corrected.  

Errors in the organism hierarchy include but are likely not limited to:

1. non-alignment with recognized taxonomic schemes,

2. duplicate concept classes,

3. conflicting classifications from dissimilar schemes,

4. incorrect logical and factual assertions and,

5. incomplete and incorrect subtypes for descriptive name concepts and terms such as 264395009 | Microorganism (organism).

Detailed analysis of reported problem, including background

In May of 2006 SNOMED hosted a Taxonomy Working Group meeting at the University of California, Davis.  At that meeting, a number of the issues addressed by this project were noted by participants.  Adequate authoring and editing resources have not been available to make the corrections.

First generation descendants of 410607006 | Organism

Most current taxonomic references list three organism "Domains" namely Domain Archaea, Domain Bacteria and Domain Eukarya.  We need to decide whether these Domains should be included.  If so, they are logical first descendants of organism.  Figure 1 shows the existing first generation of descendants of 410607006 | Organism.  The three Kingdoms (green border) are essentially placed correctly though they are properly part of Domain Eukarya.   Absent the addition of domain Eukaryota no change in their placement in the SCT organism hierarchy is being suggested.

Figure 1. First generation descendants of 410607006 | Organism (SNOMED CT January 2017 Edition)

Figure 1. First generation descendants of 410607006 | Organism (SNOMED CT January 2017 Edition)
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Concept classes in green Concept classes in red are involved in or have created logical errors (, or perhaps not appropriate for placement in the organism hierarchy.

The remaining 4 concepts classes in Figure 1 (red border) are problematic.

278306005 | Life-cycle form (organism)

Life-cycle forms are no longer present in the organism hierarchy as the result of completion of a content improvement project (IHTSDO-455).

284666000 | Trophic Life form (organism)

Descendants of 284666000 | Trophic Life form create a hierarchy of concepts that describe the various means organisms use to acquire energy.    Descendants include Autotroph and its descendants chemoautotroph and photoautotroph;  heterotroph and its descendants carnivore, epibiont, herbivore, omnivore, saprotroph, and symbiont.  Of 421 descendants of the class, only 14 are of this type.  Extant organisms that are subtypes of this class (the remainder) are particular group of trematodes (106687005 | Subclass Digenea - digenetic trematode).   This class of trematodes is correctly associated with proper Linnaean ancestor 243670002 | Class Trematoda (organism).  Association of this class with 284666000 | Trophic Life is not required and removal of 284666000 | Trophic Life form from the organism hierarchy would have no effect on their placement.

These concepts are all nouns formed from adjectives that describe characteristics of the organisms.  While it is not incorrect classify organisms as such, it is hard to imagine correctly placing all organism concept classes as subtypes of this list. Within the context of SCT, 284666000 | Trophic life form (organism) and its descendants, much like 278306005 | Life-cycle form (organism) and its descendants could be treated as characteristics of organisms rather than as organism classes.  If there is a use case for inclusion of organism trophisms in SCT, they should be moved to an appropriate attribute value sub-hierarchy.  Although it would be possible to classify organisms by their various trophisms, an attempt to actually classify ALL organisms by their “trophism(s)” would require extensive manual editing, and there is no obvious use case.

115630000 | Renotrophic organism

Renotrophic is defined as "any agent influencing the growth or nutrition of the kidney or to the action of such an agent."   It is something of a stretch to believe that this meaning can be taken literally if the agent is an organism.  In may be that it's intended to mean “any organism with a predilection to cause kidney infection(s)" but this cannot be established with certainty.    This concept and subtypes are not used in any definitions in SCT.   Its two subtypes are renotrophic bacteria and renotrophic virus, neither of which have any extant organisms as subtypes.  It seems unlikely that a list of organisms meeting this somewhat nebulous definition can be maintained or that there is any interest in doing so.

264395009 | Microorganism

"Microorganism" is an example of a common grouping name for organisms that does not align especially well with Linnaean classification.  Microorganisms are, quite simply, organisms that can only be seen using microscopy.  As subjects of the broad scientific discipline microbiology, microorganisms are reasonable and defineable "kinds of" organism.  That said, assigning and maintaining all subtypes to this seemingly familiar organism class in SCT is problematic and would be time and resource intensive.  Four major classes could reasonably be assigned to microorganism at the highest levels.  Viruses, prions, bacteria and archaea are all microscopic.  Fungi are both microscopic and macroscopic and this is also true for animals.  Finally, there are examples of organisms (e.g. Phylum Nemata) that are macroscopic as adults but diagnostic life-cycle stages such as eggs and larvae are microscopic.

Microorganism is an attribute value that is part of relationships defining 59 procedures.  The FSNs of these concept classes lack the specificity required to identify them as laboratory procedures that could be ordered in the context of patient care (they appear to be navigational).  Some would require additional specificity such as 30088009 | Blood culture, which is typically ordered by specifying the organism of interest (e.g. bacteria) and the conditions under which the test would be performed (e.g. anaerobic).  Some appear to be non-specific synonyms of actual laboratory tests such as 117011000 |Quantitative urine culture which is almost certainly a bacterial culture. 

Microorganism is the attribute value for the Causative agent relationship for a single disorder namely 4141000119104 | Necrotizing fasciitis caused by microorganism.  Taken literally, the phrase necrotizing fasciitis is a disorder associated with inflammation of the fasciae of muscles and other organs results in rapid destruction of overlying tissues. Medically, the phrase is only associated with bacteria as causative agent.  4141000119104 | Necrotizing fasciitis caused by microorganism (disorder) should be retired as "same as" 52486002 | Necrotizing fasciitis (disorder).

Microorganism is a supertype for concept classes related to antimicrobial susceptibility and resistance.  Most of the concept class fully specified names do not use the word "microorganism" (or other reference to microscopic).  Two concept classes 419708002 | Antimicrobial susceptible organism and 409792002 | Antimicrobial resistant organism are direct descendants of  264395009 | Microorganism.  Concepts in this sub-hierarchy and disorders that they define are clearly of interest from an epidemiological perspective but it is difficult to see how they would be used in laboratory reporting and the list of concept classes is certainly incomplete from that perspective.  These two concept classes are also best thought of as common grouping names and like microorganism they are difficult to align well with Linnaean classification.

1. 419708002 | Antimicrobial susceptible organism is not used in any defining relationships.  

   1. It's direct descendant 418248000 | Antimicrobial susceptible bacteria is not used in any defining relationships.

   2. 417943000 | Methicillin susceptible Staphylococcus aureus is a second generation descendant and serves as the value for the causative agent relationship for 7 findings concepts.

   3. 698216001 | Vancomycin susceptible Staphylococcus aureus is a second generation descendant and is not used in any defining relationships.
      
      

2. 409792002 | Antimicrobial resistant organism serves as value for the causative agent attribute of 7 concept classes.  Some of these uses are questionable and concepts in the target sub-hierarchy should be reviewed.

   1. 409792002 | Antimicrobial resistant organism would seem to be the correct value for two disorders 
      
      

      1. Infection caused by resistant organism (disorder) and its subtype

      2. Therapy failure due to antibiotic resistance (disorder) This relationship is inherited.  Placement of this concept as a subtype of infection should be reviewed.

   2. 409798003 | Infection caused by antimicrobial resistant virus (disorder) and 409797008 | Infection caused by antimicrobial resistant fungi (disorder) have two values in causative agent relationships.  This appears to be caused by improper grouping of relationships resulting in an error in autoclassification.  Correcting the grouping should eliminate reference to 409792002 | Antimicrobial resistant organism.

   3. The correctness of three is difficult to assess.  Based on the antimicrobial class more specific references are possible but 409792002 | Antimicrobial resistant organism would seem to be the appropriate value.
      
      

      1. Infection caused by sulfonamide resistant organism (disorder)

      2. Infection caused by tetracycline resistant organism (disorder)

      3. Infection resistant to penicillin (disorder)

   4. An additional 47 descendants serve as values for either findings or procedures.
      
      

      1. 45 descendants serve as values in causative agent relationships (45) 

      2. 2 descendants serve as values in component relationships (2)

Microorganism is a nexus for logical inconsistencies and factual errors in the organism hierarchy.  Examples include:

1. 23496000 | Fungus is a subtype of 264395009 | Microorganism and 289924001 | Fungal microorganism is a subtype of 23496000 | Fungus.  If "Fungus" is a "Microorganism" then "Fungal microorganism would appear to duplicate it's immediate supertype.

2. 415671008 | Superkingdom Eukaryota (now Domain Eukarya) is a subtype of 264395009 | Microorganism.  Some subtypes of 415671008 | Superkingdom Eukaryota certainly include microscopic organisms, however many eukaryotes are macroscopic.  Concept class 418709001 | Kingdom Metazoa a subtype of microorganism.  It may be that this concept was intended to represent "microscopic animal."  However, taken out of its hierarchical context Metazoa is redundant in SCT.

   1. Metazoa = Animal 

   2. 387961004 | Kingdom Animalia is a first generation subtype of 410607006 | Organism

   3. 414561005 | Kingdom Fungi is a subtype of 415671008 | Superkingdom Eukaryota

      1. Outside the hierarchical context, Kingdom Fungi duplicates 23496000 | Fungus

      2. many members of kingdom Fungi are microscopic, many are not

      3. descendants of 23496000 | Fungus that are extant organisms are also descendants of 414561005 | Kingdom Fungi

Changes to the concept class 264395009 | Microorganism can be managed in one of two ways.  First, it should be recognized that the concept microorganism is a commonly used non-Linnaean class.  The real problem in SNOMED CT is that it would be a huge undertaking to identify and correctly place all of its legitimate descendants.  If the descendants are not correctly placed, microorganism will not serve autoclassification properly which seems to be the intent of its current placement.  On the other hand, microorganism can be retired with very little in the way of adverse effect on classification of other hierarchies where it serves as an attribute value.  It would be necessary to substitute 410607006 | Organism for 264395009 | Microorganism as the value for either the component relationships for procedures or the causative agent relationship for organisms.  Organism is the immediate supertype of Microorganism.  Direct substitution of 410607006 | Organism for 264395009 | Microorganism in these relationships will not alter the classification of dependent procedure or disorder concepts.  This has been confirmed using the SNOMED CT authoring tool.

First generation descendants of 264395009 | Microorganism

Figure 2 shows the first generation of descendants of 264395009 | Microorganism.  Prion and Virus (green border) are certainly microscopic.    Although it is often argued that they are not free living organisms, they are etiologic agents and referenced as such in the definitions of SCT disorders and procedures.  There would have to be a very strong case made to remove them from the organism hierarchy. The disposition of the concept class "microorganism" will determine their final location. The remaining concepts (red border) present different challenges in this work.  

Figure 2. First generation descendants of 264395009 | Microorganism (SNOMED CT January 2018 Edition)

Figure 2. First generation descendants of 264395009 | Microorganism (SNOMED CT January 2018 Edition)
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Concept classes in green will likely move to first generation under 410607006 | Organism. Concept classes in red are involved in logical errors, content inconsistencies or perhaps not appropriate for placement in the organism hierarchy.

115166000 | Kingdom Prokaryote

Prokaryotes occupy two of three top-level domains, namely Domain Bacteria and Domain Archaea.   Some authors remain committed to a Two Empire System, namely Empire Prokaryota and Empire Eukaryota.  Representations of this system still include Domain Archaea and Domain Bacteria.  In the Two-Empire system, Empire Eukaryota has one subtype, the duplicative concept Domain Eukaryota (duplicative in the sense that all and only members of Domain Eukaryota make up Empire Eukaryota).  The Three Domain System being advanced as the organizing principle for SNOMED CT organisms does not include "Kingdom Prokaryote."  See "First Generation descendants of 115166000 | Prokaryote" below for details of additional editing required to align current SNOMED CT subtypes with the preferred Three Domain System.

415671008 | Superkingdom Eukaryota

If we choose to represent the first generation of the organism hierarchy as three domains, "Domain Eukarya" ("Eukarya" is already a synonym in SCT) should be made the FSN and PT for this concept class.  It's current placement as a subtype of 264395009 | Microorganism is inappropriate in any event whether or not that concept is retained.  Descendant classes should be reviewed but most do not require review at this time.  Exceptions to this are the descendants of 414561005 | Kingdom Fungi and 417396000 | Kingdom Protozoa.  There have been significant changes in modern classification of both fungi and protozoa.  The scope of a review of either of these organism classes is large enough that separate projects should be pursued.

23496000 | Fungus

Based solely on the fully specified names, 23496000 | Fungus would appear to duplicate of 414561005 | Kingdom Fungi.  However there is limited overlap between these classes.  2349600 | Fungus is an attribute value for 11 SNOMED CT Concepts, 3 findings/disorders in the causative agent role and 8 procedures in the component role.

Four subtypes of Fungus refer to environmental or host predilections of Fungi.  Anthropophilic fungus (fungi infecting man), Anthropozoophilic fungus (fungi infecting man AND animals), Geophilic fungus (soil or saprophytic fungi), and Zoophilic fungus (fungi infecting animals).  NONE of these subtypes have descendants and none are used in definitions.  They can be safely retired.

Three subtypes of Fungus and their descendants have been reclassified as part of a previous project.  Fungal morphologic state, Fungal reproductive state, Fungal structural elements.  Review these after July release.

One subtype of Fungus, 289924001 | Fungal microorganism has presently has 651 descendents.  Nearly all already have correct (single or multigeneration) connections to Kingdom Fungi.  Their association with 23496000 would seem unnecessary.  There are 14 descendents of Fungus that are not connected to Kingdom Fungi.  Most of these were corrected in a previous project.  Review these after July 2018 version release.

First generation descendants of 415671008 | Superkingdom Eukaryota

First generation descendants of 415671008 | Superkingdom Eukaryota are not misclassified per se.  Logical issues arise because 415671008 | Superkingdom Eukaryota is a subtype of Microorganism and not all descendants of these subtypes are microscopic.   Figure 3 shows the existing first generation of descendants of 415671008 | Superkingdom Eukaryota (January 2018 edition).  Three first generation descendants require correction while three are correctly placed and named.

Figure 3. First generation descendants of 415671008 | Superkingdom (Domain) Eukaryota. (SNOMED CT January 2017 Edition)

Figure 3. First generation descendants of 415671008 | Superkingdom (Domain) Eukaryota. (SNOMED CT January 2017 Edition)
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Concept classes in red are involved have naming errors, are duplicates or are involved in logic errors. Concepts in green can remain subtypes of Domain Eukaryota or can be promoted to first generation descendants of organism.

415986004 | Class Lobosea

The systematics of Amoebozoa is presently being examined and revised.  Various experts place them as subclasses of Protozoa, Protista and Ukonta (clade).   In SNOMED CT,  415986004 | Class Lobosea is a subtype of Eukaryota.  Modern classifications identify these organisms as Subphylum Lobosa.  Lobosa is part of a larger problem in that the classification of the “amoeba” (e.g. Entamoeba histolytica) is in flux. Various classifications currently place them as either Protista or Protozoa.  Some experts place Amoebozoa in an unranked class “between” Protista and Protozoa referred to as Unikonts.  

Whatever the eventual disposition of Amoebozoa in SNOMED CT, 415986004 | Class Lobosea duplicates 417341006 | Class Lobosa currently placed in the Protozoa subhierarchy.  As such, 415986004 | Class Lobosea should be retired as redundant and referred to 417341006 | Class Lobosa.

418709001 | Kingdom Metazoa

The term Metazoa was originally created by Ernst Haeckel in 1874 to distinguish multicellular animals from Protozoa (no longer considered to be animals).  When Protozoa were re-classified as a kingdom (same rank as animals), "Metazoan" effectively became a synonym of "Animal"  (387961004 | Kingdom Animalia = 418709001 | Kingdom Metazoa).  Kingdom Metazoa has no descendants in SCT (they’re all already Kingdom Animalia).  Simple retirement of Metazoa concept with referral to Animalia should be sufficient.

370570004 | Kingdom Protoctista

Modern classifications have changed Protoctista to Protista.  A member of Kingdom Protista is any eukaryotic organism (cells have nuclei) that is not an animal, plant or fungus.  As there is no common ancestor they do not form clade and technically remain "unclassified."  There are only 7 descendants of 370570004 | Kingdom Protoctista in SNOMED CT.  Given the "definition by exclusion" for this kingdom, it is not clear that these descendants are, in fact, classified as protists (most references refer to these 7 as "unclassified."  This subhierarchy should be reviewed in future especially if content requests are forthcoming.

First generation descendants of 115166000 | Kingdom Prokaryote

Figure 4 shows the first generation of descendants of 115166000 | Kingdom Prokaryote.  This figure really represents a kingdom that is no longer considered to be valid.  When Prokaryota are included in modern formal taxonomy, they are considered to be an empire that includes two domains (Bacteria and Archaea).  Given that Archaea are thought of as having characteristics of both prokaryotes and eukaryotes, this two domain system is not favored by most systematics experts.  The upper levels of the bacteria and archaea hierarchies need to be reviewed separately from this project.

Figure 4. First generation descendants of 115166000 | Kingdom Prokaryote (SNOMED CT January 2017 Edition)

Figure 4. First generation descendants of 115166000 | Kingdom Prokaryote (SNOMED CT January 2017 Edition)
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Concept classes in red are involved in logical errors, content inconsistencies or perhaps not appropriate for placement in the organism hierarchy.

Archaea

The archaea represent an area of rapid growth and change in the organisms hierarchy.  Many new organisms (and subsequently new phyla) have been discovered recently.  The scientific attention given to these organisms has generated changes in the taxonomy. Kingdom Euryarchaeota appears to be relatively stable.  Other kingdoms vary with reference source.  Some authors include unranked groups (of phyla) while others assign two additional kingdoms or phyla depending on the author: Crenarchaeota (present in SCT) and Kroarchaeota (not present in SCT).

Other specific errors in SNOMED include:

•  

  1. 115205005 | Division Mendosicutes is a sibling of 419036000 | Superkingdom Archaea.  Division Mendosicutes is an organizing "chapter" in Bergey's manual.  Mendosicutes is not used generally and Division is not a taxonomic rank.  The class Archaeobacteria (the only subtype of Division Mendosicutes) is deprecated and considered to BE the Archaea.  In SNOMED CT the incorrect subtype assignment of the genus Methanobrevibacter (a genus of Archaea) to phenotype classifications 49682003 | Gram positive coccobacillus and 59343002 | Anaerobic bacteria result in its classification as both bacteria and archaea.

  2. 419036000 | Superkingdom Archaea has a synonym “Domain Archaea."  Domain Archaea is correct and should be preferred.

  3. Current Phyla in SCT are probably not correct and are incomplete.  Euryarchaeota seems to be universally recognized as a kingdom (not a phylum).  However the rank of Crenarchaeota is debated and it may or may not be a phylum.  All existing Archaea in SNOMED can be (are) grouped under one of these two phyla.

The current classification chaos among the Archaea is one major justification for including three domains at the top of the organism hierarchy.  Other groupings and many other taxons exist.  At this time this primitive hierarchy can be isolated (so that bacteria and archaea do not intersect) and edited separately.  NONE of the Archaea (that I am aware of at this point) are not thought to be pathogenic to man or animals and are not involved in any definitions in SNOMED CT at this time. 

Subsidiary and interrelated problems

Organisms serve as values for definitions in the findings and procedures hierarchies.  Changes in the upper organism hierarchy may produce undesirable changes in classification of findings and procedures.  In some cases, errors in the organism hierarchy appear to have been induced in order to affect classification in the other hierarchies. 

Common name organism classes:

Risks / Benefits

Risks of not addressing the problem

1. Authors and editors will continue to have difficulty properly placing new content when it is requested.

2. Data retrieval and analysis based on organism hierarchy may be compromised.

3. Casual browsing by knowledgeable individuals may lead to questions about integrity and accuracy of organism hierarchy.

Risks of addressing the problem

Organism hierarchy changes may provoke need to change definitions in procedures or findings concepts.

Requirements: criteria for success and completion

Criteria for success/completion