1/28/2018 IHTSDO-455 (artf7628) Organism Life 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 Testing Construction Advisory Group Sign off required Note draft guidance (to be clarified): Approval should be sort at the end of the Elaboration/Testing phase where required Group Approval Required?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: <artf7628> Topic: <Taxon specific life cycle forms> Date <April 14, 2015> 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 Domain 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 Common name 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 biology, a taxon (plural taxa; back­formation from taxonomy) 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 plant, an animal, a bacterium, a protist, or a fungus; 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 vertebrate 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., 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.