Organism & Infectious Disease Model Project

Page tree

Resources for maintaining the Organism(s) hierarchy are limited.  It seems unlikely that the primary project we've been considering (a logical model for Microorganisms) will or even can be completed in the near term.  We have requested that the elaboration document describing this work be withdrawn.

In place of the original model project, it seems reasonable to consider changes that can be made to the existing primitive hierarchy in order to simplify current editing tasks, clarify and state principles for its organization, and eliminate existing errors.  Previously we described a subproject consider such a task (see "Editorial Guidance Subproject" document).  

In addition to the previously identified problems with microorganisms, fungi and bacteria; viruses, prions and archaea can and should be reviewed.  As an alternative to a full-scale redesign of the Organism Hierarchy and development of a functional model for organisms, Jeff Wilcke proposes to move this project to what may be a more productive and useful path.  These deliverables (subpages) describe analytical and editing challenges of the existing (all-primitive) organism hierarchy that we believe can be completed within the next two years:

Eventually, these deliverables will be associated with one or more IHTSDO project documents (Inception, elaboration, construction etc.).  The precise scope of the work (within the organism hierarchy) is difficult to describe.  It does not address a particular number of levels, specific taxonomic ranks nor is it restricted to a particular subhierarchy.

Microorganism Model Project (Withdrawn)

 

Editorial Guidance Subproject (History)

  • No labels

12 Comments

  1. Xavier GANSEL

    Hi Jeff,

    things sounds to be moving on the organism part (wink)

    what is the direction you are taking, with with schedule ?

    thks,

    Xavier

     

    1. Jeff Wilcke

      Xavier,

      I'm definitely moving towards a resurrection of this effort.  I'd like to revive a meeting schedule.   Right now I'm thinking 6 meetings a year.  I expect it will be same part of the month, day of week and hour of day.  As I have more editing to do to complete these "deliverables" I'm going to say 4th week of April.  Nothing is official.    I take it you are watching this space (thank you!).   I'm not sure anyone else is.  Have any suggestions as to how we attract a bit of attention?  I'd like this to be in front of the people (like you) who can help us most.

      -J

  2. Xavier GANSEL

    Jeff,

    I watch this space... not only because I am interested in it (I am truely) but also because I need a clean organism hierarchy to code our in vitro diagnostics test results to support results analytics.

    End of April may coincide with the IHTSDO business meeting in London. Is this an option for you ?

    Attract attention : let say we need 1 or more appealing use cases. We may propose 

    • coding pathology lab results
    • supporting data analytics

    And derive requirements for the hierarchy from these starting points and start a redesign effort.

    Isn't that what you are currently doing with those deliverables ?

    Xavier

  3. Deborah Drake

    Hi, We would also be interested from a similar point of view as Xavier and ideally have an Organism subset too post relevant updates.

    Kind regards

    Deborah (UK Terminology Centre)

     

  4. Jeff Wilcke

    A "cleaner" organism hierarchy is both a short-term and a long-term goal, no doubt.  By "attract attention" I actually meant "best means to notify everyone."  I'm hoping that you (both) have suggestions for contacting the specific user community we support.

    Concerns:

    • There is no question that this project should support "coding pathology lab results." That said, I would prefer we not mention the "c" word (let's let the computers do the coding).    (smile)  You'll note that "Laboratory Reporting" is the number one priority on our main project page.
    • As for supporting data analytics, I am always more than a little concerned that we do not have the authoring / editorial resources to ensure an accurate hierarchy at all levels.  This challenge is made even more difficult in that there is not a consistently reliable resource for correct classification and naming.    We do our best and I have no doubt that we can improve the upper levels.
    • I worry about the phrase "redesign effort."  It is what we SHOULD do, but once again authoring/editorial resources are sparse.  I don't want to promise and develop an approach that we cannot deliver.

    IHTSDO business meeting is really not an option for ME unless I discover some source of money for travel.  That said, it may be a perfect opportunity for a teleconference that would "attract some new participants."  When the opportunity presents, I will be sure to ask for a teleconference line at that meeting.

    Thanks for your input.  I'll continue to work on these new "deliverables" pages so can be ready for April.

    -Jeff

  5. Deborah Drake

    Hi Jeff,

    You could consider making the IPaLM SIG aware and having a call outside those meetings.

    It may be possible for me to find some interested clinical leads in this area if that is helpful (say after an official 'request') via the April meeting.

    Debbie.

    Advanced Terminology Specialist (Pathology) UKTC

  6. Matt Cordell

    Deborah, could I ask what you mean by "have an Organism subset"? I've encountered requests for such in Australia and our college (RCPA) has produced a subset of ~3000 organisms. Essentially just derived from the organisms participating labs had historically recorded. I did hear a comment from a microbiologist (not involved in the RCPA project) that it contained a lot of Salmonellas... And it does, over 500... (There's a few others like this, but salmonella is the largest).

    We also publish a microorganism refset in our national extension - which is just all subtypes of 264395009 | Microorganism | (not particularly exciting).

    I guess what I'm interested in is the requirement/use-case for something more specific than just a list of all the Microorganism in SNOMED CT?
    (i.e.The RCPA list is still far to big for a drop-down - so I'm not what benefit it even has over just the basic list of subtypes)

     

  7. Deborah Drake

    Matt Cordell, we have some previous work too in this area and subsets.

    I am currently trying to help sort out requirements for the UK in this area hence will take some of these queries to our specialist groups.

    I am very much interested from the same point of view as you too; also as Jeff points out resources are an issue therefore hopefully working together can help with that.

    Debbie.

     

  8. Jeff Wilcke

    I can't speak to the need for any particular organism subset.  One essential thing I want from the organism hierarchy is reliable retrieval of sub-hierarchies.  A recursive query based on "Bacteria" (Kingdom Bacteria if that's the correct concept class) should retrieve all bacteria and only bacteria.  At this time, this is not consistently so across the primary disease-causing organisms (bacteria, fungi, viruses, prions).  In fact, it can be difficult to identify which high level concept classes one should choose.

    I think we can agree that this relatively simple use case (at least) should inform authoring and editing of the organism content.   At this time, it is my primary motivation for this set of deliverables.

    1. Deborah Drake

      Jeff Wilcke that sounds like a good foundation to work from to me as well.

      Debbie.

       

      1. Xavier GANSEL

        Jeff Wilcke Deborah Drake sounds good to me too and a good foundation to the use case I envisaged 

        • assigning SNOMED concepts to IVD pathology lab results (i.e. coding pathology lab results)
        • supporting data analytic

        Xavier

  9. Xavier GANSEL

    Hi Jeff,

    A naive question : would it make sense to have 

    1. a clean nomenclature for each domain of the tree of life you try to clean up (bacteria, archea, eukaryotes, virus, ...)
    2. a set of taxonomic organisations for each of those domains according to different taxonomic principles (phenotypic, genotypic, other), thus allowing different reasoning / analytic on those taxons' names ?

    best,

    Xavier