- Created by Jeff Wilcke, last modified on 2019-May-21
Date
November 27, 2018 at 20:00 UTC
GoToMeeting Details
Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/5892670788
Attendees
Apologies
- Farzaneh Ashrafi
Objectives
- Review "fast track" document for deliverable 1: "Clarify, simplify, and correct the top levels of the SCT Organism hierarchy" (IHTSDO - 1003)
- Introduce topics and preliminary analyses for deliverable 2: "Clarify, simplify, and correct the top levels of the SCT Bacteria hierarchy" (IHTSDO - 1095)
Discussion items
| Item | Description | Owner | Notes | Action |
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| 1 | Review IHTSDO - 1003 Fast track. This is the construction document that is being reviewed. Approval is expected soon. Construction should be completed in time for inclusion in July 2019 release of SCT | Jeff Wilcke |
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| 2 | Review initial analyses of IHTSDO - 1095. IHTSDO-1095 is the next project on the list of "Deliverables" for this Project group. The file associated with this item lists the 56 concept classes that will be the first generation descendants of Domain Bacteria after removal of a redundant concept class. | Jeff Wilcke |
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| 3 | Review analysis of antimicrobial resistance content. This is another step in IHTSDO-1095. We need to develop use-cases for content classes related to resistant and determine whether concept classes that are likely useful in an epidemiological context can be related to laboratory reports. Additional problems include difficulties defining classes at the highest levels, logical errors related to both organism and pharmaceutical subtypes and terming inconsistencies. | Jeff Wilcke |
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Meeting Files
| File | Modified | |
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| Microsoft Word Document Resistance issues 20181121.docx | 2018-Nov-23 by Jeff Wilcke | |
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| Microsoft Word Document New First Generation of Bacteria.docx | 2018-Nov-26 by Jeff Wilcke | |
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| Microsoft Word Document IHTSDO_1003_fasttrack.docx | 2018-Nov-27 by Jeff Wilcke | |
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| Microsoft Word Document Top of Organism post IHTSDO 1003.docx | 2018-Nov-27 by Jeff Wilcke | |
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Previous Meetings
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6 Comments
Xavier GANSEL
Jeff,
I made a mistake in the time zone and connected 1h after the meeting
sorry for that.
I was really looking forward the discussion. may we have a rapid debrief call tomorrow ?
Xavier
Matt Cordell
Apologies, I didn't even have this meeting in my calendar so missed it. Some comments.
Item 1: I'm mixed feelings about retiring "Microorganism". It seems like a reasonable concept, though I'm not sure how useful. Some of the existing subtypes are just wrong ie. eukaryotes and fungi. (Fungi has it's own problems too (23496000|Fungus (organism)| vs 414561005|Kingdom Fungi (organism)| and subtypes of both...). Also, I only count 8 uses of |Microorganism| as of July, not a lot of impact. We do have some reference sets defined with |Microorganism|,but we can redefine (and would probably end up with a better set than we currently have).
I'll comment on the others in the respective discussion threads.
Jeff Wilcke
Microorganism IS a reasonable concept. The primary problem(s) relate to maintenance. There are certainly organism classes that are obviously and entirely microorganisms (Viruses, Bacteria for instance). Then it gets a little ugly depending on what you think SHOULD be a subtype. Not all fungi are microscopic. In fact among the dimorphic fungi that are pathogenic, the vegetative forms (that you isolate in a mycology lab) are macroscopic while the infective forms (that you'd see on histopathology) are microscopic. Same with many parasites - diagnostic forms are microscopic, adults are macroscopic. Telling the truth is VERY difficult.
So SOME of the microorganism subtypes are easy and some nearly impossible. I'm emailing you an analysis file confirming that a very small subset of organism classes can replace the single "descendants of microorganism." I can't easily fix the problems described in the previous paragraph without more human resources...
Alastair Kenworthy
Following this with interest because our lab community in NZ has just accepted using the whole microorganism hierarchy as the standard pick list everyone implements. If things are going to change, it would be very useful to have the small subset of organism classes you mention in a well-defined form to populate our microorganism refset
Jeff Wilcke
Send me an email (jwilcke@vt.edu) and I'll send you the file I shared with Matt. I would prefer you have the context of my brief report on the subject. My subset list does not correct the problems we've been discussing, it simply replaces "microorganism" with a few of its high level descendants. It's not simply a list of first generation microorganism descendants as a several other concepts e.g. Domain Eukarya (aka Superkingdom Eukaryota) must find their way to other parts of the hierarchy.
As I re-read these notes I realized that not all things microscopic (e.g. diagnostic forms of nematodes) are either listed as or generally thought of as "microscopic." That is, of course, one of the issues with common names in the organism hierarchy. Often we use them BECAUSE the are subtly ambiguous. I have no formal definition for microorganism, only intuition.
Xavier GANSEL
Jeff, could you please put me in the loop ?
this somehow comes back to discussion I had earlier this year with Mat & Alastair after the April Business meeting as well as to the fact that bioMérieux sent out its test-ID-results mapping to SCT-ID to a bMx customer in Australia (under the IHTSDO licence, of course !)
Apparently we all share the same concern and interests.