HL7 terms to SNOMED for specimen related terms.

Attached find the excel spreadsheets displaying the ready terms (simple 1:1 mappings or mappings already approved by the PHLIP working group)

and the terms for review mappings of 1:many, but straight forward.

We are working through the terms for discussion to create a few topic groups for specific SMEs to weigh in on that - stay tuned!

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NEXT LabCoP Call

September 8, 2011 from 10am to 12pm – Phone: 877.923.1669, pc: 4413979 URL: https://www.livemeeting.com/c... We will continue to discuss specimen terms related to human samples


I have attached the notes from last call, the updated spreadsheet form last call and the reference document Nancy Cornish sent to help with pre-coordinated specimen terms for bloody, liquid and soft stool.


Notes from our last human term related Lab CoP call on 9/8/2011 and the updated spreadsheet are here!


Next call is 9/22/2011 from 10AM to 12PM EDT:

Call: 877.923.1669, pc: 4413979

URL:  https://www.livemeeting.com/cc/cdc/join?id=54D3H8&role=attend

I got an email comment from Dr. James Case:
Bite wound and Scratch wound are events, not a specimen. to be more specific you would need to add some qualifier such as tissue, exudate, swab, etc.
I updated the notes accordingly - see attached file.

Notes from the call on 10/6/2011 and the updated specimen list for discussion is uploaded here.

Link to the catheter infection guidelines:


Also uploaded the IDSACatheterUrineGuidelines.pdf


Collection of Transport media for stool samples:

Cary-Blair- Meridian ParaPak C&S, 

Cary-Blair-BBL & other manufacturers (can find several through Google Search)

Buffered Glycerol Saline(BGS) This is usually prepared locally (PD}

Alkaline Peptone Water This is usually prepared locally {PD}

Amies Formulated with and without charcoal-used for transport of aerobic and anaerobic samples for bacterial isolation…usually with swab samples {PD}

Stuarts Similar to Amies {PD} and usually used for transporting swab samples

internet definitions in addition:

Transport media

Transport media should fulfill the following criteria:

  • temporary storage of specimens being transported to the laboratory for cultivation.
  • maintain the viability of all organisms in the specimen without altering their concentration.
  • contain only buffers and salt.
  • lack of carbon, nitrogen, and organic growth factors so as to prevent microbial multiplication.
  • transport media used in the isolation of anaerobes must be free of molecular oxygen.

Examples of transport media include:

  • Thioglycolate broth for strict anaerobes.
  • Stuart transport medium - a non-nutrient soft agar gel containing a reducing agent to prevent oxidation, and charcoal to neutralize
  • Certain bacterial inhibitors- for gonococci, and buffered glycerol saline for enteric bacilli.

·         Venkat-Ramakrishnan (VR) medium for v. cholerae.

and for parasites:

fixative containing zinc sulfate in polyvinyl Alcohol (i.e., Z-PVA) and a 10% formalin-physiological saline solution. Previously, 10% formalin or Shaudinn’s fixative (Mercuric chloride/alcohol/saline) or Mecuric Chloride in PVA or 10% formalin-saline were the available preservatives. Mercuric chloride-containing solutions were the superior fixatives, tending to provide the greatest clarity, of all preservatives, including the Zinc sulfate-PVA alternative introduced in the late 1980s.  The latter was introduced as a replacement for the fixatives containing mercury salts, as those were problems, as they had to be discarded as hazardous wastes. So, the available ones remaining are the zinc-PVA and 10% formalin. The PVA preparations are almost exclusively obtained commercially, and 10% formalin-saline preservatives also can be obtained commercially, but many labs prepare the 10% formalin-saline solutions on site (cheaper, fresher).



Notes from yesterday's Lab CoP call are here as well as the prioritized specimen crossmap for human terms.

Action items:

Nancy and Riki to follow up on how to create a permanent review board for maintenance of the specimen crossmappign table

Nancy and Riki to follow up on how to engage LIMS and EHRsystem vendors

Nancy to post reviewed urine terms to the listserve

Riki to continue to populate the crossmapping table with defintions and labels (prototype, preferred specimen, example, etc)

Next call is scheduled for 11/17/2011 10:00 AM - 12:00 PM ET

Call: 877.923.1669, pc: 4413979

URL:  https://www.livemeeting.com/cc/cdc/join?id=54D3H8&role=attend

Link to the CAP cancer protocols and checklists. 

These have been built to standardize surgical specimen reporting to include names for specimens as well as procedures for obtaining the specimens. This has been done in conjunction with the National Cancer Society and American College of Surgeons. It has been adopted by the Canadians and some international groups and it is consistent with SNOMED codes.


This is a collection of information taken from Texas DSHS LIMS system for rabies testing.

In our lab animal samples sent in for human rabies exposures if positive, are typed by either monoclonal antibody staining, restriction digest, or nucleotide sequencing to determine the strain of rabies virus present in the animal.



Thanks Katherine for posting - PHLIP has not yet tackled rabies, but it certainly is important next disease.

Do you have a suggestion on how to link the animal related results to the human case they relate to - did you solve that in your ELR message?


Hi Riki,

From what I am told Texas DSHS lab sends all primary animal names along with rabies typing results results (positive, negative, decomposed, inconclusive) electronically via NEDSS.  I have not been able to get an answer about what coding is used; except I was told it was "cobbled" together?

Results for human exposure to positive animals are not done electronically.  And no, I do not have any suggestions- sorry.


Notes form our call today are attached, as is the latest version of the crossmapping table for human terms (prioritized for micro/molecular/chemistry/hematology/anatomic pathology).

Next call is scheduled for 12/15/2011 10AM - 12PM ET

Call: 877.923.1669, pc: 4413979

URL:  https://www.livemeeting.com/cc/cdc/join?id=54D3H8&role=attend

Planned Topics:

  1. Model isolates – Riki to post suggested approach to phConnect by 11/30/2011
  2. Exposure (related to bites / scratches)
  3. Review Micro related specimen terms – Riki to post to phConnect prior to call (goal is 12/8/2011)
  4. Transport media / additives / preservatives terms – Riki to post file to phConnect (goal is 12/8/2011)
  5. Update on modeling for Central line specimen (triple lumen, specimen type and collection site laterality) and artificial body structure

Please find 2 documents for review prior to the 12/15 LabCoP call:

Specimen Crossmapping Table introduction and best practice

Excel spreadsheet on how to model isolates

Please feel free to comment here or send message to the listserve:

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Latest version of specimen crossmapping table - sorted by priority for micro tests - then organized by preference (?? = riki had no clue what to assign and we'll start with those). you may notice I am missing a few more of the definitions - will keep plugging along, but had to get it out for you to review prior to Thursday.



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