Forum Replies Created
If you need just a specimen type LOINC, there are several options:
66746-9 – Specimen type
31208-2 – Specimen source
The latter is widely used, in our experience.
Hope this helps!
Thank you for your persistence in getting examples into the LOINC User’s Forum. Your statement notes that “because other types of findings might be part of the Report Document….specifically is the PAP finding”, we would probably not use a Doc scale for the LOINC. The statement infers to me that there may be other portions of the report describing items like clinical history statement of adequacy, follow up recommendation. There are LOINCs for all of these.
For a.1 of your model, I would propose 19762-4 General categories [Interpretation] of Cervical or vaginal smear or scraping by Cyto stain. The answers of Normal, Low-Grade Squamous Intraepithelial Lesion, High-Grade Squamous Intraepithelial Lesion are all interpretations made by the cytology staff. Indeed, those answer values you found in SNOMED CT would be associated with the information system field mapped to 19762-4, identifying what is being reported. In the LOINC User’s Guide, there is a suggestion that LOINC maps to the field holding what is being reported and SNOMED CT identifiers map to the example answers in laboratory, cytology, and pathology reports.
I hope this conversation is of help to you. Have a great day!
There is a special property within the LOINC database for your examination: MSCNC – Mass Substance Concentration. It allows for the combination of lab values of mass/volume or substance/volume units of measure. 35194-0 is for serum or plasma Bilirubin quantitative and 35193-2 is for body fluid Bilirubin.
If you simply enter MSCNC in RELMA search window, you’ll see the covered analytes in different body fluids. If a particular analyte is’t covered, you can submit to Regenstrief for a new term.
Hope this helps. Let me know what else can be answered.
I see Mira responded to one question in your email. For the shortname display issue, keep in mind there was a time period where not all shortnames had been created. After the creation formula was decided, it took several versions to implement. So as you reverse engineer backwards, you’ll see the terms that didn’t have displays at one point in time.
I hope this helps.
If you’ll type in the display name of each field, we’ll go from there.
Please take a look at the outbound messaging format of your cytology reporting; this helps determine if the single document LOINC should be used, or if individual observations reside in separate OBX segments (pointing to individual LOINC observations).
There are individual LOINCs under Microscopic Observation with methods of cyto stain, cyto stain.thin prep, or cytology.non-gyn . Other observations such as Clinical History, General Categories and Statements of Adequacy have LOINCs as well. There is also a Pathology Biopsy Report for cervix specimen.
Please give a detail example of what you are looking for, and I’ll be glad to help. All the best, Pam
Does your assay happen to test for the galactomannan antigen, that is common across several fungi genus. Here’s the RELMA definition : Galactomannan is a polysaccharide cell wall component in certain species of fungi. The assay is used for the early diagnosis of invasive aspergillosis in immunocompromised patients undergoing hematopoietic stem cell transplantation and in patients with hematological malignancy. Other fungal sources galactomannan include Alternaria, Penicillium and Paecilomyces species, but these fungi are rarely seen in invasive disease.
This is the analyte I use in client mappings; there are several serum specimens available.
I was deferring to the HL7 CDA RMIM to define if there should be alphabetic strings or numeric code, pertaining to LOINC class. This was based on a premise that the reporting is taking place on assays with LOINC terms attached. It’s a “drill down” from the involved LOINC terms for each patient to have a table pull of the associated CLASS field in the LOINC database.
As for the second question, each LOINC term only has one class assigned it in the database. In our experience the LOINC-assigned class serves as a baseline of organization, but it does not mimic the real world laboratory workstations/departments (which I am aligning with the “lab specialty” term being used). For example, the PULM class blood gas measurements are often performed in a medical laboratory setting, rather than the pulmonary department. However, a medical laboratory will provide a variety of assays (described in their electronic Directory of Services [eDOS]) and these cross many LOINC classes.
Perhaps I am not understanding the context of the word ‘CLASS’ in the original question.
Not being familiar with Italian laws, but realizing HL7 CDA has the RMIM to identify source material; wouldn’t the HL7 CDA RMIM prescribe the format definition for the related lab specialty class? It seems the alpha character format of the CLASS field within the LOINC database (DRUGDOSE, DRUG/TOX, MOLPATH.MUT, etc) that is easily retrievable by the computer.
Thanks for helping educate me,
Your question brought three scenarios to mind. Two of the scenarios have to do with answers encoded to SNOMED CT. Any of the microbiology LOINC terms with PRID property, such as 81655-3 Respiratory pathogens DNA and RNA identified in Respiratory specimen by NAA with probe detection, have an example answer lists containing types of organisms found, and each of them would have a SNOMED CT term. Example answers for 81655-3 are No organism(s) detected, Influenza A (H3N2), Adenovirus, Parechovirus, and much more. If more than one organism’s DNA is found, there are more than one SNOMED CT term in the answer.
The second scenario is of post coordination of phrased answers. LOINC term 36903-3 is testing for Chlamydia trachomatis & Neisseria gonorrhoeae DNA; example answers here are phrases: Chlamydia trachomatis detected; Chlamydia trachomatis not detected. Multiple SNOMED CT terms would need to be used for the organism and the qualifier.
The third scenario pertains to the composition of the LOINC Parts to a single LOINC term. Translating each LOINC Part to its SNOMED CT counterpart brings up a post coordinated expression, of which there’s been two subset file releases for public review in recent years. More explanation of post coordinated expressions can be found at https://confluence.ihtsdotools.org/display/DOCSTART/7.+SNOMED+CT+Expressions
With an abundance of possibilities, I’m not sure there’s an easy answer to your second question “what does that mean about the result.” Clinically, I wouldn’t be able to speculate. Theoretically in format, I would say it means the result has complexity.
Have a great day, Hope this helps
While not being certain what you’re asking your database/use case to achieve, I would recommend you let the loinc.csv class (ALLERGY, CHEM, etc) and classtype field starnd for themselves (1,2,3,4). Are you able to link the loinc table to your database fields and cross-check that way?
Let me know what outcome you’re trying to derive, and I’ll try to help further.
All the best,
Hope all is well with you and yours. From the LOINC terms referenced, you have a molecular genetic assay for F10 gene targeted mutation analysis. I checked https://loinc.org/submissions/queue/ and didn’t find F10 or Factor X in the search. A literature reference search found https://www.ncbi.nlm.nih.gov/gene/2159 ; and http://www.omim.org/entry/613872 .
It seems totally suited for your next submission!
All the best,
Pam Banning2018-06-22 at 13:01 in reply to: use of 'sequencing' method for molecular genetic test #22478
It’s been my experience if you propose the specific genes where sequencing is being offered, Regenstrief does consider them. In June 2018 LOINC User’s Manual, section 18.104.22.168 calls out that sequencing as a particular method that will be called out. I know there are people within LabCorp, Quest Diagnostics, Mayo Medical Labs, and ARUP responsible for submissions from their test compendiums. We just never know where in their queues the sequencing assays reside. If you need any assistance in getting started on a submission, I’m happy to help direct.
Your test message came through; all is well At first glance, there is one panel established, 53775-3, with three required elements (53776-1 is an interpretation element of IgM and total). Might it be suitable for your use?
I’m unaware of any table Regenstrief provides in this manner. The UCUM documents are descriptions and instructions on translation local unit displays to the standard UCUM format. There are example UCUM tied with terms in RELMA (and therefore extrapolation is possible). In early, early LOINC days, 3M had internally used synonyms of properties to our units of measure domain. Everyone’s foundation has matured with time, and toolsets along with them.
Sorry to not help you more specifically.