FHIR Mapping

loinc2hpo can be used to convert LOINC-encoded laboratory results from FHIR.

Mapping LOINC to candidate HPO terms

LOINC observations have four main categories, quantitative(Qn), ordinal(Ord), nominal (Nom) and narrative(Nar). The majority of them are Qn (~50%) and Ord (~26%) and a smaller percentage are Nom and Nar type (<10%). Currently, loinc2hpo maps QN, Ord, and Nom codes but is not able to map Nar codes.

FHIR Interpretation codes

Test outcomes can represented with a code from the FHIR interpretation code valueset. HPO terms are qualitative. For instance, Thrombocytopenia HP:0001873 does not indicate whether there is a mild, moderate or severe degree of low blood platelets. Therefore we map FHIR codes for different degrees of severity to the same internal code (these codes are shown on the index page of this documentation).

Table 1: FHIR interpretation code set Mapping to internal code system

FHIR interpretation code value set		internal code
Code	Meaning	Code | Meaning
<	Off scale low	L	low
>	Off scale high	H	high
A	Abnormal	A	abnormal
AA	Critically abnormal	A	abnormal
AC	Anti-complementary substances present	POS	present
B	Better	N	normal
D	Significant change down	L	low
DET	Detected	POS	present
H	High	H	high
HH	Critically high	H	high
HM	Hold for Medical Review	U	unknown
HU	Very high	H	high
I	Intermediate	N	normal
IE	Insufficient evidence	U	unknown
IND	Indeterminate	U	unknown
L	Low	L	low
LL	Critically low	L	low
LU	Very low	L	low
MS	Moderately susceptible. (microbiology)	U	unknown
N	Normal	N	normal
ND	Not Detected	NEG	not present
NEG	Negative	NEG	not present
NR	Non-reactive	NEG	not present
NS	Non-susceptible	U	unknown
null	No range defined or normal ranges don’t apply	U	unknown
OBX	Interpretation qualifiers in separate OBX segments	U	unknown
POS	Positive	POS	positive
QCF	Quality Control Failure	U	unknown
R	Resistant	U	unknown
RR	Reactive	POS	present
S	Susceptible	U	unknown
SDD	Susceptible-dose dependent	U	unknown
SYN-R	Synergy - resistant	U	unknown
SYN-S	Synergy - susceptible	U	unknown
TOX	Cytotoxic substance present	POS	present
U	Significant change up	H	high
VS	Very susceptible. (microbiology)	U	unknown
W	Worse	A	abnormal
WR	Weakly reactive	POS	present

The following graph summarizes the mapping.

Nominal outcomes

Nominal observations can use coding systems that are more difficult to handle. For example, Loinc 600-7 (Bacteria identified in Blood by Culture) may use a SNOMED concept to represent the finding that Staphylococcus aureus is detected:

"coding":[{
  "system": "http://snomed.info/sct",
  "code": "3092008",
  "display": "Staphylococcus aureus"
}]

We currently map this to Bacteremia HP:0031864, but this term does not contain information about which bacterium was idenfitied in the blood.

We are currently extending the annotations to enable one to indicate what kind of bacteremia. In the above mentioned case, one would use the NCBI Taxonomy ID: 1280 for Staphylococcus aureus.