Open turbomam opened 5 years ago
LoincNumber | LongCommonName | PartNumber | PartName | PartCodeSystem | PartTypeName | LinkTypeName | Property |
---|---|---|---|---|---|---|---|
8302-2 | Body height | LP64598-3 | Body height | http://loinc.org | COMPONENT | Primary | http://loinc.org/property/COMPONENT |
8302-2 | Body height | LP6822-3 | Len | http://loinc.org | PROPERTY | Primary | http://loinc.org/property/PROPERTY |
8302-2 | Body height | LP6960-1 | Pt | http://loinc.org | TIME | Primary | http://loinc.org/property/TIME_ASPCT |
8302-2 | Body height | LP310005-6 | ^Patient | http://loinc.org | SYSTEM | Primary | http://loinc.org/property/SYSTEM |
8302-2 | Body height | LP7753-9 | Qn | http://loinc.org | SCALE | Primary | http://loinc.org/property/SCALE_TYP |
8302-2 | Body height | LP64598-3 | Body height | http://loinc.org | COMPONENT | DetailedModel | http://loinc.org/property/analyte |
8302-2 | Body height | LP6822-3 | Len | http://loinc.org | PROPERTY | DetailedModel | http://loinc.org/property/PROPERTY |
8302-2 | Body height | LP6960-1 | Pt | http://loinc.org | TIME | DetailedModel | http://loinc.org/property/time-core |
8302-2 | Body height | LP7753-9 | Qn | http://loinc.org | SCALE | DetailedModel | http://loinc.org/property/SCALE_TYP |
8302-2 | Body height | LP6985-8 | Patient | http://loinc.org | SUPER SYSTEM | DetailedModel | http://loinc.org/property/super-system |
8302-2 | Body height | LP64598-3 | Body height | http://loinc.org | COMPONENT | SyntaxEnhancement | http://loinc.org/property/analyte-core |
8302-2 | Body height | LP72681-7 | Height | http://loinc.org | COMPONENT | Search | http://loinc.org/property/search |
8302-2 | Body height | LP281538-1 | - | http://loinc.org | SYSTEM | Search | http://loinc.org/property/search |
8302-2 | Body height | LP7768-7 | BDYHGT.ATOM | http://loinc.org | CLASS | Metadata | http://loinc.org/property/CLASS |
<http://purl.bioontology.org/ontology/LNC/8302-2> a <http://www.w3.org/2002/07/owl#Class>;
<http://bioportal.bioontology.org/ontologies/umls/cui> "C0487985";
<http://bioportal.bioontology.org/ontologies/umls/hasSTY> <http://purl.bioontology.org/ontology/STY/T201>;
<http://bioportal.bioontology.org/ontologies/umls/tui> "T201";
<http://purl.bioontology.org/ontology/LNC/ASSOC_OBSERVATIONS> "89263-8";
<http://purl.bioontology.org/ontology/LNC/COMMON_ORDER_RANK> "0";
<http://purl.bioontology.org/ontology/LNC/COMMON_SI_TEST_RANK> "0";
<http://purl.bioontology.org/ontology/LNC/COMMON_TEST_RANK> "0";
<http://purl.bioontology.org/ontology/LNC/CONSUMER_NAME> "Body height";
<http://purl.bioontology.org/ontology/LNC/EXAMPLE_UCUM_UNITS> "[in_i]";
<http://purl.bioontology.org/ontology/LNC/EXAMPLE_UNITS> "inches; cm";
<http://purl.bioontology.org/ontology/LNC/IEEE_CF_CODE10> "68060";
<http://purl.bioontology.org/ontology/LNC/IEEE_DIM> "L";
<http://purl.bioontology.org/ontology/LNC/IEEE_REFID> "MDC_ATTR_PT_HEIGHT";
<http://purl.bioontology.org/ontology/LNC/IEEE_UOM_UCUM> "cm [in_i]";
<http://purl.bioontology.org/ontology/LNC/LCL> "BDYHGT.ATOM";
<http://purl.bioontology.org/ontology/LNC/LCN> "2";
<http://purl.bioontology.org/ontology/LNC/LCS> "ACTIVE";
<http://purl.bioontology.org/ontology/LNC/LCT> "MIN";
<http://purl.bioontology.org/ontology/LNC/LOINC_COMPONENT> "Body height";
<http://purl.bioontology.org/ontology/LNC/LOINC_PROPERTY> "Len";
<http://purl.bioontology.org/ontology/LNC/LOINC_SCALE_TYP> "Qn";
<http://purl.bioontology.org/ontology/LNC/LOINC_SYSTEM> "^Patient";
<http://purl.bioontology.org/ontology/LNC/LOINC_TIME_ASPECT> "Pt";
<http://purl.bioontology.org/ontology/LNC/LRN2> "Axial length; bod; Bodies; BODY HEIGHT(LENGTH).ATOM; Body length; Length; Point in time; QNT; Quan; Quant; Quantitative; Random";
<http://purl.bioontology.org/ontology/LNC/UNITS_AND_RANGE> "[in_us]:;[ft_us]:;cm:;m:;";
<http://purl.bioontology.org/ontology/LNC/VERSION_FIRST_RELEASED> "1.0h(2)";
<http://purl.bioontology.org/ontology/LNC/VERSION_LAST_CHANGED> "2.64";
<http://purl.bioontology.org/ontology/LNC/has_class> <http://purl.bioontology.org/ontology/LNC/LP7768-7>;
<http://purl.bioontology.org/ontology/LNC/has_component> <http://purl.bioontology.org/ontology/LNC/LP64598-3>;
<http://purl.bioontology.org/ontology/LNC/has_fragments_for_synonyms> <http://purl.bioontology.org/ontology/LNC/LP28569-9>;
<http://purl.bioontology.org/ontology/LNC/has_property> <http://purl.bioontology.org/ontology/LNC/LP6822-3>;
<http://purl.bioontology.org/ontology/LNC/has_scale> <http://purl.bioontology.org/ontology/LNC/LP7753-9>;
<http://purl.bioontology.org/ontology/LNC/has_supersystem> <http://purl.bioontology.org/ontology/LNC/LP6985-8>;
<http://purl.bioontology.org/ontology/LNC/has_time_aspect> <http://purl.bioontology.org/ontology/LNC/LP6960-1>;
<http://purl.bioontology.org/ontology/LNC/measures> <http://purl.bioontology.org/ontology/LNC/MTHU014711>;
<http://purl.bioontology.org/ontology/LNC/member_of> <http://purl.bioontology.org/ontology/LNC/34566-0>,
<http://purl.bioontology.org/ontology/LNC/54126-8>, <http://purl.bioontology.org/ontology/LNC/55177-0>,
<http://purl.bioontology.org/ontology/LNC/55418-8>, <http://purl.bioontology.org/ontology/LNC/58446-6>,
<http://purl.bioontology.org/ontology/LNC/62819-8>, <http://purl.bioontology.org/ontology/LNC/67795-5>,
<http://purl.bioontology.org/ontology/LNC/67871-4>, <http://purl.bioontology.org/ontology/LNC/70300-9>,
<http://purl.bioontology.org/ontology/LNC/72513-5>, <http://purl.bioontology.org/ontology/LNC/74028-2>,
<http://purl.bioontology.org/ontology/LNC/74293-2>, <http://purl.bioontology.org/ontology/LNC/74728-7>,
<http://purl.bioontology.org/ontology/LNC/75854-0>, <http://purl.bioontology.org/ontology/LNC/76046-2>,
<http://purl.bioontology.org/ontology/LNC/85057-8>, <http://purl.bioontology.org/ontology/LNC/85353-1>,
<http://purl.bioontology.org/ontology/LNC/86641-8>, <http://purl.bioontology.org/ontology/LNC/87825-6>,
<http://purl.bioontology.org/ontology/LNC/89543-3>;
<http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://purl.bioontology.org/ontology/LNC/LP248771-0>,
<http://purl.bioontology.org/ontology/LNC/MTHU000030>;
<http://www.w3.org/2004/02/skos/core#altLabel> "Body height"@en, "Body height:Length:Point in time:^Patient:Quantitative"@en;
<http://www.w3.org/2004/02/skos/core#notation> "8302-2";
<http://www.w3.org/2004/02/skos/core#prefLabel> "Body height:Len:Pt:^Patient:Qn"@en .
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX LNC: <http://purl.bioontology.org/ontology/LNC/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
select
(str(?componentlab) as ?comp)
(str(?propertylab) as ?prop)
(str(?timelab) as ?time)
(str(?systemlab) as ?sys)
(str(?scalelab) as ?scale)
(str(?methodlab) as ?meth)
(str(?classlab) as ?class)
where {
graph LNC: {
?LoincTerm skos:notation "2345-7" ;
LNC:has_class ?LoincClass ;
LNC:has_component ?LoincComponent ;
LNC:has_property ?LoincProperty ;
LNC:has_scale ?LoincScale ;
LNC:has_system ?LoincSystem ;
LNC:has_time_aspect ?LoincTime .
optional {
?LoincTerm LNC:has_method ?LoincMethod .
?LoincMethod skos:prefLabel ?methodlab .
}
?LoincComponent skos:prefLabel ?componentlab .
?LoincProperty skos:prefLabel ?propertylab .
?LoincTime skos:prefLabel ?timelab .
?LoincSystem skos:prefLabel ?systemlab .
?LoincScale skos:prefLabel ?scalelab .
?LoincClass skos:prefLabel ?classlab .
}
}
Showing results from 1 to 3 of 3. Query took 0.1s, moments ago.
row | comp | prop | time | sys | scale | meth | class |
---|---|---|---|---|---|---|---|
1 | Glucose | MCnc | Pt | Plas | Qn | CHEM | |
2 | Glucose | MCnc | Pt | Ser | Qn | CHEM | |
3 | Glucose | MCnc | Pt | Ser/Plas | Qn | CHEM |
Compare to fields from https://search.loinc.org/searchLOINC/ (requires free LOINC account)
See also https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/LNC/sourcerepresentation.html
Search Res Field | Order | Included in SPARQL above | Notes |
---|---|---|---|
search score | 0 | NA | |
LOINC | 1 | TRUE | |
LongName | 2 | FALSE | skos:altLabel ... but there may be multiple skos:altLabel s |
Component | 3 | TRUE | |
Property | 4 | TRUE | |
Timing | 5 | TRUE | |
System | 6 | TRUE | |
Scale | 7 | TRUE | |
Method | 8 | TRUE | |
exUCUMunits | 9 | FALSE | LNC:EXAMPLE_UCUM_UNITS |
exUnits | 10 | FALSE | LNC:EXAMPLE_UNITS |
Lforms | 11 | FALSE | LNC:member_of ? |
Rank | 12 | FALSE | LNC:COMMON_ORDER_RANK or LNC:COMMON_TEST_RANK ? |
SIRank | 13 | FALSE | LNC:COMMON_SI_TEST_RANK |
Class | 14 | TRUE | using LNC:has_class. see also LNC:class_of and rdfs:subClassOf. |
ShortName | 15 | FALSE | skos:altLabel ... but there may be multiple skos:altLabel s |
DisplayName | 16 | FALSE | skos:prefLabel, skos:altLabel, LNC:LRN2, LNC:LCL or LNC:CONSUMER_NAME? |
Type | 17 | FALSE | rdf:type always owl:Class |
OrderObs | 18 | FALSE | LNC:LOR |
Copyright | 19 | FALSE | LNC:COPYRIGHT or LNC:EXTERNAL_COPYRIGHT_LINK ? |
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX LNC: <http://purl.bioontology.org/ontology/LNC/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
select
?p (count( ?LoincTerm ) as ?count)
where {
graph LNC: {
?LoincTerm ?p ?o
}
}
group by ?p
order by desc (count( ?LoincTerm))
row | p | count |
---|---|---|
1 | skos:altLabel | 256165 |
2 | umls:hasSTY | 249014 |
3 | umls:tui | 249014 |
4 | rdf:type | 217363 |
5 | skos:notation | 217206 |
6 | skos:prefLabel | 217206 |
7 | umls:cui | 217079 |
8 | LNC:component_of | 213936 |
9 | LNC:has_component | 213936 |
10 | rdfs:subClassOf | 200886 |
11 | LNC:has_system | 123784 |
12 | LNC:system_of | 123784 |
13 | LNC:class_of | 94933 |
14 | LNC:has_class | 94933 |
15 | LNC:fragments_for_synonyms_of | 91277 |
16 | LNC:has_fragments_for_synonyms | 91277 |
17 | LNC:COMMON_ORDER_RANK | 86217 |
18 | LNC:COMMON_SI_TEST_RANK | 86217 |
19 | LNC:COMMON_TEST_RANK | 86217 |
20 | LNC:LCL | 86217 |
21 | LNC:LCN | 86217 |
22 | LNC:LCS | 86217 |
23 | LNC:LCT | 86217 |
24 | LNC:LOINC_COMPONENT | 86217 |
25 | LNC:LOINC_PROPERTY | 86217 |
26 | LNC:LOINC_SCALE_TYP | 86217 |
27 | LNC:LOINC_SYSTEM | 86217 |
28 | LNC:LOINC_TIME_ASPECT | 86217 |
29 | LNC:LRN2 | 86217 |
30 | LNC:VERSION_FIRST_RELEASED | 86217 |
31 | LNC:VERSION_LAST_CHANGED | 86217 |
32 | LNC:has_time_aspect | 85880 |
33 | LNC:time_aspect_of | 85880 |
34 | LNC:has_scale | 83096 |
35 | LNC:scale_of | 83096 |
36 | LNC:has_property | 82442 |
37 | LNC:property_of | 82442 |
38 | LNC:answer_to | 78544 |
39 | LNC:has_answer | 78544 |
40 | LNC:measured_by | 75772 |
41 | LNC:measures | 75772 |
42 | LNC:LOR | 71297 |
43 | LNC:analyzed_by | 69485 |
44 | LNC:analyzes | 69485 |
45 | LNC:has_method | 61707 |
46 | LNC:method_of | 61707 |
47 | LNC:LUR | 55228 |
48 | LNC:LOINC_METHOD_TYP | 45275 |
49 | LNC:has_member | 40344 |
50 | LNC:member_of | 40344 |
51 | LNC:EXAMPLE_UNITS | 34650 |
52 | LNC:EXAMPLE_UCUM_UNITS | 34413 |
53 | LNC:has_suffix | 31446 |
54 | LNC:suffix_of | 31446 |
55 | LNC:CHANGE_REASON_PUBLIC | 27531 |
56 | LNC:OID | 23021 |
57 | LNC:has_multipart | 19998 |
58 | LNC:multipart_of | 19998 |
59 | LNC:challenge_of | 18620 |
60 | LNC:has_challenge | 18620 |
61 | LNC:has_supersystem | 17881 |
62 | LNC:supersystem_of | 17881 |
63 | LNC:ANSWER_LIST_ID | 17151 |
64 | LNC:ANSWER_LIST_NAME | 17151 |
65 | LNC:LSU | 14225 |
66 | LNC:SOS | 10444 |
67 | LNC:ANSWER_CODE | 9706 |
68 | LNC:evaluation_of | 9200 |
69 | LNC:has_evaluation | 9200 |
70 | LNC:LQS | 8661 |
71 | LNC:ASSOC_OBSERVATIONS | 7296 |
72 | LNC:LQT | 7175 |
73 | LNC:HL7_ATTACHMENT_STRUCTURE | 7019 |
74 | LNC:has_imaged_location | 6270 |
75 | LNC:is_imaged_location_for | 6270 |
76 | LNC:IMAGING_DOCUMENT_VALUE_SET | 5971 |
77 | LNC:has_modality_type | 5967 |
78 | LNC:is_modality_type_for | 5967 |
79 | LNC:COPYRIGHT | 5819 |
80 | LNC:EXTERNAL_COPYRIGHT_LINK | 5819 |
81 | LNC:has_imaging_focus | 5385 |
82 | LNC:is_imaging_focus_of | 5385 |
83 | LNC:divisor_of | 5299 |
84 | LNC:has_divisor | 5299 |
85 | LNC:LEA | 4759 |
86 | LNC:PANEL_TYPE | 3622 |
87 | LNC:has_lateral_anatomic_location | 3464 |
88 | LNC:is_lateral_anatomic_location_of | 3464 |
89 | LNC:has_lateral_location_presence | 3446 |
90 | LNC:is_presence_of_lateral_location | 3446 |
91 | LNC:has_aggregation_view | 3289 |
92 | LNC:is_aggregation_view_of | 3289 |
93 | LNC:has_timing_of | 2665 |
94 | LNC:is_timing_for | 2665 |
95 | LNC:associated_with | 2490 |
96 | LNC:has_given_pharmaceutical_substance | 2392 |
97 | LNC:is_given_pharmaceutical_substance_for | 2392 |
98 | LNC:TOP_2000_LAB_RESULTS_SI | 2192 |
99 | LNC:TOP_2000_LAB_RESULTS_US | 2178 |
100 | LNC:has_pharmaceutical_route | 1909 |
101 | LNC:is_pharmaceutical_route_for | 1909 |
102 | LNC:has_view_type | 1668 |
103 | LNC:is_view_type_for | 1668 |
104 | LNC:UNIVERSAL_LAB_ORDERS_VALUE_SET | 1522 |
105 | LNC:STATUS_TEXT | 1315 |
106 | LNC:LOINC_SCORE | 1115 |
107 | LNC:has_modality_subtype | 1069 |
108 | LNC:is_modality_subtype_for | 1069 |
109 | LNC:has_action_guidance | 1021 |
110 | LNC:is_action_guidance_for | 1021 |
111 | LNC:has_presence_guidance | 999 |
112 | LNC:is_presence_guidance_for | 999 |
113 | LNC:LMP | 887 |
114 | LNC:mapped_from | 887 |
115 | LNC:mapped_to | 887 |
116 | LNC:LCD | 824 |
117 | LNC:IEEE_CF_CODE10 | 631 |
118 | LNC:IEEE_REFID | 631 |
119 | LNC:LFO | 590 |
120 | LNC:IEEE_UOM_UCUM | 589 |
121 | LNC:IEEE_DIM | 558 |
122 | LNC:IEEE_DESCRIPTION | 488 |
123 | LNC:has_exam | 431 |
124 | LNC:is_exam_for | 431 |
125 | skos:definition | 389 |
126 | LNC:has_maneuver_type | 380 |
127 | LNC:is_maneuver_type_for | 380 |
128 | LNC:has_object_guidance | 354 |
129 | LNC:is_object_guidance_for | 354 |
130 | LNC:has_approach_guidance | 340 |
131 | LNC:is_approach_guidance_for | 340 |
132 | LNC:has_quotient | 311 |
133 | LNC:quotient_of | 311 |
134 | LNC:adjustment_of | 283 |
135 | LNC:has_adjustment | 283 |
136 | LNC:LSP | 259 |
137 | LNC:UNITS_AND_RANGE | 211 |
138 | LNC:CONSUMER_NAME | 193 |
139 | LNC:has_time_modifier | 191 |
140 | LNC:time_modifier_of | 191 |
141 | rdfs:comment | 157 |
142 | rdfs:label | 157 |
143 | LNC:count_of | 147 |
144 | LNC:has_count | 147 |
145 | LNC:ANSWER_CODE_SYSTEM | 119 |
146 | LNC:HL7_FIELD_SUBFIELD_ID | 92 |
147 | LNC:HL7_ATTACHMENT_REQUEST | 80 |
148 | LNC:SUBSEQUENT_TEXT_PROMPT | 60 |
149 | LNC:has_subject | 33 |
150 | LNC:is_subject_of | 33 |
151 | LNC:ASK_AT_ORDER_ENTRY | 3 |
152 | LNC:EXAMPLE_SI_UCUM_UNITS | 2 |
153 | LNC:FROMRSAB | 1 |
154 | LNC:FROMVSAB | 1 |
155 | LNC:MAPSETRSAB | 1 |
156 | LNC:MAPSETVERSION | 1 |
157 | LNC:MAPSETVSAB | 1 |
158 | LNC:MTH_MAPFROMCOMPLEXITY | 1 |
159 | LNC:MTH_MAPFROMEXHAUSTIVE | 1 |
160 | LNC:MTH_MAPSETCOMPLEXITY | 1 |
161 | LNC:MTH_MAPTOCOMPLEXITY | 1 |
162 | LNC:MTH_MAPTOEXHAUSTIVE | 1 |
163 | LNC:TORSAB | 1 |
164 | LNC:TOVSAB | 1 |
165 | LNC:mth_expanded_form_of | 1 |
166 | LNC:mth_has_expanded_form | 1 |
167 | owl:imports | 1 |
168 | owl:versionInfo | 1 |
@cstoeckert Here are tabular and RDF representations of LOINC's glucose level. OBI has measuring glucose concentration in blood serum assay but no corresponding datum, so I have created blood glucose measurement datum in the TURBO ontology. The TURBO ontology asserts the linkage between the LOINC term and the TURBO term via the
has OMOP concept ID
(TURBO_0010147) of 8840. Glucose level is roughly the 20th most common lab in our "PDS" clinical data warehouse, out of roughly 30,000.Up until now, I have only instantiated datums (and not assays) in the Synthea-OMOP-inspired Acorn files, but I think we will need to instantiate assays (and/or orders) in order to capture context like "who ordered the assay?" and "where was it performed?".
We can use this as a staring point for templating the laboratory assays (with requester context, etc.) and output datums./
According to https://loinc.org/get-started/loinc-term-basics/, the essential LOINC parts are
From
Loinc_2.66_PartFile_3.0-Alpha.1/LoincPartLink.csv
at https://loinc.org/file-access/download-id/17948/I don't understand the LinkTypeNames yet
From http://data.bioontology.org/ontologies/LOINC/submissions/17/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb via https://bioportal.bioontology.org/ontologies/LOINC