https://github.com/thejacksonlaboratory/loinc2hpoannotation
loinc2hpo Annotation Data
https://github.com/thejacksonlaboratory/loinc2hpoannotation
hpo loinc loinc2hpo monarchinitiative
Last synced: 2 months ago
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loinc2hpo Annotation Data
- Host: GitHub
- URL: https://github.com/thejacksonlaboratory/loinc2hpoannotation
- Owner: TheJacksonLaboratory
- License: other
- Created: 2018-03-19T16:16:31.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2022-08-04T15:49:45.000Z (about 3 years ago)
- Last Synced: 2023-11-27T21:34:26.082Z (almost 2 years ago)
- Topics: hpo, loinc, loinc2hpo, monarchinitiative
- Language: Python
- Homepage: https://github.com/monarch-initiative/loinc2hpo
- Size: 1.37 MB
- Stars: 22
- Watchers: 6
- Forks: 11
- Open Issues: 16
-
Metadata Files:
- Readme: README.md
- License: License.md
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README
# loinc2hpoAnnotation
The repository contains the annotation data for the LOINC2HPO project.
Laboratory tests are uniquely identified in electronic healthcare records (EHR) with Laboratory Observation Identifier Names and Codes (LOINC), which is a universal code system that defines various kinds of clinical laboratory tests and other measurements.
The outcome of a laboratory test can be represented by a term in the [Human Phenotype Ontology (HPO)](https://hpo.jax.org/app/), which is a logically defined vocabulary for describing medically relevant abnormal phenotypes.
LOINC-coded laboratory tests can be grouped broadly into three categories, those with a quantitative outcome (Qn), an ordered categorical outcome (ordinal, or Ord) and an unordered categorical outcome (nominal, or Nom).
## Quantitative tests
A quantitative test for an analyte has a normal range, and there are three types of mappings depending on the result of the test: L (lower than normal), N (normal), and H (higher than normal). Take, for instance, a test for the concentration of potassium in the blood (LOINC:6298-4). If the result is high, our procedure infers the corresponding HPO term for [Hyperkalemia, HP:0002153](https://hpo.jax.org/app/browse/term/HP:0002153). Analogously, a low result is mapped to [Hypokalemia, HP:0002900](https://hpo.jax.org/app/browse/term/HP:0002900). The HPO is an ontology of abnormal phenotypes, and thus there is no term that specifically represents a normal test result. However, computational analysis can record negated HPO terms, and the normal test result is represented as NOT [Abnormal blood potassium concentration, HP:0011042](https://hpo.jax.org/app/browse/term/HP:0011042).
## Ordinal tests
Ordinal tests can have a series of ordered outcomes. The majority of the ordinal LOINC tests were mapped to two possible outcomes, POS (positive) or NEG (negative). For instance, the result of the test Nitrite in urine by test strip can be positive (present) or negative (absent). If present, then our approach infers the HPO term [Nitrituria, HP:0031812](https://hpo.jax.org/app/browse/term/HP:0031812); if absent, our approach infers NOT [Nitrituria, HP:0031812](https://hpo.jax.org/app/browse/term/HP:0031812).
## Nominal tests
Nominal tests have a series of outcomes that lack a natural ordering. Yet, some nominal result values are considered abnormal. For instance, LOINC 5778-6, color of urine. Currently, nine abnormal results of this test are mapped to the nine child terms of [Abnormal urinary color, HP:0012086](https://hpo.jax.org/app/browse/term/HP:0012086), including [Red urine, HP:0040318](https://hpo.jax.org/app/browse/term/HP:0040318) and [Dark urine, HP:0040319](https://hpo.jax.org/app/browse/term/HP:0040319).
# Annotations
This repository contains the annotation file for the LOINC2HPO resource. It can be used with software such as the
[loinc2hpo](https://github.com/monarch-initiative/loinc2hpo) Java library. We have curated the file using a Desktop Java application called [loinc2hpoMiner](https://github.com/pnrobinson/loinc2hpoMiner); this app is not needed to use the annotations for applications.
This is the format (version 2, from November 2021 onwards)
annotations are contained in a file called [loinc2hpo-annotations.tsv](https://github.com/TheJacksonLaboratory/loinc2hpoAnnotation/blob/master/loinc2hpo-annotations.tsv). The file has the following fields.
| Column | Explanation |
|--------------------|:--------------------:|
| loincId | LOINC ID |
| loincScale | Qn, Ord, or Nom |
| outcome | test outcome |
| hpoTermId | e.g.,HP:0031812 |
| supplementalTermId | see above |
| curation | biocuration |
| comment | (optional) |
## supplementalTermId
We need to have one additional field for the situation where there is a test for bacteremia and the test result can be any bacterium. Here, it would be good to allow software to annotate with an additional field. To guide the software, we want to
say what type of entity it could be. For instance
Bacteremia HP:0031864, NCBI Bacteria, NCBI:txid2
https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2&lvl=3&lin=f&keep=1&srchmode=1&unlock
similarly Viruses, NCBI:txid10239
https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=10239&lvl=3&lin=f&keep=1&srchmode=1&unlock
For example, we would put NCBI:txid2 into the supplement column (see below)