OMOP2OBO - Initial Release
This is the initial release of the OMOP2OBO Mappings. Additional information on this release is described here. The project workflow and all relevant data files (without PHI or licensing restrictions) are described/provided below.
New Data Sources:
- The original set of ontologies has been extended, see the Ontologies section for more information
- The National Library of Medicine's Unified Medical Language System (UMLS) MRCONSO and MRSTY. Using these data requires a NLM UMLS license agreement
Featured Functionality:
- To improve our mapping pipeline, we have created a Python-based version of Juan Banda's OHDSI Ananke
Release Data:
- All data used for this release can e downloaded directly from Zenodo (here)
Ontology Data
Downloaded Resource Information:
The specific ontologies used in this release of OMOP2OBO, including class and axiom counts, are shown in the table below. All ontologies were downloaded and processed on 09/14/20.
| Ontology | Classes | Definitions | Labels | Synonyms | DbXRefs |
|---|---|---|---|---|---|
| Cell Line Ontology (CL) | 2,238 |
1,859 |
2,238 |
2,124 |
1,376 |
| Chemical Entities of Biological Interest (CHEBI) | 126,169 |
48,824 |
126,169 |
269,798 |
231,247 |
| Human Phenotype Ontology (HPO) | 15,247 |
12,468 |
15,247 |
19,860 |
19,569 |
| Mondo Disease Ontology (MONDO) | 22,288 |
15,271 |
22,288 |
98,181 |
159,918 |
| NCBITaxon Organism Taxonomy (NCBITaxon) | 2,241,110 |
0 |
2,241,110 |
263,571 |
18,426 |
| Protein Ontology (PRO) | 215,624 |
215,598 |
215,624 |
590,190 |
195,671 |
| Uber-Anatomy Ontology (UBERON) | 13,898 |
11,026 |
13,898 |
36,771 |
51,322 |
| Vaccine Ontology (VO) | 5,783 |
1,231 |
5,789 |
6 |
0 |
Clinical Data
To create the mappings, clinical data was pulled in two waves from an OMOP (v5.0) PEDSNet (v3.0)-normalized instance of Children's Hospital of Colorado data (#15-0445).
Wiki Pages:
OMOP2OBO Mapping Sets
Data Needed to Create Mappings
Please see the README for additional details regarding the sources listed below.
omop2obo_class_relations.txt- UMLS MRCONSO and MRSTY - release uses version
2020AA(09/16/2020)
Mapping Data
Mapping data for this release can be downloaded using the links shown below.
This project is licensed under MIT - see the LICENSE.md file for details. If you intend to use any of the information on this Wiki, please provide the appropriate attribution by citing this repository:
@misc{callahan_tj_2020_4247939,
author = {Callahan, TJ},
title = {OMOP2OBO},
month = jun,
year = 2021,
doi = {10.5281/zenodo.4247939},
url = {https://doi.org/10.5281/zenodo.4247939}
}