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@callahantiff callahantiff released this 09 Nov 03:32
· 30 commits to master since this release
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Screen Shot 2020-10-14 at 20 48 36

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:

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


Screen Shot 2020-10-14 at 20 04 53

Data Needed to Create Mappings
Please see the README for additional details regarding the sources listed below.

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}
}