OMOP2OBO Versions Save

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)

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Ontology Data

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Downloaded Resource Information:

• ontology_source_list.txt
• ontology_source_metadata.txt
• master_ontology_dictionary.pickle

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

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Clinical Data

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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:

• Conditions
• Drug Exposure Ingredients
• Measurements

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OMOP2OBO Mapping Sets

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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.

• Condition Occurrence Mappings
• Drug Exposure Ingredient Mappings
• Measurement Mappings

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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}
}