| _version_ | 1866902260261322752 |
|---|---|
| author | Callahan, Tiffany J Baumgartner, William A Hunter, Lawrence D Kahn, Michael G |
| author_facet | Callahan, Tiffany J Baumgartner, William A Hunter, Lawrence D Kahn, Michael G |
| contents | <p><strong>OMOP2OBO Drug Exposure Ingredient Mappings V1.0</strong></p> <p>These mappings were created by the OMOP2OBO mapping algorithm (see links below). OMOP2OBO - the first health system-wide, disease-agnostic mappings between standardized clinical terminologies and eight Open Biomedical Ontology (OBO) Foundry ontologies spanning diseases, phenotypes, anatomical entities, cell types, organisms, chemicals, vaccines, and proteins. These mappings are also the first to be explicitly created using standard terminologies in the Observational Medical Outcomes (OMOP) common data model (CDM), ensuring both semantic and clinical interoperability across a space of N conditions [and N relationships curated in these ontologies].</p> <p>The mappings in this repository were created between OMOP standard drug exposure concepts at the ingredient-level (i.e., RxNorm) to the Chemical Entities of Biological Interest (ChEBI), the National Center for Biotechnology Information Taxon Ontology (NCBITaxon), the Protein Ontology (PRO), and the Vaccine Ontology (VO). All concepts were aligned to at least one ChEBI concept and the remaining ontologies (NCBITaxon, PR, and VO) were mapped by their drug class and/or type (e.g., biologics versus vaccines). For these OMOP domains, owl:intersectionOf (“and”), and owl:unionOf (“or”) constructors were used to construct semantically expressive mappings.</p> <p><br> <strong>Mapping Details</strong><br> Mappings included in this set were generated automatically using OMOP2OBO or through the use of a Bag-of-words embedding model using TF-IDF. Cosine similarity is used to compute similarity scores between all pairwise combinations of OMOP and OBO concepts and ancestor concepts. To improve the efficiency of this process, the algorithm searches only the top most similar results and keeps the top 75th percentile among all pairs with scores >= 0.25. Manually created mappings are also included.</p> <p><strong><em>Mapping Categories</em></strong></p> <ul> <li><strong>Automatic Exact - Concept</strong>: Exact label or synonym, dbXRef, or expert validated mapping @ concept-level; 1:1</li> <li><strong>Automatic Exact - Ancestor:</strong> Exact label or synonym, dbXRef, or expert validated mapping @ concept ancestor-level; 1:1</li> <li><strong>Automatic Constructor - Concept: </strong>Exact label or synonym, dbXRef, cosine similarity, or expert validated mapping @ concept-level; 1:Many</li> <li><strong>Automatic Constructor - Ancestor:</strong> Exact label or synonym, dbXRef, cosine similarity, or expert validated mapping @ concept-level; 1:Many</li> <li><strong>Manual: </strong>Hand mapping created using expert suggested resources; 1:1</li> <li><strong>Manual Constructor:</strong> Hand mapping created using expert suggested resources; 1:Many</li> <li><strong>Concept Similarity:</strong> score suggested mapping -- manually verified</li> <li><strong>UnMapped:</strong> No suitable mapping or not mapped type</li> </ul> <p><em><strong>Mapping Statistics</strong></em><br> Additional statistics have been provided for the mappings and are shown in the table below. This table presents the counts of OMOP concepts by mapping category and ontology:</p> <table align="center"> <thead> <tr> <th scope="col">Mapping category</th> <th scope="col">ChEBI</th> <th scope="col">NCBITaxon</th> <th scope="col">PRO</th> <th scope="col">VO</th> </tr> </thead> <tbody> <tr> <td>Automatic Exact - Concept</td> <td>3151</td> <td>155</td> <td>43</td> <td>108</td> </tr> <tr> <td>Automatic Constructor - Constructor</td> <td>404</td> <td>1</td> <td>1</td> <td>0</td> </tr> <tr> <td>Automatic Exact - Ancestor</td> <td>147</td> <td>17</td> <td>20</td> <td>4</td> </tr> <tr> <td>Automatic Constructor - Ancestor</td> <td>210</td> <td>3</td> <td>2</td> <td>2</td> </tr> <tr> <td>Concept Similarity</td> <td>109</td> <td>4241</td> <td>18</td> <td>17</td> </tr> <tr> <td>Manual</td> <td>322</td> <td>230</td> <td>157</td> <td>21</td> </tr> <tr> <td>Manual Constructor</td> <td>72</td> <td>14</td> <td>8</td> <td>2</td> </tr> <tr> <td>UnMapped</td> <td>7392</td> <td>7146</td> <td>11558</td> <td>11653</td> </tr> </tbody> </table> <p><br> <strong>Provenance and Versioning: </strong>The V1.0 deposited mappings were created by OMOP2OBO v1.0.0 on October 2022 using the OMOP Common Data Model V5.0 and OBO Foundry ontologies downloaded on September 14, 2020. </p> <p><strong>Caveats:</strong> Please note that these are the original mappings that were created for the preprint. They have not been updated to current versions of the ontologies. In our experience, this should result in very few errors, but we do suggest that you check the ontology concepts used against current versions of each ontology before using them.</p> <p> </p> <p><strong>Important Resources and Documentation</strong></p> <ul> <li>GitHub: <a href="https://github.com/callahantiff/OMOP2OBO">OMOP2OBO</a></li> <li>Project Wiki: <a href="https://github.com/callahantiff/OMOP2OBO/wiki">OMOP2OBO - wiki</a></li> <li>Zenodo Community: <a href="https://zenodo.org/communities/omop2obo">OMOP2OBO</a></li> <li>Preprint Manuscript: <a href="https://doi.org/10.5281/zenodo.5716421">10.5281/zenodo.5716421</a></li> </ul> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_6917223 |
| institution | Zenodo |
| language | eng |
| publishDate | 2020 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | OMOP2OBO Drug Exposure Ingredient Mappings Callahan, Tiffany J Baumgartner, William A Hunter, Lawrence D Kahn, Michael G OMOP2OBO OMOP Observational Medical Outcome Partnership Open Biomedical Foundry Ontologies Open Biomedical Foundry OBO ChEBI Chemical Entities of Biological Interest VO Vaccine Ontology NCBITaxon National Center for Biotechnology Information Taxon Ontology PRO Protein Ontology Concept Mappings <p><strong>OMOP2OBO Drug Exposure Ingredient Mappings V1.0</strong></p> <p>These mappings were created by the OMOP2OBO mapping algorithm (see links below). OMOP2OBO - the first health system-wide, disease-agnostic mappings between standardized clinical terminologies and eight Open Biomedical Ontology (OBO) Foundry ontologies spanning diseases, phenotypes, anatomical entities, cell types, organisms, chemicals, vaccines, and proteins. These mappings are also the first to be explicitly created using standard terminologies in the Observational Medical Outcomes (OMOP) common data model (CDM), ensuring both semantic and clinical interoperability across a space of N conditions [and N relationships curated in these ontologies].</p> <p>The mappings in this repository were created between OMOP standard drug exposure concepts at the ingredient-level (i.e., RxNorm) to the Chemical Entities of Biological Interest (ChEBI), the National Center for Biotechnology Information Taxon Ontology (NCBITaxon), the Protein Ontology (PRO), and the Vaccine Ontology (VO). All concepts were aligned to at least one ChEBI concept and the remaining ontologies (NCBITaxon, PR, and VO) were mapped by their drug class and/or type (e.g., biologics versus vaccines). For these OMOP domains, owl:intersectionOf (“and”), and owl:unionOf (“or”) constructors were used to construct semantically expressive mappings.</p> <p><br> <strong>Mapping Details</strong><br> Mappings included in this set were generated automatically using OMOP2OBO or through the use of a Bag-of-words embedding model using TF-IDF. Cosine similarity is used to compute similarity scores between all pairwise combinations of OMOP and OBO concepts and ancestor concepts. To improve the efficiency of this process, the algorithm searches only the top most similar results and keeps the top 75th percentile among all pairs with scores >= 0.25. Manually created mappings are also included.</p> <p><strong><em>Mapping Categories</em></strong></p> <ul> <li><strong>Automatic Exact - Concept</strong>: Exact label or synonym, dbXRef, or expert validated mapping @ concept-level; 1:1</li> <li><strong>Automatic Exact - Ancestor:</strong> Exact label or synonym, dbXRef, or expert validated mapping @ concept ancestor-level; 1:1</li> <li><strong>Automatic Constructor - Concept: </strong>Exact label or synonym, dbXRef, cosine similarity, or expert validated mapping @ concept-level; 1:Many</li> <li><strong>Automatic Constructor - Ancestor:</strong> Exact label or synonym, dbXRef, cosine similarity, or expert validated mapping @ concept-level; 1:Many</li> <li><strong>Manual: </strong>Hand mapping created using expert suggested resources; 1:1</li> <li><strong>Manual Constructor:</strong> Hand mapping created using expert suggested resources; 1:Many</li> <li><strong>Concept Similarity:</strong> score suggested mapping -- manually verified</li> <li><strong>UnMapped:</strong> No suitable mapping or not mapped type</li> </ul> <p><em><strong>Mapping Statistics</strong></em><br> Additional statistics have been provided for the mappings and are shown in the table below. This table presents the counts of OMOP concepts by mapping category and ontology:</p> <table align="center"> <thead> <tr> <th scope="col">Mapping category</th> <th scope="col">ChEBI</th> <th scope="col">NCBITaxon</th> <th scope="col">PRO</th> <th scope="col">VO</th> </tr> </thead> <tbody> <tr> <td>Automatic Exact - Concept</td> <td>3151</td> <td>155</td> <td>43</td> <td>108</td> </tr> <tr> <td>Automatic Constructor - Constructor</td> <td>404</td> <td>1</td> <td>1</td> <td>0</td> </tr> <tr> <td>Automatic Exact - Ancestor</td> <td>147</td> <td>17</td> <td>20</td> <td>4</td> </tr> <tr> <td>Automatic Constructor - Ancestor</td> <td>210</td> <td>3</td> <td>2</td> <td>2</td> </tr> <tr> <td>Concept Similarity</td> <td>109</td> <td>4241</td> <td>18</td> <td>17</td> </tr> <tr> <td>Manual</td> <td>322</td> <td>230</td> <td>157</td> <td>21</td> </tr> <tr> <td>Manual Constructor</td> <td>72</td> <td>14</td> <td>8</td> <td>2</td> </tr> <tr> <td>UnMapped</td> <td>7392</td> <td>7146</td> <td>11558</td> <td>11653</td> </tr> </tbody> </table> <p><br> <strong>Provenance and Versioning: </strong>The V1.0 deposited mappings were created by OMOP2OBO v1.0.0 on October 2022 using the OMOP Common Data Model V5.0 and OBO Foundry ontologies downloaded on September 14, 2020. </p> <p><strong>Caveats:</strong> Please note that these are the original mappings that were created for the preprint. They have not been updated to current versions of the ontologies. In our experience, this should result in very few errors, but we do suggest that you check the ontology concepts used against current versions of each ontology before using them.</p> <p> </p> <p><strong>Important Resources and Documentation</strong></p> <ul> <li>GitHub: <a href="https://github.com/callahantiff/OMOP2OBO">OMOP2OBO</a></li> <li>Project Wiki: <a href="https://github.com/callahantiff/OMOP2OBO/wiki">OMOP2OBO - wiki</a></li> <li>Zenodo Community: <a href="https://zenodo.org/communities/omop2obo">OMOP2OBO</a></li> <li>Preprint Manuscript: <a href="https://doi.org/10.5281/zenodo.5716421">10.5281/zenodo.5716421</a></li> </ul> |
| title | OMOP2OBO Drug Exposure Ingredient Mappings |
| topic | OMOP2OBO OMOP Observational Medical Outcome Partnership Open Biomedical Foundry Ontologies Open Biomedical Foundry OBO ChEBI Chemical Entities of Biological Interest VO Vaccine Ontology NCBITaxon National Center for Biotechnology Information Taxon Ontology PRO Protein Ontology Concept Mappings |
| url | https://doi.org/10.5281/zenodo.6917223 |