Normalization of drug and therapeutic concepts with Thera-Py

OBJECTIVE: The diversity of nomenclature and naming strategies makes therapeutic terminology difficult to manage and harmonize. As the number and complexity of available therapeutic ontologies continues to increase, the need for harmonized cross-resource mappings is becoming increasingly apparent. This study creates harmonized concept mappings that enable the linking together of like-concepts despite source-dependent differences in data structure or semantic representation. MATERIALS AND METHODS: For this study, we created Thera-Py, a Python package and web API that constructs searchable concepts for drugs and therapeutic terminologies using 9 public resources and thesauri. By using a directed graph approach, Thera-Py captures commonly used aliases, trade names, annotations, and associations for any given therapeutic and combines them under a single concept record. RESULTS: We highlight the creation of 16 069 unique merged therapeutic concepts from 9 distinct sources using Thera-Py and observe an increase in overlap of therapeutic concepts in 2 or more knowledge bases after harmonization using Thera-Py (9.8%-41.8%). CONCLUSION: We observe that Thera-Py tends to normalize therapeutic concepts to their underlying active ingredients (excluding nondrug therapeutics, eg, radiation therapy, biologics), and unifies all available descriptors regardless of ontological origin

DGIdb 5.0: Rebuilding the Drug-Gene Interaction Database for precision medicine and drug discovery platforms

The Drug-Gene Interaction Database (DGIdb, https://dgidb.org) is a publicly accessible resource that aggregates genes or gene products, drugs and drug-gene interaction records to drive hypothesis generation and discovery for clinicians and researchers. DGIdb 5.0 is the latest release and includes substantial architectural and functional updates to support integration into clinical and drug discovery pipelines. The DGIdb service architecture has been split into separate client and server applications, enabling consistent data access for users of both the application programming interface (API) and web interface. The new interface was developed in ReactJS, and includes dynamic visualizations and consistency in the display of user interface elements. A GraphQL API has been added to support customizable queries for all drugs, genes, annotations and associated data. Updated documentation provides users with example queries and detailed usage instructions for these new features. In addition, six sources have been added and many existing sources have been updated. Newly added sources include ChemIDplus, HemOnc, NCIt (National Cancer Institute Thesaurus), Drugs@FDA, HGNC (HUGO Gene Nomenclature Committee) and RxNorm. These new sources have been incorporated into DGIdb to provide additional records and enhance annotations of regulatory approval status for therapeutics. Methods for grouping drugs and genes have been expanded upon and developed as independent modular normalizers during import. The updates to these sources and grouping methods have resulted in an improvement in FAIR (findability, accessibility, interoperability and reusability) data representation in DGIdb

Cool Seq Tool

<ul> <li>fix: return type for FeatureOverlap get_grch38_mane_gene_cds_overlap by @korikuzma in <a href="https://github.com/GenomicMedLab/cool-seq-tool/commit/67a241c3ff9e01de33aeb9111d84a8278f358ff3">67a241c</a></li> </ul> <p><strong>Full Changelog</strong>: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.1.14-dev2...0.1.14-dev3</p>If you use this software, please cite it as below

Cool Seq Tool

<h2>What's Changed</h2> <ul> <li>build: properly pin pydantic v2 major version by @korikuzma in https://github.com/GenomicMedLab/cool-seq-tool/pull/215</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/GenomicMedLab/cool-seq-tool/compare/0.3.0-dev0...0.3.0-dev1</p>If you use this software, please cite it as below

VICC Variation Normalization Service

<h2>What's Changed</h2> <ul> <li>cicd: update release.yml (publish python distribution to pypi) by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/513</li> <li>fix: pin versions + fix /translate_identifier by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/516</li> <li>feat: expose cool-seq-tool feature overlap endpoint by @korikuzma in https://github.com/cancervariants/variation-normalization/pull/523</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/cancervariants/variation-normalization/compare/0.6.0-dev0...0.6.0-dev1</p>If you use this software, please cite it as below

ga4gh/vrs-python: 0.8.5

<h2>What's Changed</h2> <ul> <li>build: support python >= 3.8 by @korikuzma in https://github.com/ga4gh/vrs-python/pull/202</li> <li>docs: update pip installation + fix typos (#207) by @korikuzma in https://github.com/ga4gh/vrs-python/pull/209</li> <li>fix: gnomad_re should accept all nucleotide characters for ref/alt by @korikuzma in https://github.com/ga4gh/vrs-python/pull/277</li> <li>cicd: update release.yml to use trusted publisher by @korikuzma in https://github.com/ga4gh/vrs-python/pull/279</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/ga4gh/vrs-python/compare/0.8.4...0.8.5</p&gt

ga4gh/vrs-python: 0.8.5

<h2>What's Changed</h2> <ul> <li>build: support python >= 3.8 by @korikuzma in https://github.com/ga4gh/vrs-python/pull/202</li> <li>docs: update pip installation + fix typos (#207) by @korikuzma in https://github.com/ga4gh/vrs-python/pull/209</li> <li>fix: gnomad_re should accept all nucleotide characters for ref/alt by @korikuzma in https://github.com/ga4gh/vrs-python/pull/277</li> <li>cicd: update release.yml to use trusted publisher by @korikuzma in https://github.com/ga4gh/vrs-python/pull/279</li> <li>cicd: use single quotes in if condition for branch name by @korikuzma in https://github.com/ga4gh/vrs-python/pull/280</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/ga4gh/vrs-python/compare/0.8.4...0.8.5</p&gt

DGIdb 5.0: Rebuilding the drug-gene interaction database for precision medicine and drug discovery platforms

<p>The Drug-Gene Interaction Database (DGIdb, <a href="https://dgidb.org/">https://dgidb.org</a>) is a publicly accessible resource that aggregates genes, drugs, and drug-gene interaction records to drive hypothesis generation and discovery for clinicians and researchers. DGIdb 5.0 is the latest release and includes substantial architectural and functional updates to support integration into clinical and drug discovery pipelines. The DGIdb service architecture has been split into separate client and server applications, enabling consistent data access for users of both the API and web interface. The new interface was developed in ReactJS, and includes dynamic visualizations and consistency in the display of user interface elements. A GraphQL API has been added to support customizable queries for all drugs, genes, annotations, and associated data. Updated documentation provides users with example queries and detailed usage instructions for these new features. In addition, six sources have been added and many existing sources have been updated. New sources have been incorporated into DGIdb to enhance annotations of regulatory approval status for therapeutics. Methods for grouping drugs and genes have been expanded upon and developed as independent modular normalizers during import. The updates to these sources and grouping methods have resulted in an improvement in FAIR data representation in DGIdb. </p&gt