Release Notes for otargen v1.1.5

otargen 1.1.5

In this new release, several frequently requested query functions from Open Target are added to the package to expand the package functionality in accessing data that are key in evaluating drug targets. In addition, multiple technical bugs has been fixed to increase the efficiency of the previous query functions data retrieval. The added new query functions include:

• chemblQuery(): This function queries the Open Targets GraphQL API to retrieve ChEMBL data
  for a specified gene and disease, including evidence from the ChEMBL datasource.
  ▶️ These data are key in evaluating the tractability of a target.

• clinvarQuery(): This function queries the Open Targets GraphQL API to retrieve ClinVar data
  for a specified gene and disease, including evidence from the NCBI datasource.
  ▶️ These data are key in evaluating the target MoA and disease biology.

• knownDrugsQuery(): This function queries the Open Targets GraphQL API to retrieve known drugs data
  for a specified gene.
  ▶️ These data are key to evaluate the competitive landscape of a target.

• mousePhenotypesQuery(): This function queries the Open Targets GraphQL API to retrieve mouse phenotypes data
  for a specified gene.
  ▶️ These data are key in evaluating the target validation.

• compGenomicsQuery(): This function queries the Open Targets GraphQL API to retrieve comparative genomics data
  for a specified gene.
  ▶️ These data are key in evaluating the safety of a target.

Citing otargen in important for us 🙋‍♂️
Please cite otargen if you use it in your research 🙏🏻 : . Bioinformatics.

v1.1.1

otargen 1.1.1

Updated the examples article

• Fixed several inconsistencies between parameters naming in the functions used in the examples article and the
  main function in the package.
• Streamline the examples description to be short and organized.
• Added additional plotting case for example 7 for the additional parameters that has been added in the current version to the plot_l2g function.

Bug Fixes

• Fixed and issue with the plot_l2g() function for the cases when the disease parameter were not selected.
  The previous function were plotting only top disease for one gene. The function now updated with two more parameters to expand the plot_l2g() functionality for plotting disease agnostic scenario. These two parameters are:

• top_n_disease (default: 1): Determines the number of top diseases to plot for each gene, ranked by L2G score. Increase this value to include more diseases in the analysis. Use in conjunction with being disease-agnostic to dynamically select the top diseases for each gene.

• l2g_cutoff (default: 0.5): Sets the minimum L2G score threshold for diseases to be considered in the plot. Increasing this value can help reduce plot clutter by focusing on higher-confidence associations.

otargen v1.0.0

otargen: R Package for Tidy Data Accessing and Processing From Open Targets Genetics by GraphQL