Published February 3, 2024 | Version v2
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Collection of Reviewed Resources and Tools for Rare Disease Variant Interpretation

Creators

  • 1. ROR icon ELIXIR

Contributors

Data collector:

  • 1. University of Turin
  • 2. Istituto Superiore di Sanità
  • 3. ROR icon University of Bologna
  • 4. ROR icon University of Genoa
  • 5. Consiglio Nazionale delle Ricerche
  • 6. ROR icon University of Salerno
  • 7. ROR icon University of Naples Federico II
  • 8. Universita degli Studi di Bologna Azienda Ospedaliera Sant'Orsola-Malpighi
  • 9. Center for Technology and Innovation, Trieste

Description

Classification of the Rare Disease Resources and Tools
The Rare Disease resources and tools for annotating pathogenic variants, primarily sourced from the bio.tools registry, have been categorized into four classes:

  1. Databases of Ontologies, Gene/Protein Networks, and Variants.

  2. Tools for Variant Calling and Annotation.

  3. Resources for Gene Prioritization.

  4. Resources and Tools for Variant Interpretation.

The first class is further subdivided into three groups: Disease and Phenotype Classification Databases and Ontologies, Gene and Protein Network Databases, and Databases of Variants. Within the second class, there are distinctions between Automatic Variant Calling Tools and Pipelines, as well as Variant Annotation Tools. The resources and tools associated with variant interpretation are organized into subgroups, encompassing Pathogenicity Predictions, Protein Stability Changes, and Genotype/Phenotype Association Methods.

 

Criteria for Rare Disease Tools Evaluation
The gathered resources and tools underwent a comprehensive evaluation based on a five-star criteria framework. For the tools, our assessment considered the following key aspects:

  1. Citations: Determining whether the resource or tool had been cited more than 50 times.

  2. Download: Examining the availability of a downloadable version that can be installed locally.

  3. Web Server: Assessing whether the service is accessible online.

  4. Update: Verifying if the resource or tool had undergone updates in 2020 or later.

  5. Maturity: based on the presence of the maturity tag on the bio.tools registry.

In the case of databases, we modified the criteria slightly: Citations (point 1) was replaced with the potential to use an API for submitting queries, and Web Server (point 3) was substituted with Access, evaluating the possibility of unrestricted access.

Based on this evaluation criteria, the most reliable and user-friendly resources and tools will be distinguished with a five-star rating.

 

Files

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md5:9adcb009925ccff4170a1a2237705741
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