General Information

OLIDA was developed by the Interuniversity Institute of Bioinformatics in Brussels (IB)²

OLIDA completely overhauled DIDA, a novel database that provided for the first time detailed information on genes and associated genetic variants involved in digenic diseases, the simplest form of oligogenic inheritance, with the aim of increasing the data quality, content and accessibility. OLIDA was designed to allow storage of information on any type of oligogenic diseases in addition to the digenic diseases present in DIDA.

DIDA has been deprecated, but the table data has been kept for historical purposes on Zenodo. OLIDA provides up-to-date information, more thoroughly curated using a clearly defined protocol (see details about our curation pipeline in the documentation).

Data in DIDA has been curated by the following former curators:

• Dr Andrea Gazzo ORCID - Google Scholar
• Dorien Daneels ORCID

All the data in OLIDA was curated by dedicated biocurators:

• Dr. Sofia Papadimitriou - ORCID - Google Scholar
• Barbara Gravel - ORCID - Google Scholar
• Charlotte Nachtegael - ORCID - Google Scholar
• Inas Bosch - ORCID - Google Scholar

Special Thanks

If interested to help in the curation, let us know. Special thanks already to following external contributors:

• Dr Douglas Stewart, Consultant Paediatric Nephrologist at the Royal Hospital for Children, Glasgow
• Dr Anaïs Mottaz, Post-doctoral researcher at Hôpitaux Universitaires de Genève

Updates

v4, March 2024

Update of OLIDA content with articles published up to January 2024.

Nine existing gene combinations (18, 176, 180, 452, 552, 559, 599, 708 and 747) had their scores upgraded and involved variant combinations which were reviewed for potential change of score.

Several variant combinations had part of their scores changed:

• OLI022: Gene knowledge and Gene Metascore upgraded from 0 to 2 and 1 to 2 respectively, in consequence Functional Metascore was upgraded from 0 to 2, no change in the Final Metascore
• OLI272: Gene knowledge and Gene Metascore upgraded from 0 to 2
• OLI276: Gene knowledge and Gene Metascore upgraded from 0 to 2
• OLI633: Gene knowledge and Gene Metascore upgraded from 0 to 2
• OLI659: Gene knowledge and Gene Metascore upgraded from 0 to 2, in consequence Functional Metascore was upgraded from 0 to 2, no change in the Final Metascore
• OLI764: Gene knowledge and Gene Metascore upgraded from 0 to 2
• OLI775: Gene knowledge and Gene Metascore upgraded from 0 to 2, in consequence Functional Metascore was upgraded from 0 to 2, no change in the Final Metascore
• OLI823: Gene knowledge and Gene Metascore upgraded from 0 to 2
• OLI826: Gene knowledge and Gene Metascore upgraded from 0 to 2, in consequence Functional Metascore was upgraded from 0 to 1, no change in the Final Metascore
• OLI945: Gene knowledge and Gene Metascore upgraded from 0 to 2, in consequence Functional Metascore was upgraded from 0 to 2, no change in the Final Metascore
• OLI951: Gene knowledge and Gene Metascore upgraded from 0 to 1, in consequence Functional Metascore was upgraded from 0 to 1, no change in the Final Metascore
• OLI1008: Gene knowledge and Gene Metascore upgraded from 0 to 1
• OLI1013: Gene knowledge and Gene Metascore upgraded from 0 to 1, in consequence Functional Metascore was upgraded from 0 to 1, no change in the Final Metascore

Were added to the database:

• 198 variant combinations
• 381 variants
• 123 genes
• 141 gene combinations
• 11 diseases
• 35 references

The format for the CNVs in the Oligogenic Variant Combinations table has been changed to include their gene name when available. In consequence, the format of the downloaded table has also changed.

The terms for the gene relationships were harmonized to avoid doublons, such as "Relevant pathways for phenotype" and "Involvement in relevant pathway(s) for phenotype".

v3.3, December 2023

Update of variants ID 136, 137, 639, 947, 1661 and 2144, as they contained typos.

Many thanks to Dr Anaïs Mottaz, Post-doctoral researcher at Hôpitaux Universitaires de Genève, for finding the errors.

Update of the combination OLI1415 due to a missing variant, the missing variant was added under the ID 3399; gene combination with ID 992 was modified in consequence with their manual score and metascore downgraded to 0.

v3.2, October 2023

Update of combinations OLI1032, OLI1033, OLI1034, OLI1035, OLI1036, OLI1037 and OLI1038, to add the Meniere disease to the list of diseases linked to the variant combinations.

Special thanks to Dr Douglas Stewart, Consultant Paediatric Nephrologist at the Royal Hospital for Children, Glasgow, for finding the error.

v3.1, July 2023

Changes in diseases-related statistics plots to include gene combinations and add genes for CNVs when available.

v3, May 2023

Update of OLIDA content with articles published up to February 2023.

Three existing gene combinations (189, 606 and 635) had their scores upgraded and involved variant combinations were reviewed for potential change of score.

Several variant combinations had part of their scores changed :

• OLI285: Gene Manual harmonized and Gene Metascore upgraded from 0 to 2, in consequence Functional Metascore was upgraded from 0 to 2, increasing the Final Metascore from 0 to 1
• OLI286: Gene Manual harmonized and Gene Metascore upgraded from 0 to 2, in consequence Functional Metascore was upgraded from 0 to 2, increasing the Final Metascore from 0 to 1
• OLI834 : Gene Manual score upgraded from 0 to 2
• OLI836 : Gene Manual, Gene Manual harmonized, Gene Metascore upgraded from 0 to 2, in consequence Functional Manual and Metascore were upgraded from 0 to 2, increasing the Final Manual and Metascore from 0 to 1
• OLI847: Gene Manual harmonized and Gene Metascore upgraded from 0 to 2, in consequence Functional Metascore was upgraded from 0 to 2, increasing the Final Metascore from 0 to 1
• OLI868: Gene Manual harmonized and Gene Metascore upgraded from 0 to 1, in consequence Functional Metascore was upgraded from 0 to 1, no change in Final Metascore
• OL1108: Gene Manual harmonized and Gene Metascore upgraded from 0 to 1, in consequence Functional Metascore was upgraded from 0 to 1, no change in Final Metascore

382 new variant combinations were added to the database.

The variant combination OLI1126 was deleted and merged with a previously existing combination, OLI084, after correction of the variants coordinates.

The API was also updated to include all the metadata found in OPTIONS until now.

v2, August 2022

Update of OLIDA content with articles published up to January 2022.

v1, April 2022

Original OLIDA publication.

Contact

If you have any questions about OLIDA that are not answered in the documentation, feel free to contact us at olida@ibsquare.be. We will try to get back at you as soon as possible.

OLIDA – publications and citations

OLIDA

When using data from OLIDA please cite:

• Nachtegael C. and Gravel B., Dillen A., Smits G., Nowé A., Papadimitriou S., Lenaerts T. Scaling up oligogenic diseases research with OLIDA: the Oligogenic Diseases Database. Database, April 2022. DOI: https://doi.org/10.1093/database/baac023
  Citation files: BibTex, RIS

Predictors trained using our data

The data from digenic diseases of DIDA was used in our research group and around the world to train machine learning predictors aiming to predict and understand the cause of digenic diseases. They can be found on the about page of the website of DIDA at http://dida.ibsquare.be/about/.

VarCoPP 2.0

VarCoPP 2.0 is the update of the VarCoPP predictor, trained with the data from OLIDA with a decent confidence score, aiming to predicting potential pathogenic digenic variant combinations. The model is integrated on the ORVAL platform.

Citing VarCoPP 2.0:

• Versbraegen, N., Gravel, B., Nachtegael, C., Renaux A., Verkinderen E., Nowé A., Lenaerts T.,Papadimitriou S. Faster and more accurate pathogenic combination predictions with VarCoPP2.0. BMC Bioinformatics, May 2023. DOI: https://doi.org/10.1186/s12859-023-05291-3
  Citation files: BibTex, RIS

ORVAL

ORVAL is a sister platform to OLIDA that incorporates the VarCoPP predictor, the digenic effect predictor and other analytical tools, to explore oligogenic variant combinations and predicted pathogenic gene networks in an individual. It is available at orval.ibsquare.be.

Citing ORVAL:

• Renaux A., Papadimitriou S., Versbraegen N., Nachtegael C., Boutry S., Nowé A., Smits G., Lenaerts T. ORVAL: A novel platform for the prediction and exploration of disease-causing oligogenic variant combinations. Nucleic Acids Research, May 2019. DOI: https://doi.org/10.1093/nar/gkz437
  Citation files: BibTex, RIS

BOCK and ARBOCK

BOCK is a knowledge graph constructed to explore disease-causing genetic interactions, integrating curated information on oligogenic diseases from clinical cases with relevant biomedical networks and ontologies. Using this graph, they developed a novel predictive framework based on heterogenous paths connecting gene pairs. This method trains an interpretable decision set model that not only accurately predicts pathogenic gene interactions, but also unveils the patterns associated with these diseases. BOCK is available at https://zenodo.org/records/8124854.

Citing BOCK:

• Renaux A., Terwagne C., Cochez M., Tiddi I., Nowé A., Lenaerts T. A knowledge graph approach to predict and interpret disease-causing gene interactions. BMC Bioinformatics, August 2023. DOI: https://doi.org/10.1186/s12859-023-05451-5
  Citation files: BibTex, RIS

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