The Monarch Initiative:

Potential to be Useful

Katie Miller and Andrew Sandler

BIOL-367

Department of Biology

Loyola Marymount University

February 8, 2024

Outline

• The Monarch Initiative database contains information on genes, diseases, and phenotypes
• The database is mostly easy to use, but there are some technical issues that should be resolved to improve its function
• The scientific quality is good but could be better referenced
• The overall features of the database make it a helpful resource for identifying the causes of disease and conducting clinical diagnoses

https://monarchinitiative.org/

The Monarch Initiative Database Contains Many Types of Data

• The database stores gene, disease, and phenotype data.
• There are currently 845,539* nodes on the Monarch Initiative database.
• Each node belongs to either a gene, disease, or phenotypic feature.
• Each node contains 3 things:
• Description
• Links to additional information
• Associations between other nodes of the database
• Associations are organized in tables.

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Large Domain for Content Coverage

• We see 845539 results in the database before searching
• It is not clear if this represents all entries
• Several of these results were missing information so no content is available for that data type
• Even though an overview of the extent of the data is not available it covers a large range

Claims Coverage of Multiple Species

• “Phonemic knowledge in all forms”
• Humans are covered
• Mice are in the database but the coverage is unclear
• Unclear about other species covered
• Connects “phenotypes to genotypes across species.”

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Sandler, Andrew. Mouse and Man. 2024.

Database is Current, But Missing Information

• The current website of the Monarch Initiative is from 2024.
• They have API’s actively pulling updated data from their source databases.
• They call their pages “nodes” due to the way they have organized their tool.
• A lot of their nodes are empty at the moment.

https://monarchinitiative.org/

Monarch Initiative Could be Useful

• Monarch Initiative can be useful to help clinicians make more informed clinical decisions.
• Merges data from different fields onto a single platform
• Improves cross-discipline organization and access

Each Node has Several Types of Associations Tables

Triple-A syndrome, a disease, has three association tables:

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1. Phenotype Explorer

3. Correlated Genes

2. Causal Genes

https://monarchinitiative.org/

The Database is User-Friendly

• All Monarch Initiative resources are freely available to everyone, so any person, from any field, can use it
• Front page clearly articulates what a user can do with their website and what kind of data it contains
• The search bar is at the top of the page, which can then take you to specific “nodes”, or pages.
• Front page has several video tutorials
• There is an additional help page where user can provide feedback or contact the help desk through GitHub.

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Easy to Browse, But Hard to Download From

• It is easy to search specific phenotypic features, diseases, and genes.
• Association links make it easy to switch between nodes.
• Breadcrumbs feature shows how you got to current node from previous search history
• Links to other databases are clearly visible and their presence is explained.
• User can only download the association table
• Table is in .tsv format
• This is a standard format for tabular data

Monarch Initiative Sources Data from Other Databases

• Data is sourced from 33 other databases, which is then electronically curated into the presented format.

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• Nodes have links to databases from where the information has been sourced.
• Gene data is collected from HUGO Nomenclature Committee (HGNC).
• Disease data - MONDO program from Ontology Search (OLS)
• Phenotypic feature data - Human Phenotype Ontology (HPO)

https://academic.oup.com/nar/article/52/D1/D938/7449493?login=true

It is Difficult to Find Every Database That is Being Used

• Of the 33 databases, only 16 are directly mentioned in their article.
• The provided link to their full list is nonfunctional.
• There is no page on the website that outlines where their data is being sourced from.
• The only databases found were the ones directly linked on each node.

Monarch Initiative is an International Consortium

• Professional team made up of individuals from various schools and institutes
• Institutes are in the U.S. or Britain
• They primarily receive their funding from:
• Office of the Director National Institute of Health
• NIH National Human Genome Research Institute
• NIH National Library of Medicine
• The article and website have differing explanations of who funds the database
• Several authors received funding from the US Department of Energy
• C-Path receives funding from the FDA

Summary

• Monarch Initiative can be a helpful resource in identifying associations between data types to aid in identification and diagnosis of diseases
• The data types include genes, diseases, and phenotypes
• Monarch Initiative has the intention of being accessible to everyone, but there are some technical issues
• Difficulty to download
• Missing information
• Need to resolve issues with crediting where their data comes from and who contributes to the database

References

1. Monarch Initiative. Monarch Initiative. (n.d.). https://monarchinitiative.org/
2. Putman, T. E., Schaper, K., Matentzoglu, N., Rubinetti, V. P., Alquaddoomi, F. S., Cox, C., Caufield, J. H., Elsarboukh, G., Gehrke, S., Hegde, H., Reese, J. T., Braun, I., Bruskiewich, R. M., Cappelletti, L., Carbon, S., Caron, A. R., Chan, L. E., Chute, C. G., Cortes, K. G., … Munoz-Torres, M. C. (2024, January 5). The Monarch Initiative in 2024: An Analytic platform integrating phenotypes, genes and diseases across species. OUP Academic. https://academic.oup.com/nar/article/52/D1/D938/7449493?login=true
3. Miller, K., & Sandler, A. (2024, February 5). Monarch Initiative Week 4. Monarch Initiative Week 4 - LMU BioDB 2024. https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Monarch_Initiative_Week_4
4. Dahlquist , K. (n.d.). Week 4. Week 4 - LMU BioDB 2024. https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_4
5. Sandler, Andrew. Mouse and Man. 2024.