Migrating to the new Monarch Infrastructure
We will discontinue all previous versions of the Monarch Infrastructure (including Biolink API, OWLSim, and the underlying SciGraph and Solr services) on March 20, 2024. We request that all Monarch users transition to Monarch KG Version 3, launched on October 19, 2023.
Over the past two years, we have been hard at work to modernize the Monarch Initiative infrastructure, which involved 1) updates to a simplified knowledge graph (KG) that integrates gene, phenotype, and disease data leveraging innovative ingest and graph-building technologies and 2) a wholly renovated user interface that has been redesigned based on extensive user research. You can learn more about these updates in our recently published article in the 2024 Database Issue of Nucleic Acids Research.
Our previous infrastructure has been instrumental to the groundbreaking research our community has performed. The new Monarch KG will henceforth meet these needs. We recognize there may be some growing pains in shifting to the new framework, and we seek to empower and prepare you for these changes.
We will initiate a soft shutdown on Wednesday, February 7, 2024, changing the obsolete API endpoints to break pipelines and help our community identify dependencies intentionally. We intend to limit the impact on our community as much as possible while remaining focused on improving the Monarch KG for future research. We will discontinue all services to the obsoleted APIs on Wednesday, March 20, 2024.
If you anticipate difficulty changing to the newly released Monarch API (hosted at http://api-v3.monarchinitiative.org), please contact us immediately by making a ticket on our GitHub repository (https://github.com/monarch-initiative/monarch-app). We will work with you to find a solution with minimal disruption. During the soft shutdown, the previous version of the Monarch API will be moved from http://api.monarchinitiative.org to http://api-biolink.monarchinitiative.org until its definite shutdown on Wednesday, March 20, 2024.
Below is the complete list of resources shutting down on March 20, 2024:
http://api.monarchinitiative.org
http://api-biolink.monarchinitiative.org
http://solr.monarchinitiative.org
http://previous.monarchinitiative.org
http://owlsim.monarchinitiative.org
http://legacy.monarchinitiative.org
http://scigraph-ontology.monarchinitiative.org
http://scigraph-data.monarchinitiative.org
The new Monarch Initiative API reference is here: https://api-v3.monarchinitiative.org/v3/docs#
The obsolete Biolink API reference, which will stop working on March 20, is here: https://api.monarchinitiative.org/api
To help you port your pipeline or application to the new API as soon as possible, below are the endpoints currently in use and their corresponding new ones in the new Monarch KG Version 3.
Phenotypes for a disease
Obsolete Biolink API endpoint: https://api.monarchinitiative.org/api/bioentity/disease/MONDO%3A0019391/phenotypes
New Monarch API endpoint: https://api-v3.monarchinitiative.org/v3/api/entity/MONDO%3A0019391/biolink%3ADiseaseToPhenotypicFeatureAssociation
Phenotypes for a gene
Obsolete Biolink API endpoint: https://api.monarchinitiative.org/api/bioentity/gene/HGNC%3A9508/phenotypes
New Monarch API endpoint: https://api-v3.monarchinitiative.org/v3/api/entity/HGNC%3A9508/biolink%3AGeneToPhenotypicFeatureAssociation
Should you need help porting your existing tooling to the new endpoints, please create an issue on our GitHub repository at https://github.com/monarch-initiative/monarch-app. We value your partnership, and we will assist you with this transition.
Join our new Friends of Monarch mailing list to stay updated on the latest from the Monarch Initiative. Follow this link and click “Ask to join the group” at the top of the page.
Sincerely,
The Monarch Initiative
