Linking to External Repositories and Registries with Bioregistry

Synapse supports linking to external biological databases, repositories, and registries using standardized http://bioregistry.io prefixes. This feature allows you to create clickable links in Tables, Views, and Portals that automatically resolve to external resources, making it easier to reference data across the broader research ecosystem.

What are Bioregistry Prefixes?

The Bioregistry is an open source, community-curated registry that provides standardized prefixes for biological databases and repositories. These prefixes allow you to create compact identifiers (CURIEs) in the format prefix:identifier that can be automatically resolved to the corresponding external resource.

For example:

pubmed:38117484 is “The Epigenetic Evolution of Glioma Is Determined by the IDH1 Mutation Status and Treatment Regimen,” by Malta, Sabedot, et. al.
uniprot:Q8N653 is the Uniprot entry for the human transcriptional regulator LZTR1
geo:GSE141509 links to a Gene Expression Omnibus microarray dataset examining a mouse model of late-onset Alzheimer’s disease

How It Works in Synapse

When you include a bioregistry prefix and identifier in a Table or View cell, Synapse automatically converts it into a clickable link that opens the corresponding external resource. This works seamlessly in both Tables and Views without requiring any special formatting.

Supported Prefixes

Synapse supports a curated subset of over 200 http://bioregistry.io prefixes. You can view the complete list of Synapse-supported prefixes in the Sage-Bionetworks bioregistry-collection repository.

Some commonly used prefixes include:

pubmed - PubMed articles
cbioportal - cBioportal.org datasets
uniprot - UniProt protein database
geo - Gene Expression Omnibus data series
arrayexpress - ArrayExpress datasets
interpro - InterPro protein families
chebi - Chemical Entities of Biological Interest
go - Gene Ontology terms

Using Bioregistry Links in Tables

To add external links to a Table:

Navigate to your Table and click Table Tools, then Show Table Schema
Click Edit Schema to modify your table structure
Add a new column or use an existing text column where you want to include external links
Set the Column Type to String for text-based identifiers
In your table data, enter values using the format: prefix:identifier

For example, if you have a column for publications, you might enter:

pubmed:12345678
doi:10.1038/nature12345
pubmed:98765432

These will automatically become clickable links when viewed in the table.

Using Bioregistry Links in Views

When you create a File View, Project View, or Submission View that includes files or tables annotated with bioregistry identifiers, those links will be preserved and clickable in the view.

To include external links when creating annotations for files in a view:

Create or edit annotations on your files with keys that correspond to external databases
Use the bioregistry prefix format for the annotation values
Create a view that includes these annotated files
The bioregistry identifiers will appear as clickable links in the view

Examples

Linking to Publications

In a research dataset table, you might have a "Publication" column with values like:

pubmed:12345678 - Links to the PubMed article
doi:10.1038/s41597-022-01807-3 - Links to the DOI resolver

Linking to Protein Data

In a proteomics study, you might reference:

uniprot:P04637 - Links to the UniProt entry for the p53 protein
interpro:IPR016380 - Links to the InterPro family page

Linking to Chemical Compounds

For metabolomics or drug studies:

chebi:CHEBI:16991 - Links to the ChEBI entry for the compound
pubchem:123456 - Links to the PubChem compound page

Requesting New Prefixes

If you need to link to an external database that isn't currently supported, you can request the addition of new bioregistry prefixes by visiting the bioregistry-collection repository and creating a new issue or pull request to request the prefix.

Best Practices

Consistent Formatting: Always use the exact prefix format as specified in http://bioregistry.io . Prefixes are case-sensitive and should match exactly.

Documentation: When sharing tables or views containing external links, consider documenting which external databases are referenced and what the identifiers represent.

For additional help with Tables and Views, see Organizing Data With Tables and Views.

The http://bioregistry.io project is described in: Hoyt, C. T., et al. (2022). Unifying the identification of biomedical entities with the Bioregistry. Nature Scientific Data, 9, 714.