RRID Portal

The RRID portal displays the aggregated RRID index. The portal is accessible from the following URLs:

Guidelines:

https://scicrunch.org/resources/about/guidelines

API access is available through the developer tools via the SciCrunch platform.

RRID Index

The RRID index is a list of key biological reagents and resources aggregated from the most authoritative data sources for each resource type. Each of the records is also available from that data source. For example, the antibodyregistry.org contains the same data as the RRID portal, but displays it a little differently. The integrated index is made searchable by the SciCrunch platform and underlying data systems (e.g., ElasticSearch), but the list can be made available from any appropriate system.

Index Updates:

System updates can be viewed in the SciCrunch table view for the source (example) or in Foundry (example *must be logged in). Please note, the update of data leads the update of the index so for several days each week the new data is in staging while the index is displayed from the previous week.

Index Integrity:

The goal of the RRID index is to be a permanent system of identifiers, however it was built from data from stock centers in some cases. The stock centers are a recognized and important part of the community, making organisms, cells or samples available for reuse. However, not all stock centers are data stewards of a persistent identifier system. When possible we work with the model organism databases to draw data about organisms that are not available from stock centers. This is not uniformly available for all types of research resources, thus it is important for SciCrunch to backstop data for some index participants, therefore records are not deleted from the RRID index, but augmented with a warning sign that displays for records that are no longer available. This process is automated, but it is reviewed monthly by curators to determine if the index needs to be updated due to errors.

In all cases where errors are detected users can let the RRID staff know that a problem was found via the help box at the bottom of each page. We track these issues and strive to answer email tickets within 1 business day.

How can I become an RRID provider?

Adding an organism stock center:

The RRID index is governed by the authorities and if a new stock center wishes to register with us, we ask that they work closely with their respective model organism authority to ensure high data quality and a “backstop” at the authority for all identifiers. Please contact the help desk to get the process started or align data with your friendly model organism authority.

Adding a different resource type:

Antibody additions will all be handled by the antibodyregistry.org. Individuals can register an antibody by going to antibodyregistry.org/add and adding as little as two pieces of information about the product. The curator will reach out during the next business day to confirm the entry or to ask questions. Companies, non-profits, and labs are encouraged to add all of their antibody data to the registry. Bulk upload options are available through the help desk. For profit companies are expected to become members of the Antibody Registry to ensure long term stability of the project.

Cell line additions are all handled by the authoritative Cellosaurus database (from ExPASy). Any cell line vendor is encouraged to make all of their data available to the Cellosaurus staff so that it is included in the RRID portal. Please contact the help desk at Cellosaurus to add an individual cell line that you have created, a full catalog of cell lines, or a set of data about cell lines that will be important for other users to understand. Cellosaurus gathers, verifies, and aggregates information about each cell line, including the vendors that offer the resource, validation data, as well as any cautionary notes that come from the community, including the ICLAC.org. Typically users hear back about their requests within a business day.

BioSamples can be added to the EBI or NCBI databases by any user. This database is the authority. However, these will not be picked up as RRIDs, unless a project (like a stock center) can stand behind the data to ensure quality. To create a dataset that can be picked up by our list of approved RRIDs, projects must:

Distribute the physical samples to investigators over the longer term, and have a need to track how these are used in publications. *Biosample records that represent data for a project will not become RRIDs.
Distribution is happening in a coordinated fashion with other sample distributors. We must have evidence that your sample collection is unique.
You register a BioProject and link all of your data in BioSamples database to the BioProject number.
You must work with your users to make sure that the BioSampes IDs are visible on your website and they are communicated to your users as the method for citing the materials you provide.

Plasmids currently come entirely from Addgene. Authors are encouraged to deposit their plasmid reagents with Addgene and obtain an RRID from Addgene. There is no plasmid authority for the plasmids that are sold by various companies or by other non-profit projects. We are actively seeking an authority that would fulfill this role.