Have you ever found yourself frustrated reading through a paper to find that there is insufficient information about which reagents were used? Unambiguous identification of a reagent is crucial for reproducibility because mistakes in this can lead to wasted time or retractions.
Using a catalog number for identifying a reagent can be helpful, but it lacks context unless it links to a verified description of that reagent online. Furthermore, if the link between the catalog number and reagent description is lost (e.g. a supplier is bought out by another company and catalog number changes) the original identifier loses its meaning, making it difficult or impossible for researchers to track down that resource. A more long-term solution is the use of unique persistent identifiers (PIDs), a long-lasting way to identify and reference documents, files, or physical reagents.
What are persistent identifiers?
Perhaps the most commonly known form of a unique PID is the Digital Object Identifier (DOI). Nearly all the papers or preprints you read or produce have one. The DOI serves as a way to uniquely identify digital objects that exist on the internet so that when you click on the link it will take you directly to the original article online. It is also designed to be persistent and exist online indefinitely. PIDs historically referred to objects that exist online, but this approach has been adapted for the identification of physical materials that we use in our labs, including plasmids.
All plasmids at Addgene have unique ID numbers associated with them, which serve as unique PIDs within the Addgene catalog. These IDs allow you to unmistakably identify a plasmid available through Addgene and find verified information about each plasmid item. Given a specific Addgene ID # listed in a publication, you can quickly pull up the associated plasmid page on the Addgene website and find specific information about the plasmid: name, description, how the plasmid was generated, validated sequence information, and more.
The plasmid page also helps researchers find other publications that have used the same plasmid through the “Articles Citing this Plasmid” section. Having IDs linked to these metadata and publications help to enable reproducibility of experiments. Additionally, proper citation of these Addgene IDs in published work allows readers to quickly track down the specific plasmids used.
RRIDs and resolvable compact identifiers now exist for all Addgene plasmids!
In an effort to support standardized persistent identification of research reagents, several journals or organizations now recommend or require authors to use specific PID formats. For example, several journals like eLife, Nature, and Cell use Research Resource identifiers (RRIDs) which are supported by SciCrunch. Other well known PID formats are resolvable compact identifiers, which are Compact Uniform Resource Identifiers (CURIEs) combined with well-established prefix resolution services such as Identifiers.org and N2T.net. To help authors comply with journal policies, Addgene now provides an RRID and a resolvable compact identifier for every plasmid. In case these PID formats are new to you, we’ll go through examples to highlight the difference between them using a plasmid available through Addgene.
Let’s take a look at lenti-Cas9-VQR-Blast, which has the Addgene ID #87155.
The resolvable compact identifier format for lenti-Cas9-VQR is the URL “http://n2t.net/addgene:87155” where the Addgene registered prefix and the Addgene ID # are directly at the end of the n2t.net web address.
For the RRID format, lenti-Cas9-VQR is represented as “RRID:Addgene_87155” and the following URL (https://scicrunch.org/resolver/RRID:Addgene_87155) will take you directly to the lenti-Cas9-VQR plasmid page.
Despite their differences, both of these PID formats for lenti-Cas9-VQR contain the Addgene ID # and the information necessary to indicate that this ID is managed by Addgene.
How to cite options using the different PID formats
The instructions for how to cite any Addgene plasmid in your materials and methods section have been updated to include the option of citing with resolvable compact identifier and RRID formats. Let’s go back to our example plasmid, lenti-Cas9-VQR-Blast. If you scroll down to the bottom of this plasmid’s page you will find that the “How to cite this plasmid” section now lists the multiple PIDs separated by semi-colons.
For our example plasmid it will read “lenti-Cas9-VQR-Blast was a gift from Daniel Bauer (Addgene plasmid # 87155 ; http://n2t.net/addgene:87155 ; RRID:Addgene_87155).” So when citing, you can copy and paste the text attributing the PI who generated the plasmid, followed by the PID(s) of your choice. Or if in doubt, copy and paste the entire line.
Cite plasmid using a resolvable compact identifier and RRID
“lenti-Cas9-VQR-Blast was a gift from Daniel Bauer (Addgene plasmid # 87155 ; http://n2t.net/addgene:87155 ; RRID:Addgene_87155)”
Cite plasmid using a resolvable compact identifier
“lenti-Cas9-VQR-Blast was a gift from Daniel Bauer (Addgene plasmid # 87155 http://n2t.net/addgene:87155)”
Cite plasmid using RRID
“lenti-Cas9-VQR-Blast was a gift from Daniel Bauer (Addgene plasmid # 87155 RRID:Addgene_87155)”
Please note that we only provide recommendations for how to cite using the PIDs in the material and methods section of your publication. You should carefully read and follow the journal’s specific author guidelines for reporting your materials. If you deposit a plasmid with Addgene, your plasmid will be assigned an Addgene ID #, RRID, and resolvable compact identifier. Addgene works hard to ensure that materials available through our repository are verified and identifiable to save researchers time and make their work more reproducible. While Addgene plasmid URLs act as unique PIDs, we’re happy to support the RRID and compact identifier formats.
Acknowledgments
Many thanks to Daniela Bourges for editing this post and sharing her technical expertise in persistent identifiers.
Additional Resources on the Addgene Blog
- Read a blog post on Our Citations Feature
- Check out this post on Scientific Reproducibility
- Learn about the anatomy of a plasmid page at Addgene
Additional Resources
Topics: Scientific Sharing, Reproducibility
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