Persistent Identifiers and Open Citations: Basic Building Blocks of the Scholarly Web

45 Minutes

Learning Objectives

• Recognize the essential role of Digital Object Identifiers (DOIs) for the scholarly web
• List reasons to use DOIs
• Identify components of a DOI
• Apply basic UNIX curl commands to test and resolve DOIs for research objects
• Explain how the DOI registration system is organized and what information it yields for authors.

Introduction

Digital Object Identifiers (DOIs) are unique names assigned to information resources (including research papers and datasets) that are represented in some way on the Internet. DOIs represent an established international information standard, ISO26324:2012, and many publishers, data centers, and other information providers rely on this standard to assign unique identifiers for works under their care. The DOI assigned to a given research object distinguishes it from other works, including other versions of the same intellectual material. Examples of research-related information resources assigned DOIs include journal articles, curated datasets, theses, conference papers, pre-prints, technical reports, and books.

DOIs are actionable on the Internet: when put in URL form (https://doi.org/{DOI}, these strings automatically redirect to an online landing page that offers information about the research object. Often, but not always, the landing page contains a link to the resource itself. Where the resource is not online, the landing page indicates where to find it. For example, a DOI assigned to a physical resource such as a print book, a museum specimen, or a scientific sample will specify the repository or collection where that item resides.

The DOI is NOT by itself a seal of quality. Yet information resources that are assigned DOIs tend to be of enduring value; are likely to be used and cited by others; and are maintained by a publisher or other information provider who is committed to curating and preserving the resource over time. Because an organization is committed to curating the resource over time, the DOI is considered persistent. Some say that the DOI is basically a promise to always supply information about the information resource associated with the identifier.

A DOI is considered a persistent identifier because it reliably resolves to a human- and machine-readable landing page representing the information resource. But the DOI itself is not a guarantee that the dataset or paper is available via Open Access: rather, the DOI resolves to an Open Access landing page that may (or may not) permit linking through to the desired object. Whether or not a user can access the full content depends on various circumstances unrelated to the DOI system: format of the resource, restrictions and conditions governing access; authentication requirements; software compatibility; etc.

Nonetheless, the metadata associated with the DOI is rich enough to provide useful data for researchers. DOI metadata can tell alot about what has been published, who has published it, what works it cites, under what conditions the work was created and distributed (with what funding, whether the work is available open access, whether the work has been updated since publication, and more.)

In this session we’ll explore the anatomy of a DOI, how it is generated, and how to retrieve the rich metadata associated with a given research object and its DOI.

We’ll add to our command line repetoire by practicing a few new tools to help us acquire, examine, and use scholarly metadata available on the Web.

• curl: a unix command for transferring data from or to an Internet server without human interaction. We will use curl to retrieve data from a DOI database and to negotiate for data in the format most convenient for our use.

We’re using the example DOI ‘10.1186/s12916-015-0469-2’, which is an article

Exercise 1. Introducing the CrossRef API

CrossRef mints DOIs for most scholarly journal content. Their API contains lots of useful metadata. We’ll start by looking at the API in our web browser. APIs sound fancy, but they act much like normal web pages. They just return data files. The default data formate here is JSON. I recommend using Firefox for this exercise as it helps by formatting the JSON file for us. In browsers like Chrome, you can install plugins JSONVue to make JSON display prettier.

Open https://api.crossref.org/works/10.1186/s12916-015-0469-2 in a web browser

• what is the title of the document?
• how many references does this article cite?

Exercise 2. Practice using curl to retrieve data from the DOI database, CrossRef, and save to a file on your desktop. Then display the file on your terminal.

$ curl -o shen.json https://api.crossref.org/works/10.1186/s12916-015-0469-2
$ head shen.json

Can you find the publisher?

Extra: you can install the command line application jq to pretty print the file for easier human reading.

    >    $ jq . shen.json > shen_pretty.json

Exercise 3. You just need the citation, not the entire metadata record for this research object. Use content negotation with the CrossRef database to just get the citation for this item, in APA style. View the result on your screen.

$ curl -LH "Accept:text/x-bibliography; style=apa" https://doi.org/10.1186/s12916-015-0469-2 -o shen.txt

The -H option provides headers and the -L option tells curl to follow

redirects. See what you get when you leave off the -L

Exercise 4. It turns out that some other systems where you want to submit this citation data only take the open citation format, bibtex. Perform content negotiation with the CrossRef database again, but this time require the citation in bibtex format. Save the output to a file on your desktop for later reuse.

(For example, the ORCiD researcher profile system and certain funding agencies’ submission systems accespt bibtex citations).

$ curl -LH "Accept:application/x-bibtex" https://doi.org/10.1186/s12916-015-0469-2 -o shen.bib

$ head shen.bib

Exercise 5. Retrieve and save bibtex citations for three more research papers so you can complete your publication list for your project. Here are the DOIs for each paper:

• 10.1126/science.342.6154.60
• 10.3346/jkms.2017.32.5.713
• 10.1503/cmaj.109-4889

Challenge question: how could you use a single command line tool to quickly combine these citations into one file representing your publication list?

Solution

$ cat file1.bib file2.bib file3.bib > publist.bib

Anatomy of a DOI

The International DOI System is the overall infrastructure by which Digital Object Identifiers are assigned, registered, resolved, and associated with valuable metadata including citation, availability of full text, funder information, licensing information, and more. The following components of the DOI System together make it work:

• The International DOI Federation (IDF) is responsible for the overall governance of the system. IDF is a not-for-profit membership organization that oversees the operations of the federation of Registration Agencies which provide Digital Object Identifier (DOI) services and registration. IDF is also the registration authority for the ISO standard (ISO

26324. for the DOI system.

• Registration Agencies (RAs) provide services to Registrants (or Members) — allocating DOI name prefixes, registering DOI names and providing the necessary infrastructure to allow Registrants to declare and maintain metadata and state data. Each RA must follow basic protocols and standards of the DOI sytem, including a minimum metadata standard known as the DOI kernel. Yet each RA has the freedom to implement additional metadata standards, track a range of information about a given DOI resource, and offer public services for querying their databases. As an example, the Registration Agency CrossRef registers a range of metadata about scholarly resources including funding data, license associated with the digital object, author data including ORCiD numbers, and more – see April Ondis’ CrossRef Blog posting Beyond the DOI to richer metadata for more info about their services.
• Registrants (or Members) of a given Registration Agency register DOIs for information resources under their responsibility. Registrants include publishers, data centers, universities, libraries, university presses, and open data sharing repositories such as Zenodo. Registrants must follow the policies and procedures established by the RA in order to register DOIs. Each Registrant is given a unique member code that uniquely distinguishes them amongst all members of the RA. Each member also receives one or more unique prefix codes that forms the first part of the DOI sequence. The Registrant then uses the suffix portion of the DOI sequence to assign unique names to each resource they manage.

The metadata associated with the DOI is often rich enough to provide useful data for a researcher. We’ll look at this data throughout the rest of the lesson.

Exercise 6. Find out who owns a DOI prefix

DOI prefixes can be assigned by different Registration Agencies to different users. You can see some (slightly cryptic) information about the Registration Agency by going to doi.org with the prefix

https://doi.org/10.14291
https://doi.org/10.1021

This is also available in API form at https://doi.org/api/handles/. In most cases, the Registration Agency will be DataCite or CrossRef, which have apis for finding out about a given prefix.

https://api.crossref.org/prefixes/10.1021

https://api.datacite.org/prefixes/10.14291

If the prefix is not managed by the Registration Agency, you’ll get an error message.

Next: Register a DOI