2015 on Crossref

A healthy infrastructure needs healthy funding data

Kirsty Meddings — Wed, 16 Dec 2015 00:00:00 +0000

We’ve been talking a lot about infrastructure here at Crossref, and how the metadata we gather and organize is the foundation for so many services - those we provide directly - and those services that use our APIs to access that metadata, such as Kudos and CHORUS, which in turn provide the wider world of researchers, administrators, and funders with tailored information and tools.

The initiative formerly known as FundRef

Together Crossref’s funding data (previously known as FundRef – we simplified the name) and the Open Funder Registry, our taxonomy of grant-giving organisations, comprise a hub for gathering and querying metadata related to the questions:

“Who funded this research?” and “Where has the research we funded been published?”

To support the funding data initiative, three key pieces of metadata are needed from publishers:

Funder ID
Funder Name
DOI

Unfortunately only around half of the 950,000 Crossref DOIs with funding data contain funder IDs, the unique funder identifiers from the Open Funder Registry that are needed to link up all of the data. So, only half of the data is useful. (And 950,000 DOIs is only a fraction of the 77 million DOIs in our database, but more on that later).

When we looked at the funding data that was coming in without funder IDs we were a little surprised. We had expected that most of these would be names that simply aren’t in the Open Funder Registry yet, and we thought there would be a certain amount of incorrect information that had been entered into the “funder_name” field.

Instead, what we found was that many of the names were correct, and the funder IDs were just missing.

Tidying the data

To help correct this, we decided to match incoming names to funder IDs where we could do so with the highest level of confidence. After much testing to minimize false positives, we switched this on at the end of August 2015.

Throughout September and October, we inserted funder IDs for about 25% of the names that have been deposited without IDs. For October, the real numbers were 68,000 funder names with no IDs deposited, and 18,000 funder IDs inserted by Crossref.

In the same period 42,000 funder IDs were deposited by publishers. With our matching on top of this, we are achieving a little over a 50% overall success rate of “good” funding data (funder names and funder IDs together).

We have been very careful to distinguish the funder IDs that we have added from those deposited by publishers - provenance of data is an extremely important part of what we do. All funder IDs are tagged as provided either by the publisher or Crossref. Every time we insert an ID into a deposit, the publisher is notified in the deposit report.

We have also now added these tags to our REST API so that publishers can query to find out exactly which DOIs we have amended*. The ideal scenario at this point is that the publisher checks that they are happy with the matching and then redeposits the funding data for those DOIs, over-writing the <span >doi-asserted-by: “crossref”</span> tag and claiming the metadata as their own.

Setting some limits

The second largest problem with funding data was incorrectly entered funder name – e.g. concatenation of several names or authors entering overly long or vague program names instead of the official funder name.

To help weed this out, we have made a couple of changes to the funding data deposit system:

Funder_name field can no longer contain a numerical string over 4 digits
Funder_name field can no longer contain a text string over 200 characters
Funder names that that do not adhere to these two rules will now cause the funding data section of the metadata deposit (not the whole deposit) to fail and return an error message.

Getting the growth we need

As of today, 198 publishers deposit funding data with Crossref. This amounts to about 3.5% of Crossref’s membership (although it’s a larger proportion of our total deposits). We need more publishers to deposit funding data so that funding data search can become a truly useful tool for the community. There’s no sign-up process or additional fee - read about how to get started, and take a look at our best practices for depositing funding data.

Finally, we ask you: how can we get more and better funder metadata in 2016?

This is not a rhetorical question. Please tweet your thoughts @CrossrefOrg or email your replies to info@crossref.org. You will receive something special via snail mail if you reply to us – just Crossref’s way of saying thank you.

^{*At the time of posting our database is re-indexing and the “asserted-by” tags are still filtering through to the API. Check back in a day or two for the full picture.}

Distributed Usage Logging: A private channel for private data

Jennifer Lin — Fri, 04 Dec 2015 00:00:00 +0000

Forty wire telephone switchboard, 1907, Author unknown, Popular Science Monthly Vol 70, Wikimedia Commons.

A few months ago Crossref announced that we will be launching a new service for the community in 2016 that tracks activities around DOIs recording user content interactions. These “events” cover a broad spectrum of online activities including publication usage, links to datasets, social bookmarks, blog mentions, social shares, comments, recommendations, etc. The Event Data service collects the data and make it available to all in an open clearinghouse so that data are open, comparable, audit-able, and portable. These data are all publicly available from external platform partners, and they meet the terms of distribution from each partner.

But Crossref and its members are also concerned about privacy. We recognise that not all data can be made open and public. Particularly if it is sensitive, personally identifiable data about usage. With this in mind, we are also launching an affiliated service, Distributed Usage Logging (DUL), for external parties to transmit sensitive data on user content interactions directly to authorized end points. As researchers are increasingly using “alternative” (non-publisher) platforms to store, access and share literature, publishers are correspondingly interested in incorporating the activity on their publications into their COUNTER reports.

Interested third-party sites might include the following:

Institutional and subject repositories
Aggregator platforms (EBSCOhost, IngentaConnect)
Researcher-oriented social-networking sites (e.g. Academia.edu, ResearchGate, Mendeley)
Reading environments and tools (e.g. ReadCube, Utopia Documents)

For publishers to process such events via their COUNTER-compliant usage reporting streams, they need private usage information and a secure channel by which to receive the data from the external platforms. Crossref will provide a switchboard that will enable these non-publisher platforms can safely transmit private data directly to the publisher.

The work ahead entails close collaboration between Crossref, COUNTER, and the partners who will be sending and receiving the private data. The cross-organisational team will be working towards the following before launch: technical infrastructure development for production service, semantic definition of the usage logging message, assignment and validation of credentials to participants in the scheme, participant integration of the DUL API, and incorporation of this data type into the COUNTER Code of Practice. We will also continue to consult with data privacy and security authorities to ensure that the scheme respects all governmental obligations and community best practice regarding the processing of personal data.

We will share more about the launch of the service as we make progress along the way. Please contact Jennifer Lin for more information.

Crossref Labs plays with the Raspberry Pi Zero

Joe Wass — Wed, 02 Dec 2015 00:00:00 +0000

If you’re anything like us at Crossref Labs (and we know some of you are) you would have been very excited about the launch of the Raspberry Pi Zero a couple of days ago. In case you missed it, this is a new edition of the tiny low-priced Raspberry Pi computer. Very tiny and very low-priced. At $5 we just had to have one, and ordered one before we knew exactly what we want to do with it. You would have done the same. Bad luck if it was out of stock.

We love the way DOIs are being used in Wikipedia, but you probably already know that by now. Not only is it a brilliant source of information, mostly well cited, it’s also an organic living thing, with countless people and bots working together on countless articles. Our live stream of edits that cite (or uncite) DOIs shows new scholarly literature unfold, as it happens. From new articles to new references to improved citations to edit wars to bots cleaning up all the mess, it captivates everyone we show it to. The latest version has a live chart to show exactly how much activity is going on.

Crossref works in five ways: Rally, Tag, Run, Play, and Make and this definitely comes under ‘Play’. By the time our Raspberry Pi Zero arrived it was clear what we had to do. We ordered a servo, a driver board and a wireless adapter and got to work.

We have some new neighbours in the basement. Oxford Hackspace is a community of people who want to work on projects from electronics to metalwork, hack things to improve them or find out how they work. A diverse bunch who at the last visit were working on squeezing unprecedented color capabilities from the 30 year old ZX Spectrum, a nixie tube display, a smartphone controlled doorbell and a robotic glockenspiel. They let us use their soldering iron to solder a few header pins.

A bit of hacky Python, a pictureframe and lots of duck tape later, we have a live display of how many DOIs are cited and uncited per hour. It updates live every minute, fetches the latest numbers from the Wikipedia DOI citation stream and moves the hand.

(For the worried engineers amongst you, rest assured that sufficient duck tape was added after this picture)

It’s extraordinary to think that a fully fledged computer with very capable specifications can be manufactured and sold for $5. Within the space of a lunchtime we had it up and running, all connected and fetching data over the internet via wireless. A generation ago you would have had to use punched cards, send them by post and load them in by hand. The live stream would have been at least a month behind.

It now sits in our Oxford office reminding us that DOIs Aren’t Just for Traditional Bibliographies. Below Geoff Bilder’s reminder about what happens when you have too many standards (they’re telephone plugs from round the world).

You can find source code and instructions on the github repository so you can make your own if you want.

Watch Speaker Videos from the 2015 Annual Meeting

April Ondis — Tue, 24 Nov 2015 00:00:00 +0000

You might have missed it, but you haven’t missed out. If you want to watch – or savor re-watching – the presentations from last week’s 2015 Crossref Annual Meeting, we’ve embedded each video below in chronological order. Sit back, relax, and take it all in (again) just as though you were in an air-conditioned ballroom at the Taj.

Note: You can find the playlist containing all the videos on our YouTube channel.

Ed Pentz, Crossref Executive Director, focuses on the best practice of writing DOIs as actionable hyperlinks in his presentation, Crossref Best Practice: http://www.slideshare.net/Crossref/ed-pentz-crossref15-55435481 (slides only)

Martin Paul Eve senior lecturer at Birkbeck University, London, delivers a trenchant criticism of the process small publishers must go through when getting and depositing their first Crossref DOI in his presentation, Crossref Deposit: A Scholar-Publisher Experience:

Anne Coghill, Manager of Peer Review Operations for the American Chemical Society, detailed their process for deciding where in the manuscript workflow to insert CrossCheck plagiarism screening in her presentation, American Chemical Society Publications and CrossCheck: http://www.slideshare.net/Crossref/ann-coghill-crossref15 (slides only)

Ben Hogan, Regional Manager in Wiley’s Peer Review Management team, shares Wiley’s pain points as well as its positive experiences in using CrossCheck to detect plagiarism in his presentation, _CrossCheck Usage and Case Studies: _

Jure Triglav, Lead Developer for the PubSweet Publishing Framework at the Collaborative Knowledge Foundation, demonstrates how to mine data from the corpus of open science using Crossref’s metadata via its API and open source tools from the Collaborative Knowledge Foundation in his presentation, Making Science Writing Smarter:

Scott Chamberlain, open science researcher, shows the several advantages of using programmatic tools such as R, Python, and Ruby to mine text and data, including Crossref metadata, in his presentation, _Text and Data Mining: _

Helen Duriez, ePublishing Manager at the Royal Society, describes the Royal Society’s experience with providing Crossmark data as a means of communicating document version information in her presentation, Crossmark – a journey through time (and space?) 2015

John Chodacki, chair of Crossref’s DET committee, describes the future state of the DOI Event Tracker as an open hub for collecting and sharing data around web events that involve DOIs in his presentation, DOI Event Tracker 2015:

Marc Abrahams, editor and co-founder of the Annals of Improbable Research, makes you LAUGH, then THINK with his keynote speech, Improbable Research, the Ig Nobel Prizes, and You:

Juan Pablo Alperin describes the ways that Crossref and the Public Knowledge Project can work together to support common goals, in his presentation, _PKP and Crossref: Two P’s in a Cross

Ed Pentz, Crossref Executive Director, summarizes the organisation’s expansion over the past year with his presentation, Crossref Growth and Change:

Ginny Hendricks, Director of Member & Community Outreach, details the findings of Crossref’s recent stakeholder research and the organisation’s future plans to enhance member experience with her presentation, Member & Community Outreach:

Jennifer Lin, Director of Product Management, visualizes Crossref’s role as a map maker for the scholarly web in her presentation, Crossref: Building an Open Map for the Scholarly Enterprise:

Chuck Koscher, Director of Technology, gives us performance stats for the Crossref system, including aggregate uptimes and how long it takes to deposit metadata, in his presentation, Crossref System Performance:

Geoffrey Bilder, Director of Strategic Initiatives, sheds light on the status of current and future research projects that are part of Crossref’s new product development process in his presentation, Strategic Initiatives Update:

Scott Chamberlain, open science researcher, proposes the use of programmatic tools, such as the R programming language working with the Crossref search API, to undertake scientific research in his presentation, Thinking Programmatically:

Martin Paul Eve, senior lecturer at Birkbeck University, London, bears us back to the origins of the scholarly mission, considers the implications of the notion that researchers work within a symbolic economy, and looks at the practical challenges brought about by open access modes of publication for works in the Humanities in his wide-ranging presentation, Open Access & the Humanities: Digital Approaches:

Slideshare, Too!

Finally, each speaker has generously made their slides available here: http://www.slideshare.net/Crossref/tag/crossref15

_ _

The logo has landed

Ginny Hendricks — Wed, 11 Nov 2015 00:00:00 +0000

The rebranding of Crossref was top priority when I joined in May in a new role called “Director of Member & Community Outreach”. Since then I’ve been working to understand the array of services, attributes, and audiences we have developed; to answer the questions “What do we do, for whom, and why?”

As Crossref prepares to celebrate turning fifteen at our annual meeting next week, I am thrilled to present our new brand identity with key messages and logo. And along with “thrilled” you may also detect “nervous excitement”.

Over the last few months we have reviewed earlier research and talked with a number of members, affiliates, and academics. Turns out we’re the plain talkers of the industry, the do-ers, the scrappy people who get stuff done, chivvy others along, and in some cases we are—dare I say it—the voice of reason!

While balancing differing views within the scholarly community, we’re all about making connections – literally and figuratively. We help bring together people and metadata in pursuit of an excellent research communications system for all. And, to mirror one of Ed Pentz’s new catchphrases, we are “keeping it real”; with down-to-earth language.

Crossref Key Messages

New logos and names for all our products will come soon (in some cases it’ll be a ‘de-brand’ rather than a re-brand!). We’ll gradually phase in the new identity over the next month or two, starting with our annual meeting, and with a complete website relaunch following in 2016. We will contact all of our members and partners in the coming weeks with information about using the new logo, using a content delivery network (CDN) so that sites can reference the correct file.

Why rebrand?

We have not rebranded because we plan on doing something different but rather to better express the things we already do. Our ‘problem’ was that often people didn’t know Crossref was behind initiatives like CrossCheck, Crossmark and FundRef. Our products had become unlinked from the organisation. And since we’re all about linking things together, that just made no sense.

We needed an icon to give more flexibility across the web that a word mark cannot do alone. The icon is made up of two interlinked angle brackets familiar to those who work with metadata, and can also act as arrows depicting Metadata In and Metadata Out, two themes under which our services can generally be grouped.
Sentence case helps to avoid splitting the word; we do not want to tempt the Cross and the Ref to divide again. So that lowercase R you see in the middle of our name is indeed an official change. (Hopefully we can change the habit!)
The palette gives a nod to the history of Crossref with red & dark grey, but brings in contemporary colors for a fresh palette that is distinctive in our industry (we researched a lot - everyone has circles, and traditional shades abound). Our aesthetic embodies classic Swiss design principles and is minimalist in keeping with our straight-talking personality.

So, in the words of Board Chair, Ian Bannerman, it’s time for Crossref to step forward.

About Crossref

I’m looking forward to revealing more of the story at our annual meeting next week!

Auto-Update Has Arrived! ORCID Records Move to the Next Level

Rachael Lammey — Mon, 26 Oct 2015 00:00:00 +0000

Crossref goes live in tandem with DataCite to push both publication and dataset information to ORCID profiles automatically. All organisations that deposit ORCID iDs with Crossref and/or DataCite will see this information going further, automatically updating author records.

We’re cross-posting ORCID’s blog below with all the details:

Since ORCID’s inception, our key goal has been to unambiguously identify researchers and provide tools to automate the connection between researchers and their creative works. We are taking a big step towards achieving this goal today, with the launch of Auto-Update functionality in collaboration with Crossref and [DataCite](https://www.datacite.org/.

There’s already been a lot of excitement about Auto-Update: Crossref’s recent announcement about the imminent launch generated a flurry of discussion and celebration on social media. Our own tweet on the topic was viewed over 10,500 times and retweeted by 60 other accounts.

So why all the fuss? We think Auto-Update will transform the way researchers manage their scholarly record. Until now, researchers have had to manually maintain their record, connecting new activities as they are made public. In ORCID, that meant using Search & Link tools developed by our member organisations to claim works manually. Researchers frequently ask, “Why, if I include my ORCID iD when I submit a manuscript or dataset, isn’t my ORCID record “automagically” updated when the work is published?”

With the launch of Auto-Update, that is just what will happen.

It might seem like magic but there are a few steps to make it work:

Researchers. You need to do two things: (1) use your ORCID iD when submitting a paper or dataset, and (2) authorize Crossref and DataCite to update your ORCID record. In keeping with our commitment to ensuring that researchers maintain full control of their ORCID record, you may revoke this permission at any time, and may also choose privacy settings for the information posted on your record.

Publishers and data centers. These organisations also have two things to do: (1) collect ORCID identifiers during the submission workflow, using a process that involves authentication (not a type-in field!), and (2) embed the iD in the published paper and include the iD when submitting information to Crossref or DataCite.

Crossref and DataCite. Upon receipt of data from a publisher or data center with a valid identifier, Crossref or DataCite can automatically push that information to the researcher’s ORCID record.

More information about how to opt out of this service can be found here: the ORCID Inbox.

Why is this so revolutionary?

A bit of background, first. Crossref and DataCite, both non-profit organisations, are leaders in minting DOIs (Digital Object Identifiers) for research publications and datasets. A DOI is a unique alphanumeric string assigned to a digital object – in this case, an electronic journal article, book chapter, or a dataset. Each DOI is associated with a set of basic metadata and a URL pointer to the full text, so that it uniquely identifies the content item and provides a persistent link to its location on the internet.

Crossref, working with over a thousand scholarly publishers, has generated well over 75 million DOIs for journal articles and book chapters. DataCite works with nearly 600 data centers worldwide and has generated over 6.5 million DOIs to date. Between them, Crossref and DataCite have already received almost a half a million works from publishers and data centers that include an ORCID iD validated by the author/contributor. With Auto-Update functionality in place, information about these articles can transit (with the author’s permission) to the author’s ORCID record.

Auto-Update doesn’t stop at a researcher’s ORCID record. Systems that have integrated ORCID APIs and have a researcher’s ORCID record connected to that system — their faculty profile system, library repository, webpage, funder reporting system — can receive alerts from ORCID. Information can move easily and unambiguously across systems.

This is the beginning of the end for the endless rekeying of information that plagues researchers — and anyone involved in research reporting. Surely something to celebrate!

Questions you may have:

Q. What do I need to do to sign up for auto-update?

You need to grant permission to Crossref and DataCite to post information to your ORCID record. You can do this today by using the Search and Link wizard for DataCite available through the ORCID Registry or the DataCite Metadata Search page. We also have added a new ORCID Inbox, so that you can receive a message from Crossref or DataCite if they receive a datafile with your iD, and you can grant permission directly. See More on the ORCID Inbox.

Q. Will Crossref and DataCite be able to update my ORCID record with already published works for which I did not use my ORCID iD?

No. The auto-update process only applies to those works that these organisations receive that include your ORCID iD. For previous works that did not include your ORCID iD, you will need to use the DataCite and Crossref Search and Link wizards to connect information with your iD.

Q. What information will be posted to my record?

With your permission, basic information about the article (such as title, list of contributors, journal or publisher) or dataset (such as data center name and date of publication) will be posted, along with a DOI that allows users to navigate to the source paper or dataset landing page.

Q. What if my journal or data center doesn’t collect ORCID iDs?

Ask them to! This simple step can be accomplished using either the Public or Member ORCID APIs. Information about integrating ORCID iDs in publishing and repository workflows is publicly available.

Nov 9th - New Webinar: Crossref for Open Access Publishers

April Ondis — Mon, 19 Oct 2015 00:00:00 +0000

Register for our webinar to learn best practices for depositing metadata and ways to help with the dissemination and discoverability of OA content.

New Crossref services are being developed that have particular application to OA publishers. Did you know that our upcoming DOI Event Tracker service was inspired by a group of OASPA publishers asking if there was a way to centrally support the gathering of data that could be analyzed as altmetrics?

A large number of Crossref members classify their content as Open Access, and we’ve been thinking about how our infrastructure can support and communicate this. In many ways, it already does:

Crossref supports the deposit of license and funding information in the DOI metadata.
Crossref’s Crossmark Service is useful to OA publishers who need to have the means to update info about their content, no matter where it sits.
Crossref’s APIs allow publishers to make it easier for researchers to mine full-text content.

Register for the Crossref Open Access Webinar

Date: November 9, 2015

Time: 8:00 am (San Francisco), 11:00 am (New York), 4:00 pm (London)

Register: https://attendee.gotowebinar.com/register/4198524003003451650

Please join us for this new webinar that gives an overview of Crossref and its network of member publishers, along with information on Crossref services that have specific relevance to OA scholarly content.

Crossref will be joined by two guest speakers - Frontiers will talk about their OA workflows and how Crossref services integrate with these, and James MacGregor from PKP will show participants the Crossref Export/Registration Plugin which journals can enable to assign DOIs with Crossref and to help them participate in other Crossref services.

There will be time for questions and discussion during the webinar. The webinar will be recorded.

2015 Annual Meeting: Speakers Announced

April Ondis — Tue, 13 Oct 2015 00:00:00 +0000

Curious about who will be speaking at Crossref’s Annual Meeting this year? We have a flock of scholarly communications talent gathering at the Taj Hotel in Boston from November 17-18, 2015. In addition to our line-up of keynote speeches and technical workshops, we will be celebrating Crossref’s 15^th Anniversary with a quindecennial fête on Wednesday evening, November 18^th. There’s still time to register, so please join us!

Distinguished Guest Speaker Bios:

Marc Abrahams will be a keynote speaker at Crossref’s 2015 Annual Meeting. Marc writes about research that makes people LAUGH, then THINK. He is editor and co-founder of the magazine Annals of Improbable Research (AIR), host and main writer of the Improbable Research weekly podcast (distributed by CBS), and author of This is Improbable Too and other books. He edits and writes much of the web site and blog www.improbable.com, and for thirteen years wrote a column (called “Improbable Research”) for The Guardian newspaper.

Marc is the father and Master of Ceremonies of the Ig Nobel Prize Ceremony, honoring achievements that make people LAUGH, then THINK. The Prizes are handed out by genuine Nobel Laureates at a gala ceremony held each autumn at Harvard University and broadcast on the internet and on National Public Radio.

Marc is author of the books The Ig Nobel Prizes, The Man Who Cloned Himself, Why Chickens Prefer Beautiful Humans, This Is Improbable, This is Improbable Too, The Ig Nobel Cookbook, volume 1 (co-authored with Corky White and Gus Rancatore). He edited (and wrote much of) the science humor anthologies The Best of Annals of Improbable Research and Sex As a Heap of Malfunctioning Rubble (and other improbabilities).

Marc has a degree in applied mathematics from Harvard College, spent several years developing optical character recognition computer systems (including a reading machine for the blind) at Kurzweil Computer Products, and later founded Wisdom Simulators, a creator of educational software.

Juan Pablo Alperin will be a keynote speaker at Crossref’s 2015 Annual Meeting. Juan is an Assistant Professor and a Research Associate with the Public Knowledge Project (PKP) at Simon Fraser University. Juan started working with the PKP in 2007, and has continued to be involved as systems developer, project manager, and researcher. Juan leads and advises on several of PKP’s R&D and Scholarly Inquiry initiatives as a complement to his research and work on scholarly communications more broadly. He can be reached via @juancommander. ORCID iD: orcid.org/0000-0002-9344-7439.
Scott Chamberlain will be a keynote speaker as well as a presenter at Crossref’s 2015 Annual Meeting. Scott is a scientific programmer who contributes to the field of scholarly literature by developing software for accessing open data on the web. He co-founded a developer collective called rOpenSci to help connect open source data into the R environment, a free software environment for statistical computing and graphics that runs on all major platforms. Scott maintains a few clients to work with Crossref APIs, and a text mining client that leverages Crossref’s TDM service. In addition, Scott maintains clients in R, Ruby, and Python to interact with Legotto, a platform for collecting and delivering altmetric data. A former ecologist, Scott is currently working full time on rOpenSci at the University of California at Berkeley. He can be reached via @recology_/@opensci. ORCID iD: http://orcid.org/0000-0003-1444-9135.
John Chodacki will be a presenter at Crossref’s 2015 tech workshops. John is Director of University of California Curation Center (UC3) at California Digital Library (CDL). At UC3, John works with UC campuses and the broader community to ensure that CDL’s digital curation services meet the emerging needs of the scholarly community, including digital preservation, data management, and reuse. Prior to joining UC3, John was Product Director at PLOS where he led cross-departmental strategic projects such as the Article-Level Metrics (ALM) initiative. He has served on the Crossref board and is currently the Committee Chair for DOI Event Tracker (DET). He can be reached via @chodacki. ORCID iD: orcid.org/0000-0002-7378-2408.
Anne Coghill will be a presenter at Crossref’s 2015 Annual Meeting. Anne is Manager, Peer Review Operations, in the American Chemical Society Publications Division. She and her colleagues manage the manuscript submission and peer review environment for ACS’ scholarly journals and books publishing program. Anne holds a Bachelor of Science in chemistry from Illinois State University and a Master in Science in Management Studies from Northwestern University. She is also the co-editor of The ACS Style Guide, third edition. She can be reached via @AnneCoghill. ORCID iD: orcid.org/0000-0002-2773-2282.
Helen Duriez will be a presenter at Crossref’s 2015 tech workshops. Helen is the ePublishing Manager at the Royal Society, responsible for developing the Society’s digital journals strategy as well as the day-to-day management of its journal websites. Since digital innovation transcends the traditional boundaries of scholarly publishing, she spends a lot of time pondering a variation of Freud’s musings, ‘what do researchers want?’ Helen can be contacted via @HDuriez and @RSocPublishing.
Martin Paul Eve will be a keynote speaker as well as a presenter at Crossref’s 2015 Annual Meeting. Martin is Senior Lecturer in Literature, technology and Publishing at Birkbeck, University of London and a founder of the Open Library of Humanities. He is the author of three books: Pynchon and Philosophy: Wittgenstein, Foucault and Adorno (Palgrave, 2014); Open Access and the Humanities: Contexts, Controversies and the Future (Cambridge University Press, 2014); and Password [a cultural history (Bloomsbury, forthcoming 2016) and many journal articles. A strong advocate for open access to scholarly material, Martin has given evidence to the UK House of Commons Select Committee Inquiry into Open Access; served on the Jisc OAPEN-UK Advisory Board, the Jisc National Monograph Strategy Group, and the Jisc Scholarly Communications Advisory Board; been a member of the HEFCE Open Access Monographs Expert Reference Group; and is a member of the SCONUL Strategy Group on Academic Content and Communications. Martin is also a qualified computer programmer (Microsoft Professional in C# and the .NET Framework) and is the author of the digital publishing tools meTypeset and CaSSius. He can be reached via @martin_eve. ORCID iD: orcid.org/0000-0002-5589-8511.
Ben Hogan will be a presenter at Crossref’s 2015 tech workshops. Ben is a Regional Manager in Wiley’s Peer Review Management team, responsible for leading the North America and Open Access teams. He works with internal and external stakeholders to bring in new work and refine the peer review experience to be as efficient as possible for authors and editorial offices. Ben’s worked in publishing since 2007 in a variety of capacities, including books and journals production, training, and peer review. His interests include user experience and publication ethics.
Jure Triglav will be a presenter at Crossref’s 2015 tech workshops. His presentation,Using Crossref’s API to Make Smarter Science Writing , will explore how continuously talking to Crossref’s API can help us write better scientific content. Topics will include calling the API from JavaScript, combining Crossref data with modern web-based text editors, and more.Jure is an open science software developer. Jure graduated from medical school 4 years ago, but started working as a developer for Academia.edu shortly after. Now he focuses on technology issues present in open science and runs several projects in this space: @ScienceGist, @ScienceToolbox and @ScholarNinja. Jure also works with open science organisations like PLOS, working on software that will power the future of scientific publishing. He can be reached via @juretriglav.

Crossref Staff Speaker Bios:

Geoffrey Bilder is Director of Strategic Initiatives at Crossref, where he has led the technical development and launch of a number of industry initiatives including CrossCheck, Crossmark, ORCID and FundRef. He co-founded Brown University’s Scholarly Technology Group in 1993, providing the Brown academic community with advanced technology consulting in support of their research, teaching and scholarly communication. He was subsequently head of IT R&D at Monitor Group, a global management consulting firm. From 2002 to 2005, Geoffrey was Chief Technology Officer of scholarly publishing firm Ingenta, and just prior to joining Crossref, he was a Publishing Technology Consultant at Scholarly Information Strategies. He can be reached via @Geoffrey Bilder. ORCID iD: orcid.org/0000-0003-1315-5960.
Ginny Hendricks is Director of Member & Community Outreach for Crossref, and is responsible for Crossref’s communications, business development, member services, and product support initiatives. Before joining Crossref, she ran Ardent Marketing for nine years, where she consulted with publishers to craft multichannel marketing strategies, develop, brand, and launch online products, and build engaged communities. She previously managed Elsevier’s launch of Scopus, the abstract and citation database of peer-reviewed literature. While at Elsevier, she established advisory boards and outreach programs with library and scientific communities. In 1998, Ginny started an early e-resources help desk for Blackwell’s information Services and later led training and communication programs for Swets’ digital portfolio in Asia Pacific, Middle East, and Africa. She’s lived and worked in many parts of the world, has managed globally dispersed creative, technical, and commercial teams, and co-hosts the Scholarly Social networking events in London. She can be reached via @GinnyLDN. ORCID iD: http://orcid.org/0000-0002-0353-2702.
Chuck Koscher has been the Director of Technology for Crossref since 2002. His primary responsibility has been the development and operation of Crossref’s core services and technical infrastructure. As a senior staff member he also contributes to the definition of Crossref’s mission and the expansion of its services such as the recent launch of Fundref. His role includes management of technical support and back-end business operations. Chuck and his team interface directly with members in dealing with issues effected by new or evolving industry practices such as those involving non-journal content like books, standards and databases. Chuck has been active within the industry having served 9 years on the NISO board of directors, and a participant in initiatives such as the NISO/NFAIS Best Practices in Journal Publishing and NISO’s Supplemental Material Working Group. Prior to Crossref Chuck has over 20 years in software engineering experience primarily in the aerospace industry. ORCID iD: orcid.org/0000-0003-2181-9595.
Rachael Lammey is a Product Manager on Crossref’s Crosscheck plagiarism screening and Text and Data Mining API initiatives, among other tools that Crossref make available for publishers build upon. Rachael has been with Crossref since March 2012. She previously worked in journals publishing for Taylor & Francis for nearly six years, managing a team who worked with online submission and peer review systems. She has a degree in English Literature from St. Andrews University and a MA in Publishing Studies from the University of Stirling. She can be reached via @rachaellammey. ORCID iD: http://orcid.org/0000-0001-5800-1434.
Jennifer Lin is the Director of Product Management at Crossref. She has worked in product development, project management, community outreach, and change management within the scholarly communications, education, and public sectors since 2000. She spent four years at the Public Library of Science (PLOS) where she oversaw product strategy and development for their data program, article-level metrics initiative, and open assessment activities. Prior to PLOS, she was a consultant with Accenture, working with Fortune 500 companies as well as governments, to develop and deploy new products and services. Jennifer earned her PhD at Johns Hopkins University. Jennifer can be reached via @jenniferlin15. ORCID iD: http://orcid.org/0000-0002-9680-2328.
Ed Pentz is the Executive Director of Crossref, a not-for-profit membership association of publishers set up to provide a cross-publisher reference linking service to organise publisher metadata, run the infrastructure that makes Digital Object Identifier (DOI) links work, and rally multiple community stakeholders to develop tools and services that enable advancements in scholarly publishing. Ed was appointed as Crossref’s first Executive Director when the organisation was created in 2000. Crossref is now the largest DOI registrar in the world with over 75,000,000 DOIs. Ed is also Chair of the Board of ORCID, a registry of unique identifiers for researchers established in 2010. Prior to joining Crossref, Ed held electronic publishing, editorial and sales positions at Harcourt Brace in the US and UK and managed the launch of Academic Press’ first online journal, the Journal of Molecular Biology, in 1995. Ed has a degree in English Literature from Princeton University and lives in Oxford, England. He can be reached via @epentz. ORCID iD http://orcid.org/0000-0002-5993-8592.

DOIs in Reddit

Joe Wass — Wed, 30 Sep 2015 00:00:00 +0000

Skimming the headlines on Hacker News yesterday morning, I noticed something exciting. A dump of all the submissions to Reddit since 2006. “How many of those are DOIs?”, I thought. Reddit is a very broad community, but has some very interesting parts, including some great science communication. How much are DOIs used in Reddit?

(There has since been a discussion about this blog post on Hacker News)

We have a whole strategy for DOI Event Tracking, but nothing beats a quick hack or is more irresistible than a data dump.

What is a DOI?

If you know what a DOI is, skip this! The DOI system (Digital Object Identifier) is a link redirection service. When a publisher puts some content online they could just hand out the URL. But the URL can change, and within a very short space of time, link-rot happens. DOIs are designed to fight link rot. When a publisher mints a DOI to an article they just published, they can change the article’s URL and then update the DOI to point to the new place. DOIs are persistent. They are URLs. They’re also identifiers (kind of like ISBNs), and they’re used in scholarly publishing as to do citations.

Crossref is the DOI registration agency for scholarly publishing. That means mostly things like journal articles. There are other registration agencies, for example, DataCite, who do DOIs for research datasets. But at this point in time, most DOIs are Crossref’s.

What does finding DOIs in Reddit mean?

It means someone used a DOI to cite something! DOIs can be used for any kind of content, but because of the sheer volume of scientific publishing, lots of DOIs are for science. Having a DOI doesn’t say anything about quality or content. But it does indicate that the person who created the DOI probably intended it to be cited. We care because it means that every time a DOI is used a tiny bit of link-rot doesn’t have the opportunity to take hold. Every time something is discussed on Reddit and the DOI is used, it means that archaeologists using the data dump in 100 years will have identifiers to find the things being discussed, even if the web and URLs have long since crumbled to dust.

Or, more likely, in five year’s time when a few URLs will have shuffled around.

The results

DOIs have been used on Reddit since 2008 (the logs start in 2006). After a rocky start, we see hundreds being used per year.

That’s dozens per month.

The best subreddit to find DOIs is /r/Scholar, followed by /r/science. And then a lot of others with one or two per year.

Opportunities

It’s great to see DOIs being used in Reddit. But let’s be honest, it’s not a massive amount.

We have a list of domains that our DOIs point to. They mostly belong to publishers, so every time we see a link to a domain on the list, there’s a chance (not a certainty) that the link could have been made using a DOI. We found a large number of these, orders of magnitude more than DOIs. We’re still crunching the data.

The data

The data is quite large. It’s a 40 Gigabyte download compressed, which comes to about 170 GB that uncompressed. It contains the submissions to reddit between 2006 and 2015, not the comments, so each data point represents a thread of conversation about a DOI.

Reproducibility (updated)

You can find the source code and reproduce the figures at http://github.com/crossref/reddit-dump-experiment. We use Apache Spark for this kind of thing.

The data and methodology are very experimental. You can download all results here:

https://s3-eu-west-1.amazonaws.com/crossref-labs-data/2015-10-06/reddit-dump-experiment.zip

It includes all data for charts in this post, as well as the full list of DOIs, the full list of URLs that could possibly have DOIs, and the full JSON input line for each of these.

More info

Read about our DOI Event Tracking strategy, including our live stream of Wikipedia citations.

Scheduled Booth Presentations at the Frankfurt Book Fair

Anna Tolwinska — Tue, 29 Sep 2015 00:00:00 +0000

Oktoberfest is in full swing and that makes me think that it’s almost Frankfurt Book Fair time again!

This year in addition to individual meetings we’ll have scheduled flash presentations on our booth, M91 in Hall 4.2. These short (10-minute) presentations are great for anyone wanting a quick intro to what Crossref is all about. Running on Wednesday, Thursday, and Friday - at the following times each of those days:

10am - Small Publisher Tools
12pm - DOIs & Metadata Basics
3pm - Exploring through APIs

If you’d like to meet with us (Ed Pentz, Ginny Hendricks, Rachael Lammey, or Anna Tolwinska) please contact Rosa Morais Clark to set up a meeting.

We look forward to seeing you there!

Taxonomies Meet-up at #FBM15

Ginny Hendricks — Fri, 25 Sep 2015 00:00:00 +0000

The Taxonomies Interest Group would like to invite Crossref members to an informal drop-in at the Frankfurt Book Fair:

4-5pm on Wednesday 14th October at the TEMIS booth H76

The group would like to discuss how different publishers use their taxonomies for content enrichment and to explore the role that the Crossref interest group can play in promoting industry collaboration and emerging standards. TEMIS have kindly offered to host the event at their booth and provide refreshments: Please come by from 4pm at Booth H76.

Graham McCann from IOP Publishing and Christian Kohl from De Gruyter will be coordinating the event. For background information on the work the group is doing, take a look at this webinar recording from March 2015.

Crossref to Auto-Update ORCID Records

Ginny Hendricks — Thu, 24 Sep 2015 00:00:00 +0000

In the next few weeks, authors with an ORCID iD will be able to have Crossref automatically push information about their published work to their ORCID record. It’s something that ORCID users have been asking for and we’re pleased to be the first to develop the integration. 230 publishers already include ORCID iDs in their metadata deposits with us, and currently there are 248,000 DOIs that include ORCID iDs.

What this means for researchers

More visibility for your work! Crossref represents over 5000 scholarly publishers and many of them ask authors for their ORCID iD and include it in the publication information they send us. Also it will mean less manual searching and adding; you’ve always been able to search crossref metadata for your name and/or publications and manually add them to your ORCID record, this auto-update simply means that when your publishers include the info we can update and add work(s) to your ORCID record automatically for you. You can still choose to hide/show whatever works you choose, and, of course, you’ll have the opportunity to authorize or switch off the integration completely (though future publications may trigger a new request). Overall, you’ll benefit from a more complete and up-to-date ORCID record to showcase your work.

What this means for publishers

If you’re one of the 230 Crossref publishers who already supply ORCID iDs along with the usual metadata submissions, then you’re all good. If you don’t offer this yet, you might want to think about starting - it’s beneficial for funders, publishers, other researchers, libraries, and universities to be able to integrate with complete researcher records. You can ask for ORCIDs upon manuscript submission or acceptance and tag it in your metadata deposits with Crossref. We’ll ensure the rest.

Various caveats and important details to be aware of

Apparently not all publishers are members of Crossref (we know, crazy), and in addition only a subset of Crossref publishers (230 in total) are asking authors for ORCID iDs and/or including them in their metadata deposits.
Some publishers may choose to opt out of passing through the details to ORCID using the Crossref auto-update (perhaps they plan to send this directly at some point) but if you’ve included your ORCID with your submission and it isn’t automatically updated, then check with your publisher.
We have a “backlog” of almost 250,000 DOIs that include ORCID iDs so that may mean we do some bulk updates at a later date where authors will receive an email with a long list of works to add. Even if the works have been listed before, it’s worth accepting as it will add the most up-to-date metadata to ensure the most accurate record.

Any questions can be directed to our support team.

Annual Meeting: Join Crossref in Boston this November!

April Ondis — Fri, 18 Sep 2015 00:00:00 +0000

We’d like to invite the scholarly publishing community to get together in Boston this November with the Crossref Annual Meeting as a rally point. This is the event we hold just once a year to get the whole team under one roof, host a lively discussion with the leading voices in scholarly communications, present technical workshops, and offer you the chance to get hands’ on with our latest metadata services. Our free two-day event takes place from November 17-18, 2015 in Boston, MA.

Agenda:

Tuesday, November 17 - Tech Workshops:

The morning is an opportunity to get into small groups and talk directly with our development and support teams. We will present best practices around using Crossref’s metadata. After lunch, we will feature member case studies with tips on implementation and lessons learned. If you’re on the technical production side of scholarly publishing, you’ll want to be there — and not just for the beer & pretzels afterwards.

Wednesday, November 18 - Member Meeting:

A day to hear from thought leaders from the larger scholarly publishing community as well as from inside Crossref. Our keynote speaker will be Dr. Ben Goldacre (Bad Science), and our distinguished speakers include Dr. Scott Chamberlain (rOpenSci), Dr. Juan Pablo Alperin (Public Knowledge Project), and Dr. Martin Eve, (Open Library of Humanities). We will share details about the road map for Crossref Labs’ current and future initiatives, hear about the latest organisational developments from new members of our team, and see the debut of our new brand logo and communications strategy. Following the formal discussion, we’ll continue the conversation over cocktails as part of our celebration of Crossref’s milestone 15th Anniversary!

✱ Tickets:

Reserve your free tickets here: https://www.eventbrite.com/e/crossref15-tech-workshops-member-meeting-tickets-17921679225

Who Should Attend?

Scholarly publishers, technology providers, librarians, researchers, academic institutions, funders, journalists, and others who are keen to discuss tools and services to advance scholarly publishing are encouraged to attend.

✱ Venue:

Hotel Taj Boston
15 Arlington Street
Boston, MA 02116 USA

About Crossref Crossref is a not-for profit membership organisation that wants to improve research communication. We organize publisher metadata, run the infrastructure that makes DOI links work, and we rally multiple community stakeholders in order to develop tools and services to enable advancements in scholarly publishing.

DOI Event Tracker (DET): Pilot progresses and is poised for launch

Jennifer Lin — Tue, 15 Sep 2015 00:00:00 +0000

Publishers, researchers, funders, institutions and technology providers are all interested in better understanding how scholarly research is used. Scholarly content has always been discussed by scholars outside the formal literature and by others beyond the academic community. We need a way to monitor and distribute this valuable information.

The Crossref DOI Event Tracker (DET)

To meet this need, Crossref will be introducing a new service that tracks activity surrounding a research work from potentially any web source where an event is associated with a DOI. Following a successful pilot run started Spring 2014, the service has been approved to move toward production and is expected to launch in 2016. Any party wishing to join this phase is welcome to contact Jennifer Lin. The DOI Event Tracker (DET) registers a wide variety of events such as bookmarks, comments, social shares, citations, and links to other research entities, from a growing list of online sources. DET aggregates them, and stores and delivers the data in many ways.

Open, portable, and licensed for maximum reuse

Crossref has long served as the citation linking and metadata infrastructure provider for scholarly communication; the new DOI Event Tracker is a natural next step, providing a practical solution as a resource for the whole community. The tracker offers the following features:

Data on event activity across a common pool of online channels.
Near real-time alerting for select sources with push notifications to the system.
Cross-publisher monitoring to enable benchmarking and provide context to the data.
Common format for normalizing data results across the diverse set of sources via modern REST API.
Secure and regularly refreshed backups of critical data for long term data preservation.
Transparency of data collection so as to ensure auditable, replicable, and trustworthy results.
Query-initiated retrieval or real-time alerts when an event of interest occurs.
CC-0 license for open and flexible propagation of data.

A number of platforms are already confirmed and more parties are welcomed at any stage. So far we have confirmation to track DOI events on the following platforms:

[table id=1 /]

This set of sources reflects our initial focus on parties willing to allow their data to be redistributed in the common pool. Efforts are underway to expand the source list to include Twitter and MyScienceWork, among others. Publishers can also act as sources by publishing and distributing DOI event data via the DET when an event occurs on its platform (for example, when a PDF is downloaded, or when a comment mentions a DOI in a locally hosted discussion forum, etc.). This would make local DOI activity globally available to funders, researchers, institutions, etc.

DET provides benefits of scale and ease of access as a central point for collecting and propagating data to the community. As a single point of access, it overcomes the business and technical hurdles that are a part of managing multiple online sources where scholarly activity occurs, in a rapidly changing landscape of online channels. This resource covers content across publishers and serves as a strong foundation to support the development of tools and services by any party. DET users will always be able to combine the DET data with those individually collected via negotiated or paid access. DET remains a utility separate from any value-added amenities, such as analytics, presentation, and reporting.

DET Service-Level Agreement

For those who seek the highest level of service and a more flexible range of access options, Crossref will provide a Service-Level Agreement (SLA) service for the DOI Event Tracker. The DET SLA includes the following additional features on top of the common data offering:

Access to the complete suite of sources, which includes restricted and/or paid sources in addition to common data, providing the fullest picture of DOI usage activity possible.
Guaranteed uptime and response time to the latest raw data on the aggregate activity surrounding a DOI.
Guaranteed support response time to questions and issues surrounding data and data delivery.
Flexible data access options: on-demand real time data access and scheduled bulk downloads for processing batch analytics.
Optimum retrieval rates and accelerated delivery speeds with the dedicated SLA API.
Access to a webhook API for events of interest as an alternative to polling DET.
Standardized and enhanced linkback service for the difficult-to-track, grey literature.

The DET SLA service has a simple, value-based pricing model based on subscriber size. Register your interest in Crossref’s DOI Event Tracker and the DET SLA service if you would like stay informed of the upcoming launch. Please contact Jennifer Lin for more information.

Image modified from “Radar” icon by Karsten Barnett from the Noun Project.

Best Practices for Depositing Funding Data

Kirsty Meddings — Tue, 01 Sep 2015 00:00:00 +0000

Crossref’s funding data initiative (FundRef) encourages publishers to deposit information about the funding sources of authors’ research as acknowledged in their papers. The funding data comprises funder name and identifier, and grant number or numbers. Funding data can be deposited on its own or with the rest of the metadata for an item of content.

There are two ways that publishers can collect this funding information for any given piece of content: by asking authors to input the funder name(s) and award number(s) via their submission system, or extracting the funder names and award numbers from the acknowledgements in the paper.

The funding data is only useful if it is standardised, and so it is absolutely critical that funder names are deposited with their associated funder IDs from the Funder Registry.

For publishers considering or about to start collecting and depositing funding data, and for those already doing so, we have drawn up some guidelines that will help you to ensure good quality metadata.

If you are collecting funding information from authors via your submission system:

Provide very clear instructions for your authors. Your submission system should prompt the author towards the canonical name from Crossref’s Funder Registry as they type, or guide them through a pick-list. Make it clear to authors that they should choose funder names from this list and not copy and paste from their manuscript.
Work with your submission system vendor or adapt your in-house system to make it easy for authors to select from the Funder Registry, and more difficult to paste incorrect names or ignore the suggested names. Consider a warning message if an unknown name is entered, and offer a list of close matches.
Instruct authors to look for the name of the funding body rather than a specific program or project.

If you or one of your vendors is extracting funding information from papers:

Provide the same clear instructions to your vendor(s). Stress the importance of matching the funder names in the acknowledgements to the names in the Funder Registry.
Look for common text-extraction errors such as concatenated funder names, punctuation errors, and stop words such as “of/for” that are commonly used interchangeably, or the presence or absence of “the” at the start of a funder name.

For both workflows:

Add QA into your workflow. Many of the names sent to Crossref without IDs are very obviously funders that are in the Registry, and a check by editorial or production staff could correct misspellings or fill in blanks. Check that grant numbers have been separated and are not being deposited as one long string.
Be aware that funder names deposited without IDs are not valid funding data and will be hidden from Crossref’s search tools and APIs until such time as they are updated with a funder ID.
The funding data section of a deposit (but not the rest of the deposit) will be rejected by the Crossref deposit system if
- The funder_name field contains a numerical string longer than 4 digits
- The funder_id field contains a number that is not an ID from the Funder Registry
- The funder_name contains text that exceeds 200 characters
Consider only depositing data that has funder IDs and holding the rest to re-poll against the Funder Registry at a later date when more funder names have been added. The Funder Registry is updated at approximately two-monthly intervals. You can sign up to be alerted to updates here.
If there are funders that appear regularly in your particular subject or geographical area that are not in the Registry, send a list to funder.registry@crossref.org.

DOIs and matching regular expressions

Andrew Gilmartin — Tue, 11 Aug 2015 00:00:00 +0000

We regularly see developers using regular expressions to validate or scrape for DOIs. For modern Crossref DOIs the regular expression is short

/^10.\d{4,9}/[-._;()/:A-Z0-9]+$/i

For the 74.9M DOIs we have seen this matches 74.4M of them. If you need to use only one pattern then use this one.

The other 500K are mostly from Crossref’s early days when the battle between “human-readable” identifiers and “opaque” identifiers was still being fought, the web was still new, and it was expected that “doi” would become as well a supported URI schema name as “gopher”, “wais”, …. Ok, that didn’t go so well.

An early Crossref’s member was John Wiley & Sons. They faced the need to design DOIs without much prior work to lean on. Many of those early DOIs are not expression friendly. Nevertheless, they are still valid and valuable permanent links to the work’s version of record. You can catch 300K more DOIs with

/^10.1002/[^\s]+$/i

While the DOI caught is likely to be the DOI within the text it may also contain trailing characters that, due to the lack of a space, are caught up with the DOI. Even the recommended expression catches DOIs ending with periods, colons, semicolons, hyphens, and underscores. Most DOIs found in the wild are presented within some visual design program. While pleasant to look at the visual design can misdirect machines. Is the period at the end of the line part of the DOI or part of the design? Is that endash actually a hyphen? These issues lead to a DOI bycatch.

Adding the following 3 expressions with the previous 2 leaves only 72K DOIs uncaught. To catch these 72K would require a dozen or more additional patterns. Each additional pattern, unfortunately, weakens the overall precision of the catch. More bycatch.

/^10.\d{4}/\d+-\d+X?(\d+)\d+<[\d\w]+:[\d\w]*>\d+.\d+.\w+;\d$/i

/^10.1021/\w\w\d++$/i

/^10.1207/[\w\d]+\&\d+_\d+$/i

Crossref is not the only DOI Registration Agency and while our members account for 65-75% of all registered DOIs this means there are tens of millions of DOIs that we have not seen. Luckily, the newer RAs and their publishers can copy our successes and avoid our mistakes.

Rehashing PIDs without stabbing myself in the eyeball

Geoffrey Bilder — Thu, 11 Jun 2015 00:00:00 +0000

Anybody who knows me or reads this blog is probably aware that I don’t exactly hold back when discussing problems with the DOI system. But just occasionally I find myself actually defending the thing…

About once a year somebody suggests that we could replace existing persistent citation identifiers (e.g. DOIs) with some new technology that would fix some of the weaknesses of the current systems. Usually said person is unhappy that current systems like

DOI, Handle, Ark, perma.cc, etc. depend largely on a social element to update the pointers between the identifier and the current location of the resource being identified. It just seems manifestly old-fashioned and ridiculous that we should still depend on bags of meat to keep our digital linking infrastructure from falling apart.

In the past, I’ve threatened to stab myself in the eyeball if I was forced to have the discussion again. But the dirty little secret is that I play this game myself sometimes. After all, the best thing a mission-driven membership organisation could do for its members would be to fulfil its mission and put itself out of business. If we could come up with a technical fix that didn’t require the social component, it would save our members a lot of money and effort.

When one of these ideas is posed, there is a brief flurry of activity as another generation goes through the same thought processes and (so far) comes to the same conclusions.

The proposals I’ve seen generally fall into one of the following groups:

Replace persistent identifiers (PIDs) with hashes, checksums, etc.
Just use search (often, but not always coupled with 1 above)
Automagically create PIDs out of metadata.
Automagically redirect broken citations to archived versions of the content identified
And more recently… use the blockchain

I thought it might help advance the discussion and avoid a bunch of dead ends if I summarised (rehashed?) some of the issues that should be considered when exploring these options.

Warning: Refers to FRBR terminology. Those of a sensitive disposition might want to turn away now.

DOIs, PMIDs, etc. and other persistent identifiers are primarily used by our community as “citation identifiers”. We generally cite at the “expression” level.
Consider the difference between how a “citation identifier” a “work identifier” and a “content verification identifier” might function.
How do you deal with “equivalent manifestations” of the same expression. For example the ePub, PDF and HTML representations of the same article are intellectually equivalent and interchangeable when citing. The same applies to csv & tsv representations of the same dataset. So, for example, how do hashes work here as a citation identifier?
Content can be changed in ways that typically doesn’t effect the interpretation or crediting of the work. For example, by reformatting, correcting spelling, etc. In these cases the copies should share the same citation identifier, but the hashes will be different.
Content that is virtually identical (and shares the same hash) might be republished in different venues (e.g. a normal issue and a thematic issue). Context in citation is important. How do you point somebody at the copy in the correct context?
Some copies of an article or dataset are stewarded by publishers. That is, if there is an update, errata, corrigenda, retraction/withdrawal, they can reflect that on the stewarded copy, not on copies they don’t host or control. Location is, in fact, important here.
Some copies of content will be nearly identical, but will differ in ways that would affect the interpretation and/or crediting of the work. A corrected number in a table for example. How would you create a citation form a search that would differentiate the correct version from the incorrect version?
Some content might be restricted, private or under embargo. For example private patient data, sensitive data about archaeological finds or the migratory patterns of endangered animals.
Some content is behind paywalls (cue jeremiads)
Content is increasingly composed of static and dynamic elements. How do you identify the parts that can be hashed?
How do you create an identifier out of metadata and not have them look like this?

This list is a starting point that should allow people to avoid a lot of blind alleys.

In the mean time, good luck to those seeking alternatives to the current crop of persistent citation identifier systems. I’m not convinced it is possible to replace them, but if it is- I hope I beat you to it. 🙂 And I hope I can avoid stabbing myself in the eye.

Coming to you Live from Wikipedia

Joe Wass — Wed, 20 May 2015 00:00:00 +0000

We’ve been collecting citation events from Wikipedia for some time. We’re now pleased to announce a live stream of citations, as they happen, when they happen. Project this on your wall and watch live DOI citations as people edit Wikipedia, round the world.

View live stream »

In the hours since this feature launched, there are events from Indonesian, Portugese, Ukrainian, Serbian and English Wikipedias (in that order).

The usual weasel words apply. This is a labs project and so may not be 100% stable. If you experience any problems please email labs@crossref.org .

January 2015 DOI Outage: Followup Report

Geoffrey Bilder — Tue, 17 Mar 2015 00:00:00 +0000

Background

On January 20th, 2015 the main DOI HTTP proxy at doi.org experienced a partial, rolling global outage. The system was never completely down, but for at least part of the subsequent 48 hours, up to 50% of DOI resolution traffic was effectively broken. This was true for almost all DOI registration agencies, including Crossref, DataCite and mEDRA.

At the time we kept people updated on what we knew via Twitter, mailing lists and our technical blog at CrossTech. We also promised that, once we’d done a thorough investigation, we’d report back. Well, we haven’t finished investigating all implications of the outage. There are both substantial technical and governance issues to investigate. But last week we provided a preliminary report to the Crossref board on the basic technical issues, and we thought we’d share that publicly now.

The Gory Details

First, the outage of January 20th was not caused by a software or hardware failure, but was instead due to an administrative error at the Corporation for National Research Initiatives (CNRI). The domain name “doi.org” is managed by CNRI on behalf of the International DOI Foundation (IDF). The domain name was not on “auto-renew” and CNRI staff simply forgot to manually renew the domain. Once the domain name was renewed, it took about 48 hours for the fix to propagate through the DNS system and for the DOI resolution service to return to normal. Working with CNRI we analysed traffic through the Handle HTTP proxy and here’s the graph:

The above graph shows traffic over a 24 hour period on each day from January 12, 2015 through February 10th, 2015. The heavy blue line for January 20th and the heavy red line for January 21st show how referrals declined as the doi.org domain was first deleted, and then added back to DNS.

It could have been much worse. The domain registrar (GoDaddy) at least had a “renewal grace and registry redemption period” which meant that even though CNRI forgot to pay its bill to renew the domain, the domain was simply “parked” and could easily be renewed by them. This is the standard setting for GoDaddy. Cheaper domain registrars might not include this kind of protection by default. Had there been no grace period, then it would have been possible for somebody other than CNRI to quickly buy the domain name as soon as it expired. There are many automated processes which search for and register recently expired domain names. Had this happened, at the very least it would have been expensive for CNRI to buy the domain back. The interruption to DOI resolutions during this period would have also been almost complete.

So we got off relatively easy. The domain name is now on auto-renew. The outage was not as bad as it could have been. It was addressed quickly and we can be reasonably confident that the same administrative error will not happen again. Crossref even managed to garner some public praise for the way in which we handled the outage. It is tempting to heave a sigh of relief and move on.

We also know that everybody involved at CNRI, the IDF and Crossref have felt truly dreadful about what happened. So it is also tempting to not re-open old wounds.

But it would be a mistake if we did not examine a fundamental strategic issue that this partial outage has raised: How can Crossref claim that its DOIs are ‘persistent’ if Crossref does not control some of the key infrastructure on which it depends? What can we do to address these dependencies?

What do we mean by “persistent?”

@kaythaney tweets on definition of “persistent”

To start with, we should probably explore what we mean by ‘persistent’. We use the word “persistent” or “persistence” about 470 times on the Crossref web site. The word “persistent” appears central to our image of ourselves and of the services that we provide. We describe our core, mandatory service as the “Crossref Persistent Citation Infrastructure.”

The primary sense of the word “persistent” in the New Oxford American Dictionary is:

Continuing firmly or obstinately in a course of action in spite of difficulty or opposition.

We play on this sense of the word as a synonym for “stubborn” when we half-jokingly say that, “Crossref DOIs are as persistent as Crossref staff.” Underlying this joke is a truth, which is that persistence is primarily a social issue, not a technical issue.

Yet presumably we once chose to use the word “persistent” instead of “perpetual” or “permanent” for other reasons. “Persistence” implies longevity, without committing to “forever.” Scholarly publishers, perhaps more than most industries, understand the long term. After all, the scholarly record dates back to at least 1665 and we know that the scholarly community values even our oldest journal backfiles. By using the word “persistent” as opposed to the more emphatic “permanent” we are essentially acknowledging that we, as an industry, understand the complexity and expense of stewarding the content for even a few hundred years to say nothing of “forever.” Only the chronologically naïve would recklessly coin terms like “permalink” for standard HTTP links which have a documented half-life of well under a decade.

So “persistent” implies longevity- without committing to forever- but this still begs questions. What time span is long enough to qualify as “persistent?” What, in particular, do we mean by “persistent” when we talk about Crossref’s “Persistent Citation Infrastructure?” or of Crossref DOIs being “persistent identifiers?”

What do we mean by “persistent identifiers?”

]5 @violetailik tweets on outage and implication for term “persistent identifier”

First, we often make the mistake of talking about “persistent identifiers” as if there is some technical magic that makes them continue working when things like HTTP URIs break. The very term “persistent identifier” encourages this kind of magical thinking and, ideally, we would instead talk about “persist-able” identifiers. That is, those that have some form of indirection built into them. There are many technologies that do this- Handles, DOIs, Purls, ARKs and every URL shortener in existence. Each of them simply introduces a pointer mapping between an identifier and location where a resource or content resides. This mapping can be updated when the content moves, thus preserving the link. Of course, just because an identifier is persist-able doesn’t mean it is persistent. If Purls or DOIs are not updated when content moves, then they are no more persistent than normal URLs.

Andrew Treloar points out that when we talk about “persistent identifiers,” we tend to conflate several things:

The persistence of the identifier- that is the token or string itself.
The persistence of the thing being pointed at by the identifier. For example, the content.
The persistence of the mapping of the identifier to the thing being identified.
The persistence of the resolver that allows one to follow the mapping of the identifier to the thing being identified.
The persistence of a mechanism for updating the mapping of the identifier to the thing being identified.

If any of the above fails, then “persistence” fails. This is probably why we tend to conflate them in the first place.

Each of these aspects of “persistence” is worthy of much closer scrutiny, however, in the most recent case of the January outage of “doi.org,” the problem specifically occurred with item “D”- the persistence of the resolver. When CNRI failed to renew the domain name for “doi.org” on time, the DOI resolver was rendered unavailable to a large percentage of people over a period of about 48 hours as global DNS servers first removed, and then added back the “doi.org” domain.

Turtles all the way down*

The initial public reaction to the outage was, almost unanimous in one respect- people assumed that the problem originated with Crossref.

@iainh_z tweets to Crossref enquiring about failed DOI resoluton

@LibSkrat tweets at Crossref about DOI outage

This is both surprising and unsurprising. It is surprising because we have fairly recent data indicating that lots of people recognise the DOI brand, but not the Crossref brand. Chances are, that this relatively superficial “brand” awareness does not correlate with understanding how the system works or how it relates to persistence. It is likely plenty of people clicked on DOIs at the time of the outage and, when they didn’t work, simply shrugged or cursed under their breath. They were aware of the term ‘DOI’ but not of the promise of “persistence”. Hence, they did not take to twitter to complain about it, and if they did, they probably wouldn’t have known who to complain to or even how to complain to them (neither CNRI or the IDF has a Twitter account).

But the focus on Crossref is also unsurprising. Crossref is by far the largest and most visible DOI Registration Agency. Many otherwise knowledgeable people in the industry simply don’t know that there are even other RAs.

They also generally didn’t know of the strategic dependencies that exist in the Crossref system. By “strategic dependencies” we are not talking about the vendors, equipment and services that virtually every online enterprise depends on. These kinds of services are largely fungible. Their failures may be inconvenient and even dramatic, but they are rarely existential.

Instead we are talking about dependencies that underpin Crossref’s ability to deliver on its mission. Dependencies that not only affect Crossref’s operations, but also its ability to self-govern and meet the needs of its membership. In this case there are three major dependencies: Two of which are specific to Crossref and other DOI registration agencies and one which is shared by virtually all online enterprises today. The organisations are: The International DOI Foundation (IDF), Corporation for National Research Initiatives (CNRI) and the Internet Corporation for Assigned Names and Numbers (ICANN).

Dependency of RAs on IDF, CNRI and ICANN. Turtles all the way down.

Each of these agencies has technology, governance and policy impacts on Crossref and the other DOI registration agencies, but here we will focus on the technological dependencies.

At the top of the diagram are a subset of the various DOI Registration Agencies. Each RA uses the DOI for a particular constituency (e.g. scholarly publishers) and application (e.g. citation). Sometimes these constituencies/applications overlap (as with mEDRA, Crossref and DataCite), but sometimes they are orthogonal to the other RAs, as is the case with EIDR. All, however, are members of the IDF.

The IDF sets technical policies and development agendas for the DOI infrastructure. This includes recommendations about how RAs should display and link DOIs. Of course all of these decisions have an impact on the RAs. However, the IDF provides little technical infrastructure of its own as it has no full-time staff. Instead it outsources the operation of the system to CNRI, this includes the management of the doi.org domain which the IDF owns.

The actual DOI infrastructure is hosted on a platform called the Handle System which was developed by and is currently run by CNRI. The Handle System is part of a quite complex and sophisticated platform for managing digital objects that was originally developed for DARPA. A subset of the Handle system is designated for use by DOIs and is identified by the “10” prefix (e.g. 10.5555/12345678). The Handle system itself is not based on HTTP (the web protocol). Indeed, one of the much touted features of the Handle System is that it isn’t based on any specific resolution technology. This was seen as a great virtue in the late 1990s when the DOI system was developed and the internet had just witnessed an explosion of seemingly transient, competing protocols (e.g. Gopher, WAIS, Archie, HyperWave/Hyper-G, HTTP, etc.). But what looked like a wild-west of protocols quickly settled into an HTTP hegemony. In practice, virtually all DOI interactions with the Handle system are via HTTP and so, in order to interact with the web, the Handle System employs a “Handle proxy” which translates back and forth between HTTP, and the native Handle system. This all may sound complicated, and the backend of the Handle system is really very sophisticated, but it turns out that the DOI really uses only a fraction of the Handle system’s features. In fact, the vast majority of DOI interactions merely use the Handle system as a giant lookup table which allows one to translate an identifier into a web location. For example, it will take a DOI Handle like this:

10.5555/12345678

and redirect it to (as of this writing) the following URL:

http://psychoceramics.labs.crossref.org.pluma.sjfc.edu/10.5555-12345678.html

This whole transformation is normally never seen by a user. It is handled transparently by the web browser, which does the lookup and redirection in the background using HTTP and talking to the Handle Proxy. In the late 1990s, even doing this simple translation quickly, at scale with a robust distributed infrastructure, was not easy. These days however we see dozens if not hundreds of “URL Shorteners” doing exactly the same thing at far greater scale than the Handle System.

It may seem a shame that more of the Handle Systems features are not used, but the truth is the much touted platform independence of the Handle System rapidly became more of a liability and impediment to persistence than an aid. To be blunt, if in X years a new technology comes out that supersedes the web, what do we think the societal priority is going to be?

To provide a robust and transparent transition from the squillions of existing HTTP URI identifiers that the entire world depends on?
To provide a robust and transparent transition from the tiny subset of Handle-based identifiers that are used by about a hundred million specialist resources?

Quite simply, the more the Handle/DOI systems diverge from common web protocols and practice, then the more we will jeopardise the longevity of our so-called persistent identifiers.

So, in the end, DOI registration agencies really only use the Handle system for translating web addresses. All of the other services and features one might associate with DOIs (reference resolution, metadata lookup, content negotiation, OAI-PMH, REST APIs, Crossmark, CrossCheck, TDM Services, FundRef etc) are all provided at the RA level.

But this address resolution is still critical. And it is exactly what failed for many users on January 20th 2015. And to be clear, it wasn’t the robust and scaleable Handle System that failed. It wasn’t the Handle Proxy that failed. And it certainly wasn’t any RA-controlled technology that failed. These systems were all up and running. What happened was that the standard handle proxy that the IDF recommends RAs use, “dx.doi.org”, was effectively rendered invisible to wide portions the internet because the “doi.org” domain was not renewed. This underscores two important points.

The first is that it doesn’t much matter what precisely caused the outage. In this case it was an administrative error. But the effect would have been similar if the Handle proxies had failed of if the Handle system itself had somehow collapsed. In the end, Crossref and all DOI registration agencies are existentially dependent on the Handle system running and being accessible.

The second is that the entire chain of dependencies from the RAs down through CNRI are also dependent on the DNS system which, in turn, is governed by ICANN. We should really not be making too much of the purported technology independence of the DOI and Handle systems. To be fair, this limitation is inherent to all persistent identifier schemes that aim to work with the web. It really is “turtles all the way down.”

What didn’t fail on January 19th/20th and why?

You may have noticed a lot of hedging in our description of the outage of January 19th/20th. For one thing, we use the term “rolling outage.” Access to the Handle Proxy via “dx.doi.org” was never completely unavailable during the period. As we’ve explained, this is because the error was discovered very quickly and the domain was renewed hours after it expired. The nature of DNS propagation meant that even as some DNS servers were deleting the “doi.org” entry, others were adding it back to their tables. In some ways this was really confusing because it meant it was difficult to predict where the system was working and where it wasn’t. Ultimately it all stabilised after the standard 48-hour DNS propagation cycle.

But there were also some Handle-based services that simply were not affected at all by the outage. During the outage, a few people asked us if there was an alternative way to resolve DOIs. The answer was “yes,” there were several. It turns out that “doi.org” is not the only DNS name that points to the Handle Proxy. People could easily substitute “dx.doi.org” with “dx.crossref.org” or “dx.medra.org” or “hdl.handle.net” and “resolve” any DOI. Many of Crossref’s internal services use these internal names and so the services continued to work. This is partly why we only discovered the “doi.org” was down from people reporting it on Twitter.

And, of course, there were other services that were not affected by the outage. Crossmark, the REST API, and Crossref Metadata Search all continued to work during the outage.

Protecting ourselves

So what can we do to reduce our dependencies and/or the risks intrinsic to those dependencies?

Obviously, the simplest way to have avoided the outage would have been to ensure that the “doi.org” domain was set to automatically renew. That’s been done. Is there anything else we should do? A few ideas have been floated that might allow us to provide even more resilience. They range greatly in complexity and involvement.

Provide well-publicised public status dashboards that show what systems are up and which clearly map dependencies so that people could, for instance, see that the doi.org server was not visible to systems that depended on it. Of course, if such a dashboard had been hosted at doi.org, nobody would have been able to connect to it. Stoopid turtles.
Encourage DOI RAs to have the members point to Handle proxies using domain names under the RA’s control. Simply put, if Crossref members had been using “dx.crossref.org” instead of “dx.doi.org”, then Crossref DOIs would have continued to work throughout the outage of “doi.org”. The same with mEDRA, and the other RAs. This way each RA would have control over another critical piece of their infrastructure. It would also mean that if any single RA made a similar domain name renewal mistake, the impact would be isolated to a particular constituency. Finally, using RA-specific domains for resolving DOIs might also make it clear that different DOIs are managed by different RAs and might have different services associated with them. Perhaps Crossref would spend less time supporting non-Crossref DOIs?
Provide a parallel, backup resolution technology that could be pointed to in the event of a catastrophic Handle System failure. For example we could run a parallel system based on PURLs, ARKs or another persist-able identifier infrastructure.
Explore working with ICANN to get the handle resolvers moved under the special “.arpa” top level domain (TLD). This TLD (RFC 3172) is reserved for services that are considered to be “critical to the operation of the internet.” This is an option that was first discussed at a meeting of persistent identifier providers in 2011.

These are all tactical approaches to addressing the specific technical problem of the Handle System becoming unavailable, but they do not address deeper issues relating to our strategic dependence on several third parties. Even though the IDF and CNRI provide us with pretty simple and limited functionality, that functionality is critical to our operations and our claim to be providing persistent identifiers. Yet these technologies are not in our direct control. We had to scramble to get hold of people to fix the problem. For a while, we were not able to tell our users or members what was happening because we did not know ourselves.

The irony is that Crossref was held to account, and we were in the firing line the entire time. Again, this was almost unavoidable. In addition to being the largest DOI RA, we are also the only RA that has any significant social media presence and support resources. Still, it meant that we were the public face of the outage while the IDF and CNRI remained in the background.

And this is partly why our board has encouraged us to investigate another option:

Explore what it would take to remove Crossref dependencies on the IDF and CNRI.

Crossref is just part of a chain of dependencies the goes from our members down through the IDF, CNRI and, ultimately, ICANN. Our claim to providing a persistent identifier structure depends entirely on the IDF and CNRI. Here we have explored some of the technical dependencies. But there are also complex governance and policy implications of these dependencies. Each organisation has membership rules, guidelines and governance structures which can impact Crossref members. Indeed, the IDF and CNRI are themselves members of groups (ISO and DONA, respectively) which might ultimately have policy or governance impact for DOI registration agencies. We will need to understand the strategic implications of these non technical dependencies as well.

Note that the Crossref board has merely asked us to “explore” what it would take to remove dependencies. They have not asked us to actually take any action. Crossref has been massively supportive of the IDF and CNRI, and they have been massively supportive of us. Still, over the years we have all grown and our respective circumstances have changed. It is important that occasionally we question what we might have once considered to be axioms. As we discussed above, we use the term “persistent” which, in turn, is a synonym for “stubborn.” At the very least we need to document the inter-dependencies that we have so that we can understand just how stubborn we can reasonably expect our identifiers to be.

The outage of January 20th was a humbling experience. But in a way we were lucky: Forgetting to renew the domain name was a silly and prosaic way to partially bring down a persistent identifier infrastructure, but it was also relatively easy to fix. Inevitably, there was a little snark and some pointed barbs directed at us during the outage, but we were truly overwhelmed by the support and constructive criticism we received as well. We have also been left with a clear message that, in order for this good-will to continue, we need to follow-up with a public, detailed and candid analysis of our infrastructure and its dependencies. Consider this to be the first section of a multi-part report.

@kevingashley tweets asking for followup analysis

@WilliamKilbride tweets asking for followup and lessons learned

Image Credits

Turtle image CC-BY “Unrecognised MJ” from the Noun Project

Real-time Stream of DOIs being cited in Wikipedia

Joe Wass — Tue, 03 Mar 2015 00:00:00 +0000

TL;DR

Watch a real-time stream of DOIs being cited (and “un-cited!” ) in Wikipedia articles across the world: https://live-eventdata-crossref-org.pluma.sjfc.edu/live.html

Background

For years we’ve known that the Wikipedia was a major referrer of Crossref DOIs and about a year ago we confirmed that, in fact, the Wikipedia is the 8th largest refer of Crossref DOIs. We know that people follow the DOIs, too. This despite a fraction of Wikipedia citations to the scholarly literature even using DOIs. So back in August we decided to create a Wikimedia Ambassador programme. The goal of the programme was to promote the use of persistent identifiers in citation and attribution in Wikipedia articles. We would do this through outreach and through the development of better citation-related tools.

Remember when we originally wrote about our experiments with the PLOS ALM code and how that has transitioned into the DOI Event Tracking Pilot? In those posts we mentioned that one of the hurdles in gathering information about DOI events is the actual process of polling third party APIs for activity related to millions of DOIs. Most parties simply wouldn’t be willing handle the load of a 100K API calls an hour. Besides, polling is a tremendously inefficient process, only a fraction of DOIs are ever going to generate events, but we’d have to poll for each of them, repeatedly, forever, to get an accurate picture of DOI activity. We needed a better way. We needed to see if we could reverse this process and convince some parties to instead “push” us information whenever they saw DOI related events (e.g. citations, downloads, shares, etc). If only we could convince somebody to try this…

Wikipedia DOI Events

In December 2014 we took the opportunity of the 2014 PLOS/Crossref ALM Workshop in San Francisco too meet with Max Klein and Anthony Di Franco where we kicked off a very exciting project.

There’s always someone editing a Wikipedia somewhere in the world. In fact, you can see a dizzying live stream of edits. We thought that given that there are so many DOIs in Wikipedia, that live stream may contain some diamonds (DOIs are made of diamond, that’s how they can be persistent). Max and Anthony went away and came back with a demo that contains a surprising amount of DOI activity.

That demo is evolving into a concrete service, called Cocytus. It is running at Wikimedia Labs monitoring live edits as you read this.

For now we’re feeding that data into the DOI Events Collection app (which is an off-shoot of the Chronograph project). We are in the process of modifying the Lagotto code so that we can instead push those events into the DOI Event Tracking Instance.

The first DOI event we noticed was delightfully prosaic: The DOI for “The polymath project” is cited by the Wikipedia page for “Polymath Project”. Prosaic perhaps, but the authors of that paper probably want to know. Maybe they can help edit the page.

Or how about this. Someone wrote a a paper about why people edit Wikipedia and then it was cited by Wikipedia. And then the citation was removed. The plot thickens…

We’re interested in seeing how DOIs are used outside of the formal scholarly literature. What does that mean? We don’t fully know, that’s the point. We have retractions in scholarly literature (and our Crossmark metadata and service allow publishers to record that), but it’s a bit different on Wikipedia. Edit wars are fought over … well you can see for yourself.

Citations can slip in and out of articles. We saw the DOI 10.1001/archpediatrics.2011.832 deleted from “Bipolar disorder in children”. If we’d not been monitoring the live feed (we had considered analysing snapshots of the Wikipedia in bulk) we might never have seen that. This is part of what non-traditional citations means, and it wasn’t obvious until we’d seen it.

You can see this activity on the Chronograph’s stream. Or check your favourite DOI. Please be aware that we’re only collecting newly added citations as of today. We do intend to go back and back-fill, but that may take some time- as it * cough * requires polling again.

Some Technical Things

A few interesting things that happened as a result of all this:

Secure URLs

SSL and HTTPS were invented so you could do things like banking on the web without fear of interception or tampering. As the web becomes a more important part of life, many sites are upgrading from HTTP to HTTPS, the secure version. This is not only because your confidential details may be tampered with, but because certain governments might not like you reading certain materials.

Because of this, some time ago, Wikipedia decided to embark on an upgrade to HTTPS last year, and they are a certain way along the path. The IDF, who are responsible for running the DOI system, upgraded to HTTPS this Summer, although most DOIs are referred to by HTTP still.

We met with Dario Taraborelli at the ALM workshop and discussed the DOI referral data that is fed into the Chronograph. We put two and two together and realised that Wikipedia was linking to DOIs (which are mostly HTTP) from pages which might be served over HTTPS. New policies in HTML5 specify that referrer URL headers shouldn’t be sent from HTTPS to HTTP (in case there was something secret in them). The upshot of this is, if someone’s browsing Wikipedia via HTTPS and click on a normal DOI, we won’t know that the user came from Wikipedia. Not a huge problem today, but as Wikipedia switches over to entirely secure, we’re going to miss out on very useful information.

Fortunately, the HTML5 specification includes a way to fix this (without leaking sensitive information). We discussed this with Dario, and he did some research, and came up with a suggestion, which got discussed. It’s fascinating to watch a democratic process like this take place and take part in it.

We’re waiting to see how the discussion turns out, and hope that it all works out so we can continue to report on how amazing Wikipedia is at sending people to scholarly literature.

How shall I cite thee?

Another discussion grew out of that process, and we started talking to a Wikipedian called Nemo (note to Latin scholars: we weren’t just talking to ourselves). Nemo (real name Federico Leva) had a few suggestions of his own. Another way to solve the referrer problem is by using HTTPS URLs (HTML5 allows browsers to send the referrer domain when going from HTTPS to HTTPS).

This means going back to all the articles that use DOIs and change them from HTTP to HTTPS. Not as simple as it sounds, and it doesn’t sound simple. We started looking into how DOIs were cited on Wikipedia.

After some research we found that there are more ways that we expected to cite DOIs.

First, there’s the URL. You can see it in action in this article. URLs can take various forms.

Second there’s the official template tag, seen in action here:

<ref name="SCI-20140731">{{cite journal |title=Sustained miniaturization and anatomical innovation in the dinosaurian ancestors of birds |url=http://www.sciencemag.org.pluma.sjfc.edu/content/345/6196/562 |date=1 August 2014 |journal=[[Science (journal)|Science]] |volume=345 |issue=6196 |pages=562–566 |doi=10.1126/science.1252243 |accessdate=2 August 2014 |last1=Lee |first1=Michael S. Y. |first2=Andrea|last2=Cau |first3=Darren|last3=Naish|first4=Gareth J.|last4=Dyke}}</ref>

There’s a DOI in there somewhere. This is the best way to cite DOIs, firstly as it’s actually a proper traditional citation and there’s nothing magic about DOIs, secondly because it’s a template tag and can be re-rendered to look slightly different if needed.

Third there’s the old official DOI template tag that’s now discouraged:

<ref name="Example2006">{{Cite doi|10.1146/annurev.earth.33.092203.122621}}</ref>

And then there’s another one.

{{doi|10.5555/123456789}}

Knowing all this helps us find DOIs. But if we want to convert DOIs links in Wikipedia to use HTTPS, it means that there are more template tags to modify and more pages to re-render.

Nemo also put DOIs on the Interwiki Map which should make automatically changing some of the URLs a lot easier.

We’re very grateful to Nemo for his suggestions and work on this. We’ll report back!

The elephant in the room

Those of you who know how DOIs work will have spotted an unsecured elephant in the room. When you visit a DOI, you visit the URL, which hits the DOI resolver proxy server, which returns a message to your browser to redirect to the landing page on the publisher’s site.

Securely talking to the DOI resolver by using HTTPS instead of HTTP means that no-one can eavesdrop and see which DOI you are visiting, or tamper with the result and send you off to a different page. But the page you are sent to will be, in nearly all cases, still HTTP. Upgrading infrastructure isn’t trivial, and, with over 4000 members (mostly publishers), most Crossref DOIs will still redirect to standard HTTP pages for the foreseeable future.

You can keep as secure as possible by using HTTPS Everywhere.

Fin

There’s lots going on, watch this space to see developments. Thanks for reading this, and all the links. We’d love to know what you think.

Bootnote

Not long after this blog post was published we saw something very interesting.

That’s no DOI. We like interesting things, but they can panic us. This turned out to be a great example of why this kind of thing can be useful. A minute’s digging and we found the article edit:

It turns out that this was a typo: someone put a title when they should have put in a DOI. And, as the event shows, this was removed from the Wikipedia article.

Crossref’s DOI Event Tracker Pilot

Geoffrey Bilder — Mon, 02 Mar 2015 00:00:00 +0000

TL;DR

Crossref’s “DOI Event Tracker Pilot”- 11 million+ DOIs & 64 million+ events. You can play with it at: http://goo.gl/OxImJa

Tracking DOI Events

So have you been wondering what we’ve been doing since we posted about the experiments we were conducting using PLOS’s open source ALM code? A lot, it turns out. About a week after our post, we were contacted by a group of our members from OASPA who expressed an interest in working with the system. Apparently they were all about to conduct similar experiments using the ALM code, and they thought that it might be more efficient and interesting if they did so together using our installation. Yippee. Publishers working together. That’s what we’re all about.

So we convened the interested parties and had a meeting to discuss what problems they were trying to solve and how Crossref might be able to help them. That early meeting came to a consensus on a number of issues:

The group was interested in exploring the role Crossref could play in providing an open, common infrastructure to track activities around DOIs, they were not interested in having Crossref play a role in the value-add services of reporting on an interpreting the meaning of said activities.
The working group needed representatives from multiple stakeholders in the industry. Not just open access publishers from OASPA, but from subscription based publishers, funders, researchers and third party service providers as well.
That it was desirable to conduct a pilot to see if the proposed approach was both technically feasible and financially sustainable.

And so after that meeting, the “experiment” graduated to becoming a “pilot.” This Crossref pilot is based on the premise that the infrastructure involved in tracking common information about “DOI events” can be usefully separated from the value-added services of analysing and presenting these events in the form of qualitative indicators. There are many forms of events and interactions which may be of interest. Service providers will wish to analyse, aggregate and present those in a range of different ways depending on the customer and their problem. The capture of the underlying events can be kept separate from those services.

In order to ensure that the Crossref pilot is not mistaken for some sub rosa attempt to establish new metrics for evaluating scholarly output, we also decided eschew any moniker that includes the word “metrics” or synonyms. So the “ALM Experiment” is dead. Long live the “”DOI Event Tracker” (DET) pilot. Similarly PLOS’s open source “ALM software” has been resurrected under the name “Lagotto.”

The Technical Issues

Crossref members are interested in knowing about “events” relating to the DOIs that identify their content. But our members face a now-classic problem. There are a large number of sources for scholarly publications (3k+ Crossref members) and that list is still growing. Similarly, there are an unbounded number of potential sources for usage information. For example:

Supplemental and grey literature (e.g. data, software, working papers)
Orthogonal professional literature (e.g. patents, legal documents, governmental/NGO/IGO reports, consultation reports, professional trade literature).
Scholarly tools (e.g. citation management systems, text and data mining applications).
Secondary outlets for scholarly literature (institutional and disciplinary repositories, A&I services).
Mainstream media (e.g. BBC, New York Times).
Social media (e.g. Wikipedia, Twitter, Facebook, Blogs, Yo).

Finally, there is a broad and growing audience of stakeholders who are interested in seeing how the literature is being used. The audience includes publishers themselves as well as funders, researchers, institutions, policy makers and citizens.

Publishers (or other stakeholders) could conceivably each choose to run their own system to collect this information and redistribute it to interested parties. Or they can work with a vendor to do the same. But either case, they would face the following problems:

The N sources will change. New ones will emerge. Old ones will vanish.
The N audiences will change. New ones will emerge. Old ones will vanish.
Each publisher/vendor will need to deal with N source’s different APIs, rate limits, T&Cs, data licenses, etc. This is a logistical headache for both the publishers/vendors and for the sources.
Each audience will need to deal with N publisher/vendor APIs, rate limits, T&Cs, data licenses, etc. This is a logistical headache for both the audiences and for the publishers.
If publishers/vendors use different systems which in turn look at different sources, it will be difficult to compare or audit results across publishers/vendors.
If a journal moves from one publisher to another, then how are the metrics for that journal’s articles going to follow the journal?

And then there is the simple issue of scale. Most parties will be interested in comparing the data that they collect for their own content, with data about their competitors. Hence, if they all run their own system, they will each be querying much more than their own data. If, for example, just the commercial third-party providers were interested in collecting data covering the formal scholarly literature, they would each find themselves querying the same sources for the same 80 million DOIs. To put this into perspective, to refresh the data for 10 million DOIs once a month, would require sources to support ~ 14K API calls an hour. 60 million DOIs would require 100K API calls an hour. Current standard API caps for many of the sources that people are interested in querying hover around 2K per hour. We may see these sources lift that cap for exceptional cases, but they are unlikely to do so for many different clients all of whom are querying essentially the same thing.

These issues typify the “multiple bilateral relationships” problem that Crossref was founded to try and ameliorate. When we have many organisations trying to access the exact same APIs to process the exact same data (albeit to different ends), then it seems likely that Crossref could help make the process more efficient.

Piloting A Proposed Solution

The Crossref DET pilot aims to show the feasibility of providing a hub for the collection, storage and propagation of DOI events from multiple sources to multiple audiences.

Data Collection

Pull: DET will collect DOI event data from sources that are of common interest to the membership, but which are unlikely to make special efforts to accommodate the scholarly communications industry. Examples of this class of source include large, broadly popular services like FaceBook, Twitter, VK, Sina Weibo, etc.
Push: DET will allow sources to send DOI event data directly to Crossref in one of three ways:
- Standard Linkback: Using standards that are widely used on the web. This will automatically enable linkback-aware systems like WordPress, Moveable Type, etc. to alert DET to DOI events.
- Scholarly Linkback: A to-be-defined augmented linkback-style API which will be optimized to work with scholarly resources and which will allow for more sophisticated payloads including other identifiers (e.g. ORCIDs, FundRefs), metadata, provenance information and authorization information. This system could be used by tools designed for scholarly communications. So, for example, it could be used by publisher platforms to distribute events related to downloads or comments within their discussion forums. It could also be used by third party scholarly apps like Zotero, Mendeley, Papers, Authorea, IRUS-UK, etc. in order to alert interested parties in events related to specific DOIs.
- Redirect: DET will also be able to serve as a service discovery layer that will allow sources to push DOI event data directly to an appropriate publisher-controlled endpoint using the above scholarly linkback mechanism. This can be used by sources like repositories in order to send sensitive usage data directly to the relevant publishers.

Data Propagation

Parties may want to use the DET in order to propagate information about DOI events. The system will support two broad data propagation patterns:

one-to-many: DOI events that are commonly harvested (pulled) by the DET system from a single source will be distributed freely to anybody who queries the DET API. Similarly, sources that push DOI events via the standard or scholarly linkback mechanisms, will also propagate their DOI events openly to anybody who queries the DET API. DOI events that are propagated in either of these cases will be kept and logged by the DET system along with appropriate provenance information. This will be the most common, default propagation model for the DET system.
one-to-one: Sources of DOI events can also report (push) DOI event data directly to owner of the relevant DOI if the DOI owner provides & registers a suitable end-point with the DET system. In these cases, data sources seeking to report information relating to a DOI, will be redirected (with a suitable 30X HTTP status and relevant headers) to the end-point specified by the DOI owner. The DET system will not keep the request or provenance information. One-to-one propagation model is designed to handle use cases where the source of the DOI event has put restrictions on the data and will only share the DOI events with the owner (registrant) of the DOI. This use case may be used, for example, by aggregators or A&I services that want to report confidential data directly back to a publisher. The advantage of the redirect mechanism is that Crossref is not put into the position of having to secure sensitive data as said data will never reside on Crossref systems.

Note that the two patterns can be combined. So, for example, a publisher might want to have public social media events reported to the DET and propagated accordingly, but to also to private third parties report confidential information directly to the publisher.

So Where Are We?

So to start with, the DET Working Group has grown substantially since the early days and we have representatives from a wide variety of stakeholders. The group includes:

Cameron Neylon, PLOS
Chris Shillum, Elsevier
Dom Mitchell, Co-action Publishing
Euan Adie, Altmetric
Jennifer Lin, PLOS
Juan Pablo Alperin, PKP
Kevin Dolby, Wellcome Trust
Liz Ferguson, Wiley
Maciej Rymarz, Mendeley
Mark Patterson, eLife
Martin Fenner, PLOS
Mike Thelwell, U Wolverhampton
Rachel Craven, BMC
Richard O’Beirne, OUP
Ruth Ivimey-Cook, eLife
Victoria Rao, Elsevier

As well as the usual contingent of Crossref cat-herders including: Geoffrey Bilder, Rachael Lammey & Joe Wass.

When we announced the then-DET experiment, we said that one of the biggest challenges would be to create something that scaled to industry levels. At launch, we only loaded in about 317,500+ Crossref DOIs representing publications from 2014 and we could see the system was going to struggle. Since then Martin Fenner and Jennifer Lin at PLOS have been focusing on making sure that the Lagotto code scales appropriately and now it is currently humming along with just over 11.5 million DOIs for which we’ve gathered over 64 million “events.” We aren’t worried about scalability on that front any more.

We’ve also shown that third parties should be able to access the API to provide value added reporting and metrics. As a demonstration of this, PLOS configured a copy of its reporting software “Parascope” to point at the Crossref DET instance. The next step we’re taking is to start testing the “push” API mechanism and the “point-to-point redirect” API mechanism. For the push API, we should have a really exciting demo available to show within the next few days. And on the point-to-point redirect, we have a sub-group exploring how the point-to-point redirect mechanism could potentially be used for reporting COUNTER stats as a compliment to the Sushi initiative.

The other major outstanding task we have before us is to calculate what the costs will be of running the DET system as a production service. In this case we expect to have some pretty accurate data to go on as we will have had close to half a year of running the pilot with a non-trivial number of DOIs and sources. Note that the work group is concerned to ensure that the underlying data from the system remains open to all. Keeping this raw data open as seen as critical to establishing trust in the metrics and reporting systems that third parties build on the data. The group has also committed to leaving the creation of value-add services to third parties. As such we have been focusing on exploring business models based around service-level-agreement backed versions of the API to complement the free version of the same API. The free API will come with no guarantees of uptime, performance characteristics or support. For those users that depend on the API in order to deliver their services, we will offer paid-for SLA-backed versions of the free APIs. We can then configure our systems so that we can independently scale these SLA-backed APIs in order to meet SLA agreements.

Our goal is to have these calculations complete in time for the working group to make a recommendation to the Crossref board meeting in July 2015.

Until then, we’ll use CrossTech as a venue for notifying people when we’ve hit new milestones or added new capabilities to the DET Pilot system.

Problems with dx.doi.org on January 20th 2015- what we know.

Geoffrey Bilder — Wed, 21 Jan 2015 00:00:00 +0000

Hell’s teeth.

So today (January 20th, 2015) the DOI HTTP resolver at dx.doi.org started to fail intermittently around the world. The doi.org domain is managed by CNRI on behalf of the International DOI Foundation. This means that the problem affected all DOI registration agencies including Crossref, DataCite, mEDRA etc. This also means that more popularly known end-user services like FigShare and Zenodo were affected. The problem has been fixed, but the fix will take some time to propagate throughout the DNS system. You can monitor the progress here:

https://www.whatsmydns.net/#A/doi.org

Now for the embarrassing stuff…

At first lots of people were speculating that the problem had to do with somebody forgetting to renew the dx.doi.org domain name. Our information from CNRI was that the problem had to do with a mistaken change to a DNS record and that the domain name wasn’t the issue. We corrected people who were reporting that domain name renewal as the cause, but eventually we learned that it was actually true. We have had it confirmed that the problem originated with CNRI manually renewing the domain name at the last minute. Ugh. CNRI will issue a statement soon. We’ll link to it as soon as they do. UPDATE (Jan 21st): CNRI has sent Crossref a statement. They do not have it on their site yet, so we have can included it below.

In the mean time, if you are having trouble resolving DOIs, a neat trick to know is that you can do so using the Handle system directly. For example:

http://hdl.handle.net/10.5555/12345678

Crossref will, of course, also analyse what occurred, and issue a public report as well. Obviously, this report will include an analysis of how the outage effected DOI referrals to our members.

The amazingly cool thing is that everybody online has been very supportive and has helped us to diagnose the problem. Some have even said that the event underscores a point we often make about so-called “persistent-identifiers”- which is that they are not magic technology; the “persistence” is the result of a social contract. We like to say that Crossref DOIs are as persistent as Crossref staff. Well, to that phrase we have to add “and IDF staff” and “CNRI staff” and “ICANN staff”. It is turtles all the way down.

We don’t want to dismiss this event as an inevitable consequence of interdependent systems.And we don’t want to pass the buck. We need to learn something practical from this. How can we guard against this type of problem in the future? Again, people following this issue on Twitter have already been helping with suggestions and ideas. Can we crowd-source the monitoring of persistent identifier SLAs? Could we leverage Wikipedia, Wikidata or something similar to monitor critical identifiers and other infrastructure like purls, DOIs, handles, PMIDs, perma.cc, etc? Should we be looking at designating special exceptions to the normal rules governing DNS names? Do we need to distribute the risk more? Or is it enough cough to simply ensure that somebody, somewhere in the dependency chain had enabled DNS protection and auto-renewal for critical infrastructure DNS names?

Truly, we are humbled. For all the redundancy built into our systems (multiple servers, multiple hosting sites, Raid drives, redundant power), we were undone by a simple administrative task. Crossref, IDF and CNRI- we all feel a bit crap. But we’ll get back. We’ll fix things. And we’ll let you know how we do it.

We will update this space as we know more. We will also keep people updated on twitter on @CrossrefNews. And we will report back in detail as soon as we can.

CNRI Statement

"The doi.org domain name was inadvertently allowed to expire for a brief period this morning (Jan 20). It was reinstated shortly after 9am this morning as soon as the relevant CNRI employee learned of it. A reminder email sent earlier this month to renew the registration was apparently missed. We sincerely apologize for any difficulties this may have caused. The domain name has since been placed on automatic renewal, which should prevent any repeat of this event."

Introducing the Crossref Labs DOI Chronograph

Joe Wass — Mon, 12 Jan 2015 00:00:00 +0000

tl;dr http://chronograph.labs.crossref.org.pluma.sjfc.edu

At Crossref we mint DOIs for publications and send them out into the world, but we like to hear how they’re getting on out there. Obviously, DOIs are used heavily within the formal scholarly literature and for citations, but they’re increasingly being used outside of formal publications in places we didn’t expect. With our DOI Event Tracking / ALM pilot project we’re collecting information about how DOIs are mentioned on the open web to try and build a picture about new methods of citation.

As part of the preparation for collaborating with Wikipedia, we looked at our statistics about when DOIs are clicked and discovered that Wikipedia was, over a two year period from 2012, the eighth largest referrer of DOIs. This means that not only does Wikipedia have a lot of DOIs, but people click them too. This bit of one-off data analysis (which surprised us) gave us enough of a prod to kickstart our collaboration with Wikipedia.

At the ALM Workshop 2014 in San Francisco we talked to some Wikipedians and bibliometricians and realised that we were sitting on a really interesting data-set and that it would be churlish not to share it. At the hackathon (read the report here) we started work on a service to gather information about DOIs and, a month later, we’re ready to unveil the DOI Chronograph.

Show me the goods

You can see:

Daily referrals (clicks) from top level domains, e.g. Wikipedia.org: http://chronograph.labs.crossref.org.pluma.sjfc.edu/domain.html?domain=wikipedia.org

Daily referrals from specific subdomains, e.g. fr.wikipedia.org: http://chronograph.labs.crossref.org.pluma.sjfc.edu/domain.html?domain=fr.wikipedia.org

Daily resolutions per DOI: http://chronograph.labs.crossref.org.pluma.sjfc.edu/doi.html?doi=10.1787%2F20752288

And, the chart that kicked this all off: DOI referring domains league tables. This shows that Wikipedia is the 3rd or 4th non-traditional referrer of DOIs (i.e. excluding referrals from Publishers’ domains): http://chronograph.labs.crossref.org.pluma.sjfc.edu/top.html

Try it out

Visit the Chronograph and give it a try chronograph.labs.crossref.org on your favourite DOI (everyone has one).

More data

Talking to a bibliometrician we also realised we can correlate other data for DOIs. We’re getting the issue date (approximately the publication date) from our own metadata, as well as the date that the Crossref metadata was updated. This gives interesting results, like the resolutions for 10.1038/ncomms2953, which peak after publication and then tails off. We are attempting to collect the following information:

daily resolution counts
day on which resolution was first successful
day on which it’s possible to resolve the DOI (we’ve got a bot running for new publications)
day on which the publisher says the article was published
day on which the metadata was most recently deposited with us
day on which the metadata was first deposited with us

We’re not there yet, but we’ve made a start and we’ve already got some pretty interesting data!

Weasel words

It’s a labs project so the usual weasel words apply. Specifically, we currently have the logs for 2012 to 2014 (we’re working at digging out the rest), and the referral information for 50 million DOIs (out of 71 million). That number will be higher by the time you read this. If your page is slow to load, be patient, as it’s currently working hard crunching numbers.

This project is focused on exploring the use of DOIs outside of the formal literature. As such, we are only looking at referrals from domains that do not appear to belong to primary publishers (i.e. our members). If you try a domain and it doesn’t work, it could be that the domain belongs to one of our members. If you’ve notice any mistakes, please email us at labs@crossref.org .

Finally, these numbers contain all DOI resolutions. That’s human clicks but also content negotiation to retrieve metadata, robots etc. We might try to filter them in future, but for now be aware that not every visitor is a human.

I’ll detail some of the the technical stuff (it’s very interesting) and what happened next with Wikipedia in a future post. Watch this space.