2016 on Crossref

Included, registered, available: let the preprint linking commence.

Rachael Lammey — Mon, 05 Dec 2016 00:00:00 +0000

We began accepting preprints as a new record type last month (in a category known as “posted content” in our XML schema). Over 1,000 records have already been registered in the first few weeks since we launched the service.

By extending our existing services to preprints, we want to help make sure that:

links to these publications persist over time
they are connected to the full history of the shared research
the citation record is clear and up-to-date.

It’s not just collecting the metadata however, it’s also making it available so that it can be as widely used as possible. Preprint metadata is no different. As with all record types, we make the metadata available for machine and human access, across multiple interfaces (e.g. REST API, OAI-PMH, Crossref Metadata Search)

For example, you can see information on the preprint https://doi-org.pluma.sjfc.edu/10.20944/preprints201608.0191.v1 in a number of ways:

If you want to see all the preprint metadata deposited so far, try https://api-crossref-org.pluma.sjfc.edu/v1/types/posted-content/works. Over 1,000 records have already been registered in the first few weeks since we launched the service.

Crossref members depositing preprints need to make sure they:

Register content using the posted content metadata schema.
Respond to our match notifications that a manuscript / version of record (AM/VOR) has been registered and link to that within seven days.
Label the manuscript as a preprint clearly, above the scroll on the preprint landing page, and ensure that any link to the AM/VOR is also prominently displayed above the scroll.

It’s important to clearly label the record type so we can ensure that the connections between preprints and the associated literature are clearly visible, to both humans and machines.

As with other record types, there is a registration fee to include content in the Crossref system. For preprints, it’s $0.25 fee for current preprint files and $0.15 for back-year records.

Are you an existing Crossref member who wants to assign preprint DOIs? Let’s talk about getting started or migrating any existing content over to the dedicated preprint deposit schema.

Interested in becoming a Crossref member to assign DOIs to your preprints? Contact our membership specialist so we can answer any questions and get you set up as a member.

Using the Crossref REST API. Part 3 (with SHARE)

Rachael Lammey — Thu, 01 Dec 2016 00:00:00 +0000

As a follow-up to our blog posts on the Crossref REST API we talked to SHARE about the work they’re doing, and how they’re employing the Crossref metadata as a piece of the puzzle. Cynthia Hudson-Vitale from SHARE explains in more detail…

Cynthia Hudson-Vitale, digital data librarian in Research Data and GIS Services at Washington University in St. Louis Libraries and visiting program office for SHARE

SHARE (http://share-research.org) is building a free, open, data set about research and scholarly activities across their life cycle. It is a higher education initiative whose mission is to maximize research impact by making research widely accessible, discoverable, and reusable. SHARE’s data set is free, openly licensed, and built with open source technology developed at the Center for Open Science (COS). Launched in beta in April 2015 the data set has grown to more than 6 million records from 100+ providers, including Crossref, Social Science Research Network (SSRN), DataONE, 50+ library institutional repositories, and more.

How is the Crossref REST API used within SHARE?

SHARE currently harvests metadata from Crossref using the Crossref application programming interface (API). We pull such metadata values as journal title, author, DOI, journal name, and publisher, to name just a few. This metadata is then fed into our data processing pipeline, normalized, and aggregated into the full data set.

What are the future plans for SHARE?

Phase II of SHARE, launched in late 2015, focuses on adding metadata providers, enhancing the metadata, and making connections and links between the metadata records. These links will show the entire life cycle of research and scholarship—connecting a data management plan, grant award information, data deposits, analytic/software code, pre-publications, final manuscripts, and more.

To move these plans forward, SHARE is applying machine-learning and automation techniques and working with the community to verify metadata enhancements and curate the metadata. Current technology work focuses on imputing subject domain keywords and object types into the SHARE data set using learning models and heuristics. Data models and schemas are in development to connect the research lifecycle, connect multiple instances of an object to a single entity, and capture metadata provenance.

What else would SHARE like to see in Crossref metadata?

We would love to see rights-declaration metadata elements and article references/citations included in the metadata about digital objects. The rights-declaration information is invaluable for individuals who want to know what category the object is in (public domain, copyrighted, etc.), what constraints or permission requirements exist, contact information, and more. Additionally, networks of research can be discovered and meta-scholarship facilitated by making article reference lists machine-readable and openly available.

What’s next?

Does this give you any ideas? Feel free to get in touch with questions or take the API for a spin yourself and let us know what you can do with it!

Call for participation: Membership & Fees Committee

Ed Pentz — Tue, 29 Nov 2016 00:00:00 +0000

Crossref was founded to enable collaboration between publishers. As our membership has grown and diversified over recent years, it’s becoming even more vital that we take input from a representative cross-section of the membership. This is especially important when considering how fees and policies will affect our diverse members in different ways.

About the M&F Committee

The Membership & Fees Committee (M&F Committee) was established in 2001 and plays an important role in Crossref’s governance. Made up of 10-12 organisations of both board members and regular members, the group makes recommendations to the board about fees and policies for all of our services. They regularly review existing fees to discuss if any changes are needed. They also review new services while they are being developed, to assess if fees should be charged and if so, what those fees should be. For example, the committee recently made recommendations to the board about the fees for a new service called Event Data that we’ll launch soon, and the Content Registration fees for preprints. In addition, the board can also ask the committee to address specific issues about policies and services. Increasingly, the committee works with the outreach team to include research and survey insights.

About committee participation

The M&F Committee meets via one-hour conference calls about six times a year, although this can vary depending on what issues the committee is considering. Often proposals are developed by staff and then reviewed and discussed by the committee - so there is reading to do in preparation for the calls.

This is very important work and in order to ensure that the committee is broadly representative of Crossref’s diverse membership we are seeking expressions of interest from members who would like to serve on the M&F Committee for 2017. Appointments are for one year and members can serve multiple terms.

About you

In view of our commitment to be representative of the membership we are refreshing the committee and want to have engaged and interested people from a diverse set of members join.

If you are interested in joining the committee and helping Crossref fulfil its mission please email feedback@crossref.org with your name, title, organisation and a short statement about why you want to serve on the committee by December 19th, 2016.

Scott Delman, Director of Group Publishing, ACM is the current Chair of the committee and will review the expressions of interest with me, Ed Pentz, Executive Director, to form the committee.

Thanks for your interest.

A look back at LIVE16

April Ondis — Thu, 24 Nov 2016 00:00:00 +0000

Crossref LIVE16 opened with a Mashup Day on 1st November 2016 in London. Attendees from the scholarly communications world met to chat with Crossref team members in an open house atmosphere. The Crossref team put their latest projects on display and were met with questions, comments, and ideas from members and other metadata folks. Here’s what it looked like — you may recognize a few familiar faces.

Crossref LIVE16 in London

LIVE16 continued with the Conference Day on 2nd November, a plenary session with invited speakers and presentations by the Crossref team. Here are the presentations, in chronological order.

Dario Taraborelli speaks on “Wikipedia’s role in the dissemination of scholarship”
Ian Calvert speaks on: “You don’t have metadata (and how to befriend a data scientist)”
Ed Pentz speaks on “Crossref’s outlook & key priorities”
Ginny Hendricks speaks on “A vision for membership”
Geoffrey Bilder speaks on “The case of the missing leg”
Lisa Hart Martin speaks on “The meaning of governance”
Jennifer Lin speaks on “New territories in the Scholarly Research Map”
Chuck Koscher speaks on “Relationships and other notable things”
Carly Strasser speaks on “Funders and Publishers as Agents of Change”
April Hathcock speaks on “Opening Up the Margins”

Your survey feedback

We’re serious about making Crossref LIVE a useful and welcoming annual event for the Crossref membership as well as members of the wider scholarly communications community. That’s why we appreciate responses from the attendees who answered our survey. Here’s what we have learned from your feedback:

Content

You want speakers to tell you something new, even if you don’t agree with their points of view
Your favorite speakers were those who inspired you
You prefer an unscripted presentation style that makes complex topics accessible to all
You’re not as interested in the mechanics of Crossref’s annual election as we are

Format

You enjoyed the diversity of presenters and would like even more external speakers
You want more opportunity to ask us technical questions on the Mashup Day
You want to see panel discussions in addition to individual presentations on the Conference Day
Those who attended the Conference Day only wished they had also attended the Mashup Day

Atmosphere

You liked the casual atmosphere but wanted more seating and more dessert. So noted!

LIVE17 will be held next November 14-15 in Asia. Until then, we hope you’ll have the chance to see us at the regional Crossref LIVE events we are planning around the world throughout the year. Our next local event is Crossref LIVE in Brazil, held 13 December in Campinas and 16 December in Sao Paulo.

URLs and DOIs: a complicated relationship

Joe Wass — Fri, 04 Nov 2016 00:00:00 +0000

As the linking hub for scholarly content, it’s our job to tame URLs and put in their place something better. Why? Most URLs suffer from link rot and can be created, deleted or changed at any time. And that’s a problem if you’re trying to cite them.

Thus the Crossref DOI was born: an Identifier which is Persistent, which means that it’s designed to live forever (or, as Geoff Bilder rather more prosaically puts it, as long as we do), and also Resolvable, which means that you can click on it. A DOI is a URL, but it’s imbued with special properties. I say special, not magical, because all of the things that make Crossref DOIs what they are, are obtained through agreements and common standards rather than any kind of magic.

As part of the development of Crossref Event Data I’ve been doing some research about the relationship between DOIs and URLs. It’s a problem we have to solve in order to make Event Data work, but it’s a much broader and more interesting story, and the results have wide applicability. I’ll be telling this story at PIDapalooza. If you’re interested in Persistent Identifiers you should go and registration is open, though hurry, as it’s next week and in Rejkjavik, Iceland!

This is also a story in progress. As I write not all of the data is in, and we can be certain that it will evolve in ways we have no idea about. It’s also quite long but I’ll do my best to disqualify it from the bedtime reading list.

Full circle

Crossref was established just over fifteen years ago with the purpose of forming the linking hub between publishers. Our job was — and still is — to register content for publishers and then continue to work with them to ensure their DOIs always point to the right location of the content. To do this we need to do one main thing: send people in the right direction when they click on a DOI, and know which direction to point them in.

Today, linking is still an important part of what Crossref does, but we do a huge amount more. One of the new things we’re working on is Crossref Event Data. It’s a service for tracking how and where people use scholarly content (such as articles) across the web and social media. Early research suggested that if we limited ourselves to just looking for DOIs we wouldn’t find much. Instead we broadened our aims a little: rather than looking for mentions of registered content exclusively via their DOIs, we look for them via the most suitable mechanism. In most cases this means the actual URL of the Item. So we have come full circle: we started linking DOIs to URLs. Now we’re trying to link URLs back to DOIs.

Which URL are we talking about here? The Crossref Guidelines say:

DOI-routed reference links enabled by Crossref must resolve to a response page containing no less than complete bibliographic information about the target content …

http://www.crossref.org.pluma.sjfc.edu/02publishers/59pub_rules.html

This is what’s referred to as the Landing Page. Every Landing Page has a URL. Usually when you want to read information about an Article, it’s the Landing Page that you’re looking at. I should also say at this point that when I say Article I mean any item of Crossref Registered Content with a DOI. So the same applies to books, chapters, conference proceedings etc. But as most items are Articles, I’ll stick with that for now.

I’m going to make some assumptions. Unfortunately, and I don’t want to spoil the surprise here, they all turn out to be false. They’re all reasonable assumptions, though, and you would be forgiven for thinking, or at least wishing, that they were true.

So suspend your disbelief and follow me down the rabbit-hole…

Assumption 1: A DOI points directly to a Landing Page URL

When you click on a DOI you are taken to the Article Landing Page. It seems like a perfectly valid assumption to think that you are taken directly there.

The DOI system is essentially a big lookup table. In the first column is the DOI and in the second column is the URL. Publishers request that we register each item’s DOI and supply us with the URL it should point to. We work with CNRI and the International DOI Foundation to keep the system running and it means that when you, the reader at home, click on a DOI, you end up on the article’s Landing Page.

It would be very convenient if our assumption were true. If we wanted to turn a URL back into an article page, we could just swap the two columns and find the DOI by looking up the URL.

It turns out that it’s not quite so simple.

The Landing Page is under control of the publisher, as is the URL that they supply us with. They don’t need to supply us with the final landing page URL, only with one that leads to the landing page.

HTTP redirects

When you request a URL, either by typing it into your browser or by clicking on a link, your browser contacts the server and gets a reply. That reply can be “200 OK, here’s your page”, “303, look over there” or the dreaded “404, I can’t find it”. Other HTTP response codes are available, including well-known classics such as 201, 500 and 418.

If it’s a 303, your browser will follow the redirect URL. The response that comes back from that redirect could be another 303. You could end up following a whole chain of redirects. You wouldn’t notice anything, except having to wait an extra few milliseconds.

Extraordinary diversity

Crossref was created by a group of publishers who needed a way to link between articles. It was an ambitious goal: create a central system with which any publisher can integrate their own systems; one that allows linking to any article no matter who published it. Today we have over 5,000 members and counting, all contributing to our metadata engine. And up to 2 million DOIs are resolved every day, by all kinds of people and systems. Our wide range of members means a wide range of systems with a wide range of designs.

This brings an extraordinary diversity of behavior. If we want to make observations about DOIs we can’t just take a random sample of the over 80 million. Instead, we need to take a sample of DOIs per Publisher System. Even taking a sample per publisher might not do the job because some publishers run a variety of systems.

Experiment 1: Does Crossref know all Landing Pages?

By NASA / Paul Riedel (Great Images in NASA: Home - info - pic) [Public domain], via Wikimedia Commons

Hypothesis: Crossref knows the Landing Page URL for all DOIs.

For a sample of Items, we can follow the DOI link all the way through to the Landing Page, following any redirects, then compare the final Landing Page URL to the one that Crossref knows about. If there are extra redirects, that means that the one we have on file isn’t the final one.

We need to tighten up the terminology at this stage:

DOI URL - The full DOI, e.g. https://doi-org.pluma.sjfc.edu/10.5555/12345678 .
Resource URL - The URL that Crossref has on file (stored in our system). This is where the browser is initially redirected.
Destination URL - The URL that we end up at if we follow all the redirects.
Article Landing Page - The page that represents the item. If everything works, this should be the same as the Destination URL.

The reason we’re talking about the Destination URL as distinct from the Article Landing Page when they should be the same thing will become clear later. Consider yourself foreshadowed.

So let’s re-word our hypothesis:

Hypothesis: The Destination URL is the same as the Resource URL.

Method: A sample of DOIs was taken (most items updated in 2016, all from 2009 or earlier). The Resource URL was obtained for all of them. The DOIs were split by the domain name of the Resource URL (to give a good coverage of all Publisher systems). A sample of Resource URLs was followed per domain, at least 200 (or fewer if that exceeds the number of DOIs available). Where there were HTTP redirects they were followed.

Observations:

Number of Items sampled Destination URL: 253,381
Number where Resource URL = Destination URL: 46,995 or 19.96%

Conclusion: Not all Resource URLs are the same as the Destination URL by a long shot. Crossref does not automatically know every landing page URL.

Now we know the truth about our first assumption: DOIs don’t point directly to Landing Pages. If we want to reverse Landing Pages back into DOIs, we’re going to need to go a bit deeper…

Interlude

But first, an interlude with some information about publishers, owners, and systems, because now seems like the right time to do it.

Assumption 2: You can tell the publisher of a DOI by looking at its prefix

This is a real one one that people believe. Again, it’s entirely understandable. People look at a DOI like https://doi-org.pluma.sjfc.edu/10.1371/journal.pone.0136117.g001 , which takes them to PLoS and naturally assume that another DOI like https://doi-org.pluma.sjfc.edu/10.1371/journal.pone.0136053.t003 — because it has the same prefix of 10.1371 — is also for a PLoS item.

Whilst this turns out to be true most of the time, it’s not true for all Items, which makes it a dangerous assumption to make.

It is true that every publisher is given a prefix. They can then register DOIs with this prefix. It is also true that Items can be transferred between publishers. Because DOIs are persistent, the prefix in the DOI doesn’t change. So you might find a DOI that belongs to a publisher that has an unexpected prefix. Publishers can also be bought and sold, merged and split, which means that whilst most publishers have a single prefix, some, like Elsevier, have several. Take the case of Elsevier, who has 26 at the time of writing (you can see this in Elsevier’s entry in the Crossref Metadata API).

Every Item has an ‘owner prefix’ in addition to the prefix in the DOI. The owner prefix is the same as the DOI prefix when the Item is created, but over time, as articles are transferred, that can change to indicate that it is owned by another publisher.

Every Item has a DOI, and every DOI has a prefix. But every Item also has an Owner Prefix (you can check this in the Metadata API in the ‘prefix’ field).

So Assumption 2 has been laid to rest. The only thing you can tell from looking at a DOI is that it is, in fact, a DOI (you can tell by the “10.” index code).

Why do we care about identifying publishers anyway?

A Fair Test

We fundamentally want to conduct a fair test. The reason we can’t just take a random sample from the set of all DOIs is that there are lots of members who all do things slightly differently. Therefore we need to take a sample per publisher ‘system’. The word ‘system’ is a bit fuzzy, but my assumption is that two articles in the same system will behave the same way so we can treat them the same.

We also know that each Crossref member may be running more than one system, or a mixture. Therefore just looking at the owner of a DOI may not give accurate results if we want to conduct a survey of all the systems out there.

There’s no perfect answer, but the approach I’m taking is to look at the domain name of the Resource URL. We often find lots of subdomains for the same publisher, for example, “psw.sagepub.com”, “pol.sagepub.com”, “psx.sagepub.com” and “bpi.sagepub.com”. It’s clear that these are all operated by Sage, but they might or might not all be running on different ‘systems’.

Therefore I’m splitting DOIs up into groups based on the domain of their Resource URL. It may turn out that some publishers use a single system running on many domains, or it may turn out that some publishers use a different system for each domain they use. The key point is to find a sampling technique that broadly works, and that allows us to explore and differentiate, as keenly as possible, the variety of systems and behaviours.

Why all the redirects?

Curious minds might at this stage be wondering about all these extra redirects. Surely it’s extra stuff for the publisher to maintain. Why don’t they just point the DOI directly to the landing page?

The answer must be prefaced by repeating that there is a huge number of publishers, running a variety of systems, so we’ll never be able to completely answer that. But some humble suggestions:

They might want to be able to change the URLs of the Landing Pages. It may be easier to update their internal systems than send the update to Crossref, especially in bulk.
Different parts of their technology stack may be owned by different parts of the company, or outsourced. It’s easier to define internal boundaries than to co-ordinate business units and cross an external one.
A publisher may run a mix of different technology. As part of their systems integration process, they set up a redirect server to make everything work together.
A publisher assigns DOIs to articles but also has their own internal IDs. They maintain their own DOI-to-internal-ID lookup service.

Internal DOI resolvers

That last point is an interesting one. The DOI system is the canonical “DOI-to-URL resolver”. That doesn’t prevent publishers from running their own. Indeed, many do.

To take a real example of PLoS, an Open Access publisher who registers lots of content with Crossref. To follow one of their DOIs we go on the following journey of redirects:

http://dx.doi.org.pluma.sjfc.edu/10.1371/journal.pone.0164910
http://dx.plos.org/10.1371/journal.pone.0164910
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0164910
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0164910

Given that the last step uses a DOI, this suggests that they use the DOI as an internal identifier. All those redirects were for some purpose, but they weren’t mapping a DOI to an internal ID. This is therefore not an internal DOI resolver.

Another example from JAMA Surgery:

In this case we see a mapping from the DOI 10.1001/archsurg.142.7.595 to the ID 487551.

Can we define a heuristic for this pattern? Yes, but not a perfect one. My test is this:

Does the resource URL contain the DOI?
If so, does it redirect to a different destination URL?
If so, does the destination URL not contain the DOI?

The last step is important, because we can’t really say the publisher is running a DOI resolver if they use the DOI all the way through.

It’s not perfect and no doubt has false negatives. But we’re just trying to find out whether some publishers run their own DOI resolver systems.

Experiment 2: Determine how widespread use of internal DOI resolvers is:

Hypothesis: Some publishers run their own DOI resolvers.

Method: A number of Destination URLs were sampled per Resource URL Domain. If the Resource URL contains the DOI but the Destination URL doesn’t, that’s marked as a Publisher DOI resolver redirect.

Observations:

Number of Items sampled with Resource URL and Destination URL: 253,381
Number of Items that appear to be DOI resolvers: 166,352 = 65.6%

Conclusions: Some publishers run their own DOI resolvers.

This isn’t of much practical use, but it’s interesting to know, and hints at the way the Crossref system and DOIs are integrated with Publishers’ systems. Now that we’ve got a little insight into the reasons that publishers might run their own DOI resolvers, we can resume our journey of assumptions.

Assumption 3: We can find the Landing Page for Every DOI

Now we know that we can’t just use the lookup table in reverse, but have to follow the links all the way to their destination. Does this approach actually work?

This is a pretty big question and we need to be clear about what we mean by ‘every’ DOI. The set of DOIs I’m using (although I’m using a subset) is “all DOIs in our Metadata API that are found in doi.org”.

What is a DOI? Geoff Bilder went over it in the DOI-like-strings blog post earlier this year. The definition I’m working to here is:

A DOI is an identifier for an item of content registered in the DOI system.

That is, if you resolve the DOI on https://doi-org.pluma.sjfc.edu/ and it’s recognised, that counts as a DOI. I’m working from the set of DOIs found in the Crossref system as I’m primarily concerned with Crossref DOIs. However, we collaborate closely with DataCite.

Back to our assumption: “we can find the Landing Page for every DOI”. The answer is that we can, most of the time. But because Crossref Event Data has to work as well as possible, and therefore work with as many DOIs as possible, we have to scour all the nooks and crannies.

Assumption 4: Every DOI points somewhere unique

Stop me when you find the deliberate mistake:

Every Item corresponds to a different thing
Every Item has a single DOI
Every DOI is different
Every DOI points to a landing page
Therefore every DOI points to a different landing page

Two things immediately suggest themselves:

“Every item has a single DOI” should be true, but it isn’t. We find that sometimes two DOIs are assigned to the same item. This can happen when publications change hands between publishers, or when mistakes are made, or for a variety of other reasons. We also find that in some cases Publishers registered a DOI for the metadata and one for the article abstract. The two DOIs point to the same place. In some cases where there were two DOIs registered for the same thing we create an Alias.

When we alias a DOI we simply say “this DOI should actually point to this one”. Both DOIs still exist, and both still point to the ‘correct’ thing, it’s just that they both point to the same place. If we have two DOIs pointing to the same place, then there isn’t a one-to-one mapping, and Assumption 4 is incorrect.

Experiment 4: Aliased DOIs

Hypothesis: There isn’t a one-to-one mapping between DOIs and URLs because some DOIs are aliased to others.

Method: We collected a sample of Resource URLs from the DOI API. We count how many DOIs are classified as Aliases in the DOI system.

Observations:

From a sample of 11,227,458 DOIs
14,566 are aliased to others, or 0.129%

Conclusion: There aren’t many aliases. But there are some, and we should be aware of them.

Experiment 5: Duplicate Resource URLs

Hypothesis: There isn’t a one-to-one mapping between DOIs and URLs because some DOIs have duplicate Resource URLs.

Method: A sample of Resource URLs was collected from the DOI API. We counted how many DOIs have Resource URLs that aren’t unique. We subtract the number of deleted DOIs because all deleted DOIs have the same resource URL.

Observations:

From a sample size of 11,227,458
a total of 112,195 have duplicate resource URLs, or 0.99%
of these duplicates, 77,896 have the ‘deleted’ URL
leaving 34,229, or 0.30% having non-unique Resource URLs

Conclusion: A small number of DOIs have duplicate Resource URLs, even if we exclude those that have been deleted, which means that not every DOI can have a unique URL.

Assumption 5: The Landing Page is the same as the Destination Page.

HTTP has a very neat system for doing redirects. If it were that simple, then we could easily look up every Destination page and confidently say that it was the Landing Page. Not so.

Cookies

Web browsers aren’t the only tools that use HTTP. Most programming languages have HTTP capabilities built in.

Using cookies is a requirement of some websites, but it’s not a requirement of HTTP. Most websites use cookies in some way or another. When you log into a site, you expect cookies. But when you’re just browsing there isn’t any technical need. A small number of websites absolutely require cookies to be enabled to use the site, even if you’re just browsing and not logged in. Unfortunately, this includes some publishers.

Requiring cookies to use a publisher site means that you can’t fully resolve a DOI without enabling cookies. Most tools out there don’t. Some privacy-conscious people quite reasonably don’t enable cookies from all sites.

Using cookies when resolving a DOI adds considerable overhead and isn’t fool-proof.

Let’s try a quick experiment to see when we land up on a cookie page. Here’s an example page that tells us that we should have enabled cookies: http://www-tandfonline-com.pluma.sjfc.edu/action/cookieAbsent . It’s reachable from the DOI: https://doi-org.pluma.sjfc.edu/10.1016/j.envhaz.2007.09.007 .

Experiment 6: Some DOIs can’t be resolved without cookies

Hypothesis: We can’t resolve some DOIs to the Landing Page using standard tools because cookies are required.

Method: A sample of DOIs was taken per Resource URL Domain. They were resolved by following HTTP links. Where the Destination URL contains the word ‘cookie’, we mark that as a DOI requiring a cookie.

Observations:

A sample of 253,381 DOIs were resolved following HTTP redirects where necessary
a total of 6305 resolved to a page with ‘cookie’ in the URL or 2.48%

Conclusion: There are cookies at play for at least 2.48% of DOIs. This is probably a very conservative estimate, as we’re using a blunt tool looking for ‘cookie’ in the URL.

Cookies Required

For one DOI I found, the publisher system set cookies, then sent us on a series of redirects which set cookies that expired in the past and then, as far as I can tell, checked whether or not they were sent back. My working hypothesis is that it was profiling the behaviour to see what browser I was using.

I have also seen javascript-based redirects. This is where a web page loads a javascript file, which executes and sends the browser onto another URL. This seems to be to be a browser detection method. There is no way you can follow these DOIs without actually using a real browser.

This is a problem for Crossref Event Data. We can’t fire up a browser and follow every DOI: it isn’t practical. When I tried this for a sample as an experiment I got an email from another publisher who was worried that we were scraping data (good bot operators always put contact details in their request headers!).

The Crossref member rules leave some wiggle-room about whether this is allowed, but for the Event Data service, we can say that it’s a physical impossibility to collect all Event Data for DOIs like this.

Bring in the Browser

To quantify the size of the problem, we need to bring in a web browser. If we assume that some Publishers design their sites to work only with real browsers, that’s what we’ll use. Luckily there are web browsers packaged up into an automatable package, and we can use these to visit the DOI.

Using one of these is considerably slower than just following link headers.

I have split the ‘destination’ concept into two:

Naïve destination URL: The URL that you get from following HTTP redirects acccording to the HTTP specification
Browser destination URL: The URL that you get from letting a browser follow the DOI doing whatever a browser does.

Rather than defining a complicated spectrum of types of DOI resolution behaviour, I am classifying DOIs into two groups: those where standard HTTP redirects are sufficient and everything else.

The method I am using is to resolve a sample of URLs using the browser. I can then compare the Naïve Destination URL with the Browser Destination URL. If they are the same, then I didn’t need to use the browser after all. If they give a different result however, I trust the Browser one better and declare that DOI to require a browser to resolve.

Again, I took a sample of DOIs per Resource URL domain.

Experiment 7: Quantify proportion of DOIs that require a browser to redirect

Hypothesis: A number of DOIs can’t be resolved with standard tools but instead require a browser.

Method: A sample of DOIs was selected per Resource URL domain. The links were followed using standard HTTP and using a browser. Where the URLs between the two were different, the DOI was counted as requiring a browser to resolve.

Observations:

A total of 59,453 items were followed both using the Naïve and Browser methods.
Of these 5,883 items have a different URL between the two methods, or 9.88%

Conclusion: We can’t rely on the Naïve redirect, and would have to fire up the browser in about 10% of cases in the sample.

Other gnarly things

There are one or two supplementary gnarly things that crop up.

First, session IDs are sometimes embedded in the URL. This is a tracking technique similar to cookies, but instead of sending cookies, which are invisible to the user, a unique code is placed on the end of the URL. This means that everyone gets a different URL. The most popular of these is the JSESSIONID, which is used by servers in the Java ecosystem. An example URL is:

http://onlinelibrary.wiley.com.pluma.sjfc.edu/doi/10.1002/047084289X.rn00615.pub3/abstract;jsessionid=0D1B7AC4689A494E0EA78BD2F0A710C4.f04t04

We can easily remove these if they appear at the end of a URL. Sometimes they occur in the middle of a URL, as above. Sometimes they appear as query parameters:

http://jpharmsci.org/action/consumeSharedSessionAction?SERVER=WZ6myaEXBLGvmNGtLlDx7g%3D%3D&MAID=npYBLvZTaUI3JTHw%2BH63WQ%3D%3D&JSESSIONID=aaajjhdDL5ssK6d1HHrFv&ORIGIN=207988872&RD=RD

In this case we make no attempt to remove them. These URLs won’t be any use for matching, and we have to acknowledge that and move on.

Interpreting the results

All the above experiments involved taking as many DOIs as we had time for, gathering the Resource URLs, and then grouping the DOIs per Resource URL Domain. A sample of DOIs was investigated per each Resource URL domain to give the best chance at even coverage. The above figures have been presented as a proportion of the sampled data-set.

Now it’s time to draw some practical conclusions. I grouped the results per Resource URL Domain, so I can say that “for this domain, X% of DOIs was deleted, or aliased, or whatever”. This means that we can look at the statistics for a given domain and work out the best method for working with DOIs that belong to it.

I have created histograms of domains by their various proportions.

Our first chart is histogram of Resource URL Domains where the Naïve Destination = the Resource URL. Each domain is given a proportion which represents how many DOIs sampled on that domain have a Landing Page equal to the Resource URL.

There’s a clear bimodal distribution here. The conclusion here is “most domains require you to follow the link to find the destination URL“. Furthermore, the domains are consistent: there are virtually no domains that have a mix of DOIs that behave differently.

Our second chart is a histogram of Resource URLs where the Browser-based redirect = the Naive URL. Each domain is given a proportion which represents how many DOIs sampled on that domain require us to fire up a browser.

Overwhelmingly, the Browser Redirect URL is the same as the Naïve Redirect URL, meaning that we don’t need to fire up the browser, we can just use the Naïve URL, which is much easier to compute. There are some resource URL domains which require every DOI to be followed in a browser rather than just following links.

We know from this that we don’t have to use the browser most of the time. There is a small number of domains where we’re unsure (under 500) and a small number of domains where we know that we have to use a browser. This means we can focus our efforts.

There are lots of DOIs and they all behave differently.

There are thousands of publishers out there registering DOIs. There are thousands of domains. Some publishers have lots of domains. This makes it impossible to make many general observations about DOIs.

You can’t tell anything by looking at the DOI

Just by looking at the DOI you can’t tell who published it, or which publisher’s system is hosting it. Therefore you can’t tell how it’s going to behave.

We’ve looked at five kinds of URLs:

The DOI itself
The Resource URL
The “naïve” redirect URL
The “browser” redirect URL
The Article Landing Page

In some cases, the Resource URL, naïve redirect URL, browser redirect and Article Landing Page are the same. In some cases they aren’t. Of these, the fifth is somewhat mythical.

DOIs fall into classifications

Each DOI falls into a category, most preferable first:

The Resource URL is the same as the Landing Page.
The Landing Page can be discovered by following HTTP redirects.
The Landing Page can be discovered by firing up a web browser to follow redirects.
The Landing Page can’t be determined.

We can predictively group DOIs

We can group DOIs by their Resource URLs and take a sample per Resource URL Domain. If all samples for a domain behave a certain way, we can place the DOIs into one of the above four groups with a probability.

We’ll never know the full story.

Because of the diversity of Publisher Systems and the long history of Crossref DOIs, we’ll never be able to describe exactly what’s going on for all DOIs.

What next?

We’re continuing to develop Crossref Event Data. The part of the system that handles turning URLs back into DOIs will never be perfect, but we know from this research that we can at least work with a subset.

I’m also working on another project which will attempt to reverse a Landing Page URL back into a DOI by looking at the metadata on the Landing Page. You can read about it here. Ultimately we’re going to have to take a blended approach. Building a useful set of Landing Page URL to DOI mappings will be part of the mix.

As Event Data matures we’ll be sharing all the datasets automatically as part of our infrastructure, including our DOI-to-URL mapping.

And any members reading, please make your DOIs as easy to follow as possible! Please don’t require JavaScript or cookies when resolving DOIs.

If you’re read this far, perhaps you’re as interested in DOIs as we are. There’s a lot more to say on the subject, but that’s enough for now. See you at PIDapalooza!

Image Credits

All images from Wikipedia Commons. Click or hover on the image to see the attribution.

Preprints are go at Crossref!

Rachael Lammey — Wed, 02 Nov 2016 00:00:00 +0000

We’re excited to say that we’ve finished the work on our infrastructure to allow members to register preprints. Want to know why we’re doing this? Jennifer Lin explains the rationale in detail in an earlier post, but in short we want to help make sure that:

links to these publications persist over time
they are connected to the full history of the shared research results
the citation record is clear and up-to-date

Doing so will help fully integrate preprint publications into the formal scholarly record.

What’s new?

We’ve had to do some work on our own infrastructure to facilitate the inclusion of preprints, enabling:

Crossref membership for preprint repositories by updating our membership criteria and creating a policies for preprints
The deposit of persistent identifiers for preprints to ensure successful links to the scholarly record over the course of time via the DOI resolver.
Content Registration for preprints with custom metadata that reflect researcher workflows from preprint to formal publication (this custom metadata will then be visible to anyone using the Crossref metadata).
Notification of links between preprints and formal publications that may follow (journal articles, monographs, etc.).
Auto-update of ORCID records to ensure that preprint contributors get credit for their work.
Preprint and funder registration to automatically report research contributions based on funder and grant identification.
It will also allow for the collection of “event data” that capture activities surrounding preprints (usage, social shares, mentions, discussions, recommendations, links to datasets and other research entities, etc.).

Now we’re ready to go!

Early adopters

We have been working with various preprint publishers who are launching (or planning to launch) their own preprint initiatives.

Preprints.org is the first to successfully make preprints deposits using the dedicated schema. For example, this preprint https://doi-org.pluma.sjfc.edu/10.20944/preprints201608.0191.v1 is registered with Crossref. It is linked to a published journal article https://doi-org.pluma.sjfc.edu/10.3390/data1030014 both in the online display as well the preprint’s Crossref metadata record. Others are getting ready to go - will your organisation be next? (Technical documentation available here.)

Martyn Rittman, from Preprints, operated by MDPI said: Preprints.org is delighted to be the very first to integrate the Crossref schema for preprints. We believe it is an important step in allowing working papers and preliminary results to be fully citable as soon as they are available. It also makes it easy to link to the final peer-reviewed version, regardless of where it is published. Thanks to the hard work of Crossref and clear documentation, the schema was very simple to implement and has been applied retrospectively to all preprints at Preprints.org.

Jessica Polka, Director, ASAPbio adds: ASAPbio is a scientist-driven community initiative to promote the productive use of preprints in the life sciences. We’re thrilled to see Crossref’s development of a service that enables preprints to better contribute to the scholarly record. This infrastructure lays a necessary foundation for increasing acceptance of preprints as a valuable form of scientific communication among biologists.

Questions?

Get in touch with any questions or comments, or join our upcoming webinar to talk about preprints, infrastructure and where we go from here.

The Organisation Identifier Project: a way forward

Ed Pentz — Mon, 31 Oct 2016 00:00:00 +0000

The scholarly communications sector has built and adopted a series of open identifier and metadata infrastructure systems to great success. Content identifiers (through Crossref and DataCite) and contributor identifiers (through ORCID) have become foundational infrastructure to the industry.

But there still seems to be one piece of the infrastructure that is missing. There is as yet no open, stakeholder-governed infrastructure for organisation identifiers and associated metadata.

In order to understand this gap, Crossref, DataCite and ORCID have been collaborating to:

Explore the current landscape of organisational identifiers;
Collect the use-cases that would benefit our respective stakeholders in scholarly communications industry;
Identify those use-cases that can be more feasibly addressed in the near term; and
Explore how the three organisations can collaborate (with each other and with others) to practically address this key missing piece of scholarly infrastructure.

The result of this work is in three related papers being released by Crossref, DataCite and ORCID for community review and feedback. The three papers are:

organisation Identifier Project: A Way Forward (PDF; GDoc)
organisation Identifier Provider Landscape (PDF; GDoc)
Technical Considerations for an organisation Identifier Registry (PDF; GDoc)

We invite the community to comment on these papers both via email (oi-project@orcid.org) and at PIDapalooza on November 9th and 10th and at Crossref LIVE16 on November 1st and 2nd. To move The OI Project forward, we will be forming a Community Working Group with the goal of holding an initial meeting before the end of 2016. The Working Group’s main charge is to develop a plan to launch and sustain an open, independent, non-profit organisation identifier registry to facilitate the disambiguation of researcher affiliations.

Crossref Use Cases

Crossref has also been discussing the needs of its members over the last year and there is value in focusing on the affiliation name ambiguity problem with research outputs and contributors. In terms of the metadata that Crossref collects, something that is missing has been affiliations for the authors of publications. Over the last couple of years, Crossref has been expanding what it collects - for example, funding and licensing data and ORCID iDs - and this enables a fuller picture of what we are calling the article nexus. In order to continue to fill out the metadata we collect - and for our members to use in their own systems and publications - we need an organisation identifier.

Another use case for Crossref is identifying funders as part of collecting funder data to enable connecting funding sources with the published scholarly literature. In order to enable the reliable identification of funders in the Crossref system we created the Open Funder Registry that now has over 15,000 funders available as Open Data under a CC0 waiver. While this has been very successful, it is a very narrowly focused registry and is not suitable for a broad, community-run organisation identifier registry that addresses the affiliation use case. In future, our goal will be to merge the Open Funder Registry into the identifier registry that the organisation Identifier Working Group will work on.

By working collaboratively we can define a pragmatic and cost-effective service that will meet a fundamental need of all scholarly communication stakeholders.

Geoffrey Bilder will be focusing his talk at Crossref LIVE16 this week on this initiative, dubbed The OI Project. The talk is scheduled for 2pm UK time and will be live streamed along with the rest of that day’s program.

Smart alone; brilliant together. Community reigns at Crossref LIVE16

Ginny Hendricks — Sat, 29 Oct 2016 00:00:00 +0000

A bit different from our traditional meetings, Crossref LIVE16 next week is the first of a totally new annual event for the scholarly communications community. Our theme is Smart alone; brilliant together. We have a broad program of both informal and plenary talks across two days. There will be stations to visit, conversation starters, and entertainment, that highlight what our community can achieve if it works together.

Check out the final program.

We’re now opening the doors to all parties—our 5,000+ members of all shapes and sizes—as well as the technology providers, funders, libraries, and researchers that we work with. Our aim is to gather the ‘metadata-curious’ and have more opportunities to talk face-to-face to share ideas and information, see live demos, and get to know one another.

Mashup Day - Tuesday 1st November 12-5pm. An ‘open house’ vibe, we’ll have several stations to visit each Crossref team, a LIVE Lounge, good food, and guest areas run by our friends at DataCite, ORCID, and Turnitin. We’ll have some special programming too, on-the-hour lightning talks, including a wild talk at 2pm from a primatologist who speaks baboon!

Conference Day - Wednesday 2nd November 9am-5pm. There is more of a formal plenary agenda this day, with keynote speakers from across the scholarly communications landscape. Our primary goal is to share Crossref strategy and plans, alongside thought-provoking perspectives from our guest speakers. We’ll hear from many corners of our community including:

Funder program officer, Carly Strasser (Moore Foundation) on “Publishers and funders as agents of change“,

Data scientist, Ian Calvert (Digital Science) on “You don’t have metadata“,

Open knowledge advocate, Dario Taraborelli (The Wikimedia Foundation) on “Citations for the sum of all human knowledge“, and

Scholarly communications librarian, April Hathcock (New York University) on “Opening up the margins“.

For our part, we will set out Crossref’s “strategy and key priorities” (Ed Pentz), “A vision for membership” (me, Ginny Hendricks), “The meaning of governance” (Lisa Hart Martin), “The case of the missing leg” (Geoffrey Bilder),”New territories in the scholarly research map” (Jennifer Lin), and “Relationships and other notable things” (Chuck Koscher).

We will also set aside thirty minutes for the important Crossref annual business meeting, when we will announce the results of the membership’s vote, and welcome new board members.

I can’t wait to welcome you all.

Have you voted?

If you’re a voting member of Crossref you’ll have cast your vote already I hope! I’m so happy to see that people have voted in record numbers although it’s under 7% of our eligible members which is not high… more on member participation next week.

Important changes to Similarity Check

Madeleine Watson — Fri, 21 Oct 2016 00:00:00 +0000

New features, new indexing, new name - oh my!

TL;DR The indexing of Similarity Check users’ content into the shared full-text database is about to get a lot faster. Now we need members assistance in helping Turnitin (the company who own and operate the iThenticate plagiarism checking tool) to transition to a new method of indexing content.

For existing Similarity Check users: please check that your metadata includes full-text URLs so that Turnitin can quickly and easily locate and index your content. Full-text URLs need to be included in 90% of journal article metadata by 31st December 2016.

2016 has seen some exciting new developments

(And there are plenty more in store as we strive towards 2017). But first: in April we renamed the service from CrossCheck to Similarity Check and we now have a new service logo available to reference via our logo CDN using the following code.

<img src="https://assets-crossref-org.pluma.sjfc.edu/logo/crossref-similarity-check-logo-200.svg" width="200" height="98" alt="Crossref Similarity Check logo">

Earlier this year Crossref also signed a new contract with Turnitin. As part of this, we negotiated the inclusion of dedicated development time each year from Turnitin’s engineering and product teams to focus on developments in the iThenticate tool that will specifically support Similarity Check users and their needs. Many of our members will have been contacted recently by Turnitin and asked to complete a survey regarding how they use the tool and what improvements they would like to see made in the future. The results of this survey are currently being analyzed and will be used by Turnitin to inform a development plan.

Finally, throughout 2016 we have also been working with Turnitin to help them develop a new Content Intake System that provides a faster, more reliable and robust method for collecting data from Crossref and indexing users’ content into the Similarity Check full-text database. Previously Turnitin was only able to collect prefix data from Crossref’s system on a monthly basis whereas today, with the new Content Intake System up and running, they are able to pull full-text content links from deposited metadata on a daily basis. This means that if you are a Similarity Check user currently depositing full-text URLs with Crossref, your content is being indexed by Turnitin faster than ever before.

There are plenty of other benefits this new method provides. This is why we have agreed with Turnitin that from 1st January 2017 onwards, indexing via full-text URLs will be the only method supported for Similarity Check.

Not convinced? Let me share my top four reasons for advocating Turnitin’s exclusive use of the full-text URL indexing method for Similarity Check:

1. Reduced traffic to publisher servers. Indexing via full-text URLs means that the crawl is targeted specifically to the location of the full-text PDF or HTML content, thereby reducing the amount of traffic Turnitin puts through publisher’s servers.

2. Lower margin for error and simplified issue recovery. Turnitin will no longer need to make multiple fetches for any content item, meaning there are now fewer steps in the process. This means there will be fewer places for indexing errors to occur and also reduces the reliance on users setting meta tags or span tags correctly in their markup. Furthermore, if problems do arise, using the one method of indexing for all users will mean that Turnitin is able to pinpoint the issue faster and work with members to resolve it quickly.

3. Quicker turnaround on indexing with fewer delays. Turnitin will no longer need to investigate and set up bespoke indexing methods for different Similarity Check users and they will be able to access the location of full-text content from the one place (ie. within the specific resource tag in member’s metadata deposits). More accurate data from only one location will result in a quicker turnaround on indexing, meaning newly published content will be added into the Similarity Check content database sooner for all members to check other new manuscripts against.

4. Daily ingest is better than monthly! Full-text links can be collected daily from Crossref-rather than monthly for other methods-meaning a more regular ingest of content.

The presence of full-text URLs within the metadata is critical to the functioning of Turnitin’s new indexing system. All new Similarly Check participants are now asked to ensure they have these links in place within their deposited metadata before they participate in the service.

Already a user of Similarity Check?

If you’re an existing Similarity Check participant who joined the service before 2016, your content is likely to be currently indexed via different methods, such as following links contained in your page meta tags. If you’re not currently depositing full-text links with Crossref for Similarity Check, you will have received an email from us about this in August. If you’re unsure though, you can check your XML to see if you have included the full-text link in the field or you can send us an email at similaritycheck@crossref.org as we’d be happy to check for you.

Help, don’t leave me behind!

Us? Never! We’re here to help. But we really do need those full-text links… Everything existing Similarity Check publishers need to know about adding full-text links into new or existing metadata can be found on our help site. These URLs should be included as part of all standard metadata deposits going forward and can be easily added into existing files in bulk. So there’s no need to redeposit the full metadata, unless of course you would prefer to do so!

That’s a wrap

Looking back, it really has been a busy year for Similarity Check and it will continue to be so as we persevere in laying the groundwork for a more streamlined, robust and scalable service for 2017 and beyond. Remember, we need Similarity Check users to ensure they have full-text URLs in at least 90% of their journal article metadata by 31st December 2016 in order to continue using Similarity Check from 2017 onwards.

And please keep us updated! With over 1,200 publishers using Similarity Check, we’ll need a little nudge to know when metadata has been updated to include these links. So once updates have been deposited, please email similaritycheck@crossref.org to confirm. And of course, as always, if there are any questions or if some advice would help, we’re just an email away.

One member, one vote: Crossref Board Election opens today, September 30th

Lisa Hart Martin — Fri, 30 Sep 2016 00:00:00 +0000

Watch for two important emails on September 30th – one with a voting link and material, and one with your username and password.

Running Crossref well is a key part of our mission. It’s important that we be as neutral and fair as possible, and we are always striving for that balance. One of our stated principles is “One member, one vote”. And each year we encourage each of our members-standing at over 6000 today-to participate in the election of new board members.

It is hard to believe that November 2nd will be Crossref’s 17th annual meeting and our 16th annual Board of Directors election. How time flies, and oh, how we have grown!

Crossref’s Truths, taken from our forthcoming new website.

I am hoping that we can rally the membership to participate in this important process!

Candidates will be elected at Crossref LIVE16 for three-year terms to fill five of the 16 Board seats whose terms expire this year. The slate of candidates was recommended by the Nominating Committee, which consisted of three Board members not up for re-election, and two Crossref members that are not on the Board.

This year, Jasper Simons, APA; Paul Peters, Hindawi; Jason Wilde, AIP; Chris Fell, Cambridge University Press; and Rebecca Lawrence, f1000 served on the Nominating Committee. The Committee met to discuss the process, criteria, and potential candidates, and put forward a slate which was required to be at least equal to the number of Board seats up for election. The slate may or may not consist of Board members up for re-election.

Crossref members are welcome to run as independent candidates, as long as they have ten member endorsements sent to lhart@crossref.org with the intent to run. We sent a notification of the process in advance (this year on August 26th), so any nominations could be included in the voting materials that will be sent via email on September 30th.

You can access online voting from today at:

https://eballot4.votenet.com/PILA/admin. Watch your inbox today for emails with your username and password!

New Crossref DOI display guidelines are on the way

Ed Pentz — Tue, 27 Sep 2016 00:00:00 +0000

TL;DR

Crossref will be updating its DOI Display Guidelines within the next couple of weeks. This is a big deal. We last made a change in 2011 so it’s not something that happens often or that we take lightly. In short, the changes are to drop “dx” from DOI links and to use “https:” rather than “http:”. An example of the new best practice in displaying a Crossref DOI link is: https://doi-org.pluma.sjfc.edu/10.1629/22161

Hey Ho, “doi:” and “dx” have got to go

The updated Crossref DOI Display guidelines recommend that https://doi-org.pluma.sjfc.edu/ be used and not http://dx.doi.org.pluma.sjfc.edu/ in DOI links. Originally the “dx” separated the DOI resolver from the International DOI Foundation (IDF) website but this has changed and the IDF has already updated its recommendations so we are bringing ours in line with theirs.

We are also recommending the use of HTTPS because it makes for more secure browsing. When you use an HTTPS link, the connection between the person who clicks the DOI and the DOI resolver is secure. This means it can’t be tampered with or eavesdropped on. The DOI resolver will redirect to both HTTP and HTTPS URLs.

Timing and backwards compatibility

We are requesting all Crossref member publishers and anyone using Crossref DOIs to start following the updated guidelines as soon as possible. But realistically we are setting a goal of six months for implementation; we realize that updating systems and websites can take time. We at Crossref will also be updating our systems within six months - we already use HTTPS for some of our services and our new website (coming very soon!) will use HTTPS.

An important point about backwards compatibility is that “http://dx.doi.org.pluma.sjfc.edu/” and “http://doi.org.pluma.sjfc.edu/” are valid and will continue to work forever-or as long as Crossref DOIs continue to work-and we plan to be around a long time.

We need to do better

Reflecting on the 2011 update to the display guidelines it’s fair to say that we have been disappointed. It is still much too common to see unlinked DOIs in the form doi:10.1063/1.3599050 or DOI: 10.1629/22161 or even unlinked in this form: http://dx.doi.org.pluma.sjfc.edu/10.1002/poc.3551

What’s so wrong with this approach? To demonstrate, please click on this DOI doi:10.1063/1.3599050 - oh, you can’t click on it? How about I send you to a real example of a publisher page. What I’d like you to do is click the following link and then copy the DOI you find there and come back - http://dx.doi.org.pluma.sjfc.edu/10.1002/poc.3551.

Are you back? I expect you had to carefully highlight the “10.1063/1.3599050” and then do “edit”, “copy”. That wasn’t too bad but the next step is to put the DOI into an email and send it to someone. But wait - what are they going to do with “10.1063/1.3599050”? It’s useless. If you want it to be useful you’ll have to add “http://doi.org.pluma.sjfc.edu” or https://doi-org.pluma.sjfc.edu/ in the front.

When publishers follow the guidelines it makes things easier - if you go to https://doi-org.pluma.sjfc.edu/10.1063/1.3599050 you’ll note that you can just right click on the full DOI link on the page and get a full menu of options of what to do with it. One of which is to copy the link and then you can easily paste into an email or anywhere else.

However-putting a positive spin on the spotty adherence to the 2011 update to the DOI display guidelines-everyone has another chance with the latest set of updates to make all the changes at once!

More on HTTPS (future-proofing scholarly linking)

We take providing the central linking infrastructure for scholarly publishing seriously. Because we form the link between publisher sites all over the web, it’s important that we do our bit to enable secure browsing from start to finish. In addition, HTTPS is now a ranking signal for Google who gives sites using HTTPS a small ranking boost.

The process of enabling HTTPS on publisher sites will be a long one and, given the number of members we have, it may a while before everyone’s made the transition. But by using HTTPS we are future-proofing scholarly linking on the web.

Some years ago we started the process of making our new services available exclusively over HTTPS. The Crossref Metadata API is HTTPS enabled, and Crossmark and our Assets CDN use HTTPS exclusively. Last year we collaborated with Wikipedia to make all of their DOI links HTTPS. We hope that we’ll start to see more of the scholarly publishing industry doing the same.

So-it’s simple-always make the DOI a full link - https://doi-org.pluma.sjfc.edu/10.1006/jmbi.1995.0238 - even when it’s on the abstract or full text page of the content that the DOI identifies - and use “https://doi-org.pluma.sjfc.edu/”.

The membership boom & why metadata isn’t like beer

Susan Collins — Fri, 23 Sep 2016 00:00:00 +0000

You might recognize my name if you’ve ever applied for Crossref membership on behalf of your organisation. It recently occurred to me that, since I’ve been working in our membership department for eight years, I’ve been a part of shepherding new members for half of our history. And my, how we’ve grown.

Membership growth by country

Though it may be easy to see our membership growth by looking at the numbers, I think it’s interesting to consider where we’ve grown. The top ten member countries have dramatically changed since Crossref began sixteen years ago. At the end of our first year of operations, our membership included 54 publishers and affiliated organisations. The majority were from the US and the UK, with a small number from Germany, the Netherlands, and Japan.

In 2012, participation in our sponsors program began to increase. Sponsors are affiliated organisations that act on behalf of smaller publishers and societies who wish to register their content with Crossref. Several organisations from Turkey and South Korea were among the first sponsors to join and were very successful in representing a large number of publishers and societies from their regions. Soon to follow were sponsors from India, Ukraine, Russia and Brazil. In 2014, the Public Knowledge Project (PKP) became a sponsoring affiliate, focusing on smaller publishers with the aim of increasing the quality and global reach of scholarly publishing. With the introduction of our sponsor program, the past few years have seen a steady increase in the geographical diversity of our members.

There are 194 countries in the world. It’s pretty amazing that organisations in 112 of the world’s countries are now represented in our membership. Do I think we’ll see members joining from the other 82 nations? I don’t know but I hope so.

A look at our trending nations chart shows the diversity of our membership as we’ve grown, depicting the countries that produced the most new members over the last two years. There has been tremendous growth from South Korea! What I find just as interesting is that we have new members from so many different nations that they form their own special bloc, shown here as “Other.”

Our growth has taken place at a remarkable rate. When I joined Crossref in 2008, we had over 1800 publishers and affiliates and we were adding about 300 new members per year. In 2015, nearly 1500 members joined and we are seeing even larger numbers so far in 2016. Counting all publishers, affiliates, libraries, sponsors and represented members, our new member total through the end of August is nearly 1200 and will most certainly overtake the 2015 figure.

Member perceptions

With such a range of new members each month it’s even more important that we help people understand the benefits of joining Crossref. That it’s not just registering metadata and DOIs but maintaining and improving records over time, and participating in reference linking. We are adding and improving some educational tools that will help everyone understand how our services can enhance the discoverability of content, and why sharing richer metadata supports their full participation in the scholarly community. We are in the process of developing a new, cleaner website with videos that better explain our services-to be released in the next few weeks,-a new onboarding experience, and new and improved query and deposit tools.

Connected metadata isn’t like beer

Sometimes inviting more people to a party means there is less beer to go around. Fortunately for everyone, metadata isn’t like beer. In fact, the more metadata you draw from the tap, the more useful it becomes. So inviting new members to join Crossref makes our community better and more valuable for everyone. Every member uses that metadata to link their content to every other member’s content. This makes all members’ content easier to find, link, and cite, not just at the moment it is published, but over time.

Members from around the globe join Crossref everyday and help guide our growing community. If you are interested in joining please contact me at member@crossref.org.

Crossmark 2.0 - grab the code and you’re ready to go!

Kirsty Meddings — Thu, 15 Sep 2016 00:00:00 +0000

On September 1st we completed the final stage of the Crossmark v2.0 release and sent an email to all participating publishers containing instructions for upgrading. The first phase of v2.0 happened when we changed the design and layout of the Crossmark box back in May of this year. That allowed us to better display the growing set of additional metadata that our members are depositing, and saw the introduction of the Linked Clinical Trials feature.

Now all publishers have the opportunity to complete the upgrade by simply replacing the Crossmark button and the piece of code that calls the box. The new button designs are, we think, a much better fit for most websites, and are designed to look more like a button than a flat logo. The new buttons are also available
as .eps files for placement in PDFs.

Crossmark box on a mobile phone

Most importantly, switching to 2.0 makes the Crossmark box responsive for better display on mobile devices.

Just two weeks after the code release a number of publishers have already upgraded and are running Crossmark 2.0 on their content. Congrats to the Pan African Medical Journal who were the first member to upgrade just a couple of days after the release. Of course we realise that many members will need time to schedule the upgrade, and while we are keen to see as many early adopters as possible, we will support version 1.5 of Crossmark through to the end of March 2017.

If your content is running Crossmark 2.0 we would love to see it. Drop us a line or put a link in the comments below.

Using the Crossref Metadata API. Part 2 (with PaperHive)

Rachael Lammey — Thu, 08 Sep 2016 00:00:00 +0000

We first met the team from PaperHive at SSP in June, pointed them in the direction of the Crossref Metadata API and let things progress from there. That’s the nice thing about having an API - because it’s a common and easy way for developers to access and use metadata, it makes it possible to use with lots of diverse systems and services.

So how are things going? Alexander Naydenov, PaperHive’s Co-founder gives us an update on how they’re working with the Crossref metadata:

PaperHive

PaperHive is a web-platform for collaborative reading and a cross-publisher layer of interaction on top of research documents. It lets researchers communicate in published documents in a productive and time-saving way. PaperHive thus puts academic literature, which is integrated with the platform, in the limelight and increases content usage and reader engagement.

Transforming reading into a process of collaboration gives researchers a reason to return to the content and discover new enrichments they can benefit from. Functionality like hiving, deep linking, and the PaperHive browser extension embeds communication in the researcher’s workflow. PaperHive is free to use!

How is the Crossref API used within PaperHive?

PaperHive extends the concept of a living document and offers an innovative way of displaying content without hosting it. Instead, academic documents are dynamically pulled from the publisher’s servers thus ensuring compliance with content licensing. It enables readers to stay in touch with the articles of interest beyond just saving them in an offline folder.

Crossref is the common ground on which third party companies and initiatives can build valuable services for publishers and researchers. It facilitates the integration of content into PaperHive by providing the metadata of articles and books from numerous publishers independent of the technology behind their content platforms. Moreover, if the publishers provide ORCID identifiers of authors in the Crossref metadata, researchers can immediately interact with the readers of their works.

What are the future plans for PaperHive?

In addition to integrating further publishers’ content and extending PaperHive’s feature set for readers, we also plan to extend our partnerships with other technology providers.

As far as our cooperation with Crossref is concerned, we are looking forward to the implementation of the Crossref Event Data API.

What else would you like to see in Crossref metadata?

- The quality of the existing metadata should be improved significantly. We noticed that important fields such as author or title are missing in the metadata of many documents. PaperHive ignores articles and books with incomplete metadata because it impairs the user experience. Publishers, authors and readers can only benefit from the wider and more active usage of content, so we hope that more publishers will improve the data their provide Crossref with.

- Since researchers are working with full texts on PaperHive, it would be great if links to the full text are provided in the metadata of all articles and books. The metadata should also contain information about the format of the full text (e.g., PDF, EPUB, HTML).

Thanks Alex!

Just getting started with the API or what to know more? Get in touch via feedback@crossref.org and pass on your questions and comments.

Linking Publications to Data and Software

Jennifer Lin — Wed, 07 Sep 2016 00:00:00 +0000

TL;DR

Crossref and Datacite provide a service to link publications and data. The easiest way for Crossref members to participate in this is to cite data using DataCite DOIs and to include them in the references within the metadata deposit. These data citations are automatically detected. Alternatively and/or additionally, Crossref members can deposit data citations (regardless of identifier) as a relation type in the metadata. Data & software citations from both methods are freely propagated. This blog post also describes how to retrieve the links collected between publication and data & software.

Data & software citation is good research practice (DataCite-STM Joint Statement and FORCE11 Joint Declaration of Data Citation Principles) and is part of the scholarly ecosystem supporting research validation and reproducibility. Data & software citation is also instrumental in enabling the reuse and verification of these research outputs, tracking their impact, and creating a scholarly structure that recognises and rewards those involved in producing them.

Crossref supports the propagation of data & software citations alongside a publisher’s standard bibliographic metadata. members deposit the data citation link as part of the overall publication metadata when registering their content. Crossref partners with DataCite and together, we jointly provide a clearinghouse for the citations collected. These are all made freely available to the community as open data.

Citation practices are evolving across different communities of practice. Crossref’s offering is flexible and easily accommodates variations and changes, since it does not rely on a specific set of citation metadata elements, citation format, nor manner of credit and attribution. Publishers deposit data & software citations in their metadata deposit via a) references and/or b) relation type.

Method A: Bibliographic references

Crossref and DataCite have partnered to provide automatic linking between publications registered with Crossref and datasets bearing DataCite DOIs. This is the most efficient and effective way to ensure that data citations are fully integrated into the scholarly research information network with full and accurate metadata.

All data & software citations that include datasets bearing a DataCite DOI are eligible for auto-update linking with Crossref. In this method: authors cite the dataset or software containing the DataCite DOI per journal article submission guidelines and add it to the article citation list (c.f. FORCE11 citation placement, FORCE11 Software Citation Principles). Publishers then deposit references as part of their standard practice when registering content. Crossref checks every reference deposited for a DOI. If the DOI is identified as DataCite’s, we automatically link it to the article. With this method, no additional action is needed when publishers register their content with Crossref.

Data citation links to non-DataCite DOIs can only be exposed in the references if the publisher makes references openly available. Even in the event that the data citation is shared, it remains undifferentiated from other references. Method B described below offers another approach.

Method B: Relation type

Publishers can link their publication to a variety of associated research objects as part of the article metadata directly in the metadata deposited to Crossref, including data & software, protocols, videos, published peer reviews, preprints, conference papers, etc. Doing so not only groups digital objects together, but formally associates them with the publication. Each link is a relationship and the sum of all these relationships constitutes a ‘research article nexus.’ Data & software citations are a valuable part of this.

To tag the citation in the metadata deposit, we ask for:

description of dataset or software (optional)

dataset or software identifier

identifier type

relationship type.

Crossref can accommodate research outputs with any identifier, though we currently only validate DOI relationships during metadata processing. Technical details are documented in the [Data & Software Citations Deposit Guide][4].

Combining methods increases total available citations

The two methods are independent and can be used exclusively or jointly. Each caters to a different set of conditions and their practical considerations. See the comparison of benefits and limitations for each method in the deposit guide. We recommend that publishers use both methods where possible at this time for optimum specificity and coverage.

How to access data & software citations

Crossref and DataCite make the data & software citations deposited by Crossref members and DataCite data repositories openly available to a wide host of parties, including both Crossref and DataCite communities as well as the extended research ecosystem (funders, research organisations, technology and service providers, research data frameworks such as Scholix, etc.).

Data & software citations from references can be accessed via the Crossref Event Data API Citations included directly into the metadata by relation type can be accessed via Crossref’s APIs in a number of formats (REST, OAI-PMH, OpenURL). (A single channel containing data & software citations across interfaces is in development and will be released next year.)

Publishers, visit our detailed guide on how to deposit data and software citations. We welcome your questions and concerns at feedback@crossref.org.

Special thanks to the following who provided valuable feedback in developing the guide: Martin Fenner (DataCite), Amye Kenall (Springer Nature), Brooks Hanson (AGU), Shelley Stall (AGU), and the FORCE11 Data Citation Implementation Pilot publisher’s subgroup.

Crossref’s Annual Meeting is now Crossref LIVE16

April Ondis — Fri, 02 Sep 2016 00:00:00 +0000

Everyone is invited to our free annual event this 1-2 November in London. (Register here)!

In years past, only Crossref members typically attended the [Crossref Annual Meeting](/crossref-live-annual). This year, we looked at the event with new eyes. We realized that we’d have even richer conversations, more creative energy, and the meeting would be even better for our members if we could rally the entire community together. So we decided to re-develop our annual event from the ground-up.

The result is Crossref LIVE16, an event with a new format and a new focus on the entirety of the scholarly communications community. We are opening doors for the whole community, welcoming publishers, librarians, researchers, funders, technology providers, and Crossref members alike.

1st November - Mashup Day, from 12 noon: an afternoon of interactive activities including mingling with the Crossref team and special guests, trying out our services, live troubleshooting, and exclusive previews of some exciting things we’re working on. Plus entertainment and refreshments at an early evening reception.

2nd November - Conference Day: a full-day plenary session with distinguished keynote speakers including April Hathcock (NYU), Carly Strasser (Moore Foundation), Ian Calvert (Digital Science), and Dario Taraborelli (Wikimedia Foundation). We will provide the most important updates about our services, and share our vision and strategies for the future.

Note: You are welcome to join us for both days or just one day, as you like.

Location: The Royal Society, London, UK.

We hope you will join us, and extend this invitation to your colleagues.

This is going to be fun.

Register here

Announcing PIDapalooza - a festival of identifiers

Ginny Hendricks — Tue, 30 Aug 2016 00:00:00 +0000

The buzz is building around PIDapalooza - the first open festival of scholarly research persistent identifiers (PID), to be held at the Radisson Blu Saga Hotel Reykjavikon November 9-10, 2016.

PIDapalooza will bring together creators and users of PIDs from around the world to shape the future PID landscape through the development of tools and services for the research community. PIDs support proper attribution and credit, promote collaboration and reuse, enable reproducibility of findings, foster faster and more efficient progress, and facilitate effective sharing, dissemination, and linking of scholarly works.

We believe that by bringing together everyone who’s working with PIDs for two days of discussions, demos, workshops, brainstorming, updates on the state of the art, and more, we can make this happen faster. And you can help by giving us your input on which sessions would be most valuable. Please send us your ideas, using this form by September 18. We will send session proposal notifications the first week of October with the festival lineup.

Register to attend

Registration is now open — come join the festival with a crowd of like-minded innovators. And please help us spread the word about PIDapalooza in your community!

Stay updated with the latest news on on the PIDapalooza website and on Twitter (@PIDapalooza) in the coming weeks.

Looking forward to seeing you in November!

Preprints and Crossref’s metadata services

Chuck Koscher — Mon, 29 Aug 2016 00:00:00 +0000

We’re putting the final touches on the changes that will allow preprint publishers to register their metadata with Crossref and assign DOIs. These changes support Crossref’s Cited-by linking between the preprint and other scholarly publications (journal articles, books, conference proceedings). Full preprint support will be released over the next few weeks.

I’d like to mention one change that will be immediately visible to Crossref members who use our OAI based service to retrieve Cited-by links to their content.

This API, show in an example here, is intended to retrieve large quantities of data detailing all the Cited-by links to a given publication. The example request shows pulling the data for an IEEE conference proceeding.

example:

http://oai.crossref.org.pluma.sjfc.edu/OAIHAndler?verb=ListRecords&usr=*** pwd=****&set=B:10.1109:1070762&metadataPrefix=cr_Cited-by

With the new change, results will now identify the type of content that is doing the citing. The example results below shows that the DOI 10.1109/CSMR.2012.14 is cited by five other items and displays the DOIs of those items and their record type.

When preprint content that cites other scholarly work starts being registered with Crossref, members using this API will start seeing data like the following:

For many users of Crossref metadata the introduction of preprints will be transparent until preprint content starts being registered. However, a few changes like the one above have benefits not limited to just preprints.

The article nexus: linking publications to associated research outputs

Jennifer Lin — Thu, 25 Aug 2016 00:00:00 +0000

Crossref began its service by linking publications to other publications via references. Today, this extends to relationships with associated entities. People (authors, reviewers, editors, other collaborators), funders, and research affiliations are important players in this story. Other metadata also figure prominently in it as well: references, licenses and access indicators, publication history (updates, revisions, corrections, retractions, publication dates), clinical trial and study information, etc. The list goes on.

What is lesser known (and utilized) is that Crossref is increasingly linking publications to associated scholarly artifacts. At the bottom of it all, these links can help researchers better understand, reproduce, and build off of the results in the paper. But associated research objects can enormously bolster the research enterprise in many ways (e.g., discovery, reporting, evaluation, etc.).

With all the relationships declared across all 80+ million Crossref metadata records, Crossref creates a global metadata graph across subject areas and disciplines that can be used by all.

Research article nexus

As research increasingly goes digital, more research artifacts associated with the formal publication are stored or shared online. We see a plethora of materials closely connected to publications, including: versions, peer reviews, datasets generated or analysed in the research, software packages used in the analysis, protocols and related materials, preprints, conference posters, language translations, comments, etc. Occasionally, these resources are linked from the publication. But very rarely are these relationships made available beyond the publisher platform.

Crossref will make these relationships available to the broader research ecosystem. When publishers register content for a publication, they can identify the associated scholarly artifacts directly in the article metadata. Doing so not only groups digital objects together, but formally associates with the publication. Each link is a relationship and the sum of all these relationships constitutes a “research article nexus.”

An assortment of connections already abound in the wild today. Examples include:

F1000Research article http://doi.org.pluma.sjfc.edu/10.12688/f1000research.2-198.v3 connected to initial version http://doi.org.pluma.sjfc.edu/10.12688/f1000research.2-198.v1

OECD publication http://dx.doi.org.pluma.sjfc.edu/10.1787/empl_outlook-2014-en and its German translation http://dx.doi.org.pluma.sjfc.edu/10.1787/empl_outlook-2014-de

PeerJ article http://doi.org.pluma.sjfc.edu/10.7717/peerj.1135 and its peer review http://doi.org.pluma.sjfc.edu/10.7287/peerj.1135v0.1/reviews/3

eLife article http://doi.org.pluma.sjfc.edu/10.7554/eLife.09771 and its BioArXiv preprint http://doi.org.pluma.sjfc.edu/10.1101/018317

PLOS ONE article http://doi.org.pluma.sjfc.edu/10.1371/journal.pone.0161541 with underlying data in Dryad http://doi.org.pluma.sjfc.edu/10.5061/dryad.d2vf8

Frontiers article http://doi.org.pluma.sjfc.edu/10.3389/fevo.2015.00015 with a figshare http://doi.org.pluma.sjfc.edu/10.6084/m9.figshare.1305089.v1 video

Journal of Chemical Theory and Computation article http://doi.org.pluma.sjfc.edu/10.1021/ct400399x with software archived in Zenodo http://doi.org.pluma.sjfc.edu/10.5281/zenodo.60678

Nature Biotech article http://doi.org.pluma.sjfc.edu/10.1038/nbt.3481 with a Protocols.io protocol http://doi.org.pluma.sjfc.edu/10.17504/protocols.io.dm649d

To date, almost all these relationships are not directly recorded in the article metadata (great job, PeerJ!). And as a result, they are more than likely “invisible” to the broader scholarly research ecosystem. Publishers can remedy these gaps by depositing associations when registering content with Crossref or updating the records after registration. That is how the article nexus is formed.

(Associated datasets can also be identified in the reference list as per Joint Declaration of Data Citation Principles as with the FORCE11 Software Citation Principles. Stay tuned next week for a follow up blog post on Crossref’s support for publisher data and software citations through its metadata.)

Forming the nexus

The mechanism of declaring these relationships is straightforward and a longstanding part of the standard deposit process. For each associated research object, simply provide the identifier and identifier type for the object, an optional description of it, as well as name the relationship into the metadata record. For the latter, Crossref and DataCite share a closed list of relationship types, which ensures interoperability between mappings. See Crossref technical documentation for more details.

We maintain a list of the recommended relation types for a host of associated research objects to promote standardization across publishers. If you have relationships not specified, please contact us at feedback@crossref.org to identify a suitable one considered best practice. Common adoption of relation types will make relationship metadata useful to tool builders and systems. For example, programmatic queries on supporting materials require proper tagging of their respective relationship types.

This approach is highly extensible and accommodates the introduction of new research object forms as they emerge. It also supports associated research objects regardless of identifier type. When an associated entity has a DOI, however, we can validate the relationship during metadata processing as well as provide a more reliable representation of the article nexus.

Article nexus: a far richer scholarly map

Bibliographic metadata is like a ship’s manifest that catalogs each item of cargo in a ship’s hold - crate, drum, sack, and barrel. It identifies the components that have an internal relation to the publication (contributor, funder, article update, license, etc.), each of which are well-understood points on the scholarly map. But when we integrate the article nexus into the graph, new territories become visible - not isolated islands, but places with highways connecting them to addresses already known.

When a publication has its relationships clearly identified, the connections both go out as well as lead back to it. The more connections, the more visibility on the scholarly map, as the Art of Cartography goes. Numerous systems tap into this map: publishing, funders, research institutions, research councils, indexers & repositories, indexers, research information systems, lab & diagnostics systems, reference management and literature discovery, other PID suppliers. So publishers, you can provide the fullest value to your own publishing operation, your authors, their research communities, and the overall research enterprise by ensuring that all publications are fully linked both inside and out.

Using the Crossref Metadata API. Part 1 (with Authorea)

Rachael Lammey — Thu, 18 Aug 2016 00:00:00 +0000

Did you know that we have a shiny, not so new, API kicking around? If you missed Geoffrey’s post in 2014 (or don’t want a Cyndi Lauper song stuck in your head all day), the short explanation is that the Crossref Metadata API exposes the information that publishers provide Crossref when they register their content with us. And it’s not just the bibliographic metadata either-funding and licensing information, full-text links (useful for text-mining), ORCID iDs and update information (via Crossmark)-are all available, if included in the publishers’ metadata.

Interested? This is the kickoff a series of case studies on the innovative and interesting things people are doing with the Metadata API. Welcome to Part 1.

What can you do with the Metadata API?

Build search interfaces. We’ve built some ourselves. Check out Crossref Metadata Search to search the metadata of over 80 million journal articles, books, standards, datasets & more. Or Crossref Funder Search to search nearly 15,000 funders and the 982,162 records we have that contain funding data.

Provide cross-publisher support for text and data mining applications.

Get really interesting top-level reports on the metadata Crossref holds - or look at subsets of the information you’re interested in.

Third parties are free to build their own products and tools that build off of the Metadata API (below are some of the many examples that we will highlight in this series).

Importantly, there’s no sign-up required to use the Metadata API - the data are facts from members, therefore not subject to copyright and free to use for whatever purpose anyone chooses.

To help, Scott Chamberlain of rOpenSci has built a set of robust libraries for accessing the Metadata API. These libraries are now available in the R, Python and Ruby languages. Scott’s blog post has some great information on those. For those using the libraries, there have been a few updates since Scott’s post - to serrano, and support for field queries has been added to habanero (coming to serrano and rCrossref soon). Any feedback/bug reports can be submitted via the GitHub repos serrano or habanero. There’s also a javascript library, authored by Robin Berjon.

Who’s using the Crossref Metadata API?

We get around 30 million requests a month. We’d like to share a few case studies to showcase what they’re doing and how they’re using it. Look out for a series of posts over the next few months where we’ll open the floor to those using the API and let them explain how and why.

We’ll let Authorea kick things off…

Alberto Pepe, co-founder of Authorea explains:

Authorea is a word processor for researchers and scholars. It is a collaboration platform to write, share and openly research in real-time: write manuscripts and include rich media, such as data sets, software, source code and videos. The media-rich, data-driven capabilities of Authorea make it the perfect platform to create and disseminate a new generation of research articles, which are natively web-based, open, and reproducible. Authorea is free to use.

How is the Crossref Metadata API used within Authorea?

Authorea is specifically made for scholarly documents such as research articles, conference papers, grey literature, class notes, student papers, and problem sets. What makes scholarly documents so peculiar are their citations and references, mathematical notation, tables, and data. For citations and references, we built a citation tool which allows authors to search and cite scholarly papers with ease, without having to leave the editor. While in the middle of writing a sentence, authors can click the “cite” button and a citation tool opens up:

We currently use two engines for searching scholarly literature via their APIs: Crossref and Pubmed. Our authors love being able to search (by author name, paper title, topic, etc) and add references to their papers on the fly, in one click.

What are the future plans for Authorea?

Among the many plans we have for the future, there is one which is also tied to Crossref: we are going to let authors assign DOIs to Authorea articles such as blog posts, preprints, “data papers”, “software papers” and other kinds of grey literature which does not fit in the traditional scholarly journals.

What else would you like to see in our metadata?

Well, since you ask: we would love to see unique BibTex IDs being served by the Metadata API (right now, you create the ID automatically using author name and year). Also, in some cases, some important metadata fields are missing (even author or title). I think it is actually more important to fix existing metadata rather than add new fields!

Keen to share what you’re doing with the Crossref Metadata API? Contact feedback@crossref.org and share your story.

Get ready for Crossmark 2.0!

Kirsty Meddings — Wed, 17 Aug 2016 00:00:00 +0000

TL;DR… In a few weeks, publishers can upgrade to the new and improved Crossmark 2.0 including a mobile-friendly pop-up box and new button. We will provide a new snippet of code for your landing pages, and we’ll support version v1.5 until March 2017.

We recently revealed a new look for the Crossmark box, bringing it up-to-date in design and offering extra space for more metadata. The new box pulls all of a publication’s Crossmark metadata into the same space, so readers no longer have to click between tabs. Linked Clinical Trials and author names (including ORCID iDs) now have their own sections alongside funding information and licenses. Feedback so far tells us that the new box is a vast improvement.

However, this was only phase one of the Crossmark makeover. We will soon complete the upgrade to display a fully responsive, mobile-friendly box. The Crossmark button has been given a facelift too, and we are excited to offer the first public preview today:

The new button brings the Crossmark icon up to date and is designed to be more “clickable” than the current button. It will be available in several different ratios and also in greyscale.

The first phase of the new design was rolled out in the existing Crossmark pop up window (Crossmark v1.5) without the need for changes within publisher systems. For the Crossmark v2.0 upgrade, publishers will need to update their landing pages with a new snippet of code, to ‘unlock’ the new button and functional enhancements.

Crossmark 2.0 will be available to adopt in a few weeks, and each publisher can decide when to switch over. We encourage members to upgrade sooner rather than later to get the benefits of the new box, but we also understand there are planned development schedules and the need for a testing period so we will continue to support Crossmark v1.5 until March 2017.

Many thanks to all of those who completed our surveys to help us shape the new button. And congratulations to Elizabeth Ramsey, a researcher from Trent University in Canada, who will be receiving a limited edition Crossref Moleskine notebook from the survey prize draw.

Our User Experience Designer, Rakesh Masih, will be blogging soon with details about the research and testing for this project, as well as more about our new approach to user experience at Crossref.

Getting ready to run with preprints, any day now

Jennifer Lin — Tue, 16 Aug 2016 00:00:00 +0000

While preprints have been a formal part of scholarly communications for decades in certain communities, they have not been fully adopted to date across most disciplines or systems. That may be changing very soon and quite rapidly, as new initiatives come thick and fast from researchers, funders, and publishers alike. This flurry of activity points to the realization from these parties of preprints’ potential benefits:

Accelerating the sharing of results;

Catalyzing research discovery;

Establishing priority of discoveries and ideas;

Facilitating career advancement; and

Improving the culture of communication within the scholarly community.

To acknowledge them as a legitimate part of the research story, we need to fully build preprints into the broader research infrastructure. Preprints need infrastructure support just like journal articles, monographs, and other formal research outputs. Otherwise, we (continue to) have a two-tiered scholarly communications system, unlinked and operating independently.

Infrastructure for preprints

For this reason, the team at Crossref is extending its infrastructure services to allow members to register preprints. This new development is designed to provide custom support for preprints. It will ensure that: links to these publications persist over time; they are connected to the full history of the shared research results; and the citation record is clear and up-to-date. We established this preprints service to fully integrate preprint publications into the formal scholarly record with features such as:

Crossref membership for preprint repositories, joining the community of publishers who have made a commitment to maintain and connect scholarly publications.

Persistent identifiers for preprints to ensure successful links to the scholarly record over the course of time via the DOI resolver.

Content Registration for preprints with custom metadata that reflect researcher workflows from preprint to formal publication.

Notification of links between preprints and formal publications that may follow (journal articles, monographs, etc.).

Collection of “event data” that capture activities surrounding preprints (usage, social shares, mentions, discussions, recommendations, links to datasets and other research entities, etc.).

Reference linking for preprints, connecting up the scholarly record to associated literature

Auto-update of ORCID records to ensure that preprint contributors get credit for their work.

Preprint and funder registration to automatically report research contributions based on funder and grant identification.

Supporting utility & effectiveness of preprints for all

To build the service, we are listening to the research community tell us their vision of what preprints will do. We solicited use cases from the community and have built a registry of preprint user stories with researchers, publishers, funding agencies, tenure and promotion committees in academic institutions, and technology providers.

To realize the user stories, the research enterprise will no doubt need brand new tools and existing systems enhancements. Crossref’s preprints infrastructure will support the development of all needs currently registered. The community at large can focus on building effective solutions, instead of finding or securing access to data. All data are available without restriction to all so that participants as well the services and systems supporting them can access the data and reuse it for advancing early dissemination, literature discovery, research tracking, promotion and funding assessment, etc.

These are exciting days for scholarly communications. Over time, we envision an even more vibrant ecosystem of research outputs that include existing artefacts linked up to preprints. And Crossref is committed to providing infrastructure for the dynamic enterprise all along the way.

We plan to announce the availability of the preprints infrastructure and further technical details within the next few weeks. If you’re interested in learning more about how these will be supported, get in touch!

Using AWS S3 as a large key-value store for Chronograph

Joe Wass — Tue, 02 Aug 2016 00:00:00 +0000

One of the cool things about working in Crossref Labs is that interesting experiments come up from time to time. One experiment, entitled “what happens if you plot DOI referral domains on a chart?” turned into the Chronograph project. In case you missed it, Chronograph analyses our DOI resolution logs and shows how many times each DOI link was resolved per month, and also how many times a given domain referred traffic to DOI links per day.

We’ve released a new version of Chronograph. This post explains how it was put together. One for the programmers out there.

Big enough to be annoying

Chronograph sits on the boundary between normal-sized data and large-enough-to-be-annoying-size data. It doesn’t store data for all DOIs (it includes only those that are used on average once a day), but it has information on up to 1 million DOIs per month over about 5 years, and about 500 million data points in total.

Storing 500 million data points is within the capabilities of a well-configured database. In the first iteration of Chronograph a MySQL database was used. But that kind of data starts to get tricky to back up, move around and index.

Every month or two new data comes in for processing, and it needs to be uploaded and merged into the database. Indexes need to be updated. Disk space needs to be monitored. This can be tedious.

Key values

Because the data for a DOI is all retrieved at once, it can be stored together. So instead of a table that looks like

<td>
<span >2010-01-01</span>
</td>
<td>
<span >5</span>
</td>

<td>
<span >2010-02-01</span>
</td>
<td>
<span >7</span>
</td>

<td>
<span >2010-03-01</span>
</td>
<td>
<span >3</span>
</td>

10.5555/12345678

Instead we can store

<td>
{&#8220;2010-01-01&#8221;: 5, &#8220;2010-02-01&#8221;: 7, &#8220;2010-03-01&#8221;: 3}
</td>

10.5555/12345678

This is much lighter on the indexes and takes much less space to store. However, it means that adding new data is expensive. Every time there’s new data for a month, the structure must be parsed, merged with the new data, serialised and stored again millions of times over.

After trials with MySql, MongoDB and MapDB, this approach was taken with MySQL in the original Chronograph.

Keep it Simple Storage Service Stupid

In the original version of Chronograph the data was processed using Apache Spark. There are various solutions for storing this kind of data, including Cassandra, time-series databases and so on.

The flip side of being able to do interesting experiments is wanting them to stick around without having to bother a sysadmin. The data is important to us, but we’d rather not have to worry about running another server and database if possible.

Chronograph fits into the category of ‘interesting’ rather than ‘mission-critical’ projects, so we’d rather not have to maintain expensive infrastructure if possible.

I decided to look into using Amazon Web Services Simple Storage Service (AWS S3) to store the data. AWS itself is a key-value store, so it seems like a good fit. S3 is a great service because, as the name suggests, it’s a simple service for storing a large number of files. It’s cheap and its capabilities and cost scale well.

However, storing and updating up to 80 million very small keys (one per DOI) isn’t very clever, and certainly isn’t practical. I looked at DynamoDB, but we still face the overhead of making a large number of small updates.

Is it weird?

In these days of plentiful databases with cheap indexes (and by ‘these days’ I mean the 1970s onward) it seems somehow wrong to use plain old text files. However, the whole Hadoop “Big Data” movement was predicated on a return to batch processing files. Commoditisation of services like S3 and the shift to do more in the browser have precipitated a bit of a rethink. The movement to abandon LAMP stacks and use static site generators is picking up pace. The term ‘serverless architecture’ is hard to avoid if you read certain news sites.

Using Apache Spark (with its brilliant RDD concept) was useful for bootstrapping the data processing for Chronograph, but the new code has an entirely flat-file workflow. The simplicity of not having to unnecessarily maintain a Hadoop HDFS instance seems to be the right choice in this case.

Repurposing the Wheel

The solution was to use S3 as a big hash table to store the final data that’s served to users.

The processing pipeline uses flat files all the way through from input log files to projections to aggregations. At the penultimate stage of the pipeline blocks of CSV per DOI are produced that represent date-value pairs.

<td>
2010-01
</td>
<td>
2010-01-01,05<br /> 2010-02-01,02<br /> 2010-01-03,08<br /> &#8230;
</td>

<td>
2010-02
</td>
<td>
2010-02-1,10<br /> 2010-02-01,7<br /> 2010-02-03,22<br /> &#8230;
</td>

10.5555/12345678

At the last stage, these are combined into blocks of all dates for a DOI

<td>
2010-01
</td>
<td>
2010-01-01,05<br /> 2010-02-01,02<br /> 2010-01-03,08<br /> &#8230;<br /> 2010-02-1,10<br /> 2010-02-01,7<br /> 2010-02-03,22<br /> &#8230;
</td>

10.5555/12345678

The DOIs are then hashed into 12 bits and stored as chunks of CSV

day-doi.csv-chunks_8841:

10.1038/ng.3020
2014-06-24,4
2014-06-25,4
2014-06-26,3
...
10.1007/978-94-007-2869-1_7
2012-06-01,12
2012-06-02,8
...
10.1371/journal.pone.0145509
2016-02-01,13
2016-02-02,75
2016-02-03,30
...

There are 65,536 (0x000 to 0xFFFF) possible files, each with about a thousand DOIs worth of data in each.

When the browser requests data for a DOI, it is hashed and then the request for the appropriate file in S3 is made. The browser then has to perform a linear scan of the file to find the DOI it is looking for.

This is the simplest possible form of hash table: simple addressing with separate linear chaining. The hash function is a 16-bit mask of MD5, chosen because of availability in the browser. It does a great job of evenly distributing the DOIs over all 65,536 possible files.

Striking the balance

In any data structure implementation, there are balances to be struck. Traditionally these concern memory layout, the shape of the data, practicalities of disk access and CPU cost.

In this instance, the factors in play included the number of buckets that need to be uploaded and the cost of the browser downloading an over-large bucket. The size of the bucket doesn’t matter much for CPU (as far as the user is concerned it takes about the same time to scan 10 entries as it does 10,000), but it does make a difference asking user to download a 10kb bucket or a 10MB one.

I struck the balance at 4096 buckets, resulting in files of around 100k, which is the size of a medium sized image.

It works

The result is a simple system that allows people to look up data for millions of DOIs, without having to look after another server. It’s also portable to any other file storage service.

The approach isn’t groundbreaking, but it works.

A fairer approach to waiting for deposits

Chuck Koscher — Wed, 20 Jul 2016 00:00:00 +0000

If you ever see me in the checkout line at some store do not ever get in the line I’m in. It is always the absolute slowest.

Crossref’s metadata system has a sort of checkout line, when members send in their data they got processed essentially in a first come first served basis. It’s called the deposit queue. We had controls to prevent anyone from monopolizing the queue and ways to jump forward in the queue but our primary goal was to give everyone a fair shot at getting processed as soon as possible. With many different behaviors by our members this could often be a challenge and at times some folks were not 100% happy.

We recently made a change where the queue now cycles through all waiting users and selects a job from each. This means that low-frequency users will always get a pretty fast service even if there are a lot of unique users waiting. Everyone gets one bite of the apple on each cycle through the waiting list. Of course, we still have some special controls to help deal with large quantities of files from a single user and ways to jump the queue under really special circumstances.

We believe this will, on average, yield a better experience and minimize the backups that formerly required administrator attention to resolve.

2016 upcoming events - we’re out and about!

Rosa Morais Clark — Wed, 06 Jul 2016 00:00:00 +0000

Check out the events below where Crossref will attend or present in 2016. We have been busy over the past few months, and we have more planned for the rest of year. If we will be at a place near you, please come see us (and support these organisations and events)!

Upcoming Events
SHARE Community Meeting, July 11-14, Charlottesville, VA, USA
Crossref Outreach Day - July 19-21 - Seoul, South Korea
CASE 2016 Conference - July 20-22 - Seoul, South Korea
ACSE Annual Meeting 2016 - August 10-11 - Dubai, UAE
Vivo 2016 Conference - August 17-19 - Denver CO, USA
SciDataCon - September 11-17 - Denver CO, USA
ALPSP - September 14-16 - London, UK
OASPA - September 21-22 - Arlington VA, USA
3:AM Conference - September 26 - 28 - Bucharest, Romania
ORCID Outreach Conference - October 5-6 - Washington DC, USA
Frankfurt Book Fair - October 19-23 - Frankfurt, Germany (Hall 4.2, Stand #4.2 M 85)
Crossref Annual Community Meeting #Crossref16 - November 1-2 - London, UK**
PIDapalooza - November 9-10 - Reykjavik, Iceland
OpenCon 2016 - November 12-14 - Washington DC, USA
STM Digital Publishing Conference - December 6-8 - London, UK

The Crossref outreach team will host a number of outreach events around the globe. Updates about events are shared through social media so please connect with us via @CrossrefOrg.

DOI-like strings and fake DOIs

Geoffrey Bilder — Wed, 29 Jun 2016 00:00:00 +0000

TL;DR

Crossref discourages our members from using DOI-like strings or fake DOIs.

Details

Recently we have seen quite a bit of debate around the use of so-called “fake-DOIs.” We have also been quoted as saying that we discourage the use of “fake DOIs” or “DOI-like strings”. This post outlines some of the cases in which we’ve seen fake DOIs used and why we recommend against doing so.

Using DOI-like strings as internal identifiers

Some of our members use DOI-like strings as internal identifiers for their manuscript tracking systems. These only get registered as real DOIs with Crossref once an article is published. This seems relatively harmless, except that, frequently, the unregistered DOI-like strings for unpublished (e.g. under review or rejected manuscripts) content ‘escape’ into the public as well. People attempting to use these DOI-like strings get understandably confused and angry when they don’t resolve or otherwise work as DOIs. After years of experiencing the frustration that these DOI-like things cause, we have taken to recommending that our members not use DOI-like strings as their internal identifiers.

Using DOI-like strings in access control compliance applications

We’ve also had members use DOI-like strings as the basis for systems that they use to detect and block tools designed to bypass the member’s access control system and bulk-download content. The methods employed by our members have fallen into two broad categories:

Spider (or robot) traps.
Proxy bait.

Spider traps

A “spider trap” is essentially a tripwire that allows a site owner to detect when a spider/robot is crawling their site to download content. The technique involves embedding a special trigger URL in a public page on a web site. The URL is embedded such that a normal user should not be able see it or follow it, but an automated bot (aka “spider”) will detect it and follow it. The theory is that when one of these trap URLs is followed, the website owner can then conclude that the ip address from which it was followed harbours a bot and take action. Usually the action is to inform the organisation from which the bot is connecting and to ask them to block it. But sometimes triggering a spider trap has resulted in the IP address associated with it being instantly cut off. This, in turn, can affect an entire university’s access to said member’s content.

When a spider/bot trap includes a DOI-like string, then we have seen some particularly pernicious problems as they can trip-up legitimate tools and activities as well. For example, a bibliographic management browser plugin might automatically extract DOIs and retrieve metadata on pages visited by a researcher. If the plugin were to pick up one of these spider traps DOI-like strings, it might inadvertently trigger the researcher being blocked- or worse- the researcher’s entire university being blocked. In the past, this has even been a problem for Crossref itself. We periodically run tools to test DOI resolution and to ensure that our members are properly displaying DOIs, Crossmarks, and metadata as per their member obligations. We’ve occasionally been blocked when we ran across the spider traps as well.

Proxy bait

Using proxy bait is similar to using a spider trap, but it has an important difference. It does not involve embedding specially crafted DOI like strings on the member’s website itself. The DOI-like strings are instead fed directly to tools designed to subvert the member’s access control systems. These tools, in turn, use proxies on a subscriber’s network to retrieve the “bait” DOI-like string. When the member sees one of these special DOI-like strings being requested from a particular institution, they then know that said institution’s network harbours a proxy. In theory this technique never exposes the DOI-like strings to the public and automated tools should not be able to stumble upon them. However, recently one of our members had some of these DOI-like strings “escape” into the public and at least one of them was indexed by Google. The problem was compounded because people clicking on these DOI-like strings sometimes ended having their university’s IP address banned from the member’s web site. As you can imagine, there has been a lot of gnashing of teeth. We are convinced, in this case, that the member was doing their best to make sure the DOI-like strings never entered the public. But they did nonetheless. We think this just underscores how hard it is to ensure DOI-like strings remain private and why we recommend our members not use them.

Pedantry and terminology

Notice that we have not used the phrase “fake DOI” yet. This is because, internally, at least, we have distinguished between “DOI-like strings” and “fake DOIs.” The terminology might be daft, but it is what we’ve used in the past and some of our members at least will be familiar with it. We don’t expect anybody outside of Crossref to know this.

To us, the following is not a DOI:

10.5454/JPSv1i220161014

It is simply a string of alphanumeric characters that copy the DOI syntax. We call them “DOI-like strings.” It is not registered with any DOI registration agency and one cannot lookup metadata for it. If you try to “resolve” it, you will simply get an error. Here, you can try it. Don’t worry- clicking on it will not disable access for your university.

http://doi.org.pluma.sjfc.edu/10.5454/JPSv1i220161014

The following is what we have sometimes called a “fake DOI”

10.5555/12345678

It is registered with Crossref, resolves to a fake article in a fake journal called The Journal of Psychoceramics (the study of Cracked Pots) run by a fictitious author (Josiah Carberry) who has a fake ORCID (http://orcid.org/0000-0002-1825-0097) but who is affiliated with a real university (Brown University).

Again, you can try it.

http://doi.org.pluma.sjfc.edu/10.5555/12345678

And you can even look up metadata for it.

https://api-crossref-org.pluma.sjfc.edu/v1/works/10.5555/12345678

Our dirty little secret is that this “fake DOI” was registered and is controlled by Crossref.

Why does this exist? Aren’t we subverting the scholarly record? Isn’t this awful? Aren’t we at the very least hypocrites? And how does a real university feel about having this fake author and journal associated with them?

Well- the DOI is using a prefix that we use for testing. It follows a long tradition of test identifiers starting with “5”. Fake phone numbers in the US start with “555”. Many credit card companies reserve fake numbers starting with “5”. For example, Mastercard’s are “5555555555554444” and “5105105105105100.”

We have created this fake DOI, the fake journal and the fake ORCID so that we can test our systems and demonstrate interoperable features and tools. The fake author, Josiah Carberry, is a long-running joke at Brown University. He even has a Wikipedia entry. There are also a lot of other DOIs under the test prefix “5555.”

We acknowledge that the term “fake DOI” might not be the best in this case- but it is a term we’ve used internally at least and it is worth distinguishing it from the case of DOI-like strings mentioned above.

But back to the important stuff….

As far as we know, none of our members has ever registered a “fake DOI” (as defined above) in order to detect and prevent the circumvention of their access control systems. If they had, we would consider it much more serious than the mere creation of DOI-like strings. The information associated with registered DOIs becomes part of the persistent scholarly citation record. Many, many third party systems and tools make use of our API and metadata including bibliographic management tools, TDM tools, CRIS systems, altmetrics services, etc. It would be a very bad thing if people started to worry that the legitimate use of registered DOIs could inadvertently block them from accessing content. Crossref DOIs are designed to encourage discovery and access- not block it.

And again, we have absolutely no evidence that any of our members has registered fake DOIs.

But just in case, we will continue to discourage our members from using DOI-like strings and/or registering fake DOIs.

This has been a public service announcement from the identifier dweebs at Crossref.

Image Credits

Unless otherwise noted, included images purchased from The Noun Project

Outreach Day DC. Next Up? You Tell Us

Jennifer Kemp — Tue, 28 Jun 2016 00:00:00 +0000

Rallying the community is a key Crossref role. Sometimes this means collaborating on new initiatives but it is also an ongoing process, a cornerstone of our outreach efforts. Part of rallying the community is bringing people together, literally, in a series of outreach days around the globe. It means we encourage dialog with us and among members and non-publisher affiliates. We want to hear from the community and we hope to facilitate conversations in it. Not just about Crossref, but larger issues of scholarly communications and your particular part in it. The Crossref outreach team is doing a number of events around the world to bring together the community for updates, feedback and discussion.

On 16 June, Crossref hosted an all day session in Washington, DC where we were joined by about 35 attendees from the region, mostly publishers. The size of the group made for lots of discussion, and we are grateful for the feedback. Here is what we took away from the event:

We all need a better understanding of who is using Crossref metadata and how

Sure, we all know that, for example, submission systems, libraries and hosting platforms use Crossref metadata (‘metadata out’), but pinpointing where in workflows (often multiple instances) and the interplay between publishers and these systems? Not so much. Help us change that: take this short survey to tell us how publisher metadata quality affects your systems and workflows and we will, in turn, make use cases (anonymized if you wish) available as part of an ongoing effort to promote the value of more, better and enriched metadata.

Here I must say a big thank you to our guest speaker for the day, Carly Robinson, who provided an excellent presentation on the work of OSTI, of the U.S. Department of Energy. Carly shared examples of how OSTI uses the Crossref metadata in their systems to aid compliance and compliment the DOE public access model. A live use case is a welcome way to partner with our community!

The more things change, the more they emphasize core best practices

A good part of the day was spent on new initiatives such as: DOIs for preprints, auto-update of ORCID records, ‘early content registration’ , linked clinical trials and more. All good stuff-the industry evolves and workflows must keep pace-but none of which generated a great deal of questions or expressed concern.

One session that did spur a lot of discussion was a simple overview of where Crossref services sit in the publishing process (including pre- and post-). Perhaps this is because it was early in the day but the much-appreciated discussion underscored the need to make the case for enriched metadata in a well-understood workflow that reflects the roles of publishers and affiliate users of metadata.

Outreach is an experiment in which we are all subjects

Finally, it must be noted here that we actively seek feedback on our Community Outreach days! We are not a large team and we can’t do as many outreach days as we’d like, but we are very open to hearing from you: So, tell us in this quick survey: what should we discuss? And where should we head next?

Hello preprints, what’s your story?

Jennifer Lin — Thu, 23 Jun 2016 00:00:00 +0000

The role of preprints

Crossref provides infrastructure services and therefore we support scholarly communications as it evolves over time. Today, preprints are increasingly discussed as a valuable part of the research story (beyond physics, math, and a small set of sub-disciplines). Preprints might play a positive role in catalyzing research discovery, establishing priority of discoveries and ideas, facilitating career advancement, and improving the culture of communication within the scholarly community.

As we shared in an earlier blog post last month, members will be able to register Crossref DOIs for preprints later this year. We will connect the full history of a research work, and ensure the citation record is clear and up-to-date. As we build out this new record/resource type, we’d love to hear how the research community envisions what preprints will do.

What’s your story, preprint?

So we can develop a service that supports the whole host of potential uses for all stakeholders, we ask the entire research community to contribute preprints user stories . User stories are concrete descriptions of a specific need, typically used in technology development: As a [x], I want to [y] to that I can [z]. User stories take the “end-user’s” perspective as they focus on a discrete result and its value. They are essential when implementing solutions that must meet a wide range of needs, across a diverse set of constituents. For example:

As an author, I want to share results before my paper is submitted to a journal so that I can get rapid feedback on it and make improvements before publication.

As a researcher who is part of a tenure and promotion committee or funder review panel, I want to know the reach of early results published from the candidate so that I can more quickly track the impact of results, rather than relying only on journal articles that take much longer to publish.

As a journal publisher, I want to know whether a preprint exists for a manuscript submitted to me so that I can decide whether I will accept the submission based on my editorial policy.

We aim to assemble a full catalog that cuts across research disciplines and stakeholder groups. We want to hear from you: researchers, publishers, funding agencies, scholarly societies, academic institutions, technology providers, other infrastructure providers , etc .

Tell us your story here

To ensure that your needs are included, please send us your user stories via this user story “deposit” form . They will be added to the full registry of contributions from the community, which we hope will serve as a key resource for all those developing preprints into a core part of scholarly communications (e.g., ASAPbio, etc.).

Linked Clinical Trials initiative gathers momentum

Kirsty Meddings — Tue, 21 Jun 2016 00:00:00 +0000

We now have linked clinical trials deposits coming in from five publishers: BioMedCentral, BMJ, Elsevier, National Institute for Health Research and PLOS. It’s still a relatively small pool of metadata - around 4000 DOIs with associated clinical trial numbers - but we’re delighted to see that “threads” of publications are already starting to form.

If you look at this article in The Lancet and click on the Crossmark button you will see that in the Clinical Trials section there are links to three other articles reporting on the same trial: two from the American Heart Journal and one from BMJ’s Heart. Readers can navigate between these four articles in three separate journals using the Crossmark functionality- a new set of links and routes for discovery have appeared.

In another example, three articles from PLOS ONE are threaded together around a trial for the treatment of Type 1 diabetes. And here another PLOS journal, Neglected Tropical Diseases links through to a PLOS ONE article about the same trial.

If you publish in the health sciences please do consider joining this exciting initiative so that we can expand these threads and build up the metadata. Read the tech specs here or drop me an email if you have questions.

Distributing references via Crossref

Geoffrey Bilder — Fri, 17 Jun 2016 00:00:00 +0000

Known unknowns

If you follow this blog, you are going to notice a theme over the coming months- Crossref supports the deposit and distribution of a lot more kinds of metadata than people usually realise.

We are in the process of completely revamping our web site, help documentation, and marketing to better promote our metadata distribution capabilities, but in the mean time we think it would be useful highlight one of our most under-promoted functions- the ability to distribute references via Crossref.

One of the questions we most often get from members is- “can we distribute references via Crossref?” The answer is an emphatic yes. But to do so, you have to take an extra and hitherto obscure step to enable reference distribution. [EDIT 6th June 2022 - all references are now open by default with the March 2022 board vote to remove any restrictions on reference distribution].

How?

Many members deposit references to Crossref as part of their participation in Crossref’s Cited-by service. However - for historical reasons too tedious to go into - participation in Cited-by does not automatically make references available via Crossref’s standard APIs. In order for publishers to distribute references along with standard bibliographic metadata, publishers need to either:

Contact Crossref support and ask them to turn on reference distribution for all of the prefixes they manage.
Set the reference_distribution_opt element to any for each content item registered where they want to make references openly available.

Either of these steps will allow references for the affected member DOIs to be distributed without restriction through all of Crossrefs APIs and bulk metadata dumps.

Note that by doing this, you are not enabling the open querying of your Cited-by data- you are simply allowing the references that you already deposit to be redistributed to interested parties via our public APIs.

Who?

So who does this now? Well, at the moment not many members have enabled this feature. How could they? They probably didn’t know it existed. At the time of writing this 29 publishers have enabled reference distribution for at least some of their DOIs.

But that’s why we are writing this post. Given the interest expressed by our members, we expect the list to start growing quickly over the next few months. Particularly now that they know they can do it and have clear instructions on how to do it. 🙂

If you are of a geeky persuasion and want to see the list of publishers who are doing this, you can check via our API.

The following query will just show you the total number of members who are distributing references for at least some of their DOIs.

https://api-crossref-org.pluma.sjfc.edu/v1/members?filter=has-public-references:true&rows=0

And this query will allow you to page through the member records and see who is distributing references.

https://api-crossref-org.pluma.sjfc.edu/v1/members?filter=has-public-references:true

That cool, but can you see how many total DOIs have reference distribution enabled? No, but will will be adding that capability to our API soon.

OMG! OMG! OMG! Does this mean I can get references from api.crossref.org?

Yep. But before you get too excited- note above that not many of our members are doing this yet and that our API is still being updated to allow you to better query this information. At the moment references are not included in our JSON representation- they are only included in our XML representation. You can get the XML for a Crossref DOI either through content negotiation, or by using the following incantation on our API (using an eLife DOI as an example):

~~https://api-crossref-org.pluma.sjfc.edu/v1/works/10.7554/eLife.10288.xml~~

~~As we update our API to better support querying DOIs that include references, you will see the new functionality reflected in our documentation at:~~

Yes. 🤗. See the API docs below.

https://api-crossref-org.pluma.sjfc.edu

Beyond the DOI to richer metadata

April Ondis — Wed, 15 Jun 2016 00:00:00 +0000

The act of registering a DOI (Digital Object Identifier) for scholarly content is sometimes conflated with the notion of conferring a seal of approval or other mark of good quality upon an item of content. This is a fundamental misunderstanding.

A DOI is a tool, not a badge of honor.

The presence of a Crossref DOI on content sends a signal that:

The owner of the content would like to be formally cited if the content is used in a scholarly context.
The owner of the content considers that it is worthy of being made persistent.

Beyond the DOI

For Crossref, a DOI is just one of several types of metadata we register, albeit an important one.

Metadata about scholarly works extends beyond the DOI. In addition to bibliographic details, layers of information accompanying published works may now extend to data that describes the research, such as the source of research funding. It may also include non-descriptive information that facilitates usage, such as copyright and access permissions.

In fact, this “richer” metadata can tell you more about the context of the content deposited for a published work than you might realize.

For example:

Author data - Crossref metadata may include information specifying the author’s unique ORCID, allowing you to find other works by the same person.

Copyright and access indicators - You can view the license terms under which the full content may be available, which is very helpful for scholars who want to access the full content for research and teaching or for text and data mining.

Funding data - Metadata may also include the identity of the grant-making institution that funded the research, so that the funder and, in the case of publicly funded research, the general public and other researchers, have visibility on the resulting research outputs.

Clinical Trials data - Similarly, when research involves a clinical trial, (testing of medicines and treatments on human beings), Crossref metadata can enhance output visibility by displaying the clinical trial number and the related clinical trial registry.

Like the full content they describe, these metadata have become research resources in their own right. Unfortunately, too much metadata is entered into Crossref with missing, incomplete, or duplicated fields. This “bad” metadata slows the pace of discovery, confounding attempts to find and understand scholarly content and its context.

As a community, we really need to do something about that.

“The Map is not the Territory”

And the metadata is not the content. In Metadata (MIT Press), Jeffrey Pomerantz quotes Alfred Korzybski’s insight that a map is a simplified representation of a territory, a tool of abstraction that allows us to find our way. Jennifer Lin contributed the concept of the scholarly road map as a useful metaphor for the way we use metadata about scholarly works to find our way between and among them in the digital world.

Metadata deposited with Crossref amounts to pieces of information-structured, descriptive, administrative, contextual-about published works that humans can read and machines can use to automate linking and retrieval. The systematic development of such metadata allows us to make sense of such complex information by finding, linking, citing, and assessing scholarly content.

If you want to understand how Crossref acts as a map of scholarly metadata, try searching for content on search.crossref.org (our human API interface). Or simply talk with us @CrossrefOrg and via member@crossref.org.

Our memories of #SSP2016

April Ondis — Wed, 08 Jun 2016 00:00:00 +0000

Last week a bunch of Crossref’s staff traveled to the 2016 Society for Scholarly Publishing Annual Meeting in Vancouver, BC. After we returned en masse, all nine of us put our heads together to share some of our personal memories of the event.

Crossref’s Rosa and Susan at the Fun Walk/Run sponsored by High Wire. 5K before breakfast!

On Cybersecurity and the Scholarly World —“The session described the many and complicated security threats that IT systems face and how threat detection and defense is a constantly ongoing activity. Certainly system administrators are challenged with the technology issues that build firewalls, block intrusions and divert disruptive activity. But perhaps even more important are the social issues that must be managed to develop an informed user community that is immune to the less technical but probably more effective hacks like phishing for user passwords.”

On Persistent Identifiers in Scholarly Communications: What, Why, How, Where, and Who? “Everyone from Crossref loved this panel, which should come as no surprise (wink). Persistent identifiers such as DOIs and ORCID iDs enable machine and human readers to discover, cite, link, and correctly attribute works across different platforms. David Crotty of the Oxford University Press said it best with ‘If you’re not actively building these persistent identifiers into your systems, get busy!’ Alice Meadows of ORCID represented the scholarly communications infrastructure with an image of shiny copper plumbing - don’t tell me we don’t have glamorous jobs! Laura Rueda of DataCite had particularly helpful diagrams to explain how persistent identifiers ease and speed the workflow of a research object as it travels from researcher to publisher to the greater community.”

On Crossing Boundaries: Encouraging Diversity in Scientific Communication with Dr. Margaret-Ann Armour — “I decided to attend this keynote when I saw that men as well as women were in the audience. Dr. Armour had great anecdotes that supported formal data on women’s roles in STEM. It made me reflect on how the path to a career in scholarly publishing is often not direct, and relies on personal networking. She was very witty and deserved her standing ovation.”

On Standards and Recommended Practices to Support Adoption of Altmetrics — “Todd Carpenter summed up the intent behind many altmetrics initiatives when he said that understanding how many people are using and reading scholarly content is important because ‘we all want to know how we’re doing’ but ‘this project should never become the number’ because the intent is about ‘trying to add flavor and nuance to the conversation in a meaningful way’. Stuart Maxwell of Scholarly IQ also made a really astute observation that “all assessment is in some way subjective - impact is relative to how you compare yourself to other researchers in your field.” What especially appealed to me about this session was learning that NISO extends its remit to include the data quality performance of altmetrics aggregators themselves. Asking each aggregator to self-report a publicly available, annual accounting of how they comply with the Altmetrics Data Quality Code of Conduct will likely increase consistency, transparency and trust.”

SSP receptions & evening events, where mashed potato sundaes were a thing

Yes, the sessions are great, but some of the really interesting sights, sounds and discussions occur at the evening events. It’s impossible for one person to cover all of them (or is it?), but our idea of a few memorable highlights from this year’s SSP are, in no particular order:

“Tuesday’s reception—bar conveniently located just steps from the Crossref booth meant lots of good traffic! The convivial atmosphere made it easy to ignore that we were all tantalizingly close to the glorious view just outside the hotel doors. Wednesday’s reception was a chance to meet all the folks who didn’t make it in Tuesday. Though it seems most of us were delayed arriving in Vancouver, it was well worth the trip and arriving to find a few hundred colleagues all enjoying happy hour is a fine way to start a meeting.”

“HighWire’s reception at the Vancouver Rowing Club provided a lovely walk on the way there, a great band at the party and a shrimp tower almost (but not quite) too good looking to eat. The pouring rain on the walk back made for a memorable bonding experience.”

“Wildebeest was the atmospheric site of the Silverchair reception and great chance to see a bit of downtown before enjoying some good cheese and fine company. At least two of us attending made plans to save the world through better metadata. Over sparkling rose wine no less.”

“Dolphins and sea otters made merry in a pool outside the Sheridan Group reception at the Vancouver Aquarium, while we noshed and drank with the fishes inside. But the food rivalled the undersea sights. A very nice gentleman with an ice cream scoop filled a parfait glass with a perfectly round dollop of mashed potatoes and told me to help myself to toppings. Shut the front door! I got the works. Delicious creamy mashed (whipped) potatoes of a perfect consistency, a ladle full of warm brown gravy topped with a generous sprinkle of finely sliced green onions (scallions), and a healthy spray of large, crispy bacon pieces!! It looked like a sundae … that you eat with a fork!!”

“The President’s reception was in the world’s largest hotel suite (approximately), with some very photogenic desserts and a lot of happy people who know that it’s well worth sacrificing some sleep for the event.”

Of course, the hotel bar in the evenings had some memorable discussions too but what happens in the bar stays in the bar, right? And we should probably all be grateful for the early last call …

’Til next year!

HTTPS and Wikipedia

Joe Wass — Tue, 31 May 2016 00:00:00 +0000

This is a joint blog post with Dario Taraborelli, coming from WikiCite 2016.

In 2014 we were taking our first steps along the path that would lead us to Crossref Event Data. At this time I started looking into the DOI resolution logs to see if we could get any interesting information out of them. This project, which became Chronograph, showed which domains were driving traffic to Crossref DOIs.

You can read about the latest results from this analysis in the “Where do DOI Clicks Come From” blog post.

Having this data tells us, amongst other things:

where people are using DOIs in unexpected places
where people are using DOIs in unexpected ways
where we knew people were using DOIs but the links are more popular than we realised

By the time the ALM Workshop 2014 rolled around there was some preliminary data and we realised that Wikipedia came into the third category. There are lots of DOIs in Wikipedia and people click them!

I met with Dario Taraborelli, head of research at the Wikimedia Foundation, and shared the data. Dario — who co-authored in 2010 the Altmetrics Manifesto — has been interested in understanding how scholarly citations are used in Wikipedia. Over the years, Wikipedia contributors have made extensive use of references to the scientific literature using DOIs, and by doing so they have created a resource that represents today in many ways the “front matter to all research”. There is growing interest in the community in understanding how DOIs are being used in Wikipedia and in non traditional scholarship.

During our discussions the subject of Wikipedia’s gradual transition to HTTPS was raised: we anticipated that this change would affect our data gathering.

Changes

When you’re reading webpage and click on a link to another page, your web browser will usually tell the server of that second page the last page you were on. This forms the basis of trackers like Google Analytics.

In the days before HTTPS, the next site would know the full URL that you were previously on. With the change to HTTPS, this was reduced to just sending the domain name and not the full URL, or no data at all if you click from an HTTPS page to HTTP.

DOI hyperlinks are just like any other hyperlink, and are mostly HTTP not HTTPS.

Up until 2015, Wikipedia was served over HTTP, only switching to HTTPS when users were logged in or if they requested it. The Wikimedia Foundation started planning to move to HTTPS and we knew that if they did that, and continued to use HTTP DOIs then we would lose valuable research data.

A Plan

We decided that the best course of action was to try and change the DOIs in Wikipedia to use HTTPS. Simple, right?

After some further research, Dario posted a proposal on how to mitigate the impact of the HTTPS rollout, to make sure that Wikipedia can still signal its importance as a traffic source, while preserving the privacy of its users. Discussion followed and the conclusion was to change the format of every single DOI on Wikipedia, which fortunately could be done without having to edit millions of pages. You can read the full story in this post from a year ago.

The result of this effort was that well in advance of the HTTPS switchover, the DOI links were ready to continue reporting referral data.

The Switch

In June 2015 the Wikimedia foundation made the announcement that they were finalising the switch, and that within a few weeks all traffic would be HTTPS.

We held our breath. Would it work? Would we lose all referral data from Wikipedia sites? In February 2016 the last piece of the puzzle fell into place as Wikipedia gained a ‘meta referrer’ tag to explicitly specify how they would like referrers to be sent: a detailed report on the effect of this change is coming up on the Wikimedia Foundation’s blog.

The results

As detailed in the last blog post the traffic that we measured coming from Wikipedia doesn’t seem to have slowed down during 2015:

I’d call that a success! Over the period covered in the graph, Wikipedia remained prominent as a non-publisher referral of traffic to DOIs.

Looking at the balance of HTTP vs HTTPS traffic coming from wikipedia.org, the switchover was dramatic:

Thank you to Dario Taraborelli, Nemo (Federico Leva), Aaron Halfaker, Alex Stinson and everyone who put in this effort.

I’ll leave the last word to Dario:

It’s great to see this data. It shows that the switchover happened successfully, which better protects the privacy of our users whilst still reporting the fact that Wikipedia is a prominent source of traffic. This is important validation of the increasing role that Wikipedia plays in the education and scientific community.

Where do DOI clicks come from?

Joe Wass — Thu, 19 May 2016 00:00:00 +0000

As part of our Event Data work we’ve been investigating where DOI resolutions come from. A resolution could be someone clicking a DOI hyperlink, or a search engine spider gathering data or a publisher’s system performing its duties. Our server logs tell us every time a DOI was resolved and, if it was by someone using a web browser, which website they were on when they clicked the DOI. This is called a referral.

This information is interesting because it shows not only where DOI hyperlinks are found across the web, but also when they are actually followed. This data allows us a glimpse into scholarly citation beyond references in traditional literature.

Last year Crossref Labs announced Chronograph, an experimental system for browsing some of this data. We’re working toward a new version, but in the meantime I’d like to share the results for 2015 and some of 2016. We have filtered out domains that belong to Crossref member publishers to highlight citations beyond traditional publications.

Top 10 DOI referrals from websites in 2015

This chart shows the top 10 referring non-primary-publisher domains of DOIs per month. Note that if browsers don’t send the referrer (e.g. from an HTTPS page), we don’t get to find out. Because the top 10 can be different month to month, the total number of domains mentioned can be more than 10. Subdomains are combined, which means that, for example, the wikipedia.org entry covers all Wikipedia languages. This chart covers all of 2015 and the first two months of 2016.

The top 10 referring domains for the period:

webofknowledge.com
baidu.com
serialssolutions.com
scopus.com
exlibrisgroup.com
wikipedia.org
google.com
uni-trier.de
ebsco.com
google.co.uk

It’s not surprising to see some of these domains here: for example serialssolutions.com and exlibrisgroup.com are effectively proxies for link resolvers, Baidu and Google are incredibly popular search engines which would show up anywhere. But it is exciting to see Wikipedia ranked amongst these. For more detail look out for the new Chronograph.

HTTP vs HTTPS in 2015

We’ve also seen a steady increase in HTTPS referral traffic, i.e. people clicking on DOIs from sites that are using HTTPS. While it is still dwarfed by HTTP, there was a steady uptick throughout 2015.

This chart shows HTTP vs HTTPS referrals per day, which shows up the weekly spikes. It doesn’t include resolutions where we don’t know the referrer.

Increasing numbers of people are moving to HTTPS for reasons of security, privacy and protection from tampering. Google has announced plans to take HTTPS into account when ranking search results. Wikipedia has moved exclusively to HTTPS, and I’ll be telling the story of how Crossref and Wikipedia collaborated in an upcoming blog post.

Chronograph

Another version of Chronograph will be available soon. It will contain full data for all non-primary-publisher referring domains. Stay tuned!

Clinical trial data and articles linked for the first time

Daniel Shanahan — Tue, 17 May 2016 00:00:00 +0000

It’s here. After years of hard work and with a huge cast of characters involved, I am delighted to announce that you will now be able to instantly link to all published articles related to an individual clinical trial through the Crossmark dialogue box. Linked Clinical Trials are here!

In practice, this means that anyone reading an article will be able to pull a list of both clinical trials relating to that article and all other articles related to those clinical trials – be it the protocol, statistical analysis plan, results articles or others – all at the click of a button.

Linked Clinical Trials interface

Now I’m sure you’ll agree that this sounds nifty. It’s definitely a ‘nice-to-have’. But why was it worth all the effort? Well, simply put: “to move a mountain, you begin by carrying away the small stones”.

Science communication in its current form is an anachronism, or at the very least somewhat redundant.

You may have read about the ‘crisis in reproducibility’. Good science, at its heart, should be testable, falsifiable and reproducible, but an historical over-emphasis on results has led to a huge number of problems that seriously undermine the integrity of the scientific literature.

Issues such as publication bias, selective reporting of outcome and analyses, hypothesising after the results are known (HARKing) and p-hacking are widespread, and can seriously distort the literature base (unless anyone seriously considers Nicholas Cage to be causally related to people drowning in swimming pools).

This is, of course, nothing new. Calls for prospective registration of clinical trials date back to the 1980s and it is now becoming increasingly commonplace, recognising that the quality of research lies in the questions it asks and the methods it uses, not the results observed.

Uptake of trial registration year-on-year since 2000

Building on this, a number of journals and funders – starting with BioMed Central’s Trials over 10 years ago – have also pushed for the prospective publication of a study’s protocol and, more recently, statistical analysis plan. The idea that null and non-confirmatory results have value and should be published has also gained increasing support.

Over the last ten years, there has been a general trend towards increasing transparency. So what is the problem? Well, to borrow an analogy from Jeremy Grimshaw, co-Editor-in-Chief of Trials – we’ve gone from Miró to Pollock.

Although a results paper may reference a published study protocol, there is nothing to link that report to subsequent published articles; and no link from the protocol itself to the results article.

A single clinical trial can result in multiple publications: the study protocol and traditional results paper or papers, as well as commentaries, secondary analyses and, eventually, systematic reviews, among others, many published in different journals, years apart. This situation is further complicated by an ever-growing body of literature.

Researchers need access to all of these articles if they are to reliably evaluate bias or selective reporting in a research object, but – as any systematic reviewer can tell you – actually finding them all is like looking for a needle in a haystack. When you don’t know how many needles there are. With the haystack still growing.

That’s where we come in. The advent of trial registration means that there is a unique identifier associated with every clinical trial, at the study-level, rather than the article level. Building on this, the Linked Clinical Trials project set out to connect all articles relating to an individual trial together using its trial registration number (TRN).

By adapting the existing Crossmark standard, we have captured additional metadata about an article, namely the TRN and the trial registry, with this information then associated with the article’s DOI on publication. This means that you will be able to pull all articles related to an individual clinical trial from the Crossmark dialogue box on any relevant article.

This obviously has huge implications for the way science is reported and used. By quickly and easily linking to related published articles, it will enable editors, reviewers and researchers to evaluate any selective reporting in the study, and help to provide far greater context for the results.

As all the metadata will be open access (CC0), with no copyright, it will also be possible to access this article ‘thread’ through the Crossref Metadata Search, or independently through an application programming interface (API). This provides a platform for others to build on, with many already looking to take the next step, such as Ben Goldacre’s new Open Trials initiative.

However, in order for this to work, we must capture as many articles and trials as possible to create a truly comprehensive thread of publications. We currently have data from the NIHR Libraries, PLoS and, of course, BioMed Central, but need more publishers and journals to join us in depositing clinical trial metadata. After all, without metadata, this is all merely wishful thinking.

Let’s hope we’re the pebble that starts the landslide.

Members will soon be able to assign Crossref DOIs to preprints

Geoffrey Bilder — Thu, 05 May 2016 00:00:00 +0000

TL;DR

By August 2016, Crossref will enable its members to assign Crossref DOIs to preprints. Preprint DOIs will be assigned by the Crossref member responsible for the preprint and that DOI will be different from the DOI assigned by the publisher to the accepted manuscript and version of record. Crossref’s display guidelines, tools and APIs will be modified in order to enable researchers to easily identify and link to the best available version of a document (BAV). We are doing this in order to support the changing publishing models of our members and in order to clarify the scholarly citation record.

Background

Why is this news? Well, to understand that you need to know a little Crossref history.

(cue music and fade to sepia)

When Crossref was founded, one of its major goals was to clarify the scholarly record by uniquely identifying formally published scholarly content on the web so that it could be cited precisely. At the time, our members had two primary concerns:

That a Crossref DOI should point to one intellectually discrete scholarly document. That is, they did not want one Crossref DOI to be assigned to two documents that appeared largely similar, but which might vary in intellectually significant ways.
That two DOIs should not point to the same intellectually discrete document. They wanted it to be easy for all to tell when the same discrete intellectual content was cited.

As such, when Crossref was founded, we developed a complex set of rules that were colloquially known by our members as Crossref’s rules “prohibiting the assignment of DOIs to duplicative content.”

(cue music, show wavy lines, return to color)

Well… as we gained experience in assigning DOIs, many of these rules have been amended or discarded when it became apparent that they didn’t actually support common scholarly citation practice and/or otherwise muddied the scholarly citation record.

For example, sometimes a document will be re-published in a special issue or an anthology. Before the advent of the DOI, it was common citation practice to always cite a document in the context in which it was read. The context of the document could, after all, affect the interpretation or crediting of the work. But it would be impossible to support this common citation practice if we were to assign the same Crossref DOI to the article on both its original context and in its re-published form. Our current recommendation in these situations is to assign separate DOIs to content that is republished in another context.

Another example occurs when a particular copy of a two identical documents has been annotated. For example, though the Handbook to The birds of Australia By John Gould has its own Crossref DOI (http://doi.org.pluma.sjfc.edu/10.5962/bhl.title.8367), another copy of the same book has been hand-annotated by Charles Darwin and also has its own, different Crossref DOI (http://doi.org.pluma.sjfc.edu/10.5962/bhl.title.50403). Historians of science quite reasonably may want to refer and cite the particular annotated copy of this historic document.

__[So much for not assigning two separate Crossref DOIs to identical documents.]

Finally, we should note a far more common example practice in our industry. Our members often make content available online with a Crossref DOI before they consider it to be formally published. This practice goes by a number of names including “publish ahead of print,” “article in progress,” “article in press,” “online ahead of print,” “online first”, etc.

But in each case, the process is the same- the publisher is assigning a Crossref DOI to the document soon after it has been accepted for publication and this same Crossref DOI is carried over to the finally published article. Again, this practice just reflects that the “intellectual” content of the accepted manuscript should not change between the point of acceptance and the point of publication, so of the purposes of “citation” they are largely interchangeable.

[So much for not assigning one Crossref DOI to two versions of the same document.]

Now, in the above cases it also helps to clarify the scholarly record to also specify that the respective Crossref DOIs of the original and the “duplicative” work are related, and we encourage our members to make these connections explicit when they can. Nonetheless, it is paramount in both cases to allow the “duplicative works” to be cited precisely and independently.

Which brings us back to preprints.

The case for preprints

First we should define what was meant by preprints because even this commonly used term sometimes means different things to different communities. We have historically considered preprints to be any version of a manuscript that is intended for publication but that has not yet been submitted to a publisher for formal review. Note that this definition does not include “accepted manuscripts” which -as we noted above- often already have Crossref DOIs assigned to them soon after acceptance.

Crossref members originally worried that, by assigning DOIs to preprints, we would end up muddying the scholarly record. They worried that the very presence of a Crossref DOI would be interpreted to mean that the content to which it had been applied had gone through a formal publishing process. And unlike the case with “accepted manuscripts”, the difference between intellectual content of a preprint and the final published version can sometimes be substantial. At the time, it seemed that the scholarly record would be clarified by prohibiting the assignment of DOIs to preprints.

But again, changes in the scholarly communication landscape have led us to -as the youngsters say- pivot.

A Koan

When is a preprint a preprint?

Crossref has always been catholic in its definition of “publisher.” Many of our members do not consider “publishing” to be their primary mission. The OECD and World Bank are two obvious cases here. But our membership also includes government departments, universities and archives. In these latter cases they have traditionally assigned Crossref DOIs to things like internal reports, grey literature, working papers, etc. This activity was clearly within the original rules set out by Crossref. And this is where our koan comes into play- “when is a preprint a preprint?”

It is often difficult to predict when something might eventually be formally published. How do you a priori know that working paper will never be submitted for publication? After all, everything could potentially be submitted for publication (Sometimes it seems everything is.)

This is the dilemma that was faced by a few of our members. For example, Cold Spring Harbor Laboratory, which runs bioRxiv has been a Crossref member since 2000 and has assigned over 35,000 Crossref DOIs. They have been assiduous in trying to stick to Crossref’s rules about preprints. Furthermore, they have taken equal care to ensure that preprints in bioRxiv are labeled as such and linked to the final publication (via a Crossref journal DOI) when it is available. This takes a lot of work.

But often bioRxiv simply has no way of telling when the authors of a working paper or report might suddenly decide to submit their work for publication. So they have found themselves occasionally and inadvertently violating Crossref’s rules on preprints because they had no way of predicting when something would magically transform from being an innocuous working paper into a fraught preprint.

It is a testament to bioRxiv that they have persevered. We have other members who face the same problem. They have not given up. They have not gone elsewhere for their DOIs.

Which brings us to our next point.

Not All DOIs

Have you noticed how often we use the phrase “Crossref DOIs?” Were you wondering if this was an annoying affectation or an example of a marketing department gone mad? It’s neither. It is an essential distinction that we make because Crossref is just one of several DOI registration agencies. Although all DOIs are “compatible” in the minimal sense that you can “resolve” them to a location on the web, that does not mean that all DOIs work identically. Different DOI registration agencies have different constituencies, different services, different governance models and different rules covering what their members can assign their respective DOIs to.

This was not the case when Crossref was founded and our rules were first drafted. At the time, Crossref was the only registration agency and, as such, the rule which prohibited the assignment of Crossref DOIs to preprints kinda worked. But it was unworkable in the longer term.

Quite naturally, new DOI registration agencies have been established for different communities with different primary use-cases. While Crossref could have a rule prohibiting the assignment of Crossref DOIs to preprints, there was nothing stopping another registration agency from allowing (indeed, encouraging) its members to assign DOIs to preprints.

So the simple fact is that DOIs could be assigned to preprints regardless of Crossref’s old rules. By continuing to prohibit the practice at Crossref we were just making life for some of our existing members more difficult.

And it has become clear that the situation would only get worse as more of our members started to roll-out new publishing and business models.

Business model neutral

Crossref has always been business model neutral. We need to adapt and change to support our members’ business models, not the other way around.

A number of our members are starting to adopt publishing workflows that are more fluid and public than established publishing models. These new workflows make much of the submission and review process open, which, in turn often blurs the historically hard distinctions between a draft manuscript, a preprint, a revised proof, an accepted manuscript, the “final” published version, and subsequent corrections and updates. Where as in classic publishing models a document went through a series of discrete state-changes (some in public, many in private) new publishing workflows treat document versions as a continuum, most of which are made available publicly and which consequently may be used cited at almost any point in the publishing process.

In short, Crossref’s members increasingly need the flexibility to assign DOIs at different points in the publishing lifecycle. Rather than enforce rules that enshrined an existing publishing or business model, we need to work with our members to establish and adopt new DOI assignment practices which support evolving publishing models whilst maintaining a clear citation record and which lets researchers easily identify the best available version (BAV) of a document or research object.

So you see, not all of our motivations for this change in policy are opportunistic or prosaic. Underneath our gruff and flinty exterior is a soft, idealistic center. There are principles at work here as well.

What next

So this isn’t just matter of changing our rules and display guidelines. We also have to make some schema changes, and adjust our services and APIs to clearly distinguish between preprints and accepted manuscripts/versions of record. Additionally, we will be building tools to make it much easier for our members to link preprints to the final published article (and vice versa). Finally, we need to update our documentation to help our members take advantage of the new functionality. We expect that everything will be in place by the end of August, 2016, at which point you will see another announcement from us.

Crossref Brand update: new names, logos, guidelines, + video

Ginny Hendricks — Fri, 29 Apr 2016 00:00:00 +0000

It can be a pain when companies rebrand as it usually requires some coordinated updating of wording and logos on websites, handouts, and slides. Nevermind changing habits and remembering to use the new names verbally in presentations.

Why bother?

As our infrastructure and services expanded, we sometimes branded services with no reference to Crossref. As explained in our The Logo Has Landed post last November, this has led to confusion, and it was not scalable nor sustainable.

With a cohesive approach to naming and branding, the benefits of changing to (some) new names and logos should help everyone. Our aim is to stem confusion and be in a much better position to provide clear messages and useful resources so that people don’t have to try hard to understand what Crossref enables them to do.

So while it may be a bit of a pain short-term, it will be worth it!

What are the new names?

As a handy reference, here is a slide-shaped image giving an overview of our services with their new names:

Overview of brand name changes, April 2016

It’s a lowercase ‘r’ in Crossref

That’s right, you’ve spent fifteen years learning to capitalize the second R in Crossref, and now we’re asking you to lowercase it! Please say hello to and start to embrace the more natural and contemporary Crossref.

Reference logos from our new CDN via assets.crossref.org

I’m hoping we can count on our community to update logos and names on your end, keeping consistent with new brand guidelines. And I hope we can make it as easy as possible to do:

This Content Delivery Network (CDN) at assets.crossref.org allows you to reference logos using a snippet of code. Please do not copy/download the logos.
This set of brand guidelines for members.

We also have a new website in development which will put support and resources front and center of the user experience. More on that in the next month or two.

By using the snippets of code provided via our new CDN at assets.crossref.org, these kind of manual updates should never be a problem in the future if the logo changes again (no plans anytime soon!).

Of course, we don’t expect people to update new logos and names immediately, there is always a period of transition. Please let us know let us know if we can help you to update your sites and materials in the coming weeks.

Also, check out the launch video, which presents five key Crossref brand messages:

Getting Started with Crossref DOIs, courtesy of Scholastica

Anna Tolwinska — Mon, 25 Apr 2016 00:00:00 +0000

I had a great chat with Danielle Padula of Scholastica, a journals platform with an integrated peer-review process that was founded in 2011. We talked about how journals get started with Crossref, and she turned our conversation into a blog post that describes the steps to begin registering content and depositing metadata with us. Since the result is a really useful description of our new member on-boarding process, I want to share it with you here as well. As always, comments and questions are welcome here, at member@Crossref.org, and @CrossrefOrg. - Anna_

The internet is in a constant state of change, with new content being added to the web by the minute and old content sometimes getting moved around. While the benefit of publishing scholarly outputs online is that it’s possible to update them at any moment, moving or modifying content can also …

Crossref Event Data: early preview now available

Madeleine Watson — Mon, 18 Apr 2016 00:00:00 +0000

Test out the early preview of Event Data while we continue to develop it. Share your thoughts. And be warned: we may break a few eggs from time to time!

Chicken by anbileru adaleru from the The Noun Project

Want to discover which research works are being shared, liked and commented on? What about the number of times a scholarly item is referenced? Starting today, you can whet your appetite with an early preview of the forthcoming Crossref Event Data service. We invite you to start exploring the activity of DOIs as they permeate and interact with the world after publication.

But first, a bit of background

Discussion around scholarly research increasingly occurs online after publication, for example on blogs, sharing services, social media, and wikis. These ‘events’ occur across the web on numerous platforms and are a critical part of the scholarly enterprise. We are developing an infrastructure service (Crossref Event Data) that collects, stores, and delivers raw data of the events occurring with Crossref DOIs. We will store the data in an open, auditable and portable form for the community to access. Publishers, platforms, funders, bibliometricians and service providers may benefit from access to this raw data, and it can be used to feed into research records or proprietary tools and services that offer aggregation and analysis.

For more information, see our pilot blog post and description of potential use cases.

Collaborative, transparent development

Developers Martin Fenner (DataCite) and Joe Wass (Crossref) enjoy a tofu break

Lagotto, the software originally developed at PLOS, has been extended and improved in a joint effort between DataCite and Crossref. The two DOI Registration Agencies have partnered to envision, build and release the service. On the 13th of April, after a year of collaboration, we jointly released Lagotto 5.0. You can read about the collaboration on the DataCite blog post.

Crossref and DataCite will continue to work closely together to develop Lagotto and the Event Data service. Although Crossref Event Data has mostly Crossref DOIs at launch, you will be able to find DataCite DOIs if they are cited in Crossref or Wikipedia.

All of the software that runs Event Data, including Lagotto, is developed in the open and is open source. Please refer to the Crossref Event Data Technical User Guide for full details.

Preview the data

This service is currently under development with a full launch expected the second half of 2016. Before it is launched however, we invite you to take a look around and preview a subset of the data sources we plan to include. You may experience occasional hiccups while we continue building the service.

At this stage, we are working with data from three sources although we will greatly expand the variety of platforms from which we collect data as development progresses. At this stage, you can view Mendeley bookmarks, Wikipedia references, and Crossref to DataCite links.

Mendeley

Mendeley is a reference manager and academic social network for scholars. View the number of social bookmarks from scholars or groups on Mendeley.

For example, doi.org/10.1016/J.JIP.2016.03.007 currently has 8 readers on Mendeley to date.

Wikipedia

Wikipedia is an online encyclopaedia, the Internet’s largest and most popular general reference work. View references in Wikipedia of Crossref publications in Wikipedia articles in all languages.

For example, doi.org/10.3897/ZOOKEYS.565.7185 was referenced in the Russian Wikipedia page on Oxyscelio

Crossref to DataCite links

DataCite is a global consortium that assigns DOIs to research data. This enables people to find, share, use, and cite data. You can view all the data citations to DataCite research outputs found in Crossref publications (work is underway to make the links found in DataCite metadata available in Event Data).

For example, Global, Regional, and National Fossil-Fuel CO2 Emissions (doi.org/10.3334/CDIAC/00001) dataset has been referenced by six Crossref publications to date. Software links are also included. Another example is PGOPHER (doi.org/10.5523/bris.huflggvpcuc1zvliqed497r2), a general purpose software for simulating and fitting rotational, vibrational and electronic spectra, which has been referenced by seven Crossref publications to date.

Ready to take a spin?

You can explore the Crossref Event Data early preview by visiting http://eventdata.crossref.org.pluma.sjfc.edu and following the links to featured examples within our interim application for inspecting the data, technical documentation, and our Quick Start guide.

This service is currently under development and as such we welcome your thoughts and feedback on the data we are collecting currently from our three active sources. As a reminder, we expect to include the following sources as part of our full service launch later this year (pending confirmation):

[table id=1 /]

We’re also on the lookout for new data sources to investigate for future inclusion in the Event Data service so please do get in touch with requests and recommendations. As we continue to build the service throughout 2016, we will be committing to a model of continuous development so that we can make new sources available as they are completed.

Watch this blog for regular updates on our progress, or subscribe to receive new blog posts by email (just add your details to the upper right side of this page).

What are there 80 million of?

Ginny Hendricks — Fri, 08 Apr 2016 00:00:00 +0000

As of this week, there are 80,000,000 scholarly items registered with Crossref!

By the way, we update these interesting Crossref stats regularly and you can search the metadata.

The 80 millionth scholarly item is [drumroll…] Management Approaches in Beihagi History from the journal Oman Chapter of Arabian Journal of Business and Management Review, published by Al Manhal in the United Arab Emirates.

There have been loads of changes since Wiley registered “Designer selves: Construction of technologically mediated identity within graphical, multiuser virtual environments” with the DOI http://dx.doi.org.pluma.sjfc.edu/10.1002/(SICI)1097-4571(1999)50:10<855::AID-ASI3>3.0.CO;2-6), which happens to have been Crossref’s first official DOI (after many prototype deposits).

In the beginning, most of our new members came from the United States and Europe. Now, lots of our members and affiliates come from other parts of the world.

Ed Pentz was Crossref’s first (and only) employee in February 2000. Now it takes 30 of us to manage the 80 million records and over 5,300 participating organisations and to work on projects like Crossref Event Data, ‘early content registration’ , and all the new stuff you’ll be hearing about later this year.

Maybe in the context of social media services (e.g. Facebook users) 80,000,000 does not seem like such a big number. But 80,000,000 is an important milestone. Just think —

There are also 80 million microbes in a 10 second kiss [Microbiome, 2014, 2:41, Kort et al].

And after 80 million years of extinction events, we’re all still here!

What else is 80 million? Tell us in a tweet using #Crossref80mil. There may be a prize!

Crossref has 80 million registered content items

Dr Norman Paskin

Ed Pentz — Wed, 06 Apr 2016 00:00:00 +0000

Dr Norman Paskin

It was with great sadness and shock that I learned that Dr Norman Paskin had passed away unexpectedly on the 27th March. This is a big loss to the DOI, Crossref and digital information communities. Norman was the driving force behind the DOI System and was a key supporter and ally of Crossref from the start. Norman founded the International DOI Foundation in 1998 and ran it successfully until the end of 2015 when he moved to a strategic role as an Independent Board Member.

Norman was an early proponent of the value of persistent digital identifiers paired with standardised metadata and laid the groundwork for the system and infrastructure that has made Crossref and eight other Registration Agencies so successful. Norman was also a key adviser and participant in many standards organisations and initiatives where he regularly provided key intellectual input to help improve digital communications.

Personally, it was a great pleasure to work with Norman over the last twenty years and I greatly appreciated his intelligence, humour, advice, and particularly his help and generous support when I relocated to Oxford.

The International DOI Foundation has posted a notice, and has created condolences@doi.org for people to send messages.

The Wikipedia Library: A Partnership of Wikipedia and Publishers to Enhance Research and Discovery

Rachael Lammey — Mon, 04 Apr 2016 00:00:00 +0000

Back in 2014, Geoffrey Bilder blogged about the kick-off of an initiative between Crossref and Wikimedia to better integrate scholarly literature into the world’s largest knowledge space, Wikipedia. Since then, Crossref has been working to coordinate activities with Wikimedia: Joe Wass has worked with them to create a live stream of content being cited in Wikipedia; and we’re including Wikipedia in Event Data, a new service to launch later this year. In that time, we’ve also seen Wikipedia importance grow in terms of the volume of DOI referrals.

Alex Stinson, Project Manager for the Wikipedia Library, and our guest blogger! This file is licensed under the Creative Commons Attribution-Share Alike 3.0 Unported license (Source: Myleen Hollero Photography)

Alex Stinson, Project Manager for the Wikipedia Library, and guest blogger! This file is licensed under the Creative Commons Attribution-Share Alike 3.0 Unported license (Source: Myleen Hollero Photography)

How can we keep this momentum going and continue to improve the way we link Wikipedia articles with the formal literature? We invited Alex Stinson, a project manager at The Wikipedia Library (and one of our first guest bloggers) to explain more:

Wikipedia provides the most public gateway to academic and scholarly research. With millions of citations to academic as well as non-academic but reliable sources, like those produced by newspapers, its ecosystem of 5 million English Wikipedia articles and 35 million articles in hundreds of languages provides the first stop for researchers in both scholarly and informal research situations. The practice of “checking Wikipedia” has become ubiquitous in a number of fields; for example, Wikipedia is the most visited source of medical information online, even providing the first stop for many medical students and medical practitioners when looking for medical literature.

The Wikipedia Library program helps Wikipedia’s volunteer editors access and use the best sources in their research and citations. Through partnerships with over fifty leading publishers and aggregators, like JSTOR, Project Muse, Elsevier, Newspapers.com, Highbeam, Oxford University Press and others, we have been able to give over 3000 of our most prolific volunteers access to over 5500 accounts. These are clear, win-win relationships where Wikipedia editors get to use these databases to improve Wikipedia, while in turn linking to authoritative resources and enhancing their discovery.

JSTOR has been working with us since 2012, providing over 500 accounts to our editors. Kristen Garlock at JSTOR writes:

“We’re very happy to collaborate with the Wikipedia Library to provide JSTOR access to Wikipedia editors. Supporting the initiative to increase editor access to scholarly resources and improve the quality of information and sources on Wikipedia has the potential to help all Wikipedia readers. In addition to providing more discoverability for our institutional subscribers, introducing new audiences to the scholarship on JSTOR them discover access opportunities like our Register & Read program.”

There are strong signals that Wikipedia’s role in the citation ecosystem helps ensure the best materials reach the public through its over 400 million monthly readers:

The latest estimates by Crossref show that Wikipedia has risen from the 8th most prolific referrer to DOIs to the 5th.

Two of our access partners have found that around half of the referrals arriving from Wikipedia were able to authenticate into their subscription resources, suggesting that a large portion of our readers can take advantage of subscriptions provided by scholarly institutions.

Wikipedia is highly influential in the open access ecosystem as well, with a recent study showing higher citation rates for OA materials than those behind a paywall.

Altmetrics tools (such as Altmetric.com, ImpactStory or Plum Analytics) are recognizing Wikipedia’s importance by including Wikipedia citations in their impact metrics.

Despite these advances, we think this is only the beginning of Wikipedia’s impact on the landscape of scholarly research and discovery. Wikipedia can become a highly integrated research platform within the broader research ecosystem, where the best scholarship is summarized and discoverable-where Wikipedia effectively becomes the front matter to all research.

However, there are some clear barriers to fulfilling this vision. Currently, most citations on Wikipedia are stored in free-text and not readily available in machine-readable formats; our community is working to fix this. Wikipedia also has major systematic gaps in topics where either we lack volunteer interest or Wikipedia reflects larger systemic biases within society or scholarship.We need the help of volunteers, experts, industry partners, and information technologists to grow Wikipedia’s collection of citations, especially around key missing areas, and to transform existing citations into structured formats.

WikiData, Wikipedia’s sister project which crowdsources structured metadata, offers an excellent opportunity for improving the impact of Wikipedia in research. Having Wikipedia citations stored in this structured ecosystem, connecting metadata with semantic meaning, would allow the citations in Wikipedia to become the backbone for discovery tools which emphasize the hand-curated interrelationships between authoritative sources and the knowledge collected by Wikipedia and Wikidata editors.

We need more collaborators to realize the full vision of Wikipedia supporting research in the most effective ways:

We need help from publishers with subscription databases, to help us give our editors access to the databases through The Wikipedia Library’s access partnership program. These high-quality source materials allow our editors to expose that research in a number of languages and for millions of readers.

We need help from the open access community, to figure out how to better support increased citation and strategic use of open access materials within Wikipedia and other Wikimedia projects. Our community has some ideas, but we need your input and collaboration.

We need your expertise to build our structured metadata ecosystem, by helping Wikidata map and collect citation data.

We need the larger research community to promote Wikipedia as a scholarly communications tool and make contributing to Wikipedia an important part of the social responsibility of experts. Wider citation of sources in Wikipedia ensures widespread discovery and dissemination of that research.

If you think you can help, we invite you to contact us at wikipedialibrary@wikimedia.org or via Twitter @WikiLibrary.

Python and Ruby Libraries for accessing the Crossref API

Scott Chamberlain — Fri, 04 Mar 2016 00:00:00 +0000

I’m a co-founder with rOpenSci, a non-profit that focuses on making software to facilitate reproducible and open science. Back in 2013 we started to make an R client working with various Crossref web services. I was lucky enough to attend last year’s Crossref annual meeting in Boston, and gave one talk on details of the programmatic clients, and another higher level talk on text mining and use of metadata for research.

Crossref has a newish API encompassing works, journals, members, funders and more (check out the API docs), as well as a few other services. Essential to making the Crossref APIs easily accessible—and facilitating easy tool/app creation and exploration—are programmatic clients for popular languages. I’ve maintained an R client for a while now, and have been working on Python and Ruby clients for the past four months or so.

The R client falls squarely into the analytics/research use cases, while the Python and Ruby clients are ideal for general data access and use in web applications (the Javascript library below as well).

I’ve strived to make each client in idiomatic fashion according to the language. Due to this fact, there is not generally correspondence between the different clients with respect to data outputs. However, I’ve tried to make method names similar across Ruby and Python; although the R client is quite a bit older, so method names differ from the other clients and I’m resistant to changing them so as not to break current users’ projects. In addition, R users are likely to want a data.frame (i.e., table) of results, so we give back that - whereas with Python and Ruby we give back dictionaries and hashes, respectively.

Crossref clients

Python:
- Source: https://github.com/sckott/habanero
- Pypi: https://pypi.python.org/pypi/habanero
Ruby:
- Source: https://github.com/sckott/serrano
- Rubygems: https://rubygems.org/gems/serrano
- serrano also comes with a command line tool of the same name that’s installed when you install serrano (examples below)
R:
- Source: https://github.com/ropensci/rcrossref
- CRAN: https://cran.rstudio.com/web/packages/rcrossref/
Javascript:
- Source: https://github.com/scienceai/crossref
- NPM: https://www.npmjs.com/package/crossref

I’ll cover the Python, Ruby, and R libraries below.

Installation

Python

on the command line

pip install habanero

Ruby

on the command line

gem install serrano

in an R session

install.packages("rcrossref")

Examples

Output is indicated by the syntax #> in all examples below.

Python

in a Python REPL (e.g. iPython)

Import the Crossref module from within habanero, and initialize a client

from habanero import Crossref
cr = Crossref()

Query for the phrase “ecology”

x = cr.works(query = "ecology", limit = 5)

Index to various parts of the output

x['message']['total-results']
#> 276188

Extract similar data items from each result. The records are in the “items” slot

[ z['DOI'] for z in x['message']['items'] ]
#> [u'10.1002/(issn)1939-9170',
#> u'10.4996/fireecology',
#> u'10.5402/ecology',
#> u'10.1155/8641',
#> u'10.1111/(issn)1439-0485']

In habanero for some methods we require you to instantiate a client.

You can set a base URL and API key. This is a future looking feature

as Crossref API does not require an API key.

Note: I’ve tried to make sure habanero is Python 2 and 3 compatible. Hopefully you’ll find that’s true.

Ruby

in a Ruby repl (e.g., pry), load serrano

require 'serrano'

Query for “peerj” on the journals route

x = Serrano.journals(query: "peerj")

Collect just ISSN’s from each result

x['message']['items'].collect { |z| z['ISSN'] }
#> => [["2376-5992"], ["2167-8359"]]

Shell

The serrano command line tool is quite powerful if you are used to doing things there.

Here, search for one article; summary data is shown.

serrano works 10.1371/journal.pone.0033693
#> DOI: 10.1371/journal.pone.0033693
#> type: journal-article
#> title: Methylphenidate Exposure Induces Dopamine Neuron Loss and Activation of Microglia in the Basal Ganglia of Mice

There’s also a -json flag to give back JSON data, which can be parsed with the command line tool jq.

serrano works --filter=has_full_text:true --json --limit=5 | jq '.message.items[].link[].URL'
#> "http://api.wiley.com.pluma.sjfc.edu/onlinelibrary/tdm/v1/articles/10.1002%2F9781119208082.ch9"
#> "http://api.wiley.com.pluma.sjfc.edu/onlinelibrary/tdm/v1/articles/10.1002%2F9781119208082.index"
#> "http://api.wiley.com.pluma.sjfc.edu/onlinelibrary/tdm/v1/articles/10.1002%2F9781119208082.ch11"
#> "http://api.wiley.com.pluma.sjfc.edu/onlinelibrary/tdm/v1/articles/10.1002%2F9781119208082.ch15"
#> "http://api.wiley.com.pluma.sjfc.edu/onlinelibrary/tdm/v1/articles/10.1002%2F9781119208082.ch4"

In an R session, load rcrossref

library("rcrossref")

Search the works route for the phrase “science”

res <- cr_works(query = "science", limit = 5)
#> $meta
#> total_results search_terms start_index items_per_page
#> 1 4333827 science 0 5
#>
#> $data
#> Source: local data frame [5 x 23]
#>
#> alternative.id container.title created deposited DOI funder indexed
#> (chr) (chr) (chr) (chr) (chr) (chr) (chr)
#> 1 2013-11-21 2013-11-21 10.1126/science <NULL> 2015-12-27
#> 2 Science Askew 2004-11-26 2013-12-16 10.1887/0750307145/b426c18 <NULL> 2015-12-24
#> 3 2006-04-10 2010-07-30 10.1002/(issn)1557-6833 <NULL> 2015-12-25
#> 4 2013-08-27 2013-08-27 10.1002/(issn)1469-896x <NULL> 2015-12-27
#> 5 2013-12-19 2013-12-19 10.5152/bs. <NULL> 2015-12-28
#> Variables not shown: ISBN (chr), ISSN (chr), issued (chr), link (chr), member (chr), prefix (chr), publisher
#> (chr), reference.count (chr), score (chr), source (chr), subject (chr), title (chr), type (chr), URL
#> (chr), assertion (chr), author (chr)
#>
#> $facets
#> NULL

Index through to get the DOIs

res$data$DOI
#> [1] "10.1126/science" "10.1887/0750307145/b426c18" "10.1002/(issn)1557-6833"
#> [4] "10.1002/(issn)1469-896x" "10.5152/bs."

rcrossref also has faster versions of most functions with an underscore at the end (_) which only do the http request and give back json (e.g., cr_works_())

Comparison of Crossref Client Methods

After installation and loading the libraries above, the below methods are available

<th>
<span >Python</span>
</th>
<th>
<span >Ruby</span>
</th>
<th>
<span >R</span>
</th>

<td>
<span ><code>cr.works()</code></span>
</td>
<td>
<span ><code>Serrano.works()</code></span>
</td>
<td>
<span ><code>cr_works()</code></span>
</td>

<td>
<span ><code>cr.members()</code></span>
</td>
<td>
<span ><code>Serrano.members()</code></span>
</td>
<td>
<span ><code>cr_members()</code></span>
</td>

<td>
<span ><code>cr.funders()</code></span>
</td>
<td>
<span ><code>Serrano.funders()</code></span>
</td>
<td>
<span ><code>cr_funders()</code></span>
</td>

<td>
<span ><code>cr.types()</code></span>
</td>
<td>
<span ><code>Serrano.types()</code></span>
</td>
<td>
<span ><code>cr_types()</code></span>
</td>

<td>
<span ><code>cr.licenses()</code></span>
</td>
<td>
<span ><code>Serrano.licenses()</code></span>
</td>
<td>
<span ><code>cr_licenses()</code></span>
</td>

<td>
<span ><code>cr.journals()</code></span>
</td>
<td>
<span ><code>Serrano.journals()</code></span>
</td>
<td>
<span ><code>cr_journals()</code></span>
</td>

<td>
<span ><code>cr.members()</code></span>
</td>
<td>
<span ><code>Serrano.members()</code></span>
</td>
<td>
<span ><code>cr_members()</code></span>
</td>

<td>
<span ><code>cr.registration_agency()</code></span>
</td>
<td>
<span ><code>Serrano.registration_agency()</code></span>
</td>
<td>
<span ><code>cr_agency()</code></span>
</td>

<td>
<span ><code>cr.random_dois()</code></span>
</td>
<td>
<span ><code>Serrano.random_dois()</code></span>
</td>
<td>
<span ><code>cr_r()</code></span>
</td>

API Route
works
members
funders
types
licenses
journals
members
registration agency
random DOIs

Other Crossref Services

<th>
<span >Python</span>
</th>
<th>
<span >Ruby</span>
</th>
<th>
<span >R</span>
</th>

<td>
<span ><code>cn.content_negotiation()</code><a href="#footnote-1">[1]</a></span>
</td>
<td>
<span ><code>Serrano.content_negotiation()</code></span>
</td>
<td>
<span ><code>cr_cn()</code></span>
</td>

<td>
<span ><code>cn.csl_styles()</code><a href="#footnote-1">[1]</a></span>
</td>
<td>
<span ><code>Serrano.csl_styles()</code></span>
</td>
<td>
<span ><code>get_styles()</code></span>
</td>

<td>
<span ><code>counts.citation_count()</code><a href="#footnote-2">[2]</a></span>
</td>
<td>
<span ><code>Serrano.citation_count()</code></span>
</td>
<td>
<span ><code>cr_citation_count()</code></span>
</td>

Service
content negotiation
CSL styles
citation count

[1] from habanero import cn

[2] from habanero import counts

Features

These are supported in all 3 libraries:

Filters (see below)
Deep paging (see below)
Pagination
Verbose curl output

Filters

Filters (see API docs for details) are a powerful way to get closer to exactly what you want in your queries. In the Crossref API filters are passed as query parameters, and are comma-separated like filter=has-orcid:true,is-update:true . In the client libraries, filters are passed in idiomatic fashion according to the language.

Python

from habanero import Crossref
cr = Crossref()
cr.works(filter = {'award_number': 'CBET-0756451', 'award_funder': '10.13039/100000001'})

Ruby

require 'serrano'
Serrano.works(filter: {award_number: 'CBET-0756451', award_funder: '10.13039/100000001'})

library("rcrossref")
cr_works(filter=c(award_number=TRUE, award_funder='10.13039/100000001'))

Note how syntax is quite similar among languages, though keys don’t have to be quoted in Ruby and R, and in R you pass in a vector or list instead of a hash as in the other two.

All 3 clients have helper functions to show you what filters are available and what the options are for each filter.

<th>
<span >Python</span>
</th>
<th>
<span >Ruby</span>
</th>
<th>
<span >R</span>
</th>

<td>
<span ><code>filters.filter_names</code><a href="#footnote-3">[3]</a></span>
</td>
<td>
<span ><code>Serrano::Filters.names</code></span>
</td>
<td>
<span ><code>filter_names()</code></span>
</td>

<td>
<span ><code>filters.filter_details</code><a href="#footnote-3">[3]</a></span>
</td>
<td>
<span ><code>Serrano::Filters.filters</code></span>
</td>
<td>
<span ><code>filter_details()</code></span>
</td>

Action
Filter names
Filter details

[3] from habanero import filters

Deep paging

Sometimes you want a lot of data. The Crossref API has parameters for paging (see rows and offset), but large values of either can lead to long response times and potentially timeouts (i.e., request failure). The API has a deep paging feature that can be used when large data volumes are desired. This is made possible via Solr’s cursor feature (e.g., blog post on it). Here’s a run down of how to use it:

cursor: each method in each client library that allows deep paging has a cursor parameter that if you set to * will tell the Crossref API you want deep paging.
cursor_max: for boring reasons we need to have feedback from the user when they want to stop, since each request comes back with a cursor value that we can make the next request with, thus, an additional parameter cursor_max is used to indicate the number of results you want back.
limit: this parameter when not using deep paging determines number of results to get back. however, when deep paging, this parameter sets the chunk size. (note that the max. value for this parameter is 1000)

For example, cursor=”*” states that you want deep paging, cursor_max states maximum results you want back, and limit determines how many results per request to fetch.

Python

from habanero import Crossref
cr = Crossref()
cr.works(query = "widget", cursor = "*", cursor_max = 500)

Ruby

require 'serrano'
Serrano.works(query: "widget", cursor: "*", cursor_max: 500)

library("rcrossref")
cr_works(query = "widget", cursor = "*", cursor_max = 500)

Text mining clients

Just a quick note that I’ve begun a few text-mining clients for Python and Ruby, focused on using the low level clients discussed above.

Python: https://github.com/sckott/pyminer
Ruby: https://github.com/sckott/textminer

Do try them out!

Community responses to our proposal for early content registration

Geoffrey Bilder — Tue, 01 Mar 2016 00:00:00 +0000

TL;DR:

We will proceed with implementing the proposed support for registering content before online availability. Adopting the workflow will be optional and will involve no extra fees.

Background

At the end of January, Crossref issued a “request for community comment” on a proposed new process to support the registration of content including DOIs before online availability. We promised that we would summarize the results of the survey once we had received and analyzed all the responses.

Support for Crossref implementing the proposed new workflow was overwhelming. Of the 104 responses, 90 were positive, 7 were neutral and 7 were negative. As such we will proceed to make the necessary changes to better support registering content before online availability. We aim to enable this functionality in the second half of 2016.

We received survey responses varying in length from one or two sentences to multiple pages. A lot of the responses also interspersed questions and observations about entirely different issues that were of interest to respondents. As such, it has taken a while for us to analyze the results. We also found it was pretty much impossible for us to tabulate a summary of the responses to the direct questions. Instead we’ll summarize the responses at a high level and then drill down into some of the nuances in the answers and issues that were raised from the responses.

The positive responses

By “positive” we mean the respondent understood the issues we were trying to address and thought what we were proposing was a reasonable way to address the problems. Here are a few (anonymized) excerpts from the responses:

“[This] is very timely as we have been made aware of changes to manuscript deposit requirements for UK authors. Authors who partake in the REF system will have to deposit articles at their manuscript stage before publication. We need to set an embargo on the articles so that they only become discoverable at some point after the publication date. Ideally we would like this to happen with all articles regardless of where they are from as authors will put their own work up on open access sites.”

“Your proposal and the associated workflow look good to us and will help with our media embargo timelines, as well as our authors’ institutional requirements.”

“The workflows and solutions seem reasonable … The temporary landing page seems like a sustainable technical solution. Hosting by Crossref is key to this – there is no way that all publishers would otherwise take on maintaining temporary pages. And having a standard display for metadata consistency is crucial too.”

“Early assignment and recording of DOIs from the point of acceptance forms a key step in [the university’s] proposed ‘Submit-accept-deposit’ workflow. We welcome the proposal by Crossref to enable early assignment of DOIs for publications.”

Note that a positive response did not mean the respondents thought the problems necessarily applied to them or that they would necessarily be implementing the changes - just that what we were proposing seemed sound for those who needed to address the issues.

“While not directly relevant to our business the proposal seems aimed to protect the integrity of DOIs and Crossref’s role and that is not a bad thing.”

“I would consider it an irresponsible use of the system on the part of a publisher to circulate dois that don’t (yet) work. This is bound to lead to frustration with users encountering errors. However I appreciate that this situation may arise in some workflows and therefore your proposals to implement temporary landing pages make sense.”

“I was not aware of these issues, but think that your solutions seem feasible. We are a small journal and generally don’t add doi’s or publish until the article is complete (i.e., we don’t post anything that’s just accepted - only finalized). So we would be unlikely to update our workflow.”

Also, though respondents might have been generally positive about the proposal - that didn’t always mean they were also sanguine about it. For example, several shared concerns about the potential costs of changing their workflows.

“[we] would consider implementing this change into our workflow. Limiting factors would include the effort and additional cost to enable our paper management system vendor…”

“My only comment is that the process needs to be streamlined as much as possible so small publishers without great technical capacity will not be burdened with twice the work or with additional expense. After reading through Crossref’s proposal, I believe you have taken such things into account and will implement an efficient and worthwhile system.”

“The workflow makes sense as a solution to the problem you describe […] but will require extensive workflow changes on our end in order to implement. Speaking for a small publishing house I’m not sure it’s reasonable to expect this from us on any short term.”

Several of the positive respondents also wondered about how we would handle particular edge cases (e.g. rescinding acceptances) and/or offered suggestions to improve the proposal. We will discuss these further at the end of this post.

The neutral responses

The responses we categorised as “neutral” were generally too short to conclude much about. They consisted of one or two sentences that said something like “this doesn’t apply to me.” It wasn’t clear whether it didn’t apply to them because they didn’t have the problems we described or because they’d already solved the problems we described (e.g. by providing their own interim landing pages). They also didn’t comment on the applicability to other members or whether they thought the issues might eventually affect them.

The negative responses

We categorised responses as “negative” when the member rejected that the issues we outlined were actual problems or they rejected the mechanisms we were proposing to address the problems.

“…a formal letter of acceptance on a letter in PDF will be OK for authors. Why a DOI is better?”

“…I am aware of funder and institutional requirements for authors to take action on acceptance of manuscripts for publication in journals but don’t think the time pressure is so high that it has to happen in short time between acceptance and published ahead of print online…”

“Of all the accepted-but-not-yet-published papers in existence at any time, the number whose existence must be demonstrated to promotion and tenure review boards must be awfully small.”

There are a few common themes here. The first is that, historically, the industry has been content with acceptance letters as proof of publication and that it was relatively rare for authors to have to produce such proof.

The problem that has led us to propose support for a modified workflow is that now we have situations where all the researchers in a country require such letters on a regular basis - not just when they are up for promotion or tenure. This is the new reality faced by researchers and institutions who are subject to regular national evaluation schemes like the REF and ERA.

One of the negative respondents added:

“This is very familiar territory. It’s definitely coming out of STEM.”

Indeed, the initial pressure to support the earlier registration of DOIs is certainly falling on our members who focus on STEM publishing. Researchers in the STEM fields are generally under more pressure to publish articles frequently and they are primarily affected by emerging funder mandates. The relatively high research output in STEM fields combined with the need for regular compliance checks and regular evaluation schemes is creating an environment that requires more automated mechanisms to keep track of publications. Asking for and processing letters of acceptance in these situations just doesn’t scale.

Some of the negative responses also questioned our assertions about the hazards of promulgating unregistered DOI-like strings and/or the problems associated with the delay between when content is made available online and when the content is registered.

“I don’t buy the argument that people lose trust in DOIs in general because they once tried to resolve one and it didn’t lead to an article. By the same argument, URLs in general are similarly undermined.”

“where authors ask me for their DOIs so they can accurately cite the paper in another publication or use it for grants and applications. I explain that it won’t work until the issue as a whole posts and I have never heard back about confusion or distrust of the system.”

To this all we can say is, we have the data. Next to typos, unregistered DOIs account for the second greatest category of failed resolutions on the Crossref system. Our help desk has to explain them to researchers constantly. We have promoted DOIs as being more robust, persistent identifiers than ordinary URLs. People are not surprised when URLs don’t work. They are surprised when DOIs don’t work. We’d like to keep it that way.

What seems to be at the the root of the few negative responses - is that most assumed that Crossref was mandating that publishers change their workflow - even if they didn’t face any of the issues outlined in the proposal. There is very little that Crossref mandates to participate. This is by design. Our membership is just too diverse for us to have mandates that can be sensibly applied to all. Still - we should have made it clearer in the proposal that the proposed changes would not be mandated. We will certainly need to make this clearer when we roll out support for the new processes.

Oh yeah - one respondent called us out for using the phrase “advanced publication” instead of “advance publication”. For this we are truly sorry. The employee who made this mistake has been dragged out and shotted.

Issues raised and questions asked

Both the positive and negative respondents raised issues, asked questions and provided suggestions regarding the proposal. We will make sure that, when the proposal is implemented, we address all of these issues more clearly, but in the meantime, we thought it would be helpful if we answered some of them briefly here.

Q: Would Crossref charge extra for the new workflow?

A: No. We should have made this clear in the proposal. We should have also mentioned that, in the “Crossref-facilitated Early Registration” scenario members will only be charged once they have replaced the “registered_content” metadata with metadata for the published item using one of the existing content schemas (e.g. article, book, confproc).

Q: Would Crossref require that publishers adopt the new proposed workflows?

A: No. But we will recommend them to members who need to address the issues outlined in the proposal. And in general, we will recommend that our members register DOIs as early in the process as practicable.

Q: What does “acceptance” mean? It was pointed out that there were lots of variations of “acceptance” including “acceptance pending revisions”, etc.

A: We would expect that “contingent acceptance” does not constitute final acceptance and that in this case “acceptance” should mean that the publisher has a copy of the manuscript in which the author has made all of the changes asked of them.

Q: Doesn’t “acceptance” works both ways? A researcher has to grant permission to publish to the publisher.

A: This is a vital point - the publisher should only register content for which they have already secured the rights to publish.

Q: Collecting and verifying the metadata associated with a paper is expensive and time consuming. As such, some publishers only produce complete and robust metadata after a paper has been accepted. We face a Catch-22. if we deposit metadata immediately after acceptance, it will be sparse and unreliable. If we wait to collect and verify the metadata, then we risk violating some of the emerging mandates. How do we resolve this dilemma?

A: This is clearly beyond our control, but we expect that those issuing the mandates will have to make some reasonable accommodations if they expect publishers to register content both early and with reasonably useful metadata.

Q: How would publishers handle rescinded acceptances?

A: Publishers can handle this the same way they handle retractions or withdrawals. Additionally, the registered record type and the “intent to publish” landing page will both support Crossmark for those members who use Crossmark to promulgate corrections to the literature. We will explore adding a new “acceptance rescinded” update type to the Crossmark schema.

Q: The Crossref DOIs we generate contain embedded publication information such as volume and issue. We don’t know these details at acceptance so how can we register DOIs early?

A: Many of our members generate Crossref DOIs with embedded semantic information in them such as volume/issue, publication date or even author initials and title. After 16 years of experience, we have found that this tends to be a bad idea. Publication schedules slip. Metadata changes. We will soon be revising our guidelines on DOI best practice in Crossref DOI generation to recommend against embedding such information into the DOI itself. Clearly, if you decide to assign Crossref DOIs at acceptance, you will need to adopt a DOI structure that accommodates this.

Q: Our hosting provider manages DOI registrations for us. If we have to register DOIs earlier in the process, can we have one party (e.g. a manuscript tracking system vendor) register the initial “registered_content” metadata and then have different party (e.g. hosting provider or typesetter) replace that record with the final metadata?

A: Yes.

Q: Will you be working with industry vendors to help them support this new workflow?

A: Yes.

Q: Will we support the pre-registration of DOIs in the the deposit forms on the Crossref site?

A: Yes.

Q: If Crossref hosts the “intent to publish” landing page, how will publishers be able to account for visits to the page and incorporate that information into their metrics?

A: While visitors to the Crossref hosted page will not show up in the publisher’s own hosting platform logs, publishers will be able to easily see how many times their “intent to publish” landing page was accessed by looking at their standard Crossref DOI resolution logs.

Q: Could the Crossref-hosted landing page also include the URL that the DOI will eventually be associated with?

A: This is an interesting idea and was suggested by two separate respondents. The challenge will be in explaining to the user that the URL might or might not work. We are also concerned that this would reduce the incentive for publishers to replace the holding page in a timely manner. We’ll explore this option as we continue to work on implementation.

Q: Would the Crossref-hosted landing page be open to indexing by Google and others? If so, wouldn’t this undermine articles under press embargoes?

A: The idea behind the limited metadata required for registering content is that it allows the publisher to control the balance between discovery (needed to meet funder requirements) and discretion (needed to manage publicity). So yes, the Crossref-hosted landing pages would be open to indexing, but publishers can still control what gets indexed by withholding metadata as needed.

Q: The table of required metadata elements for the “registered content” type does not include the author. How are such records supposed to be used as proof of acceptance if they do not include the author name?

A: ~~We made a mistake. The table should have included the contributor in the required element column.~~ Update: We retract our retraction! We are trying to accommodate several different use cases for ’early content registration’ and these different use cases often have contradictory metadata implications. So, for example, including the author is certainly important for monitoring mandate compliance. However, including the author might be problematic when the publisher is trying to manage publicity around an upcoming publication. Again, Crossref is not in a position to resolve this dilemma and we expect that those issuing the mandates will make some reasonable accommodations with publishers who need to manage publicity around publications. In short, “authors” will remain optional metadata.

Summary and conclusions

We were delighted with the response rate on the proposal. It is clear to us that a lot of the respondents really appreciated both being alerted to a set of issues that they were not yet aware of and that they valued the chance to comment on our proposed mechanisms for addressing said issues. We also learned some lessons on how to better structure any such future surveys in order to make them easier for us to summarise and respond to. The wide variety of responses and detailed descriptions of different workflows reconfirmed our sense that Crossref members vary widely in their working practices. We need to continue to work directly with members and understand these different working practices so that we can provide appropriately flexible services to our membership and to the scholarly community in general.

Finally, the feedback we received will be used by our product team and our communications & outreach teams to refine our rollout plans for registering content before online availability. We expect that we will rollout this functionality in the second half of 2016.

Thanks to those who responded to our RFC. Some of those responses included questions about other matters relating to Crossref. We have attempted to extract these and answer them directly- but if we have not yet answered one of your questions, please follow-up with us at feedback@crossref.org

Event Data: open for your interpretation

Madeleine Watson — Thu, 25 Feb 2016 00:00:00 +0000

What happens to a research work outside of the formal literature? That’s what Event Data will aim to answer when the service launches later this year.

Following the successful DOI Event Tracker pilot in Spring 2014, development has been underway to build our new service, newly re-named Crossref Event Data. It’s an open data service that registers online activity (specifically, events) associated with Crossref metadata. Event Data will collect and store a record of any activity surrounding a research work from a defined set of web sources. The data will be made available as part of our metadata search service or via our Metadata API and normalised across a diverse set of sources. Data will be open, audit-able and replicable.

We expect to include the following sources at the launch of the clearinghouse in Q3 (pending final confirmation):

[table id=1 /]

What could you achieve?

Anyone interested in metrics and analytics will have direct and open access to a single collection of DOI activity data of events occurring outside of the formal literature. As Event Data records are time-stamped, you can be assured that the data you receive is both auditable and replicable. Collected and stored by Crossref in the one location, we invite researchers, publishers, funders and altmetrics providers to consider the possibilities Event Data offers to enrich and expand your work.

With such a corpus of open, transferable and auditable raw data at your fingertips, what could you achieve?

General and altmetrics service providers

Crossref Event Data is a centrally-managed resource, therefore as a third party vendor you will have the ability to collect real-time data from a central location to enrich, analyze, interpret and report via your own tools. Using our API, you will gain regular access to our collection of raw, auditable data to feed into your own tools and services ready for aggregation and analysis. Additionally, the optional benefit of an SLA with Crossref will ensure that your clients have access to a reliable and flexible source of event data.

Journal editors

Using the data collected in our service, as an editor you can attract authors by offering data on the audience’s research interest, track the full-scope of article dissemination and gain a better understanding of how the publications you manage compare to each other. By analysing the Event Data records, you can quickly find reviewers based on publication network analysis, identify new areas to grow author submissions and track the reach of submissions selected for publication.

Funders

As a Funder, you can use Event Data to isolate and track the dissemination and usage of the research you funded outside of the scholarly literature. As the data is portable, you can be assured that should a journal move, your ability to track its dissemination moves with it. Using the Event Data records collection, you can:

Efficiently track progress of the research impact of grant awardees in an automated fashion, with the signals most relevant to your organisation

Develop measurements of research engagement at the article level which reflect your mission and current funding priorities

Gain visibility into the potent success stories highlighting the impact of your work for your development campaigns

Analyze trends of past and future funding programs

More effectively pursue your funding strategy and manage your portfolio based on data-driven decision making.

Publishers and publishing platforms

By analyzing and interpreting the Event Data collection, as a publisher or content distributor you can use the records to undertake the following metric-lead analysis to help drive your business needs:

Conduct more robust publication growth analysis across titles, subject areas, or all published literature

Gain a balanced understanding of the engagement on your publications across subject areas, titles, or managing editors

Enhance author services (personalization, content discovery, profile management, etc.)

Focused and data-driven product development of tools and services to drive audience engagement

Provide content distributors data on downstream reach of publications.

Bibliometricians

Event Data heavily supports Bibliometric research by facilitating the tracking of DOI-related research activity across different platforms and channels. As a Bibliometrician, use trusted raw data as the underlying data for your research, which you can easily obtain from Crossref in a single, normalized format across a variety of sources. Additionally, as Event Data data is replicable, portable and auditable, you will be assured of high quality results in your research projects.

Research institutions

All of the stakeholders in your institution, from the research, development and marketing offices to the researchers themselves, will benefit from access to data about where and how your research is being discussed in mainstream and social media. As a research institution, Event Data can help you:

Track dissemination of publications (types of channels, rate of growth, etc.) by members of the institution

Access up-to-date information on the research progress of faculty members, useful for tenure and promotion decisions

View data on downstream impact of publications

Roll up data for custom reporting of department’s research activities

Stay tuned, testing begins soon!

With development work on the MVP (Minimum Viable Product) scheduled to complete shortly, we will soon be releasing a small subset of data sources that are collecting event data as well as a testing environment for interested parties to explore a very preliminary version of the software as we continue to work towards implementation of the full Event Data clearinghouse release in Q3. Look out for our MVP announcement, with full technical specifications and confirmation of the selected initial pull and push sources, over the coming weeks.

Revived: Crossref Books Interest Group

April Ondis — Wed, 24 Feb 2016 00:00:00 +0000

We’re reviving the Books Interest Group, and inviting new members!

After a hiatus, Crossref’s Books Interest Group is back. We’re excited to announce that Emily Ayubi of the American Psychological Association has agreed to chair the group.

In reviving the group, our intention is to create opportunities to talk about issues that are important to scholarly book publishers. For example, we hope to explore whether it is time to revise the Crossref best practices for depositing, versioning, and linking book content.

We are seeking interested members from the book publishing community, and want to hear your ideas for agenda items and topics for discussion.

Our first meeting will be a teleconference held at 11:00 am Eastern time on Wednesday, March 23rd. You will receive dial-in details by email. ** **

If you’d like to join—and we’re hoping you will—please email me at aondis@crossref.org.

Request for Community Comment: registering content before online availability

Ginny Hendricks — Thu, 21 Jan 2016 00:00:00 +0000

Crossref is proposing a process to support the registration of content—including DOIs and other metadata—prior to that content being made available, or published, online. We’ve drafted a paper providing background on the reasons we want to support this and highlighting the use cases. One of the main needs is in journal publishing to support registration of Accepted Manuscripts immediately on or shortly after acceptance, and dealing with press embargoes.

Proposal doc for community comment

We request community comment on the __proposed approach as outlined in this report.

Some examples of what we’d like to know:

Are you aware of the issues outlined in this proposal?
Are you aware of the funder and institutional requirements for authors to take action on acceptance of manuscripts for publication in journals?
Do you think the proposed solution and workflows are reasonable?
Are you likely to update your workflow to register content early?
If you are likely to update your workflow, how long do you estimate it will take?
Any other general comments, questions or feedback on anything raised in this document.

Please send comments, feedback and questions to me, Ginny, at feedback@crossref.org. The deadline for comments is February 4th. Thanks!

Linking clinical trials = enriched metadata and increased transparency

Kirsty Meddings — Mon, 18 Jan 2016 00:00:00 +0000

We will shortly be adding a new feature to Crossmark. In a section called “Clinical Trials” we will be using new metadata fields to link together all of the publications we know about that reference a particular clinical trial.

Most medical journals make clinical trial registration a prerequisite for publication. Trials should be registered with one of the fifteen WHO-approved public trial registries , or with clinicaltrials.gov which is run by the US National Library of Medicine. Once registered, a trial is assigned a clinical trial number (CTN) which is subsequently used to identify that trial in any publications that report on it.

Publications that result from any one trial are likely to be released in multiple journals from different publishers and at different times, for example secondary analyses coming some time after the publication of the initial results. Cross-publisher collaboration is paramount to linking all of these publications together so that researchers, funders, and regulatory agencies can understand the whole set of results from clinical trials. With this in mind, a group of medical publishers, led by BioMedCentral, approached Crossref to establish a working group, and here, they designed an approach to address this problem: “thread” all the various documents together surrounding a clinical trial.

Updated upstream

To implement threaded publications, publishers extract clinical trial numbers from papers, or ask authors to submit those numbers to them. Publishers add the CTNs to the Crossref DOI metadata via three new fields: clinical trial number, clinical trial registry where trial is registered, and trial stage (pre-results, results or post-results of the trial). Crossref has assigned unique IDs to each trial registry (much the same as we have done for funders in our Funder Registry and for the same reason - trial registry names and URIs can change over time and we need a persistent identifier). Using a combination of trial registry ID and clinical trial number, we can easily identify other content in the Crossref database that cites the same trial. Finally, Crossref displays the clinical trial metadata on the respective papers for all participating Crossmark publishers. Crossmark is a convenient place for readers to access the clinical trial information and is readily accessible directly from the journal article (online and PDF versions). And of course all of the data also goes into our open API so that anyone can make use of it.

The reporting of clinical trial results is notoriously inconsistent, something that the AllTrials initiative is also seeking to address. Publishers can help by collecting this information upstream and disseminating it using the existing Crossref infrastructure.

We ask all publishers to deposit the clinical trial data which is so critical to transparency in this area of research, and have already had the first data in from Crossref member the National Institute of Health Research. Once we launch the initial set of linked clinical trials, we will expand coverage of the threaded publications to include all content that reports on or references a clinical trial, from protocol to results to supporting data and systematic reviews.

Stay tuned and watch this space as threaded publications rolls out to journal articles across publishers!

Crossref & the Art of Cartography: an Open Map for Scholarly Communications

Jennifer Lin — Fri, 08 Jan 2016 00:00:00 +0000

In the 2015 Crossref Annual Meeting, I introduced a metaphor for the work that we do at Crossref. I re-present it here for broader discussion as this narrative continues to play a guiding role in the development of products and services this year.

Metadata enable connections

At Crossref, we make research outputs easy to find, cite, link, and assess through DOIs. Publishers register their publications and deposit metadata through a variety of channels (XML, CSV, PDF, manual entry), which we process and transform into Crossref XML for inclusion into our corpus. This data infrastructure which makes possible scholarly communications without restrictions on publisher, subject area, geography, etc. is far more than a reference list, index or directory.

If research builds on what came before, one could claim that the process of knowledge production is partly the story of the very relationships between results disseminated (i.e., publications). So let’s consider each publication as a node in a graph where each has a coordinate and is connected by its citations to other publications (as well those that cite it). Additionally, each is associated with a set of people and places, along with a whole host of elements involved in the research and dissemination process.

But take a wider berth, and we begin to capture relationships between all such contributing agents and objects involved in the research process. Here we find an array of entities belonging to the scholarly graph, including different types of research artifacts, publisher and journal, funders, ORCIDs, peer reviews, publication status updates (corrections, retractions, etc.), citations, license information, additional URLs (machine destinations, hosting platforms, etc.), underlying data, software and protocols, materials, discussions and blog posts, recommendations, reference work mentions, etc. The entities on the graph multiply at an even higher rate as researchers share more outputs across more channels. And over time, the graph expands exponentially, producing a webbing that is far more dense and far more vast than we can currently imagine. Perhaps even to the point we realize Borges’ story where a cartographer builds a map so large it replicates the territory itself (On Exactitude in Science)!

From graph to cartography

At the heart of Borges’s poignant story is the map. Crossref’s graph of scholarly communications could be seen in the same light. It has a representational aspect, which is not purely abstract and can be visualized. Here, a map becomes an incredibly potent metaphor. Each link enabled by publisher-deposited metadata is a new street, bridge, or highway that takes us to a particular place (i.e., entity) of interest. These roads lead to articles, researchers, funders, institutions, etc., and in doing so, make them discoverable. They tell a story about the roles of each in the broader research in the landscape dotted with a plethora of places.

The scholarly web has a growing corpus of more than 78 million publications at this very moment registered with Crossref. On average ten to fifteen thousand new objects appear every day. Maps are all the more essential for getting around in a bewildering environment of new and unfamiliar places, even for known ones in areas of exploding growth. They are critical for orienteering, discovering relationships, identifying sets of associated objects, naming new neighborhoods that emerge (i.e., new research specialties), etc. And if each connection on the map is seen as an event, maps can also represent micro-narratives about the research process and the agents involved. A multi-dimensional map containing all these entities, which serves as an evolving representation of spacetime that is constantly updated and always available, would finally begin to depict the process of scholarly activity as a dynamic, evolving, almost living system.

An open map for scholarly communication

Crossref builds such a scholarly map of the research enterprise and makes it openly available for the entire research ecosystem. Call this a meta map or, more recently, call it metastructure. No matter what name it goes by we call it infrastructure at Crossref.

Crossref’s open map for scholarly communications is a core part of the open information infrastructure for scholarly research. Crossref map data are open, portable, as well as licensed and provisioned for maximum reuse to serve the whole community. This open resource has two entrances: one for humans, another for machines. The Crossref REST API enables machines to traverse this environment and mine it in equal measure to the humans behind them. It is configured so that a robot can learn, a phone can access, and platforms can be built.

OpenStreetMap and Google Maps, both widely used and mature infrastructure maps, are instructive examples when we consider a map of this kind for scholarly communications. Map data can be represented in unlimited ways, depending on any variety of needs and users. Third parties can add content via interactive layers that tell different stories such as health expenditure by country based on GDP and coral reefs at risk. They have a broad base of users across business models from philanthropic services aimed at disaster relief (Refugeemaps.eu) to commercial entities providing drivers with locations on open parking spaces (AppyParking on Google Map, PocketParker on OpenStreetMap). They power platforms and services that build maps for others (MapQuest, MapBox). They have applications far beyond the business of maps. For example, Place picker is a Google Maps widget that supports easy auto-complete the entry of any place or location on a mobile app where typing is a chore. And as far use cases close to home, the two have served as raw data for academic research (ex: workflow for generating multi-agent traffic simulation scenarios, automatic classification of GPS trajectories for transportation modes, etc.).

In kind, the Crossref infrastructure map also supports: the development of any variety of new maps which re-present the data, the makers of map platforms that power the research enterprise, tools that use map data, as well as academic research (bibliometrics). We extract slices of data of common interest from the map and add them as additional layers by which anyone can access and create applications on or across these bands of data:

Contributors (authors, editors, reviewers)
Funding information (funding body, grant number)
Trial & study information (clinical trials registry number, registered report, replication study)
Publication history (versions, updates, revisions, corrections, retractions, dates received/accepted/published)
Peer review (status, type, reviews)
Access indicators (publication license for text & data mining, machine mining URLs)
Resources & associated research artifacts (preprints, figures & tables, datasets, software, protocols, research resource IDs)
Activity surrounding the publication (peer reviews, comments & discussions, bookmarks, social shares, recommendations).

Today, the map powers a host of public and commercial organisations alike for a wide range of scholarly and non-scholarly purposes:

<td style="border: 1px solid #ffffff;">
<ul>
<li>
<span >Indexing services</span>
</li>
<li>
<span >Publishing vendors</span>
</li>
<li>
<span >Peer review systems</span>
</li>
<li>
<span >Reference manager systems</span>
</li>
<li>
<span >Lab & diagnostics suppliers</span>
</li>
<li>
<span >Info management systems</span>
</li>
<li>
<span >Educational tools</span>
</li>
<li>
<span >Data analytics systems</span>
</li>
<li>
<span >Literature discovery services</span>
</li>
</ul>
</td>

Publishers
Funders
Research institutions
Archives & repositories
Research councils
Data centres
Professional networks
Patent offices
Registration Agencies

We will follow up this post to highlight a cross-section of these consumers in the Crossref map ecosystem and elaborate on what & how they have built from our data. An infrastructure map offers endless potential to third parties across publishers, funders, research institutions, and vendors working to serve the scholarly research enterprise.

The art of cartography

In the Crossref Product Management team, we have ambitious plans for map enhancements this year. They focus on expanding information density and ease of access to the data. In the former case, we will introduce a new class of locations where activity surrounding the publications are occurring when we launch the DOI Event Tracker. We will also initiate an extensive publisher campaign to achieve full metadata deposit completeness across our membership. No one can keep pace with the sheer volume of research activity happening online nor wander the Lonely Web of research alone. The more metadata publishers provide for a publication, the more roads lead to its map location. After all, discoverability is closely associated with connectedness on a map. And finally, in the latter case, we will refresh and enhance the user interface to make it more powerful for humans to traverse the ever-changing landscape (as easily as the REST API enables machines!).

I gratefully acknowledge the feedback received from the following who served as generous and insightful sounding boards: Virginia Barbour, Theo Bloom, Martin Eve, Daniel S. Katz, Amye Kenall, Catriona MacCullum, Cameron Neylon, Mark Patterson, Kristen Ratan, Carly Strasser, and Kaitlin Thaney.

ORCID tipping point?

Ginny Hendricks — Thu, 07 Jan 2016 00:00:00 +0000

Today eight publishers have presented an open letter that sets out the rationale for making ORCID iDs a requirement for all corresponding authors, a move that is being backed by even more publishers and researchers as the news spreads on twitter with #publishORCID. Crossref is a founding organisation of ORCID and an ongoing supporter so it’s great to see further uptake and even more benefit for the research community.

We encourage all our members to strive for complete metadata and that should include ORCID iDs, whether their workflows are able to require them at submission or not. Since we launched the ORCID auto-update process a couple of months ago, over 10,000 authors have given Crossref permission to automatically update their ORCID records.

The open letter—signed by eLife, PLOS, The Royal Society, AGU, EMBO, Hindawi, IEEE, and Science—also offers minimum implementation guidelines for the process:

Require. ORCID iDs are required for corresponding authors of published papers, ideally at submission.
Collect. The collection of ORCID iDs is done via the ORCID API, so authors are not asked to type in or search for their iD.
Auto-update. Crossref metadata is updated to include ORCID iDs for authors, so this information can automatically populate ORCID records.
Publish. Author/co-author ORCID iDs are embedded into article metadata.

ORCID’s own announcement gives further background and describes the benefits for researchers, such as single sign-on across journals and ultimately, increased discovery of their works. Everybody wins.