Buying & Selling DOIs...and the same for specimens

A previous post of mine described the business model for digital object identifiers in albeit simplistic terms. But, perhaps I should back up a second. Just what the heck is a DOI and why should the average systematist care? [Later in this post, I'll describe an interesting business model for biodiversity informatics]

Rod Page recently wrote a post in iPhylo that does a great job of selling the concept. Permit me to summarize and to add my own bits:

1. DOIs are strings of numbers & letters that uniquely identify something in the digital realm. In the case of published works, they uniquely identify that work.
2. DOIs are resolvable and can be made actionable. i.e. you can put http://dx.doi.org/ in front of a DOI and, through the magic of HTTP, you get redirected to the publisher's offering or the PDF or HTML version of the paper
3. DOIs have metadata. If you have for example a citation to a reference, you can obtain the DOI. Conversely, if you have a DOI, you can get the metadata
4. DOIs are a business model. Persistent URLs (championed by many) are not a business model because there is no transfer of funds & confidences

Systematists have lamented that their works on delineating & describing species don't get cited in the primary literature. If they published in journals that stamped DOIs on their works or if they participated in helping journals get DOIs for back-issues or future publications, then outfits like the Biodiversity Heritage Library would have an easier time mapping taxon names to published works. For example, searching not for a publication but a taxon name in Biodiversity Heritage Library (protoype HERE) would not only provide a list of works in BHL that used the name somewhere in its text, it could provide a forward-linking gadget from CrossRef. The end user would have an opportunity to do his or her own cognitive searching:

There is nothing stopping an outfit like the Biodiversity Heritage Library from using Handles or some other globally unique identifer. But, doing so cuts off the possibility of injecting old works back into contemporary use because they will not be embedded into a widely used cross-linking framework.

MOIs for Sale

The Global Biodiversity Information Facility and The Encyclopedia of Life must also be active participants in the adoption of globally unique identifiers. But again, there must be a business model. So, here's a business model in relation to museum specimens:

1. A registry sells a "MOI" - Museum Object Identifier (my creation of course) at 1 cent per labelled specimen.
2. The price will go up to 2 cents a specimen after 2020, the usual year given for various National Biodiversity Strategies. Translation: get your act together because it'll cost more later.
3. All MOIs must have DarwinCore metadata
4. The registry sets up a resolver identical in functionality to DOIs

Now, before all the curators out there scream bloody murder, let's stop and think about this and put a creative, financial spin on the possibilities. Craig Newmark, the founder of the ever popular Craig's List, was recently interviewed on Stephen Colbert's Colbert Report where he mentioned Donor's Choose (see interview). If you're not familiar with that new service, here's the slogan: "Teachers ask. You choose. Students learn."

DonorsChoose.org is a simple way to provide students in need with resources that our public schools often lack. At this not-for-profit web site, teachers submit project proposals for materials or experiences their students need to learn. These ideas become classroom reality when concerned individuals, whom we call Citizen Philanthropists, choose projects to fund.

There's a lot of interest in The Encyclopedia of Life and the Biodiversity Heritage Library now. Let's set-up a global "Donor's Choose" clone called something like "Biodiversity Knowledge Fund" (though that's not catchy enough) to be locally administered by daughter organizations to EOL and the BHL in countries throughout the world. Funds then are transferred to institutions of the donor's choosing. Museums then accept the funds donated to them and turn around and buy "MOIs". What would prevent a museum from taking the money specifically donated to them and spending it on things other than MOIs? Nothing. But, their specimens then aren't indexed. Are you a philanthropist or have 20 dollars (or francs, rubles, pounds, pesos, dinar, lira, etc.) you'd like to donate? Want to fund biodiversity but don't know how? Here's an answer. But is such a "Biodiversity Knowledge Fund" sustainable? No, but it's a start.

Biodiversity Informatics Needs a Business Model

Publishers and (most) librarians understand that digital object identifiers (doi) associated with published works are more than just persistent codes that uniquely identify items. They are built into the social fabric of the publishing industry. Because monies are transferred for the application and maintenance of a doi, the identifier is persistent. It's really because of this "feature" that tools like cross-linking and forward-linking can be built and that these new tools will themselves persist. The nascent biodiversity informatics community is attempting to do all the fun stuff (myself included) like building taxonomic indices, gadgetry to associate names and concepts with other things like literature, images, and specimens without first establishing a long-term solution for how the persistence of all these new tools will be established. Let me break it down another way:

Publishers buy dois and pay an annual subscription. In turn, the extra fee for the doi is passed down the chain to the journal & its society. The society then passes the extra fees on to either an author in the way of page fees or to the subscribers of the journal. Since the majority of subscribers are institutions and authors receive research grants from federal agencies, ultimately, the fractions of pennies that merge to pay for a single doi come from tax payers' wallets and purses. So, dois fit nicely into the fabric of society and really do serve a greater purpose than merely uniquely identifying a published object. Then, and only then, can the nifty tools CrossRef provides be made available. Then, third parties may use these tools with confidence.

Not surprisingly, the biodiversity informatics community has latched on to the nifty things one can do with globally unique identifiers because everybody wants to "do things" by connecting one another's resources. Some very important and extremely interesting answers to tough questions can only be obtained by doing this work. Also not suprisingly, there is now a mess of various kinds of supposed globally unique identifiers (GUIDs) because big players want to be the clearinghouse much as CrossRef is the clearinghouse for dois. But they have all missed the point.

So, how do we instill confidence in the use of LSIDs, ITIS TSNs, the various NCBI database id's, etc. without a heap of silos with occasional casualities? Get rid of them or at least clearly associate what kind of object gets what kind of identifier along with a business model where there will be persistent, demonstrable transfer of funds. The use of Semantic Web tools is merely a band-aid for a gushing wound. When I say persistent transfer of funds, I don't mean assurances that monies will come from federal grants or wealthy foundations in order to maintain those identifiers. I mean an identifier that is woven into the fabric and workflow of the scientific community. This may be easier said than done because other than publications, the scientific community (especially systematists and biologists) aren't in the business of producing anything tangible except publications. CrossRef has that angle very well covered. So, what else do scientists (the systematics community is what I'm most interested in) produce that can be monetized? Specimens, gene sequences, and perhaps a few other objects. We need several non-profits like CrossRef with the guts to demand monies for the assignment of persistent identifiers. Either we adopt this as a business model or we monetize some services (e.g. something like Amazon Web Services as previously discussed) that directly, clearly, and unequivocally feed into the maintenance of all the shiny new GUIDs.

DOIs in the References Cited Section

I just read a recent post by Ed Pentz (Executive Director of CrossRef) who alerted his readers to some recent changes to recommended American Medical Association and American Psychological Association style guides. Ed also provides two examples. Essentially, a string like "doi:10.1016/j.ssresearch.2006.09.002" is to be tagged at the end of each reference (if these dois exist) in the literature cited section of journals that use AMA or APA styles. Cool! It would be a snap to write a JavaScript to recognize "doi:" on a page and magically add the "http://dx.doi.org/" and I have no doubt publishers can do something similar prior to producing PDF reprints. Ed seemed puzzled by the exclusion of "http://dx.doi.org/", but this is a really smart move by the AMA and the APA. DOIs afterall are URNs so it's best to avoid any confusion. If paper publishers want to make these actionable, then they can do so. If web publishers want to do the same, then a simple little JavaScript can do it.

So, what we need now are style editors to pick-up this recommedation across the board in all journals in all disciplines. This simple addition would do a world of good for human discoverability and for machine consumption/repurposing. It shouldn't just be a recommendation, it should be mandatory.

Hopefully, this will step-up the drive for including XMP metadata within PDF reprints. It may be a pain for authors to track down DOIs if they're not stamped on the covering page (usually hovering around the abstract or the very top of the page) and consequently, adoption of this new recommendation may be rather slow. If the DOI were embedded in the XMP, then reference managers like EndNote and RefMan will naturally read these metadata. In other words, building your reference collection would be as simple as dropping a PDF in a watched file folder and letting your reference manager do the rest. This would also open the door to zero local copies of PDFs or an intelligent online storage system. EndNote and RefMan need only have the DOI and they can pull the rest using CrossRef's DOI look-up services.

Forward Thinking

I previously criticized CrossRef for the implementation of new restrictive rules for use of its OpenURL service, but Ed Pentz, Executive Director of CrossRef, stopped by and reassured us that CrossRef exists to fill the gaps. The most restrictive rule has now been relaxed. Well done, Ed.

While browsing around new publications in Biodiversity and Conservation, I caught something called "Referenced by" out of the corner of my eye. This may be old hat to most of you and I now feel ashamed that I have not yet discovered it. Perhaps I have subconsciously dismissed boxes on web sites because Google AdWare panels have constrained my eyeball movements. Anyhow, CrossRef have used the power of DOIs to provide a hyperlinked list of more recent publications that have referenced the work you are currently examining. Ed Pentz has blogged about this new feature. Now, this is cool and is the stuff dreams are made of. For example, a paper by Matt Greenstone in '83 entitled, "Site-specificity and site tenacity in a wolf spider: A serological dietary analysis" (doi:10.1007/BF00378220) is referenced by at least 6 more recent works as exemplified in that panel including several by Matt himself. Besides the obvious way that this permits someone to peruse your life's work (provided you reference yourself and publish in journals that have bought into CrossRef), this is a slick way to keep abreast of current thinking. If your initial introduction to subject matter is via pre-1990 publications, you can quickly examine how and who has used previous works regardless of what journal that article has appeared. Hats off CrossRef!

Now, what we need are publishing firms still mired in the dark ages to wake-up to the power of DOIs. If you participate in the editorial procedures for a scientific society and your publisher has not yet stepped-up by providing you with DOIs, get on the phone and jump all over them! You would be doing your readers, authors, and society a disservice if you accepted anything less than full and rapid cooperation by your chosen publisher.

So Ed, will "Forward Linking" be a web service we can tap into?

CrossRef Takes a Step Back

UPDATE Sept. 8/2007: Please read the response to this post by Edward Pentz, Executive Director of CrossRef in the comments below.

Mission statement: "CrossRef is a not-for-profit membership association whose mission is to enable easy identification and use of trustworthy electronic content by promoting the cooperative development and application of a sustainable infrastructure."

Not-for-profilt, hunh? Money-grabbing in the professional publishing industry has once again proven to be more important than making scientific works readily accessible. As of September 7, 2007, CrossRef will roll out new rules for its OpenURL and DOI lookups. Unless you become a card carrying CrossRef "affiliate", there will be a daily cap of 100 lookups using their OpenURL service, which will require a username/password. If >100 lookups are performed, CrossRef will reserve the right to cancel the account and will force you to buy into their senseless pay-for-use system. Here are the new rules as described at http://www.crossref.org/04intermediaries/60affiliate_rules.html:

1. Affiliates must sign and abide by the term of the CrossRef Affiliate Terms of Use
2. Affiliates must pay the fees listed in the CrossRef Schedule of Fees
3. The Annual Admininstrative Fee is based on the number of new records added to the Affiliates service(s) and/or product(s) available online
4. There are no per-DOI retrieval fees. There are no fees based on the number of links created with the Digital Identifiers.
5. Affiliates may "cache" retrieved DOIs (i.e. store them in their local systems)
6. The copyright owner of a journal has the sole authority to designate, or authorize an agent to designate, the depositor and resolution URL for articles that appear in that journal
7. A primary journal (whether it is hosted by the publisher or included in an aggregator or database service) must be deposited in the CrossRef system before a CrossRef Member or Affiliate can retrieve DOIs for references in that article. For example, an Affiliate that hosts full text articles can only lookup DOIs for references in an article if that journal's publisher is a PILA Member and is depositing metadata for that journal in the CrossRef System
8. Real-time DOI look-up by affiliates is not permitted (that is, submitting queries to retrieve DOIs on-the-fly, at the time a user clicks a link). The system is designed for DOIs to be retrieved in batch mode.

So what's the big deal?
The issue has to do with scientific society back-issues like the kind served by JStore. Without some sort of real-time DOI look-up, it is near impossible to learn of newly scanned and hosted PDF reprints for older works. After September 7, the only solution available to developers and bioinformaticians is to periodically "batch upload" lookups. CrossRef sees Rod Page's bioGUID service and my simple, real-time gadget as a threat to their steady flow of income even though it clearly fits within their general purpose "...to promote the development and cooperative use of new and innovative technologies to speed and facilitate scholarly research."