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While working on an internal project, we developed “pdfstamp“, a command-line tool that allows one to easily apply linked images to PDFs. We thought some in our community might find it useful and have released it on github. Some more PDF-related tools will follow soon.

Just a quick heads-up to say that we’ve had a go at incorporating InChIs and ontology terms into our PDFs with XMP. There isn’t a lot of room in an XMP packet so we’ve had to be a bit particular about what we include.

• InChIs: the bigger the molecule the longer the InChI, so we’ve standardized on the fixed-length InChIKey. This doesn’t mean anything on its own, so we’ve gone the Semantic Web route of including an InChI resolver HTTP URI. Alternatively you can extract the InChIKeys with a regular expression.
• Ontology terms: we’re using HTTP URIs again and pointing to either Open Biomedical Ontology URIs (biology, biomedicine; slashy) or RSC ontology terms (chemistry; hashy). Often the OBO URIs resolve to a specific web page, but for the moment the RSC URIs just point to a large OWL file. Slashy URIs are quite a bit more involved so we’ll have to see what the demand is like.

There’s only about 4K to play with, so it’s only ever going to be a best-of. More detailed article metadata has to go in either a sidecar file, as Tony has pointed out before, or ideally on the article landing page. The example files are here and I’ve posted something with a different slant on the RSC technical blog.

Since I’ve already blogged about this a number of times before here, I thought I ought to include a link to a fuller writeup in this month’s D-Lib Magazine of our nature.com OpenSearch service which serves as a case study in OpenSearch and SRU integration:

doi:10.1045/july2010-hammond

(Click image for full size graphic.)

I thought I could take this opportunity to demonstrate one evolution path from traditional record-based search to a more contemporary triple-based search. The aim is to show that these two modes of search do not have to be alternative approaches but can co-exist within a single workflow.

Let me first mention a couple of terms I’m using here: ‘graphs’ and ‘properties’. I’m using ‘property’ loosely to refer to the individual RDF statement (or triple) containing a property, i.e. a triple is a ‘(subject, property, value)’ assertion. And a ‘graph’ is just a collection of ‘properties’ (or, more properly, triples). Oh, and I’ll also use the term ‘records’ when considering ‘graphs’ as pre-fabricated objects returned within a result set.

Since last month’s threads (here, here, here and here) talking about the issues involved in making the DOI a first-class identifier for linked data applications, I’ve had the chance to actually sit down with some of the thread’s participants (Tony Hammond, Leigh Dodds, Norman Paskin) and we’ve been able sketch-out some possible scenarios for migrating the DOI into a linked data world.

I think that several of us were struck by how little actually needs to be done in order to fully address virtually all of the concerns that the linked data community has expressed about DOIs. Not only that- but in some of these scenarios we would put ourselves in a position to be able to semantically-enable over 40 million DOIs with what amounts to the flick of a switch.

(This post is just a repost of a comment to Geoff’s last entry made because it’s already rather long, because it contains one original thought - FRBR as OSI - and because, well, it didn’t really want to wait for moderation.)

Hi Geoff:

First off, there is no question but that Crossref was established to take on the reference linking challenge for scholarly literature. (Hell, it’s there, as you point out, in the organization name - PILA - as well as in the application name - Crossref.)

Tony’s recent thread on making DOIs play nicely in a linked data world has raised an issue I’ve meant to discuss here for some time- a lot of the thread is predicated on the idea that Crossref DOIs are applied at the abstract “work” level. Indeed, that it what it currently says in our guidelines. Unfortunately, this is a case where theory, practice and documentation all diverge.

When the Crossref linking system was developed it was focused primarily on facilitating persistent linking amongst journals and conference proceedings. The system was quickly adapted to handle books and more recently to handle working papers, technical reports, standards and “components”- a catchall term used to refer to everything from individual article images to database records.

(Update - 2010.02.10: I just saw that I posted here on this same topic over a year ago. Oh well, I guess this is a perennial.)

I am opening a new entry to pick up one point that John Erickson made in his last comment to the previous entry:

“I am suggesting that one “baby step” might be to introduce (e.g.) RDFa coding standards for embedding the doi:D syntax.”

Yea!

It might be worth consulting the latest Crossref DOI Name Information and Guidelines to see what that has to say about this. Section 6.3 - The response page has these two specific requirements for publishers:

(Click image for full size graphic.)

Following the JISC seminar last week on persistent identifiers (#jiscpid on Twitter) there was some discussion about DOI and its role within a Linked Data context. John Erickson has responded with a very thoughtful post DOIs, URIs and Cool Resolution, which ably summarizes how the current problem with DOI in that the way the DOI is is implemented by the handle HTTP proxy may not have kept pace with actual HTTP developments. (For example, John notes that the proxy is not capable of dealing with ‘Accept’ headers.) He has proposed a solution, and the post has attracted several comments.