Thursday, June 30, 2016

Aggregating annotations on the scientific literature: a followup on the ReCon16 hackday

In the previous post I sketched out a workflow to annotate articles using and aggregate those annotations. I threw this together for the hackday at ReCon 16 in Edinburgh, and the hack day gave me a chance to (a) put together a crude visualisation of the aggregated annotations, and (b) recruit CrossRef's Rachael Lammey (@rachaellammey) into doing some annotations as well so I could test how easy it was to follow my garbled instructions and contribute to the project.

We annotated the paper A new species of shrew (Soricomorpha: Crocidura) from West Java, Indonesia (doi:10.1644/13-MAMM-A-215). If you have the extension installed you will see our annotations on that page, if not, you can see them using the proxy:

Rachael and I both used the IFTTT tool to send our annotations to a central store. I then created a very crude summary page for those annotations: When this page loads it queries the central store for annotations on the paper with DOI 10.1644/13-MAMM-A-215, then creates some simple summaries.

For example, here is a list of the annotations. The listed is "typed" by tags, that is, you can tell the central store what kind of annotation is being made using the "tag" feature in On this example, we've picked out taxonomic names, citations, geographical coordinates, specimen codes, grants, etc.

Screenshot 2016 06 30 12 30 53

Given that we have latitude and longitude pairs, we can generate a map: Screenshot 2016 06 30 12 31 15

The names of taxa can be enhanced by adding pictures, so we have a sense of what organisms the paper is about:

Screenshot 2016 06 30 12 31 24

The metadata on the web page for this article is quite rich, and does a nice job of extracting it, so that we have a list of DOIs for many of the articles this paper cites. I've chosen to add annotations for articles that lack DOIs but which may be online elsewhere (e.g., BioStor).

Screenshot 2016 06 30 12 31 34

What's next

This demo shows that it's quite straightforward to annotate an article and pull those annotations together to create a central database that can generate new insights about a paper. For example, we can generate a map even if the original paper doesn't provide one. Conversely, we could use the annotations to link entities such as museum specimens to the literature that discusses those specimens. Given a specimen code in a paper we could look up that code in GBIF (using GBIF's API, or a tool like "Material Examined", see Linking specimen codes to GBIF). Hence we could go from code in paper to GBIF, or potentially from GBIF to the paper that cites the specimen. Having a central annotation store potentially becomes a way to build a knowledge graph linking different entities that we care about.

Of course, a couple of people manually annotating a few papers isn't scalable, but because has an API we can scale this approach (for another experiment see revisited: annotating articles in BioStor). For example, we have automated tools to locate taxonomic names in text. Imagine that we use those tools to create annotations across the accessible biodiversity literature. We can then aggregate those into a central store and we have an index to the literature based on taxonomic name, but we can also click on any annotation and see that name in context as an annotation on a page. We could manually augment those annotations, if needed, for example by correcting OCR errors.

I think there's scope here for unifying the goals of indexing, annotation, and knowledge graph building with a fairly small set of tools.

Thursday, June 23, 2016

Aggregating annotations on the scientific literature: a hack for ReCon 16

7iUlfzBpI will be at ReCon 16 in Edinburgh (hashtag #ReCon_16), the second ReCon event I've attended (see Thoughts on ReCon 15: DOIs, GitHub, ORCID, altmetric, and transitive credit). For the hack day that follows I've put together some instructions for a way to glue together annotations made by multiple people using It works by using IFTTT to read a user's annotation stream (i.e., the annotations they've made) and then post those to a CouchDB database hosted by Cloudant.

Why, you might ask? Well, I'm interested in using to make machine-readable annotations on papers. For example, we could select a pair of geographic co-ordinates (latitude and longitude) in a paper, tag it "geo", then have a tool that takes that annotation, converts it to a pair of decimal numbers and renders it on a map.

Screenshot 2016 06 23 15 53 07

Or we could be reading a paper and the literature cited lacks links to the cited literature (i.e., there are no DOIs). We could add those by selecting the reference, pasted in the DOI as the annotation, and tagging it "cites". If we aggregate all those annotations then we could write a query that lists all the DOIs of the cited literature (i.e., it builds a small part of the citation graph).

By aggregating across multiple users we effectively crowd source the annotation problem, but in a way that we can still collect those annotations. For this hack I'm going to automate this collection by enabling each user to create an IFTTT recipe that feeds their annotations into the database (they can switch this feature off at any time by switching off the recipe).

Manual annotation is not scalable, but it does enable us to explore different ways to annotate the literature, and what sort of things people may be interested in. For example, we could flag scientific names, great numbers, localities, specimens, concepts, people, etc. We could explore what degree of post-processing would be needed to make the annotations computable (e.g., converting 8°07′45.73″S, 63°42′09.64″W' into decimal latitude and longitude).

If this project works I hope to learn something about people want to extract from the literature, and to what extent having a database of annotations can provide useful information. This will also help inform my thinking about automated annotation, which I've explored in revisited: annotating articles in BioStor.

Wednesday, June 22, 2016

What happens when open access wins?

The last few days I've been re-reading articles about Ted Nelson's work (including ill-fated Project Xanadu), reading articles celebrating his work (brought together in the open access book "Intertwingled"), playing with, and thinking about annotation and linking. One of the things which distinguishes Nelson's view of hypertext from the current web is that for Nelson links are first class citizens, they are persistent, they are bidirectional, and can be links not just documents but between parts of documents. In the web we have links that are unidirectional, when I link to something, the page I link to has no idea that I've made that link. Knowing who links to you turns out to be both hard to work out, and very valuable. In the academic world, links between articles (citations) form the basis of commercial databases such as the Web of Science. And of course, the distribution of links between web pages forms the basis of Google's search engine. Just as attempts to build free and open citation databases have come to nothing, there is no free and open search engine to compete with Google.

The chapters in "Intertwingled" make clear that hypertext had a long and varied history before being subsumed by the web. One project which caught my eye was Microcosm, which lead me to the paper "Dynamic link inclusion in online PDF journals" (doi:10.1007/BFb0053299, there's a free preprint here). This article tackles the problem of adding links to published papers. These links could be to other papers (citations), to data sets, to records in online databases (e.g., DNA sequences), names of organisms, etc. The authors outline four different scenarios for adding these links to an article.

In first scenario the reader obtains a paper from a publisher (either open access from behind a paywall), then using a "linkbase" that they have access too they add link to the paper.


This is very much what offers, you use their tools to add annotations to a paper, and those annotations remain under your control.

In the second scenario, the publisher owns the linkbase and provides the reader with an annotated version of the paper.


This is essentially what tools like ReadCube offer. The two remaining scenarios cover the case where the reader doesn't get the paper from the publisher but instead gets the links. In one of these scenarios (shown below) the reader sends the paper to the publisher and gets the linked paper back in return, in the other (not shown) the reader gets the links but uses their own tools to embed them in the paper.


If you're still with me at this point you may be wondering how all of this relates to the title of this essay ("What happens when open access wins?"). Well, imagine that academic publishing eventually becomes overwhelmingly open access, so that publishers are making content available for free. Is this a sustainable business model? Might a publisher, seeing the writing on the wall, start to think about what they can charge for, if not articles (I'm deliberately ignoring the "author pays" model of open access as I'm not convinced this has a long term future).

In the diagrams above the "linkbase" is on the publisher's side in two of the three scenarios. If I was a publisher, I'd be looking to assembling proprietary databases and linking tools to create value that I could then charge for. I'm sure this is happening already. I suspect that the growing trend to open access for publications is not going to be enough to keep access to scientific knowledge itself open. In many ways publications themselves aren't terribly useful, it's the knowledge they contain that matters. Extracting, cross linking, and interpreting that knowledge is going to require sophisticated tools. The next challenge is going to be ensuring that the "linkbases" generated by those tools remain free and open, or an "open access" victory may turn out to be hollow.