Monday, February 10, 2014

Mark-up of biodiversity literature

UnknownI gave a remote presentation at a proiBioSphere workshop this morning. The slides are below (to try and make it a bit more engaging than a desk of Powerpoints I played around with Prezi).

There is a version on Vimeo that has audio as well.

I sketched out the biodiversity "knowledge graph", then talked about how mark-up relates to this, finishing with a few questions. The question that seems to have gotten people a little agitated is the relative importance of markup versus, say, indexing. As Terry Catapano pointed out, in a sense this is really a continuum. If we index content (e.g., locate a string that is a taxonomic name) and flag that content in the text, then we are adding mark-up (if we don't, we are simply indexing, but even then we have mark-up at some level, e.g. "this term occurs some where on this page"). So my question is really what level of markup do we need to do useful work? Much of the discussion so far has centered around very detailed mark-up (e.g., the kind of thing ZooKeys does to each article). My concern has always been how scalable this is, given the size of the taxonomic literature (in which ZooKeys is barely a blip). It's the usual trade off, do we go for breadth (all content indexed, but little or no mark-up), or do we go for depth (extensive mark-up for a subset of articles)? Where you stand on that trade off will determine to what extent you want detailed mark up, versus whether indexing is "good enough".