Cisco Pit Stop: Digitising the Natural History Museum’s collections

Last week (25-26 February) I was in London for CISCO Pit Stop event. Thursday evening was at the Natural History Museum where I gave a talk extolling the virtues of linking stuff together:

from @rdmpage digitization is the body of knowledge: literature+specimens+dna barcodes #CISCOpitstop @NHM_Science pic.twitter.com/HnbLCT9mHO

— Deborah Paul (@idbdeb) February 25, 2016

My slides are here:

Cisco Digital Catapult from Roderic Page

Friday we assembled at the Digital Catapult Centre, which as Sandy Knapp notes, has some amazing views from it's 9th floor.

Surreal!! Amazing view from #ciscopitstop pic.twitter.com/CB8Z2R1nGt

— Sandra Knapp (@SandyKnapp) February 26, 2016

A group of experts (loosely defined, at least, if they include me in that category) and small businesses (with backgrounds in digitisation, text-mining, publishing, etc.) got together to try and come up with workable ideas where we could marry issues in digitisation and subsequent use of that data with tools and markets. A fascinating experience, although I'm not yet sure what the outcome will be. But it's always useful talking (and listening) to people with very different backgrounds and notions of what matters (and what is possible).

GBIF specimens in BioStor: who are the top ten museums with citable specimens?

Brief update on yesterday's post about finding specimens in BioStor. BioStor has some 66,000 articles from BHL, from which I've extracted 143,000 cases of a specimen code being cited in the text. Of these 143,000 occurrences, 81,000 have been matched to an occurrence in GBIF.

The top ten collections with specimens in BioStor are:

Dataset	Number of specimens
NMNH Vertebrate Zoology Herpetology Collections (National Museum of Natural History)	11194
Herpetology Collection (University of Kansas Biodiversity Research Center)	9619
Herpetology Collection (University of Kansas Biodiversity Research Center)	9328
NMNH Invertebrate Zoology Collections (National Museum of Natural History)	9061
CAS Herpetology Collection Catalog (California Academy of Sciences)	6720
MCZ Herpetology Collection (Museum of Comparative Zoology, Harvard University)	5818
NMNH Vertebrate Zoology Fishes Collections (National Museum of Natural History)	4642
MCZ Herpetology Collection - Reptile Database (Museum of Comparative Zoology, Harvard University)	4380
FMNH Herpetology Collections (Field Museum)	2110
FMNH Fishes Collections (Field Museum)	2061

This is pretty much what I expected. Virtually complete runs of publications from The Field Museum at Chicago, the University of Kansas, and the Biological Society of Washington are available in BHL, and many of these have been added to BioStor. These journals have extensive taxonomic treatments of vertebrate taxa, particularly frogs, hence herpetology collections dominate the rankings.

There will inevitably be errors in the mapping between specimen codes and GBIF occurrences. I've tried to minimise these by mapping codes within taxonomic groups, but it's clear that there are duplicate codes even within some collections. There is also all manner of variation in the way people cite museum specimens, and these are often different from the codes that appear in GBIF. There will also be issues with extracting specimen codes, and I'm also discovering a few *cough* duplicates of articles in BioStor, so the numbers I present above are liable to change as I clean things up.

But one could imagine a "league table" of museum collections, where we can measure both the extent to which those collections have been digitised, and the extent to which material from those collections have been cited. We could use this to compute measures of the impact of a collection.

But for now I'm browsing the results trying to get a sense of how successful the mapping has been. There are some interesting examples. The specimen codes extracted from the article Review Of The Chewing Louse Genus Abrocomophaga (Phthiraptera : Amblycera), With Description Of Two New Species are those for the mammalian hosts of the lice. Hence someone viewing the records for these specimens and following the link to this paper would discover that these mammals had parasitic lice. If we add other sorts of links to the mix, such as between specimens and DNA sequences, then we can start to build a rich network of connections between the basic data of biodiversity.

DeepDyve - renting scientific articles

Bit late, but I stumbled across DeepDyve, which provides rental access to scientific papers for as little as $0.99. The pitch to publishers is:

Today, scholarly publisher sites receive over 2 billion visits per year from users who are unaffiliated with an institution yet convert less than 0.2% into a purchase or subscription. DeepDyve’s service is designed for these ‘unaffiliated users’ who need an easy and affordable access to authoritative information vital to their careers.

Renting a paper means you get to read it online, but you can't print or download it, and access is time limited (unless you purchase the article outright). You can also purchase monthly plans (think Spotify for papers).

It's an interesting model, and the interface looks nice. Here's a paper on Taxonomy and Diversity (http://dx.doi.org/10.1023/A:1003602221172):


Leaving aside the issue of whether restricted access to the scientific literature is a good idea (even if it is relatively cheap) I'm curious about the business model and the long tail. One could imagine lots of people downloading a few high-visibility papers, and my sense (based on no actual data I should stress) is that DeepDyve's publishing partners are providing access to their first-tier journals.

Taxonomic literature is vast, but most individual papers will have few readers (describing a single new species is usually not big news, with obvious exceptions). But I wonder if in aggregate the potential taxonomic readership would be enough to make cheap access to that literature economic. Publishers such as Wiley, Taylor and Francis, and Springer have digitised some major taxonomic journals, how will they get a return on this? I suspect the a price tag of, say, €34.95 for an article on seabird lice (e.g., "Neue Zangenläuse (Mallophaga, Philopteridae) von procellariiformen und charadriiformen Wirten" http://dx.doi.org/10.1007/BF00260996) will be too high for many people, but the chance to rent it for 24 hours for, say, $0.99, would be appealing. If this is the case, then maybe this would encourage publishers to digitise more of their back catalogue. It would be nice if everything is digitised and free, but I could live with digitised and cheap.