University of Glasgow

Roderic Page

Last week (25-26 February) I was in London for [CISCO Pit
Stop](http://www.digitalcatapultcentre.org.uk/open-calls/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](https://twitter.com/rdmpage) digitization is the body
> of knowledge: literature+specimens+dna barcodes
> [\#CISCOpitstop](https://twitter.com/hashtag/CISCOpitstop?src=hash)
> [@NHM_Science](https://twitter.com/NHM_Science)
> [pic.twitter.com/HnbLCT9mHO](https://t.co/HnbLCT9mHO)
>
> --- Deborah Paul (@idbdeb) [February 25,
> 2016](https://twitter.com/idbdeb/status/702950123119185920)

My slides are
[here](http://www.slideshare.net/rdmpage/cisco-digital-catapult):

::: {style="margin-bottom:5px"}
**[Cisco Digital
Catapult](//www.slideshare.net/rdmpage/cisco-digital-catapult "Cisco Digital Catapult"){target="_blank"}**
from **[Roderic Page](//www.slideshare.net/rdmpage){target="_blank"}**
:::

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](https://twitter.com/hashtag/ciscopitstop?src=hash)
> [pic.twitter.com/CB8Z2R1nGt](https://t.co/CB8Z2R1nGt)
>
> --- Sandra Knapp (@SandyKnapp) [February 26,
> 2016](https://twitter.com/SandyKnapp/status/703236567951876096)

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).


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:    My slides are here:
<strong>
 Cisco Digital Catapult
</strong>
from
<strong>
 Roderic Page
</strong>
Friday we assembled at the Digital Catapult Centre, which as Sandy Knapp notes, has some amazing views from it's 9th floor.

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

![Gbif](http://lh4.ggpht.com/-xUNNB8qt0bo/T0zlTrh5XaI/AAAAAAAABKo/gkNPg4kwKXU/gbif.gif?imgmax=800 "gbif.gif"){border="0"
width="128" height="124" style="float:right;"}Brief update on
[yesterday\'s
post](http://iphylo.blogspot.com/2012/02/linking-gbif-and-biodiversity-heritage.html)
about finding specimens in [BioStor](http://biostor.org). 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](http://biostor.org/reference/81065) 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.  
  
  


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.

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

![Deepdyve
button](http://lh6.ggpht.com/-ZdvCr84lFfE/TpP2xcIt4GI/AAAAAAAABAk/LVDU2bVZYI4/deepdyve_button.gif?imgmax=800 "deepdyve_button.gif"){border="0"
width="54" height="54" style="float:right;"}Bit late, but I stumbled
across [DeepDyve](http://www.deepdyve.com), which provides rental access
to scientific papers for as little as \$0.99. The [pitch to
publishers](http://www.deepdyve.com/corp/partners/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](http://www.spotify.com/) for papers).  
  
It\'s an interesting model, and the interface looks nice. Here\'s a
paper on [Taxonomy and
Diversity](http://www.deepdyve.com/lp/springer-journals/taxonomy-and-biodiversity-43Fw0dtaJ4)
(<http://dx.doi.org/10.1023/A:1003602221172>):  
  
![Deepdyvescreenshot](http://lh5.ggpht.com/-Q5A2eSgpemo/TpP2yB8JOSI/AAAAAAAABAs/4ETfMUCTN1w/deepdyvescreenshot.png?imgmax=800 "deepdyvescreenshot.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="400" height="313"}  
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.


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: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.

Messages de Rogue Scholar

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

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

DeepDyve - renting scientific articles