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).

Towards a wiki of phylogenies

At the start of this week I took part in a biodiversity informatics workshop at the Naturhistoriska riksmuseets, organised by Kevin Holston. It was a fun experience, and Kevin was a great host, going out of his way to make sure myself and other contributors were looked after. I gave my usual pitch along the lines of "if you're not online you don't exist", and talked about iSpecies, identifiers, and wikis.

I also ran a short, not terribly successful exercise using iTaxon to demo what semantic wikis can do. As is often the case with something that hasn't been polished yet, the students found the mechanics of doing things less than intuitive. I need to do a lot of work making data input easier (to date I've focussed on automated adding of data, and forms to edit existing data). Adding data is easy if you know how, but the user needs to know more than they really should have to.

The exercise was to take some frog taxa from the Frost et al. amphibian tree (doi:10.1206/0003-0090(2006)297[0001:TATOL]2.0.CO;2) and link them to GenBank sequences and museum specimens. The hope was that by making these links new information would emerge. You could think of it as an editable version of this. With a bit of post-exercise tidying, we got someway there. The wiki page for the Frost et al.
paper now shows a list of sequences from that paper (not all, I hasten to add), and a map for those sequences that the students added to the wiki:

Although much remains to be done, I can't help thinking that this approach would work well for a database like TreeBASE, where one really needs to add a lot of annotation to make it useful (for example, mapping OTUs to taxon names, linking data to sequences and specimens). So, one of the things I'm going to look at is dumping a copy of TreeBASE (complete with trees) into the wiki and seeing what can be done with it. Oh, and I need to make it much, much easier for people to add data.

Phyloinformatics workshop online

Slides from the recent Phyloinformatics workshop in Edinburgh are now online at the e-Science Institute. In case the e-Science Institute site disappears I've posted the slides on slideshare.

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Heiko Schmidt has also posted some photos of the proceedings, demonstrating how distraught the particpants were that I couldn't make it.

Phyloinformatics workshop - primal scream

Argh!!! The phyloinformatics workshop at Edinburgh's eScience Centre is underway (program of talks available here as an iCalendar file), and I'm stranded in Germany for personal reasons I won't bore readers with. The best and brightest gather less than an hour from my home town to talk about one of my favourite subjects, and I can't be there. Talk about frustration!

How can they they possibly proceed without yours truly to interject "it sucks" at regular intervals? What, things are going just fine? Next, you'll be suggesting that Systematic Biology can function without me as editor … wait, what's that you say? Jack's running the show without a hitch … gack, I'm redundant.