Biblio autocomplete

A new Drupal module: Biblio autocomplete.

Previsoulsy as part of eMonocot we started to use the IPNI webservice to autocomplete some fields in the Biblio content type. As one of the eMonocot objectives is to "Ensure that the tools developed are compliant with zoological nomenclature" I have extended this functionality to use the ZooBank API which is currently in a testing phase. In addition values for the autocomplete suggestions can be made from values previous entered in other Biblio nodes.

Instead of having either previsously entered values, IPNI or ZooBank attempt to autocomplete the field this module has been developed to allow any combination of these plugins to attempt the autocompletion. This will have uses in cases like the recent Lyme Regis Geo-BioBlitz where a single classification spand both animal and plant kingdoms (in this case the Dictioanry of UK Species).

The module is designed so that additional plugin modules can easily contribute results for other webservices.

This work was done as part of eMonocot as a contribution to the Scratchpads project.

Measuring the Impact of Wikipedia for organisations (Part 1)

The following series of posts will be about analysing the impact and use of Wikipedia by organisations. For convenience I have used the example of the Natural History Museum (NHM), as it's the one I am most familiar with. Doing such studies on an unfamiliar organisation might prove difficult.

The linkypedia project set out to answer these kinds of questions.  A local installation of linkypedia,  with modifications, has been used to generate the statistics presented here. All links are from pages on Wikipedia to pages on the domain http://www.nhm.ac.uk/.

Measuring Impact via Page Views
One (probably flawed) measure of an organisation's Wikipedia impact is the number of page views on Wikipedia pages that reference that organisation.

 The following data are total page view from December 2007 to December 2012 (and ignores the fact that these pages might not have had links for all of this time).

Wikipedia Page	Number of links to www.nhm.ac.uk	Page views Dec' 07 - Dec' 12
Cat	1	19,958,264
Charles Darwin	1	15,323,809
Dinosaur	1	10,740,744
Horse	1	10,692,007
Great Britain	1	9,669,059
Chocolate	1	9,243,390
Tomato	2	6,756,291
Tyrannosaurus	3	6,012,785
Cattle	1	5,868,187
Homeopathy	1	5,378,978
Taxonomy	3	5,303,333
Dodo	2	5,210,713
James Cook	2	4,977,016
Nature	1	4,874,884
Pangaea	1	4,827,257
Binomial nomenclature	2	4,514,425
Moose	1	4,432,025
Giant squid	1	4,209,529
Eggplant	2	3,910,621
Largest organisms	3	3,585,714

There's a pretty good correlation between this list and things the NHM is known for, I guess some people might be surprised that homoeopathy makes the list but the link is to a debate between Peter Fisher and Ben Goldacre held at the museum.

The graph below shows that of the 13,000+ articles linking to www.nhm.ac.uk most are in the long tail of page views, and relatively few articles with links to the NHM have over 1,000,000 page views.

 Another way of measuring Wikipedia impact might be to see how many links to an organisation's website there are on pages that relate to the organisation's core activities. The following table shows the Wikipedia articles with the most links to the NHM's website.

Wikipedia Page	Number of links to www.nhm.ac.uk	Page views Dec' 07 - Dec' 12
Sematurinae	62	5,722
Wildlife Photographer of the Year	9	24,226
Chris Stringer	7	48,001
Natural History Museum	6	945,997
Nemapogon granella	6	5,996
Bumblebee	6	2,567,265
Systematic & Applied Acarology Society	5	96
Nemapogon	5	3,001
Systematic & Applied Acarology	4	209
Amastus	4	3,833
Tinea pellionella	4	23,723
Niditinea	4	1,805
Niditinea fuscella	4	3,045
Tinea trinotella	4	3,443
Tineola bisselliella	4	196,615
Monopis laevigella	4	6,212
Monopis obviella	4	2,359
Ectropis	4	6,279
Perizoma	4	6,880
Drepanogynis	4	1,492

Most of these are species or genera or months, so there is some obvious scope for improvements in other areas of study. (In fact there are a few thousand stub articles on lepidoptera that have little more than a link to a catalogue on the NHM website).  Chris Stringer is a member of NHM staff, and the Wildlife Photographer of the Year is owned jointly by the NHM and the BBC.

More results to follow.


Measuring the Impact of Wikipedia for organisations (Part 1) by Ed Baker is licensed under a Creative Commons Attribution 3.0 Unported License.

Adobe Acrobat JavaScript for extracting first page of PDFs

Just so I don't forget!

ViBRANT Citizen Science Workshop (24-25 January 2013)

Organised by Ed Baker (me) & Sarah Faulwetter to set a framework for future development of the Scratchpads BioBlitz profile (demo site) and the HCMR's ViBRANT deliverable of a Citizen Science module for Drupal.

Workshop Day 1: What can we learn from successful citizen science projects?

Morning (workshop participants & invited NHM staff)

Presentations from successful citizen science projects (background to the project and what has made them successful)

• COMBER (Citizens' Network for the Observation of Marine BiodivERsity)
  Hellenic Centre for Marine Research
• iSPOT
  Open University / OPAL
• ExCiteS (Extreme Citizen Science)
  University College London
• Notes from NatureVizzuality
• Global Canopy Programme
• Overview of other European Citizen Science projectsSarah Faulwetter & Ed Baker

Afternoon (workshop participants)

Round table discussion on how ViBRANT and Scratchpads can participate in citizen science with emphasis on:

• What would be useful for us to do and how we might be able to engage with existing projects?
• What user-groups exist, how are they served by existing projects, and who can Scratchpads/ViBRANT target?
• What are the outcomes of these projects (fun/educational awareness/scientific data)?
• What quality of data can be collected?
• How can data gathered be reused (Biodiversity Data Journal/GBIF/EoL)?

Workshop Day 2: Creating a citizen science plan for Scratchpads & ViBRANT

ViBRANT attendees

• Development plan for HCMR’s citizen science module and can we incorporate it into the BioBlitz profile
• Can we incorporate citizen science tools into Scratchpads in general (e.g. crowdsourcing image transcription).

Playing with Flickr and CartoDB

Last Friday we had a ViBRANT sponsored workshop about CartoDB, the open source mapping and visualisation product from Madrid/New York based Vizzuality. The context of the workshop was possible integration of CartoDB with the Scratchpads and OBOE projects in the context of visualising biological datasets. The notes for the workshop demonstrations are here and are what the work done here is based on.

Not having a suitable dataset to hand I have been playing with making maps of the photos I have shared on Flickr. Flickr does provide a map view of a user's photographs (here's mine) although it is very limited in functionality - and unless you only have a handful of photographs you can't get a map view of all of your photographs.

I have previously visualised my Flickr stream by hacking the Drupal flickrsync module to save geolocation data with the Location module. Even with clustering the map points for 7,000+ images the results are slow to load: Drupal Flickr map of my photographs. The plus side of this work was that with just modifying the output of the view I could get a CSV file of my Flickr stream which I easily imported into CartoDB.

The basic map produced by CartoDB from this file is below:

Next I wanted to make a map of countries that are represented in my Flickr stream (perhaps I really wanted to play with PostGIS and polygons). This required downloading a shape file of all the countries from thematicmapping and uploading the file to a new table in CartoDB (CartoDB will accept the URL to the zip file so you can do it without downloading the file if you choose). The following SQL was applied to the world countries table:

This results in the following map:


Finally using some PostGIS I was able to make this map a little more accurate by splitting the countries into separate polygons (e.g. separating Hawaii from the continental United States, Northern Ireland from Great Britain).


Here's the new map:
 

Drupal Developer | Natural History Museum, London

Become part of an expanding team of developers working at the cutting edge of information science and biodiversity research. The Natural History Museum London is recruiting a Drupal developer (fixed term until end of November 2013, £34,853 per annum plus benefits) to work on the Scratchpad project (http://scratchpads.eu) as part of a major effort to help researchers share and manage biodiversity data on the Web.

Key tasks and responsibilities include:

•   Development and support of Drupal Modules and Themes

•   Data parsing and content construction

•   Supporting users in the development of their sites

•   Interfacing with the user support team

Applicants should be able to work on their own initiative and be proficient in module development, theming and quality assurance. Mentored training and support will be provided. Successful applicants will work with members of the developer and user communities to manage and parse biodiversity data, in addition to helping with the design, construction and testing of Drupal modules and sites.  The project includes opportunities for international travel as part of the development team.

Applicants should have at least 1-2 years experience in Drupal development (version 6 & 7) with hands on experience configuring Views, CCK and other contributed Drupal modules. This includes working with PHP, MySQL, SQL, XML, HTML and CSS. If you have a profile page on Drupal.org, please make reference to this within your application along with Drupal websites you have developed.

For job specific enquiries contact s.rycroft@nhm.ac.uk

Absolutely, Positively, Strictly - NO RECRUITMENT AGENCIES.

For a full job description and to apply online please visit the Natural History Museum website. http://www.nhm.ac.uk/jobs

Closing date: 30th November 2012

Audible for iPhone - crashing and can't delete files

 

This is an annoying bug I have found in the latest Audible for iPhone app. Audiobooks seem to download entirely but the fact they have finished doesn't seem to register with the system. The result is the app crashes when you try to play them (or on start up) and you can't delete the files from your library. Everything is fine however if you are offline.

This problem can be fixed by turning your phone into airplane mode in Settings, and then reopening the app. You can now play the audio files without the app crashing - but it is still not possible to delete them from your Library, it is however still possibly to delete them via the Now Playing / Last Played screen. Play the troublesome file and then click the button in the top right of the screen to bring up the Bookmarks/Details/Chapters screen.

Select the Details tab and scroll to the bottom of the page.

You can now remove the problematic audiobook from the device. You can then download it again after turning off airplane mode and everything should be fine.

This problem seems to occur when downloading from patchy connections and/or when the app is downloading in the background.