scratchpads: biodiversity online, redefining publication

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Simon D. Rycroft Vincent S. Smith & Dave Roberts Scratchpads “Biodiversity online” “Redefining publication”

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Scratchpad talk presented by Simon Rycroft at BNCOD 2008 Biodiversity Informatics Workshop, Cardiff University, 10th July 2008

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Page 1: Scratchpads: Biodiversity online, Redefining publication

Simon D. RycroftVincent S. Smith & Dave Roberts

Scratchpads“Biodiversity online”“Redefining publication”

Page 2: Scratchpads: Biodiversity online, Redefining publication

Your data1

Published and reviewedon your site

3Uploaded

and tagged

2

What is a Scratchpad?

Page 3: Scratchpads: Biodiversity online, Redefining publication

Your dataSpecimens

ImagesLiterature

DNA & PhylogeniesDescriptions

Page 4: Scratchpads: Biodiversity online, Redefining publication

Taxonomy backbone• Classification import from uBio Classification Bank

• Import from tab delimited files in three differentformats

• Makes use of a core feature of Drupal

Page 5: Scratchpads: Biodiversity online, Redefining publication

Auto tagging• Quick and easy

• Data available immediately after upload

• Works with any extra data that may be added to ataxonomy (vernacular names, synonymy)

Page 6: Scratchpads: Biodiversity online, Redefining publication

Sucking lice (Anoplura) have around 500 species andrepresent the smaller of the two traditional suborders of lice.The Anoplura are all blood-feeding ectoparasites of mammals.They can cause localised skin irritations and are vectors ofseveral blood-borne diseases.

Children appear particularly susceptible to attracting lice,possibly due to their fine hair.

At least three species of Anoplura are parasites of humans; thehuman condition of being infested with sucking lice is calledpediculosis. Pediculus humanus is divided into two subspecies,Pediculus humanus humanus, or the body louse, sometimesnicknamed "the seam squirrel" for its habit of laying of eggs inthe seams of clothing, and Pediculus humanus capitis, or thehead louse. Phthirus pubis (the pubic louse) is the cause of thecondition known as crabs.

http://dev.catlife.myspecies.info/

Page 7: Scratchpads: Biodiversity online, Redefining publication

On your site

Page 8: Scratchpads: Biodiversity online, Redefining publication

Taxon pages• Content is displayed in “Panels” on “taxon pages”

• Panels is a plugin feature for Drupal provided by athird party

• Extended with “View controls”

Page 9: Scratchpads: Biodiversity online, Redefining publication

Curate the web• View controls allows a user of a Scratchpad to

effectively curate content from the web.

• Currently have panels for:– Wikipedia

– Flickr

– Yahoo Images

– Biodiversity Heritage Library / Google scholar

– NCBI

– GBIF specimen location maps

Page 10: Scratchpads: Biodiversity online, Redefining publication

Default Panels

Page 11: Scratchpads: Biodiversity online, Redefining publication

Additional features• Enterprise backup

– TSM on the Scratchpads’ server

– Intend to include an additional tape archive

• Additional modules– Nested set query

– Tinytax taxonomy browser

– Autocomplete taxonomic name browsing

Page 12: Scratchpads: Biodiversity online, Redefining publication

Scratchpad statisticsOver100,000 pages, and 650 contributors

• Contributors:– No more than 10% significantly active– Contributors in more than 30 countries

• Pages– Over 60 Sites– Largely made up of definitions and references, but also includes images,

specimens, descriptions, DNA sequences and maps.

Page 13: Scratchpads: Biodiversity online, Redefining publication

Visitors

Key monthly statistics- 50,000 page views - 6,000 visitors- 8 minutes on site- 50% returning visits

Page 14: Scratchpads: Biodiversity online, Redefining publication

Future developments• Help

• Improved taxonomy handling

• Export of data

Page 15: Scratchpads: Biodiversity online, Redefining publication

Sand box & Information• http://scratchpads.eu

• http://sandbox.scratchpads.eu

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