Projects at Center for Biodiversity Informatics

Missouri Botanical Garden

Trish Rose-SandlerData Projects Coordinator

SLA St Louis Chapter meeting St Louis MO March 29 2014

3 projects I’ll cover:• Art of Life• Purposeful Gaming and BHL • Mining Biodiversity

What is BHL?

• A consortium of natural history, botanical libraries and research institutions

• An open access digital library for historic biodiversity literature

• An open data repository of taxonomic names and bibliographic information

16 BHL Member Institutions as of March 2014• American Museum of Natural History • California Academy of Sciences Library• Cornell University Library • Harvard University Botany Libraries • Ernst Mayr Library of the Museum of Comparative Zoology • Library of Congress • Marine Biological Laboratory / Woods Hole Oceanographic Institution Library• Missouri Botanical Garden Library• National Library Board (Singapore)• Natural History Museum, London• The New York Botanical Garden • Royal Botanic Gardens, Kew• Smithsonian Institution Libraries • United States Geological Survey Libraries• Washington University St Louis• University of Illinois, Urbana-Champaign

BHL Global

BHL Scientific Names

What is Art of Life?

• Full title - The Art of Life: Data Mining and Crowdsourcing the Identification and Description of Natural History Illustrations from the Biodiversity Heritage Library (BHL)

• Grant given to Missouri Botanical Garden in St Louis. Partners :Indianapolis Museum of Art, University of Colorado, Boulder

• Funded by National Endowment for the Humanities

• Runs May 2012-April 2014 (extended 1 yr til April 15)

BHL Problem statement – users want access to images, access to images is

limited – How to broaden the audiences for BHL content?

5 Primary Objectives of Art of Life

Objective 1: Define an appropriate metadata schema for natural history illustrations

Objective 2: Build software tools to automatically identify illustrations in the BHL corpus

Objective 3: Enhance existing tools to enable the initial sorting, viewing, and editing of these identified visual resources.

Objective 4: Integrate tagging applications to enable a community of users to edit descriptive metadata for the illustrations

Objective 5: Integrate the descriptive metadata generated by users back into BHL portal both for access and preservation

What is Purposeful Gaming and BHL?

• Full title - Purposeful gaming and BHL: engaging the public in improving and enhancing access to digital texts

• National Leadership Grant for Libraries given to Missouri Botanical Garden in St Louis.

• Partners include Harvard, Cornell, New York Botanical Garden

• Funded by IMLS

• Runs Dec 2013-Nov 2015

BHL Problem statement – major challenge for digital libraries: full-text searching of

texts is significantly hampered by poor output from Optical Character Recognition (OCR) software.

– Historic literature has proven to be particularly problematic because of its tendency to have varying fonts, typesetting, and layouts that make it difficult to accurately render

Sample of poor OCR output from an 18th century publication.This page is from Linneaus' Species Plantarum published in 1753An image of the original text is on the left. The OCR is on the rightthe right

A sample of poor OCR output from a hand written text. This page is from the Diaries of William Brewster, 1865-1919

8 primary objectives of Purposeful Gaming and BHL

1) digitizing horticultural catalogs2) transcribing field notebooks and horticultural catalogs3) building a technical framework for management of digital text outputs4) comparing digital outputs for accuracy5) developing and deploying a game6) evaluating accuracy scores from the game against ground truth pages 7) generating an error matrix for clean-up8) producing a report and disseminating findings.

Like reCaptcha …….

…..but a lot more fun!

What is Mining Biodiversity?

• Full title – Mining Biodiversity: Enriching Biodiversity Heritage with Text Mining and Social Media

• 3 separate grants given to The National Centre for Text Mining, University of Manchester (UK), Missouri Botanical Garden (USA); Dalhousie University’s Big Data Analytics Institute (Canada) and Social Media Lab (Canada)

• Mining Biodiversity is one of the projects that won in the third round of the transatlantic Digging Into Data Challenge, a competition aiming to promote the development of innovative computational techniques that can be applied to big data in the humanities and social sciences.

• Runs March 2014- Sept 2015

Goals• enriching a large-scale library, i.e., the BHL, via innovative

application of text mining techniques to produce semantic metadata and a term inventory,

• providing improved access to biodiversity-related digital artifacts via an enhanced search engine and visualisation of results, and

• stimulating increased collaboration, interaction and sharing of information amongst BHL users via the social media environment.

http://biodivlib.wikispaces.com/Art+of+Life

http://biodivlib.wikispaces.com/Purposeful+Gaming

http://miningbiodiversity.org/

Contact: Trish Rose-Sandler trish.rose-sandler@mobot.org

For more info and to track progress of these projects