Expanding Access to Biodiversity Literature. Mining Biodiversity.
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Transcript of Expanding Access to Biodiversity Literature. Mining Biodiversity.
Expanding Access to Biodiversity Literature
Presented by: William Ulate Center for Biodiversity Informatics, MBG
May 26, 2016
Biodiversity Heritage Library
• a consortium of botanical and natural history libraries
• stores digitised legacy literature on biodiversity
• currently holds 180,000 volumes = millions of pages (PDFs and OCR-generated text)
• open-access
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Mining Biodiversity
• Transform BHL into a next-generation social digital library
• A multi-disciplinary approach – Text Mining
– Machine learning
– History of Science
– Environmental History & Studies
– Library and Information Science
– Social Media
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What have we done so far?
Social Media
Visualisation
Semantic
Metadata
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Making Biodiversity Digital Objects More Social and Shareable
Follow us on Twitter: @SMLabTO
We also partnered with Altmetric to better understand who and why people share BHL content across various social media platforms
Follow us on Twitter: @SMLabTO
“My Tweeps” app mytweeps.com
Helping BHL (and other organizations) to get daily insights about their Twitter followers (or Tweeps) and what they are interested in.
We call it a "reverse" Twitter because instead of seeing tweets from people whom you follow, the app shows you tweets from people who follow you.
Follow us on Twitter: @SMLabTO
Current features
• supports keyword-based search
• species names annotated and linked to the Encyclopedia of Life
• integrates automatic taxonomic name finding tools (uBio Taxonfinder / GNRDS)1
• data access through export functionalities and Web services
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1 Global Names Recognition and Discovery tools and Services (GNRDS). See http://gnrd.globalnames.org/
What’s wrong with keyword-based search: Polysemy
•Ambiguity!
Boxwood
historic place in Alabama?
North American term for plants in the Buxaceae
family?
Box
container?
Boxwood for other English-speaking countries?
What’s wrong with keyword-based search: Polysemy
•Ambiguity!
California bay
hardwood tree?
location?
Semantic metadata generation
• Entity types
– species
– location
– habitat
– anatomical parts
– qualities
– persons
– temporal expressions
• Association types
– observation
– Habitation
– nutrition
– trait
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How does semantic information help?
SPECIES California bay
hardwood tree
location
California bay LOCATION
•Word sense disambiguation
What’s wrong with keyword-based search: Synonymy
Campanula portenschlagiana Schult.
Campanula portenschlagiana Schult.
Campanula affinis Rchb. ex Nyman
Campanula muralis Port ex. A. DC.
What’s wrong with keyword-based search: Synonymy
Clematis L.
Clematis L.
Clematopsis Bojer ex Hutch.
Atragene L.
Archiclematis tamura
How does semantic information help?
Campanula portenschlagiana Schult.
Campanula portenschlagiana
Schult.
Campanula affinis Rchb. ex Nyman
Campanula muralis Port ex. A. DC.
•Query expansion
Term Inventory
• compilation of species names (flowering plants, mammals, birds)
• acts as a thesaurus, as each name is linked to its synonyms as well as other semantically related names
• “semantically relatedness”: defined in terms of a contextual similarity measure, computed over the entire BHL corpus
Sources we leveraged
• Names
– Encyclopedia of Life (EOL)
– Catalogue of Life
– Global Biodiversity Information Facility (GBIF)
• Images
– Encyclopedia of Life (EOL)
Experiments
• Training data: all English texts from the BHL – about 26 million pages with a size of 49GB
• Evaluation data: synonymous terms from the Catalogue of Life
• Select 500 scientific names and their synonyms from the CoL
• Results at top-20
Category Class #terms in
CoL
#terms in
BHL
#average synonyms
in CoL
Birds Aves 1140 818 2.28
Mammals Mammalia 1131 726 2.26
Plants Plantae 1141 826 2.28
Category Pre@20 Re@20
Birds 69.41% 63%
Mammals 62.12% 53.84%
Plants 56.17% 21.43%
Application to Query Expansion
• an interface for searching BHL documents using a species name as a query
• query is automatically expanded by retrieving synonyms/semantically related names from the term inventory
• documents mentioning all of the names in the expanded query are returned
https://www.youtube.com/watch?v=lF2ManWhljM
http://nactem10.mib.man.ac.uk/va/MiBio/Search/queryExpansion.html?prot=thumb
Some Magnoliopsida species (common) names
CHOICE 1 CHOICE 2 CHOICE 3
Phaseolus multiflorus Garden pea Argemone alba
Citrus nobilis Sweetheart Arabis perfoliata
Spergularia marina Aster pauciflorus Mimosa
Canavalia ensiformis Physic nut Mung bean
Chrysanthemum inodorum Guilandina bonducella Tilia parvifolia
Fraxinus pubescens Arabidopsis thaliana Pulsatilla vulgaris
Symphoricarpos orbiculatus Turritis glabra Medick
Sorbus domestica Lespedeza reticulata Hypericum galioides
Haematoxylon campechianum Scaevola lobelia Alliaria petiolata
Kerria japonica Clematis indivisa Erythrina glauca
Petasites officinalis Ptychotis ajowan Aster multiflorus
Salix cinerea Ribes vulgare Sword bean
More Magnoliopsida species (common) names
CHOICE 1 CHOICE 2 CHOICE 3
Peucedanum ostruthium Cynoglossum sylvaticum Allamanda schottii
Windsor bean Common haricot Ranunculus pusillus
Sambucus canadensis Field bean Dwarf bean
Gaillardia bicolor Ipomoea nil Monniera monniera
Arnica alpina Indian laburnum Eastern redbud
Calocarpum mammosum Ribes americanum Lactuca alpina
Polygonum maritimum Erica mediterranea Paronychia canadensis
Imperatoria ostruthium Rubus lasiocarpus Melochia corchorifolia
Valerianella olitoria Sonchus oleraceus Vicia hirsuta
Mountain ebony Carduus lanceolatus Salix rubra
Ledum groenlandicum Sida abutilon Tecoma radicans
Gilia coronopifolia Corydalis canadensis Lacinaria spicata
And more Magnoliopsida species (common) names
CHOICE 1 CHOICE 2 CHOICE 3
Pyrus cydonia Barbados pride Prenanthes alba
Clianthus dampieri White lupin Yellow pea
Geum intermedium Pyrus melanocarpa Erigeron canadensis
Pyrola uniflora Japanese pagoda tree Epilobium hirsutum
Ampelopsis engelmanni Soybean Salix pentandra
Solanum nodiflorum Exogonium purga Lathyrus montanus
Ribes floridum Impatiens biflora Stellaria media
Orobus tuberosus Cassia marilandica Cnicus discolor
Medicago maculata Melilotus indica Apium nodiflorum
Glycine soja Balsam of tolu Juglans laciniosa
Stellaria longifolia Salix arctica Purging cassia
Echinospermum lappula Umbrella tree Potentilla pumila
Thank you
William Ulate Missouri Botanical Garden
Photo: W.Ulate. Corcovado National Park, Costa Rica. 2013
This project was made possible in part by
[LG-00-14-04-0032-14]
Riza Batista-Navarro NaCTeM, University of Manchester