Knowledge Extraction and Semantic Linking in the Encyclopedia of Life

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This talk describes work I have been doing with Cyndy Parr at EOL to annotate text with DBpedia URIs and to generate a species associations network. It was presented to the Boston Python User Group in April 2013.

Technologie

Knowledge extraction and
semantic linking in the
Encyclopedia of Life
Anne Thessen
annethessen@gmail.com

Performance Metrics
• 1631 URIs assigned to 487 text objects from 21 test
species
• 83% were correct
• 20% of the text objects were not assigned a URI
• 239 keys in the dictionary
• Precision 0.89, Recall 1, F1 Score 0.942

Challenges and Errors
• Many ways to say the same thing
– Uterine cannibalism = oophagy
• Negation (9%)
• Describing related taxa (30%)
• Word/phrase part (27%)
• Generalities (15%)
• Homonym (13%)

Challenges
Koko
Горилла
Guerilla
Eastern Lowland Gorilla
Gorilla
graueri
Gorilla berengei
Gorilla beringei
MatschieGorilla beringei mikenensis
King kong
Gorilla gorilla
Virunga
Gorila
Gorille
Mountain
gorilla
大猩猩
ゴリラ

Challenges
Contextual data
Primate
Monkey
Eyes
Food
Panama
Aotus nancymaae
Disambiguate by
authority, species, conte
xtual data
Contextual data
Legume
Plant
Flower
Mirbeliea
Australia
Aotus mollis

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Knowledge Extraction and Semantic Linking in the Encyclopedia of Life

1. Knowledge extraction and semantic linking in the Encyclopedia of Life Anne Thessen annethessen@gmail.com

4. Performance Metrics • 1631 URIs assigned to 487 text objects from 21 test species • 83% were correct • 20% of the text objects were not assigned a URI • 239 keys in the dictionary • Precision 0.89, Recall 1, F1 Score 0.942

5. Challenges and Errors • Many ways to say the same thing – Uterine cannibalism = oophagy • Negation (9%) • Describing related taxa (30%) • Word/phrase part (27%) • Generalities (15%) • Homonym (13%)

7. Finding Taxonomic Names

9. Challenges Koko Горилла Guerilla Eastern Lowland Gorilla Gorilla graueri Gorilla berengei Gorilla beringei MatschieGorilla beringei mikenensis King kong Gorilla gorilla Virunga Gorila Gorille Mountain gorilla 大猩猩ゴリラ

10. Challenges Contextual data Primate Monkey Eyes Food Panama Aotus nancymaae Disambiguate by authority, species, conte xtual data Contextual data Legume Plant Flower Mirbeliea Australia Aotus mollis