Dictionary-based named entity recognition

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Lars Juhl Jensen

Dictionary-based named entity recognition

Lars Juhl Jensen
Dictionary-based
named entity recognition

>10 km

too much to read

computer

as smart as a dog

teach it specific tricks

named entity recognition

comprehensive dictionary

synonyms

cyclin dependent kinase 1

CDC2

normalization

CDK1_HUMAN

dictionary compilation

genes/proteins

UniProtKB

Ensembl

RefSeq

chemical compounds

PubChem

species/organisms

NCBI Taxonomy

functions

pathways

compartments

Gene Ontology

tissues

Brenda Tissue Ontology

diseases

Disease Ontology

phenotypes

Human Phenotype Ontology

environments

Environment Ontology

filters

redundant terms

insulin

broad synonyms

CDK holoenzyme

related synonyms

polyubiquitin

wrong synonyms

BRCA1

dictionary expansion

shortened forms

protein kinase activity

protein kinase

Wnt signaling pathway

Wnt signaling

synonymous forms

metabolic disease

metabolic disorder

plural forms

protein kinase

protein kinases

mitochondrion

mitochondria

cancer

cancers

adjective forms

mitochondrion

mitochondrial

abbreviated forms

Escherichia coli

E. coli

prefixes and suffixes

CDC2

hCDC2

mCDC2

Cdc28

Cdc28p

huge dictionary

additional ambiguity

handling ambiguity

three options

allow

disallow

disambiguate

acceptable ambiguity

orthologous genes

overlapping ontologies

disease

phenotype

unacceptable ambiguity

unrelated entities

APC

adenomatous polyposis col

naphase promoting comple

disambiguation

ranking of name sources

remove unlikely meanings

acronym definitions

three letter acronym (TLA)

other names mentioned

C. sativa

Camelina sativa

Cannabis sativa

Castanea sativa

marijuana

species autodetection

two rounds of NER

species/organisms

genes/proteins

text matching

uppercase / lowercase

spaces and hyphens

punctuation

too many variants

flexible matching

finite state automaton

LINNAEUS

custom hash function

C++ tagger

efficiency

Pafilis et al., PLOS ONE, 2013

performance

~85% precision

~75% recall

“black list”

bad names

SDS

web resources

indexing of literature

term co-occurrence

iHOP

Hoffmann & Valencia, Nature Genetics, 2004www.ihop-net.org

STRING

Szklarczyk et al., Nucleic Acids Research, 2015string-db.org

real-time text mining

Reflect

augmented browsing

Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009reflect.ws

EXTRACT

interactive annotation

Pafilis et al., Proceedings of BioCreative V, 2015extract.hcmr.gr

Pafilis et al., Proceedings of BioCreative V, 2015extract.hcmr.gr

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Dictionary-based named entity recognition

1. Lars Juhl Jensen Dictionary-based named entity recognition

3. too much to read

5. as smart as a dog

6. teach it specific tricks

7.

8.

9. named entity recognition

10. comprehensive dictionary

12. cyclin dependent kinase 1

14. normalization

16. dictionary compilation

17. genes/proteins

21. chemical compounds

23. species/organisms

24. NCBI Taxonomy

27. compartments

28. Gene Ontology

30. Brenda Tissue Ontology

32. Disease Ontology

34. Human Phenotype Ontology

35. environments

36. Environment Ontology

38. redundant terms

40. broad synonyms

41. CDK holoenzyme

42. related synonyms

43. polyubiquitin

44. wrong synonyms

46. dictionary expansion

47. shortened forms

48. protein kinase activity

49. protein kinase

50. Wnt signaling pathway

51. Wnt signaling

52. synonymous forms

53. metabolic disease

54. metabolic disorder

55. plural forms

56. protein kinase

57. protein kinases

58. mitochondrion

59. mitochondria

62. adjective forms

63. mitochondrion

64. mitochondrial

65. abbreviated forms

66. Escherichia coli

68. prefixes and suffixes

74. huge dictionary

75. additional ambiguity

76. handling ambiguity

77. three options

80. disambiguate

81. acceptable ambiguity

82. orthologous genes

83. overlapping ontologies

86. unacceptable ambiguity

87. unrelated entities

89. adenomatous polyposis col

90. naphase promoting comple

91. disambiguation

92. ranking of name sources

93. remove unlikely meanings

94. acronym definitions

95. three letter acronym (TLA)

96. other names mentioned

98. Camelina sativa

99. Cannabis sativa

100. Castanea sativa

102. species autodetection

103. two rounds of NER

104. species/organisms

105. genes/proteins

106. text matching

107. uppercase / lowercase

108. spaces and hyphens

109. punctuation

110. too many variants

111. flexible matching

112. finite state automaton

114. custom hash function

115. C++ tagger

116. efficiency

117. Pafilis et al., PLOS ONE, 2013

118. performance

119. ~85% precision

120. ~75% recall

121. “black list”

124. a

125. an

126. web resources

127. indexing of literature

128. term co-occurrence

130. Hoffmann & Valencia, Nature Genetics, 2004www.ihop-net.org

132. Szklarczyk et al., Nucleic Acids Research, 2015string-db.org

133. real-time text mining

135. augmented browsing

136. Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009reflect.ws

138. interactive annotation

139. Pafilis et al., Proceedings of BioCreative V, 2015extract.hcmr.gr

140. Pafilis et al., Proceedings of BioCreative V, 2015extract.hcmr.gr