Download - Dictionary-based named entity recognition
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Lars Juhl Jensen
Dictionary-basednamed entity recognition
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>10 km
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too much to read
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computer
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as smart as a dog
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teach it specific tricks
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named entity recognition
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comprehensive dictionary
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synonyms
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cyclin dependent kinase 1
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CDC2
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normalization
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CDK1_HUMAN
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dictionary compilation
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genes/proteins
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UniProtKB
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Ensembl
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RefSeq
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chemical compounds
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PubChem
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species/organisms
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NCBI Taxonomy
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functions
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pathways
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compartments
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Gene Ontology
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tissues
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Brenda Tissue Ontology
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diseases
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Disease Ontology
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phenotypes
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Human Phenotype Ontology
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environments
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Environment Ontology
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filters
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redundant terms
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insulin
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broad synonyms
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CDK holoenzyme
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related synonyms
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polyubiquitin
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wrong synonyms
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BRCA1
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dictionary expansion
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shortened forms
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protein kinase activity
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protein kinase
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Wnt signaling pathway
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Wnt signaling
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synonymous forms
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metabolic disease
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metabolic disorder
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plural forms
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protein kinase
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protein kinases
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mitochondrion
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mitochondria
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cancer
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cancers
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adjective forms
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mitochondrion
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mitochondrial
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abbreviated forms
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Escherichia coli
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E. coli
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prefixes and suffixes
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CDC2
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hCDC2
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mCDC2
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Cdc28
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Cdc28p
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huge dictionary
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additional ambiguity
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handling ambiguity
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three options
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allow
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disallow
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disambiguate
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acceptable ambiguity
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orthologous genes
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overlapping ontologies
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disease
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phenotype
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unacceptable ambiguity
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unrelated entities
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APC
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adenomatous polyposis coli
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anaphase promoting complex
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disambiguation
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ranking of name sources
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remove unlikely meanings
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acronym definitions
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three letter acronym (TLA)
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other names mentioned
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C. sativa
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Camelina sativa
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Cannabis sativa
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Castanea sativa
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marijuana
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species autodetection
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two rounds of NER
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species/organisms
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genes/proteins
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text matching
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uppercase / lowercase
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spaces and hyphens
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punctuation
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too many variants
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flexible matching
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finite state automaton
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LINNAEUS
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custom hash function
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C++ tagger
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efficiency
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Pafilis et al., PLOS ONE, 2013
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performance
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~85% precision
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~75% recall
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“black list”
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bad names
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SDS
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a
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an
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web resources
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indexing of literature
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term co-occurrence
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iHOP
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Hoffmann & Valencia, Nature Genetics, 2004www.ihop-net.org
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STRING
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Szklarczyk et al., Nucleic Acids Research, 2015string-db.org
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real-time text mining
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Reflect
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augmented browsing
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Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009reflect.ws
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EXTRACT
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interactive annotation
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Pafilis et al., Proceedings of BioCreative V, 2015extract.hcmr.gr
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Pafilis et al., Proceedings of BioCreative V, 2015extract.hcmr.gr