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Text mining

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Lars Juhl Jensen
Lars Juhl Jensen

Text mining

Science
1 of 126
Text mining Lars Juhl Jensen
>10 km
too much to read
exponential growth
~40 seconds per paper
computer
as smart as a dog
teach it specific tricks
learning objectives
information retrieval
named entity recognition
information extraction
benchmarking
information retrieval
find the relevant papers
ad hoc retrieval
user-specified query
“yeast AND cell cycle”
PubMed
indexing
fast lookup
stemming
word endings
dynamic query expansion
MeSH terms
Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5- dependent Swe1 hyperphosphorylation and degradation
no tool will find that
named entity recognition
identify the concepts
Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5- dependent Swe1 hyperphosphorylation and degradation
comprehensive lexicon
genes/proteins
CDC2
cyclin dependent kinase 1
chemical compounds
organisms
diseases
orthographic variation
flexible matching
upper- and lower-case
CDC2
Cdc2
spaces and hyphens
cyclin dependent kinase 1
cyclin-dependent kinase 1
expansion rules
prefixes and suffixes
CDC2
hCDC2
abbreviated forms
Saccharomyces cerevisiae
S. cerevisiae
plural/adjective forms
mitochondrion
mitochondria
“black list”
SDS
augmented browsing
EXTRACT
interactive annotation
Pafilis et al., Database, 2016extract.hcmr.gr
extract.hcmr.gr Pafilis et al., Database, 2016
information extraction
formalize the facts
Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5- dependent Swe1 hyperphosphorylation and degradation
two approaches
the formal way
NLP Natural Language Processing
part-of-speech tagging
what you learned in school pronoun pronoun verb preposition noun
sentence parsing
Gene and protein names Cue words for entity recognition Verbs for relation extraction [nxexpr The expression of [nxgene the cytochrome genes [nxpg CYC1 and CYC7]]] is controlled by [nxpg HAP1] Saric et al., Proceedings of ACL, 2004
association type
direction
high precision
poor recall
domain-specific
the pragmatic way
guilt by association
co-mentioning
counting
within documents
within paragraphs
within sentences
quality score
generic
protein–protein
protein–chemical
protein—disease
organism—disease
high recall
high precision
undirected associations
unknown type
benchmarking
prove that it works
the formal way
manually annotated corpus
precision
recall
shared tasks
BioCreative
BioNLP
existing corpora
not novel
create your own
much work
the pragmatic way
inspect text-mining output
precision
no recall
much less work
summary
keep it simple
domain knowledge
technical knowhow
Thanks for your attention

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