Semantic Search Engine for the Life Science Web
Heiko Dietze, Michael Schroeder
BIOTEC, TU-Dresden
heiko.dietze@biotec.tu-dresden.de
Semantic Web Applications and Tools for Life Sciences
November 28, 2008
e-Science Institute, Edinburgh, Scotland, UK
Searching for an answer
1. What is the diagnosis for the symptoms for
multiple spinal tumors and skin tumors?
2. Which model organisms are used to study the
Fgf8 protein?
3. Which functions does Rag C have?
4. How do Bop-Pes interactions affect cell growth?
5. How do Ret-GDNF interactions affect liver
development?
The web holds answers to all of these questions!
But how can we find them?
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Is Google enough?
• Googling for a diagnosis, Tang et al., BMJ,
2006
• 58% success rate
Question: What is the
diagnosis for multiple spinal
tumors and skin tumors?
Answer:
Neurofibromatosis type 2
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Is Google enough?
• Google does have an answer to
Question 1
• But Google does not have
answers for Question 2-5 in the
top ten
• Note, 80% of users just check
first page and top left corner
• Google key-word search is not enough:
– Which organisms is FGF8 studied in?
– Web page: “... fgf8 expression in Zebrafish ...”
– Organism is not mentioned, but we know
Zebrafish is an organism
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semantic search for the life
science web
Combine: web search, text-mining and ontologies
for question answering
Outline:
• Existing approaches
• GoWeb architecture and examples
• GoWeb evaluation
– Genes and Functions
– Symptoms and Diseases
– Proteins, Diseases and Evidences
• Discussion
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How to answer questions
• Key-word search
– Works only if question and document contain the
keywords
• Search formal RDF/OWL statement
– Works if RDF available, but problem is
presentation to users
• Natural language processing of queries and text
– Computationally intensive, natural language can be
very complex
• Key-word search plus clustering
• Key-word search plus text-mining & ontology
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Semantic search with RDF/OWL
Search for “endosome”
List of related
RDF/OWL Resources
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Search with natural language
Question:
What causes diabetes?
Question:
How far is the
Earth from Mars?
Answers extracted with NLP:
• Facts, e.g. Mutations, Distances
• Sentences
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Key-Word Search plus Clustering of Results
• Clusty, Carrot,
Keyword search:
Fgf8 model organism
Clusters containing:
• Mouse
• Zebrafish
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Key-Word Search plus Text-Mining & Ontology
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Question: Which organism is Fgf8 studied?
Keyword:
Fgf8
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Answer: Mice, Zebrafish
GoWeb: 1000 of
5986 web-sites
What:
MeSH-Branch: Organisms
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Answer: Mice, Zebrafish
In Yahoo
Pos 79
In zebrafish, Fgf3 and Fgf8
have been implicated …
biomdecentral.com
Zebrafish
44 of 1000
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Answer: Cichlids
Evolution of novelty in the cichlid dentition
Cichlids
4 of 1000
Fgf8 is expressed more proximally and
specifies the molar tooth field ...
In Yahoo
Pos 939
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Who, Where, When
Who:
• Person,
• Organisation,
• Company
Where:
• Domains,
• Locations
When:
• Dates
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GoWeb Evaluation
• Three Benchmarks:
– Genes and Functions
– Symptoms and Diseases
– Proteins, Diseases and Evidences
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Gene and Function
Example:
Benchmark:
GoWeb:
• Gene: “Rag C”
• Function: cytoplasm, RNA splicing,
transcription, GDP binding
• 457 genes and 1352 ontology terms
• Manually curated from full-text articles
• BioCreAtIvE 1 (Task 2) Blaschke et al.
• Recall: 58.1% (785 of 1352)
• Query for gene name
• Induced ontology contains the terms
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Symptoms and Diseases
Example:
Benchmark:
Google,
Tang et al:
GoPubMed:
GoWeb:
• Symptoms: fever, anterior mediastinal mass,
and central necrosis
• Disease: Lymphoma
• 26 diagnostic case records
(New England Journal of Medicine)
• 15/26 (58%) symptoms as keywords, results
manually curated
• 13/26 (50%) cases
• 20/26 (77%) cases correct answer
• 10 cases, answer directly in top categories
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Symptoms and Diseases
hypertension
"adrenal mass"
40 articles
"Cushing
Syndrome"
eMedicine.com
oncologychannel.com
jcem.endojournals.org
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Proteins, Diseases and Evidences
Example:
Benchmark:
GoWeb:
• What is the role of MMS2 in cancer?
• 28 questions, TREC Genomics 2006
• Passage retrieval for question
answering
• Biomedical literature, full-text
•
•
•
•
22 of 28 (78,6%) answer possible
Transform question to keywords
Find snippet with a valid answer
13 cases, semantic filter
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Q: What is the role of MMS2 in cancer
DNA damage
10 of 1000
... concerted action of RAD5
with UBC13 and MMS2 in DNA
damage repair is given by ...
nar.oxfordjournals.org
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Discussion
• Pro
– Let Yahoo do the hard work
– Snippets ≈ sentence, surprisingly good results
– Users are familiar with keywords, semantics only to
guide users
• Con
– Snippets are not sentences
– Co-occurrence is only statistical
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• GoWeb explores web search results with
ontologies (what, where, who, when)
• GoWeb can help to answer questions
– Definition, reference, entities (Tomuro 2001) ✔
– “meaning of life” ✘
• 3 Benchmarks
–
–
–
–
Gene and Function
Symptoms and Disease
Protein and Disease
Success rate up to 80%
• Try it at gopubmed.org/goweb
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Acknowledgements
• People
– Andreas Doms, Thomas Wächter
– GoPubMed team from Transinsight
M. Alvers, L. Barrio-Alvers, J. Mönnich,
C. Plake, M. Zschunke.
• Funding
European Union for the Sealife Project,
Project Reference IST-2006-027269
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Try it at gopubmed.org/goweb
Thank your, for your Attention.
Questions?
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Questions that & can’t be answered
Not
Noteverything
everythingcan
canbe
beanswered
answered
•• What’s
What’sthe
themeaning
meaningof
oflife?
life?
•• When
Whenshould
shouldIIsell
sellmy
myLehman
LehmanBrothers
Brothersshares?
shares?
Classification
Classificationby
byTomuro
Tomuroand
andLytinen
Lytinen2001
2001
✔
✔ definition
definition('What
('Whatdoes
doesXXdo?'),
do?'),reference
reference('What',
('What','Which')
'Which')or
orentities
entities
('Who')
('Who')
✘
✘ manner
mannerof
ofaction,
action,degree
degreeor
orinterval
interval('how
('howmany',
many','how
'howmuch'
much'or
or'how
'how
long',
long',e.g.
e.g.What
Whatpercentage
percentageof
ofchildren
childrenare
arevaccinated?)
vaccinated?)and
and
procedure
procedure('how
('howto')
to')
Medical
Medicalquestion
questiontaxonomy
taxonomyby
byEly
Elyet
etal.
al.2000
2000
✔
✔ questions
questionsrelated
relatedto
todiagnosis
diagnosis
✘
✘ treatment
treatmentbranch
branch(What
(Whatare
arethe
theoptions
optionsfor
fortreatment
treatmentof
ofcondition
conditionyy
ininsituation
situationz?),
z?),management
management(What
(Whatisisthe
thebest
bestway
wayto
todiscuss
discussor
or
approach
approachdiscussion
discussionof
ofdifficult
difficultissue
issuex?),
x?),nonclinical
nonclinical(What
(Whatare
arethe
the
legal
legalconsiderations
considerationsininsituation
situationy?)
y?)
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