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Andreas DomsBiotechnology Center
Technical UniversityDresden
ontology-based literature search
life scienceliterature
gopubmed
hands-on
curation tool
examples
agenda
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Andreas DomsBiotechnology Center
Technical UniversityDresden
ontology-based literature search
life scienceliterature
gopubmed
hands-on
curation tool
agenda
examples
• Part I: GoPubMed• Part II: practical
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Life science literature
• 600.000 researches work in the life sciences
• PubMed literature database contains 17.000.000 scientific abstracts
• Annual growth ca. 500.000
agenda
life science literature
• most important source for researchers
• a lot of unstructured information • growth rapidly• common vocabulary helps searching
ontology-based literature search
gopubmed
hands-on
curation tool
examples
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PubMed
• Great resource if one knows what one is looking for–“Kox1” has 17 hits
• But “diabetes” will produce >279.394
How can the common vocabulary of the GeneOntology be used to facilate literature search?
agenda
life science literature
• most important source for researchers
• a lot of unstructured information • growth rapidly• common vocabulary helps searching
ontology-based literature search
gopubmed
hands-on
curation tool
examples
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The Gene Ontologyagenda
life scienceliterature
ontology-based literature search
• Gene Ontology• long result lists• concept regonition• the idea of ontology-based search
gopubmed
hands-on
curation tool
examples
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Searching in PubMedagenda
life scienceliterature
ontology-based literature search
• Gene Ontology• long result lists• concept regonition• the idea of ontology-based search
gopubmed
hands-on
curation tool
examples
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Searching in PubMedagenda
life scienceliterature
ontology-based literature search
• Gene Ontology• long result lists• concept regonition• the idea of ontology-based search
gopubmed
hands-on
curation tool
examples
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Identification of ontology terms…
Concept recognitionagenda
life scienceliterature
ontology-based literature search
• Gene Ontology• long result lists• concept regonition• the idea of ontology-based search
gopubmed
hands-on
curation tool
examples
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We all know sequence alignmentagenda
life scienceliterature
ontology-based literature search
• Gene Ontology• long result lists• concept regonition• the idea of ontology-based search
gopubmed
hands-on
curation tool
examples
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Idea: Use it for concept identification
agenda
life scienceliterature
ontology-based literature search
• Gene Ontology• long result lists• concept regonition• the idea of ontology-based search
gopubmed
hands-on
curation tool
examples
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Examples
PMID 7578980: ”Primed monocytes transcribed TNF mRNA at a higher rate than freshly isolated monocytes upon activation with LPS.”
(for monocyte activation (GO:0042117))
PMID 7612661: ”Although all nm23 proteins contain nucleoside diphosphate (NDP) kinase activity, it has not been established that the enzyme activity mediated the various functions of nm23 proteins.”
(for protein kinase activity (GO:0004672)).
agenda
life scienceliterature
ontology-based literature search
• Gene Ontology• long result lists• concept regonition• the idea of ontology-based search
gopubmed
hands-on
curation tool
examples
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Concept recognition
• difficult as terms are not used in their lexical base form
• Inter-annotator agreement between 65 to 85%
• Good entity recognition systems: ~90% f-value
• Generel concepts may be mis-interpreted („development“ has 8 meanings in WordNet)
• Machine learning can achieve very good results for disambiguation but you need training data
agenda
life scienceliterature
ontology-based literature search
• Gene Ontology• long result lists• concept regonition• the idea of ontology-based search
gopubmed
hands-on
curation tool
examples
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• thioredoxin-disulfide reductase activity (GO:0004791)
• small-molecule carrier or transporter (GO:0005468)
• Endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5’-phosphomonoesters (GO:0016893)
• [methionine synthase] reductase activity (GO:0030586)
• structural constituent of chorion (sensu Insecta) (GO:0005213)
Concept recognitionagenda
life scienceliterature
ontology-based literature search
• Gene Ontology• long result lists• concept regonition• the idea of ontology-based search
gopubmed
hands-on
curation tool
examples
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Ontology-based literature searchagenda
life scienceliterature
ontology-based literature search
• Gene Ontology• long result lists• concept regonition• the idea of ontology-based search
gopubmed
hands-on
curation tool
examples
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Ontology-based literature searchagenda
life scienceliterature
ontology-based literature search
• Gene Ontology• long result lists• concept regonition• the idea of ontology-based search
gopubmed
hands-on
curation tool
examples
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Ontology-based literature searchagenda
life scienceliterature
ontology-based literature search
• Gene Ontology• long result lists• concept regonition• the idea of ontology-based search
gopubmed
hands-on
curation tool
examples
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Ontology-based literature searchagenda
life scienceliterature
ontology-based literature search
• Gene Ontology• long result lists• concept regonition• the idea of ontology-based search
gopubmed
hands-on
curation tool
examples
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levamisole inhibitor
agenda
life scienceliterature
gopubmed
ontology-based literature search
hands-on
curation tool
examples
• user interface• using GoPubMed• browsing results
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helicobacter pylori
Which anatomical structure is affected by helicobacter pylori?
agenda
life scienceliterature
examples
ontology-based literature search
hands-on
curation tool
gopubmed
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rab5
Which biological process is the protein Rab5 involved in and where is located in the cell?
agenda
life scienceliterature
examples
ontology-based literature search
hands-on
curation tool
gopubmed
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aspirin
Which enzymes are inhibited by aspirin?
agenda
life scienceliterature
examples
ontology-based literature search
hands-on
curation tool
gopubmed
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leukemia
Is „leukemia“ a hot research topic?
agenda
life scienceliterature
examples
ontology-based literature search
hands-on
curation tool
gopubmed
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nurse [au] london [ad]
What is Paul Nurse working on?
agenda
life scienceliterature
examples
ontology-based literature search
hands-on
curation tool
gopubmed
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What is Paul Nurse working on?agenda
life scienceliterature
examples
ontology-based literature search
hands-on
curation tool
gopubmed
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blobel g[au] new york[ad]
What is Günther Blobel working on?
agenda
life scienceliterature
examples
ontology-based literature search
hands-on
curation tool
gopubmed
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Blobel donated the whole money for the Frauenkirche
in Dresden
What is Günther Blobel working on?
agenda
life scienceliterature
examples
ontology-based literature search
hands-on
curation tool
gopubmed
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• GoPubMed can answer bio-medical Questions
• GoPubMed gives a good overview about current bio-medical literature
• GoPubMed provides a bibliometric analysis
ontology-based literature search
life scienceliterature
gopubmed
hands-on
curation tool
examples
agenda
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Thank you so much!
ontology-based literature search
life scienceliterature
gopubmed
hands-on
curation tool
examples
agenda