Andreas Doms Biotechnology Center Technical UniversityDresden ontology-based literature search life science literature gopubmed hands-on curation tool

Andreas DomsBiotechnology Center

Technical UniversityDresden

ontology-based literature search

life scienceliterature

gopubmed

hands-on

curation tool

examples

agenda

Andreas DomsBiotechnology Center

Technical UniversityDresden



gopubmed

hands-on

curation tool

agenda

examples

• Part I: GoPubMed• Part II: practical

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


gopubmed

hands-on

curation tool

examples

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


gopubmed

hands-on

curation tool

examples

The Gene Ontologyagenda



• Gene Ontology• long result lists• concept regonition• the idea of ontology-based search

gopubmed

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Searching in PubMedagenda




gopubmed

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Searching in PubMedagenda




gopubmed

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Identification of ontology terms…

Concept recognitionagenda




gopubmed

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We all know sequence alignmentagenda




gopubmed

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Idea: Use it for concept identification

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gopubmed

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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




gopubmed

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curation tool

examples

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

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gopubmed

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curation tool

examples

• 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




gopubmed

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Ontology-based literature searchagenda




gopubmed

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levamisole inhibitor

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gopubmed


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• user interface• using GoPubMed• browsing results

helicobacter pylori

Which anatomical structure is affected by helicobacter pylori?

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rab5

Which biological process is the protein Rab5 involved in and where is located in the cell?

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gopubmed

aspirin

Which enzymes are inhibited by aspirin?

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leukemia

Is „leukemia“ a hot research topic?

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nurse [au] london [ad]

What is Paul Nurse working on?

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What is Paul Nurse working on?agenda


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blobel g[au] new york[ad]

What is Günther Blobel working on?

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Blobel donated the whole money for the Frauenkirche

in Dresden

What is Günther Blobel working on?

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gopubmed

• GoPubMed can answer bio-medical Questions

• GoPubMed gives a good overview about current bio-medical literature

• GoPubMed provides a bibliometric analysis



gopubmed

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curation tool

examples

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Thank you so much!



gopubmed

hands-on

curation tool

examples

agenda

Documents

Andreas Doms Biotechnology Center Technical UniversityDresden ontology-based literature search life science literature gopubmed hands-on curation tool