Andreas Doms Biotechnology Center Technical UniversityDresden ontology-based literature search life...

Andreas DomsBiotechnology Center

Technical UniversityDresden

ontology-based literature search

life scienceliterature

gopubmed

hands-on

curation tool

examples

agenda

Andreas DomsBiotechnology Center

Technical UniversityDresden

ontology-based literature search

life scienceliterature

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

ontology-based literature search

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

ontology-based literature search

gopubmed

hands-on

curation tool

examples

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

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

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

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

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

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

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

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

• 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

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

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

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

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

levamisole inhibitor

agenda

life scienceliterature

gopubmed

ontology-based literature search

hands-on

curation tool

examples

• user interface• using GoPubMed• browsing results

helicobacter pylori

Which anatomical structure is affected by helicobacter pylori?

agenda

life scienceliterature

examples

ontology-based literature search

hands-on

curation tool

gopubmed

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

aspirin

Which enzymes are inhibited by aspirin?

agenda

life scienceliterature

examples

ontology-based literature search

hands-on

curation tool

gopubmed

leukemia

Is „leukemia“ a hot research topic?

agenda

life scienceliterature

examples

ontology-based literature search

hands-on

curation tool

gopubmed

nurse [au] london [ad]

What is Paul Nurse working on?

agenda

life scienceliterature

examples

ontology-based literature search

hands-on

curation tool

gopubmed

What is Paul Nurse working on?agenda

life scienceliterature

examples

ontology-based literature search

hands-on

curation tool

gopubmed

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

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

• 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

Thank you so much!

ontology-based literature search

life scienceliterature

gopubmed

hands-on

curation tool

examples

agenda