agenda life science literature ontologybased literature search gopubmed

agenda life science literature ontology-based literature search gopubmed examples hands-on curation tool Andreas Doms Biotechnology Center Technical University. Dresden

agenda • Part I: Go. Pub. Med • Part II: practical life science literature ontology-based literature search gopubmed examples hands-on curation tool Andreas Doms Biotechnology Center Technical University. Dresden

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 examples hands-on curation tool Life science literature • 600. 000 researches work in the life sciences • Pub. Med literature database contains 17. 000 scientific abstracts • Annual growth ca. 500. 000

agenda life science literature Pub. Med • most important source for researchers • a lot of unstructured information • growth rapidly • common vocabulary helps searching • Great resource if one knows what one is looking for ontology-based literature search • But “diabetes” will produce >279. 394 gopubmed examples hands-on curation tool –“Kox 1” has 17 hits How can the common vocabulary of the Gene. Ontology be used to facilate literature search?

agenda life science literature ontology-based literature search • Gene Ontology • long result lists • concept regonition • the idea of ontologybased search gopubmed examples hands-on curation tool The Gene Ontology

agenda life science literature ontology-based literature search • Gene Ontology • long result lists • concept regonition • the idea of ontologybased search gopubmed examples hands-on curation tool Searching in Pub. Med

agenda life science literature ontology-based literature search • Gene Ontology • long result lists • concept regonition • the idea of ontologybased search gopubmed examples hands-on curation tool Searching in Pub. Med

agenda life science literature Concept recognition ontology-based literature search • Gene Ontology • long result lists • concept regonition • the idea of ontologybased search gopubmed examples hands-on curation tool Identification of ontology terms…

agenda life science literature ontology-based literature search • Gene Ontology • long result lists • concept regonition • the idea of ontologybased search gopubmed examples hands-on curation tool We all know sequence alignment

agenda life science literature ontology-based literature search • Gene Ontology • long result lists • concept regonition • the idea of ontologybased search gopubmed examples hands-on curation tool Idea: Use it for concept identification

agenda life science literature ontology-based literature search • Gene Ontology • long result lists • concept regonition • the idea of ontologybased search Examples PMID 7578980: ”Primed monocytes transcribed TNF m. RNA at a higher rate than freshly isolated monocytes upon activation with LPS. ” (for monocyte activation (GO: 0042117)) gopubmed examples PMID 7612661: ”Although all nm 23 proteins contain nucleoside diphosphate (NDP) kinase activity, it has not been established that the enzyme activity mediated the various functions of nm 23 proteins. ” hands-on curation tool (for protein kinase activity (GO: 0004672)).

agenda life science literature ontology-based literature search • Gene Ontology • long result lists • concept regonition • the idea of ontologybased search gopubmed examples hands-on curation tool 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% fvalue • Generel concepts may be mis-interpreted („development“ has 8 meanings in Word. Net) • Machine learning can achieve very good results for disambiguation but you need training data

agenda life science literature ontology-based literature search • Gene Ontology • long result lists • concept regonition • the idea of ontologybased search gopubmed examples hands-on curation tool Concept recognition • 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)

agenda life science literature ontology-based literature search • Gene Ontology • long result lists • concept regonition • the idea of ontologybased search gopubmed examples hands-on curation tool Ontology-based literature search

agenda life science literature ontology-based literature search • Gene Ontology • long result lists • concept regonition • the idea of ontologybased search gopubmed examples hands-on curation tool Ontology-based literature search

agenda life science literature ontology-based literature search • Gene Ontology • long result lists • concept regonition • the idea of ontologybased search gopubmed examples hands-on curation tool Ontology-based literature search

agenda life science literature ontology-based literature search • Gene Ontology • long result lists • concept regonition • the idea of ontologybased search gopubmed examples hands-on curation tool Ontology-based literature search

agenda life science literature ontology-based literature search gopubmed • user interface • using Go. Pub. Med • browsing results examples hands-on curation tool levamisole inhibitor

agenda life science literature ontology-based literature search gopubmed examples Which anatomical structure is affected by helicobacter pylori? helicobacter pylori hands-on curation tool

agenda life science literature ontology-based literature search gopubmed examples Which biological process is the protein Rab 5 involved in and where is located in the cell? rab 5 hands-on curation tool

agenda life science literature ontology-based literature search gopubmed examples Which enzymes are inhibited by aspirin? aspirin hands-on curation tool

agenda life science literature ontology-based literature search gopubmed examples Is „leukemia“ a hot research topic? leukemia hands-on curation tool

agenda life science literature ontology-based literature search gopubmed What is Paul Nurse working on? examples nurse [au] london [ad] hands-on curation tool

agenda life science literature ontology-based literature search gopubmed examples hands-on curation tool What is Paul Nurse working on?

agenda life science literature ontology-based literature search gopubmed examples What is Günther Blobel working on? blobel g[au] new york[ad] hands-on curation tool

agenda life science literature What is Günther Blobel working on? ontology-based literature search gopubmed examples hands-on curation tool Blobel donated the whole money for the Frauenkirche in Dresden

agenda life science literature ontology-based literature search gopubmed examples hands-on curation tool • Go. Pub. Med can answer biomedical Questions • Go. Pub. Med gives a good overview about current biomedical literature • Go. Pub. Med provides a bibliometric analysis

agenda life science literature ontology-based literature search gopubmed examples hands-on curation tool Thank you so much!