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

2. Andreas Doms Biotechnology Center Technical UniversityDresden ontology-based literature search life science literature gopubmed hands-on curation tool agenda examples Part I: GoPubMed Part II: practical

3. 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

4. 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

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

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

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

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

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

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

11. 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 science literature ontology-based literature search Gene Ontology long result lists concept regonition the idea of ontology- based search gopubmed hands-on curation tool examples

12. 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 science literature ontology-based literature search Gene Ontology long result lists concept regonition the idea of ontology- based search gopubmed hands-on curation tool examples

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

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

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

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

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

18. levamisole inhibitor agenda life science literature gopubmed ontology-based literature search hands-on curation tool examples user interface using GoPubMed browsing results

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

35. rab5 Which biological process is the protein Rab5 involved in and where is located in the cell? agenda life science literature examples ontology-based literature search hands-on curation tool gopubmed

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

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

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

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

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

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

56. 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 science literature gopubmed hands-on curation tool examples agenda

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