Swan Annotation Framework: running text mining services and curating the results.

1. © Massachusetts General Hospital, All Rights Reserved Oct 25, 2010 - Paolo Ciccarese, PhD
SWAN Annotation Framework and
Text Mining Services
Paolo Ciccarese, PhD
Oct 25, 2010
1
Mass General Hospital Harvard Medical School
paolo.ciccarese@gmail.com

2. © Massachusetts General Hospital, All Rights Reserved Oct 25, 2010 - Paolo Ciccarese, PhD
Running text mining services
2

3. © Massachusetts General Hospital, All Rights Reserved Oct 25, 2010 - Paolo Ciccarese, PhD
3 – Loading a news

4. © Massachusetts General Hospital, All Rights Reserved Oct 25, 2010 - Paolo Ciccarese, PhD
4 – Selecting one or more of the available text mining services

5. © Massachusetts General Hospital, All Rights Reserved Oct 25, 2010 - Paolo Ciccarese, PhD
5 – Running the selected text mining services

6. © Massachusetts General Hospital, All Rights Reserved Oct 25, 2010 - Paolo Ciccarese, PhD
6 – Display of the results

7. © Massachusetts General Hospital, All Rights Reserved Oct 25, 2010 - Paolo Ciccarese, PhD
7 – List of the results in the summary panel

8. © Massachusetts General Hospital, All Rights Reserved Oct 25, 2010 - Paolo Ciccarese, PhD
8 – Display of items in text through the summary panel

9. © Massachusetts General Hospital, All Rights Reserved Oct 25, 2010 - Paolo Ciccarese, PhD
9 - Sets summary panel

10. © Massachusetts General Hospital, All Rights Reserved Oct 25, 2010 - Paolo Ciccarese, PhD
10 – Display of all the items belonging to the selected set

11. © Massachusetts General Hospital, All Rights Reserved Oct 25, 2010 - Paolo Ciccarese, PhD
11 – Curation of one annotation item

12. © Massachusetts General Hospital, All Rights Reserved Oct 25, 2010 - Paolo Ciccarese, PhD
12 – The returned term is too broad

13. © Massachusetts General Hospital, All Rights Reserved Oct 25, 2010 - Paolo Ciccarese, PhD
13 – Introducing a comment in the curation token

14. © Massachusetts General Hospital, All Rights Reserved Oct 25, 2010 - Paolo Ciccarese, PhD
14 – Applying the curation token

15. © Massachusetts General Hospital, All Rights Reserved Oct 25, 2010 - Paolo Ciccarese, PhD
15 – Another example of curation

16. © Massachusetts General Hospital, All Rights Reserved Oct 25, 2010 - Paolo Ciccarese, PhD
16 – Another example of curation

17. © Massachusetts General Hospital, All Rights Reserved Oct 25, 2010 - Paolo Ciccarese, PhD
17 – First term is an exact match

18. © Massachusetts General Hospital, All Rights Reserved Oct 25, 2010 - Paolo Ciccarese, PhD
Extending the automatically
generated set
18

19. © Massachusetts General Hospital, All Rights Reserved Oct 25, 2010 - Paolo Ciccarese, PhD
19 – For adding annotation on the text span ‘APP’ it is necessary to select the text and…

20. © Massachusetts General Hospital, All Rights Reserved Oct 25, 2010 - Paolo Ciccarese, PhD
20 - … attach the right term

21. © Massachusetts General Hospital, All Rights Reserved Oct 25, 2010 - Paolo Ciccarese, PhD
21 – New annotation added to the NCBO result set

22. © Massachusetts General Hospital, All Rights Reserved Oct 25, 2010 - Paolo Ciccarese, PhD
22 – Displaying the new annotation in context

23. © Massachusetts General Hospital, All Rights Reserved Oct 25, 2010 - Paolo Ciccarese, PhD
23 – Displaying all the items of the set