1. Topic Maps applied to PubMed, Extreme’07, August 20071 Topic Maps applied to PubMed Giovani Rubert Librelotto Mirkos Martins Henrique Machado Franciscan University UNIFRA Brazil José Carlos Ramalho Pedro Gabriel Ferreira Pedro R. Henriques Department of Informatics University of Minho Portugal

2. Topic Maps applied to PubMed, Extreme’07, August 20072 Outline Motivation PubMed Topic Maps Metamorphosis PubMed knowledge representation Conclusion

3. Topic Maps applied to PubMed, Extreme’07, August 20073 Motivation Write down what you want to find! Underline the key concepts Consider how best to combine and refine the concepts

4. Topic Maps applied to PubMed, Extreme’07, August 20074 Identify Key Concepts Is it risky for pregnant women to take antidepressants? Risky – (Synonyms) Harm, adverse effects Anti-depressants – Name of drug or drug(s)?

5. Topic Maps applied to PubMed, Extreme’07, August 20075 PubMed PubMed is a free search engine that provides very full coverage of the related biomedical sciences, such as biochemistry and cell biology. It also offers access to the MEDLINE database with citations and abstracts of biomedical research articles.

6. Topic Maps applied to PubMed, Extreme’07, August 20076 PubMed (2) The PubMed core subject is medicine and its related fields. It is offered by the United States National Library of Medicine as part of the Entrez information retrieval system.

7. Topic Maps applied to PubMed, Extreme’07, August 20077 PubMed (3) The inclusion of an article in PubMed does not endorse the article's contents, as other indexes. Nevertheless, many PubMed citations contain links to full text articles which are freely available, often in the PubMed Central digital library.

8. Topic Maps applied to PubMed, Extreme’07, August 20078 MEDLINE MEDLINE database covers over 4.900 journals published around the world primarily from 1966 to the present and is composed of more than 17 millions of citations.

9. Topic Maps applied to PubMed, Extreme’07, August 20079 Milestones MEDLINE 35 years young –15.8 million records PubMed approximately 10 years old –17 million records MEDLINE database covers over 4.900 journals

10. Topic Maps applied to PubMed, Extreme’07, August 200710 PubMed architecture

11. Topic Maps applied to PubMed, Extreme’07, August 200711 PubMed web site

12. Topic Maps applied to PubMed, Extreme’07, August 200712 Querying PubMed

13. Topic Maps applied to PubMed, Extreme’07, August 200713 Query Results Formats Summary Basic Bibliographic Citation (default) Abstract Includes abstract if available Brief First author, first few words, PMID Citation Citation, Abstract & Subject Headings

14. Topic Maps applied to PubMed, Extreme’07, August 200714 Changing Results Format Pull down menu on display bar Select desired format Change occurs automatically

15. Topic Maps applied to PubMed, Extreme’07, August 200715 Information indexed in PubMed Subject or journal title Title Abbreviation NLM ID (NLM'sunique journal identifier) ISO abbreviation Both the print and electronic International Standard Serial Numbers (pISSN and eISSN).

16. Topic Maps applied to PubMed, Extreme’07, August 200716 PubMed data structure - CFG MedlineCitation ==> PMID, DateCreated, DateCompleted, Article, MedlineJournalInfo, ChemicalList, CitationSubset, MeshHeadingList Article ==> Journal, ArticleTitle, Pagination, Abstract, Affiliation, AuthorList, Language, PublicationTypeList Journal ==> ISSN, JournalIssue, Title JournalIssue ==> Volume, Issue, PubDate PubDate ==> Year, Month, Day, Hour?, Minute?, Second? MedlineJournalInfo ==> Country, MedlineTA, NlmUniqueID ChemicalList ==> Chemical+ Chemical ==> RegistryNumber, NameOfSubstance MeshHeadingList ==> MeshHeading+ MeshHeading ==> DescriptorName, QualifierName? AuthorList ==> Author+ Author ==> LastName, ForeName, Initials PublicationTypeList ==> PublicationType+

17. Topic Maps applied to PubMed, Extreme’07, August 200717 PubMed XML Schema

18. Topic Maps applied to PubMed, Extreme’07, August 200718 Available PubMed Concepts Publication Date Language Literature Type Journal Author Gender Age Journal Subset

19. Topic Maps applied to PubMed, Extreme’07, August 200719 Available PubMed Association Author writes article; Keyword describes article; Article was published in an year; Article is published in a journal; Article is written in a language; Article refers to chemical substances; Author publishes in an year; Author writes paper in a language; Journal refers to the keywords;

20. Topic Maps applied to PubMed, Extreme’07, August 200720 What’s the idea? 1.To create an ontology based on PubMed concepts and associations 2.To use that ontology to present query results.

21. Topic Maps applied to PubMed, Extreme’07, August 200721 How? Structure level Catalog level 1.Prebuild ontology’s structure level 2.Populate the ontology with query results (occurrences)

22. Topic Maps applied to PubMed, Extreme’07, August 200722 Metamorphosis

23. Topic Maps applied to PubMed, Extreme’07, August 200723 Metamorphosis

24. Topic Maps applied to PubMed, Extreme’07, August 200724 XSTM editor

25. Topic Maps applied to PubMed, Extreme’07, August 200725 Structure level through XSTM Article Year... <xpath id="PMID” name="Article/ArticleTitle"> //MedlineCitation Article Article/Abstract PMID Article/Pagination/MedlinePgn

26. Topic Maps applied to PubMed, Extreme’07, August 200726 Topic Maps applied to PubMed

27. Topic Maps applied to PubMed, Extreme’07, August 200727 New architecture Metamorphosis Extracting the base ontology Qresults intersection Semantic Browser

28. Topic Maps applied to PubMed, Extreme’07, August 200728 One of the advantages of this approach is that no new database is created and no redundant data is produced; Information is interconnected within a huge knowledge network navigable in any direction.

29. Topic Maps applied to PubMed, Extreme’07, August 200729 Future work Integration of Topic Maps and MeSH headings Minimizing “false hits” and saving time Identifying other useful – but frequently overlooked – features of the PubMed database.

30. Topic Maps applied to PubMed, Extreme’07, August 200730 MeSH Medical Subject Headings (MeSH) is a controlled vocabulary designed by the National Library of Medicine to search MEDLINE and other health sciences databases

31. Topic Maps applied to PubMed, Extreme’07, August 200731 MeSH example by Wikipedia

32. Topic Maps applied to PubMed, Extreme’07, August 200732 MeSH qualifiers In addition to the descriptor hierarchy, MeSH contains a small number of standard qualifiers (also known as subheadings), which can be added to descriptors to narrow down the topic.

33. Topic Maps applied to PubMed, Extreme’07, August 200733 MeSH qualifiers example For example, "Measles" is a descriptor and "epidemiology" is a qualifier; "Measles/epidemiology" describes the subheading of epidemiological articles about Measles. The "epidemiology" qualifier can be added to all other disease descriptors. Not all descriptor/qualifier combinations are allowed since some of them may be meaningless. In all there are 83 different qualifiers

34. Topic Maps applied to PubMed, Extreme’07, August 200734 Conclusion This paper described the integration of data from PubMed information system using the ontology paradigm, in order to generate an homogeneous view of this resources. The proposal uses an environment, called Metamorphosis, for the automatic construction of Topic Maps with data extracted from the various data sources, and a semantic browser to navigate among the information resources.

35. Topic Maps applied to PubMed, Extreme’07, August 200735 Questions? Short announcement: XATA2008: Portuguese XML conference, Feb. 2008 Becoming international English will be the language We are seeking people for PC commitee...