Exploration, sharing and privacy of data

1. Exploration, sharing and privacy
of data
Linked Data – challenges for Imagiology and Radiology
Francisco Couto
Ciências ULisboa
FISMED 2017 – 6 Nov 2017

3. Images
Text
Data
Linked Data

4. Linked Data
Spouse
Daughter

5. Application
• Similar medical images?
• Computer-assisted image processing
• Related medical images ?
• Which are not necessarily similar
• Linked Data

6. Example
Discover new drugs to treat Alzheimer’s
what proteins are involved in signal transduction
and
are related to pyramidal neurons?
Tim Berners-Lee’s Linked Data slides, from TED 2009
best known as the inventor of the World Wide Web
http://www.ted.com/talks/tim_berners_lee_on_the_next_web.html

7. Many hits but no relevant results

8. Linked healthcare data
32 hits, 32 results

9. LINKED DATA

10. Definition
The term Linked Data refers to a set of best
practices for publishing and connecting
structured data on the Web using international
standards of the World Wide Web Consortium

11. Wikipedia
• Infopages
• box in the upper right of the page
• names, dates, places
• DBpedia project
• extracts this structured data
• publish as Linked Data
http://dbpedia.org

13. Topic Datasets %
Government 183 18.05%
Publications 96 9.47%
Life Sciences 83 8.19%
User-generated content 48 4.73%
Cross-domain 41 4.04%
Media 22 2.17%
Geographic 21 2.07%
Social Web 520 51.28%
Total 1014
State of the LOD Cloud 2014

14. Important properties
• easily combined with other Linked Data
• best reason to explore and use Linked Data
• Important for data sharing
• self-documenting
• immediately figure out what a term means
• Linked Data can be private
• widely deployed behind enterprise firewalls on
private networks

15. Linked Data from Forms
• Manual human annotation like in wikipedia
• only works with a wide set of users
• Selecting the right terms is non-trivial
• takes time
• requires knowledge
• Common problems
• missing values
• too generic to be useful
B. Inácio, J. Ferreira, and F. Couto, Metadata analyser: measuring metadata quality, in Practical Applications
of Computational Biology and Bioinformatics (PACBB), pp. 197-204, 2017

16. Alternatives for Imagiology
• Explore the written reports
• Text mining approaches
• Use a specialized terminology (RadLex)
• multilingual approaches
• Sharing and privacy
• Not images only the metadata
• Still there are privacy concerns

17. Imagiology Written Reports
• written in free-text
• well structured
• more than any other clinical notes
• since the information has to pass from one health
care professional to another

18. Text Mining Tools
• Dictionary-based
• only requires a common terminology
• limited to that terminology
• ambiguity of terms
• Machine Learning
• requires a trainning set
• not limited to a terminology
• learns with experience

19. RadLex
• RSNA has produced RadLex(R)
• ontology focused on radiology
• terms (i.e. a lexicon) and the relationships
• over 75,000 terms and synonyms
https://www.rsna.org/RadLex.aspx

20. WHY USING A COMMON
TERMINOLOGY?

21. Cell

22. 22
London Bills of Mortality
listed possible ways to die throughout the
sixteenth, seventeenth and eighteenth centuries
Source: http://faculty.up.edu/asarnow/popular7.htm

23. 23
Aggregated Stats

24. <?xml version="1.0"?>
<rdf:RDF
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:dc= "http://purl.org/dc/elements/1.1/">
<rdf:Description rdf:about="http://en.wikipedia.org/wiki/Sintra_Collar">
<dc:description>
Gold collar. It was made from three circular sectioned and tapering gold bars that are
fused at the ends forming a penannular neck-ring.
</dc:description>
<dc:date>1250BC-800BC (circa)</dc:date>
<dc:location>
Sintra, Portugal
</dc:location>
<dc:type>
Gold
</dc:type>
</rdf:Description>
</rdf:RDF>

25. <?xml version="1.0"?>
<rdf:RDF
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:dc= "http://purl.org/dc/elements/1.1/">
<rdf:Description rdf:about="http://en.wikipedia.org/wiki/Sintra_Collar">
<dc:description>
Gold collar. It was made from three circular sectioned and tapering gold bars that are
fused at the ends forming a penannular neck-ring.
</dc:description>
<dc:date>1250BC-800BC (circa)</dc:date>
<dc:location>
Sintra, Portugal
http://yboss.yahooapis.com/geo/placefinder?woeid=748874
</dc:location>
<dc:type>
Gold
http://purl.obolibrary.org/obo/CHEBI_30050
</dc:type>
</rdf:Description>
</rdf:RDF>

26. Metal
Silver
CoinagePrecious
Palladium GoldPlatinum Copper
is-a
mappings

27. Example
• MER
• Minimal Entity Recognizer
http://labs.fc.ul.pt/mer/
Couto, F. M., Campos, L., & Lamurias, A. MER: a minimal named-entity recognition tagger and
annotation server. Proceedings of the BioCreative, 2017
• DiShIn
• Semantic Similarity Measures using Disjunctive
Shared Information
http://labs.fc.ul.pt/dishin/
F. Couto and M. Silva, Disjunctive shared information between ontology concepts: application to Gene
Ontology, Journal of Biomedical Semantics, vol. 2, no. 5, pp. 1-16, 2011

32. Language
 Usually written in the native language
 Text Mining tools mostly developed for
English
 RadLex is currently only available in English
 German and Portuguese translations of RadLex
are currently in development
 Obstacle in the sharing information

33. Two approaches
1) Translate the lexicon itself
• new version of lexicon requires translation
2) Translate the reports
• efficient automatic translation services nowadays
available
• state-of-the-art Text Mining tools tuned for English

34. Multilingual Reports
• reports accessible to any doctor
• who understands English
• tourists access their reports in their language
• send them to their personal doctor at home
• hospital can get a highly specialized second
opinion
• in complex clinical cases from international
experts

35. Translation Efficiency
• 51 Research Articles related to Radiology
• originally written in Portuguese
• a human translation in English was available
• We measured NER accuracy
• using Yandex, Google and Unbabel
L. Campos, V. Pedro, and F. Couto, Impact of translation on named-entity recognition in radiology texts,
Database, vol. 2017, no. bax064, pp. 1-9, 2017

37. Multilingual System Prototype
• Given a report
• Automatically translates the report
• Find the most similar reports
• According to most similar RadLex terms

41. PRIVACY

42. Privacy in Imagiology
• Like sharing photos
• After being in the web stays in the web
• An issue can be passed from family to family
• Encrypt data
• If important is a question of time
• Cloud storage
• Is it secure?
• Split through different providers.

43. Privacy in linked data
• You can share metadata without sharing really
privacy sensitive information
• show what kind of images are available
• You control which person to give that data
• using a secure channel
M. Fernandes, J. Decouchant, F. Couto, and P. Verissimo, Cloud-assisted read alignment and privacy, in
Practical Applications of Computational Biology and Bioinformatics (PACBB), pp. 220-227, 2017

44. Final Remarks (1)
• Linked Data is not free or open data
• is not sound data
• it can have access restrictions
• be incomplete and have errors
• But many successful use cases in the Life and
Health Sciences
M. Barros and F. Couto, Knowledge representation and management: a linked data perspective, IMIA
Yearbook of Medical Informatics, pp. 178-183, 2016

45. Final Remarks (2)
• go beyond technological advances
• create motivation mechanisms
• encourage data owners to share their data
• in a meaningful way
• Science is about replication
• without access to data there is no replication

46. Thanks!
Current Team:
• André Lamúrias
and Tânia Maldonado (Text Mining)
• Gonçalo Figueiró (MRIR)
• Maria Fernandes
and Mariana Pinhão (Genomic Privacy)
Publications & Tools
• http://labs.fc.ul.pt/
• http://webpages.fc.ul.pt/~fjcouto/?page_id=100