An ontology driven module                for accessing chronic                 pathology literature                       ...
Motivation, problem area      Chronic diseases are the leading causes of death and disability          for a large amount...
Motivation, problem area             New monitoring and treatment of chronic                  patients are becoming possi...
Context: the Project    An Open, Ubiquitous and Adaptive Chronic Disease Management    Platform for Chronic Obstructive Pu...
Context: The CHRONIOUS                            project20 October 2011           SWWS-OTM2011   Copyright 2011 CHRONIOUS...
Literature search module:                      design requirements      Using explicit medical terminology (e.g., control...
The developedsystem                  Document                   upload                  Automatic                  Upload ...
Terminology to index scientific                   literature                                          COPD, CKD Ontologies...
The adopted approach         RDF URI as a kind of lingua franca          MeSH (provided by the US medical library) has be...
Natural Language Processing                 Based on General Architecture for Text Engineering (GATE) framework          ...
Ontology enrichment    Semi-automatic process - candidate concepts are rated according to       Corpus relevance:determin...
Tool – Relevance                        details20 October 2011         SWWS-OTM2011   Copyright 2011 CHRONIOUS -- IMATI-CNR
Search Interface20 October 2011         SWWS-OTM2011   Copyright 2011 CHRONIOUS -- IMATI-CNR
Search results:           (black Box Testing) intial           comparison with PubMed                                     ...
Conclusions        The CHRONIOUS search system can become a specialized        indexing and search system for the hospital...
Critical and open issues                          for future work        User notifications                  • about chang...
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An ontology driven module for accessing chronic pathology literature- CHRONIOUS-Swws2011

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  • In this respect, the European community has funded the Chronious project, which include an European wide consortium (14 partners) aims at developing a …
  • An ontology driven module for accessing chronic pathology literature- CHRONIOUS-Swws2011

    1. 1. An ontology driven module for accessing chronic pathology literature Riccardo Albertoni, Institute for Applied Mathematics and Information Technology C.N.R., Genova, Italy Joint work with Stephan Kiefer, Jochen Rauch, Marco Attene, Franca Giannini, Simone Marini, Luc Schneider, Carlos Mesquita, Xin Xing20 October 2011 SWWS-OTM2011 Copyright 2011 CHRONIOUS -- IMATI-CNR
    2. 2. Motivation, problem area  Chronic diseases are the leading causes of death and disability for a large amount of people in most industrialized nations.  Chronic diseases have a deep impact on today’s society costs: 1. Costs of medical care in relation to diagnosis and treatment of disease 2. Loss of human resources caused by morbidity or premature death 3. Intangible costs capture the psychological dimensions of illness including pain and anxiety New technologies for acquiring and analyzing vital signals are arising20 October 2011 SWWS-OTM2011 Copyright 2011 CHRONIOUS -- IMATI-CNR
    3. 3. Motivation, problem area  New monitoring and treatment of chronic patients are becoming possible  No already existent guidelines are available  Knowledge in the domain is rapidly evolving Need of tools for indexing and retrieving well focused documentation accordingly to continuously evolving knowledge20 October 2011 SWWS-OTM2011 Copyright 2011 CHRONIOUS -- IMATI-CNR
    4. 4. Context: the Project An Open, Ubiquitous and Adaptive Chronic Disease Management Platform for Chronic Obstructive Pulmonary Disease (COPD) and Chronic Kidney disease (CKD), FP7-ICT-2007–1– 216461 CHRONIOUS, February 2008 – January 2012 (48 months) http://www.chronious.eu/20 October 2011 SWWS-OTM2011 Copyright 2011 CHRONIOUS -- IMATI-CNR
    5. 5. Context: The CHRONIOUS project20 October 2011 SWWS-OTM2011 Copyright 2011 CHRONIOUS -- IMATI-CNR
    6. 6. Literature search module: design requirements  Using explicit medical terminology (e.g., controlled vocabularies)  Specific to the considered pathologies, but also terminology allowing different levels of granularity in search (searching by coarse- and fine- grained concepts)  Terminology as much as possible Modular and Extendable  CKD and COPD are a kind of test-bed for Chronious, but other chronic diseases should be pluggable eventually  Knowledge in these domains evolves, so do related terminologies! we should support in keeping terminologies up-to-date  Offering multilingual capabilities  Search must be possible in different languages, at least when well established translations of terminologies are available20 October 2011 SWWS-OTM2011 Copyright 2011 CHRONIOUS -- IMATI-CNR
    7. 7. The developedsystem Document upload Automatic Upload tool Document processing Manual Format NLP Concept upload tool Transformation Associator CKD COPD MeSH Ontology ontology thesaurus OWL/RDF SKOS/RDF enrichment tool mapping API Indexer Document Search Conceptual search Metadata search Free Text search NLP20 October 2011 SWWS-OTM2011 Copyright 2011 CHRONIOUS -- IMATI-CNR
    8. 8. Terminology to index scientific literature COPD, CKD Ontologies  Medical Subject Headings (MeSH) is a well known controlled vocabulary used for indexing articles Layer Ontology for Clinical Care (MLOCC) Middle from MEDLINE/PubMed  it isn’t enough specialized to deeply cover COPD and CKD domains  Ontologies have been defined to deepen COPDBiological and Biomedicalby Open and CKD diseases (OWL IFOMIS) Ontology (OBO) Foundry: Basic Formal Ontology (BFO) +  However MeSH is still required in Chronious Relation Ontology (RO) + Foundational Model  The search is not always made at the same level of granularity, often keyword search can be done moving back and forwardof Anatomy Ontology (FMA) from coarse to very disease- specialized concepts  Multilingual support, some “certified” translations are available for example in Italian, Portuguese, Spanish  Terminological de facto standard, clinicians expect MeSH is included  How to combine ontologies and MeSH in CHRONIOUS ?20 October 2011 SWWS-OTM2011 Copyright 2011 CHRONIOUS -- IMATI-CNR
    9. 9. The adopted approach RDF URI as a kind of lingua franca  MeSH (provided by the US medical library) has been encoded in SKOS/RDF (W3C)  Italian, Portuguese and Spanish translations of MeSH (provided by national authorities) have been encoded in SKOS/RDF  We kept RDF ID consistent to the original MESH descriptor identifiers  A semi-automatic mapping between MeSH in SKOS and developed Ontologies  A script compares MeSH terms with lexical representation of concepts form OWL ontologies  The suggested mapping are validated in two stages-process by Ontology Engineers and Clinicians20 October 2011 SWWS-OTM2011 Copyright 2011 CHRONIOUS -- IMATI-CNR
    10. 10. Natural Language Processing  Based on General Architecture for Text Engineering (GATE) framework  Open Source, JAVA suite, originally developed at the University of Sheffield beginning in 1995  used worldwide by a wide community of scientists, companies, teachers and students for all sorts of natural language processing tasks, including information extraction in many languages  Default processes applied to extract headwords of a text:  Sentence splitter, Tokeniser, Part-of-speech tagger, Morphological analyzer  Modules included for the Ontology Enrichment Tool and the Indexer  OntoRootGazetteer: A GATE plug-in that produces ontology aware annotations for extracted terms;  Shallow Parser: it identifies word groups such as “chronic diseases” and “lung function”;  RegEx-Pattern Matcher: it matches a lemma of a token with word patterns defined as regular expression;  Thesaurus Matcher: it matches the lemma of a token to a domain thesaurus, a JAPE resources has been developed to access MEsH and the mapped ontology concepts through MeSH Mapping API20 October 2011 SWWS-OTM2011 Copyright 2011 CHRONIOUS -- IMATI-CNR
    11. 11. Ontology enrichment Semi-automatic process - candidate concepts are rated according to  Corpus relevance:determined by its average Term Frequency Inverted Document Frequency (TF.IDF) value with respect to the whole document corpus;  Concept co-occurrences average distance in the text between the candidate concept and a concept within the corpus is calculated as a benchmark.  Domain relevance: matching with common dictionary (WordNet), domain thesaurus (MeSH) and with regular expression patterns;  Subclass-of relations: extraction of vertical relations, linguistic patterns or dictionary hypernyms.  Candidateconcepts are marked as “new”, “to validate”, “postponed”,20 October 2011 “accepted” or “rejected” by ontology engineers and clinicians SWWS-OTM2011 Copyright 2011 CHRONIOUS -- IMATI-CNR
    12. 12. Tool – Relevance details20 October 2011 SWWS-OTM2011 Copyright 2011 CHRONIOUS -- IMATI-CNR
    13. 13. Search Interface20 October 2011 SWWS-OTM2011 Copyright 2011 CHRONIOUS -- IMATI-CNR
    14. 14. Search results: (black Box Testing) intial comparison with PubMed “Inhaler Device” “Inhaler device” “PostBronchodilatorSpirometryHorizontal axis: Number of considered/retrieved documentsVertical axis: F-measureAlso glass box testing has been performed to ensure ontologiesrepresent therightconcepts20 October 2011 SWWS-OTM2011 Copyright 2011 CHRONIOUS -- IMATI-CNR
    15. 15. Conclusions The CHRONIOUS search system can become a specialized indexing and search system for the hospital:  It can manage internal hospital documents to be indexed into the database  It can cover other medical domains and languages using MeSH  It is already specialized in COPD and CKD by using specific ontologies  It provides the tools for ontology maintenance thus well suited to domains characterized by rapidly evolving knowledge20 October 2011 SWWS-OTM2011 Copyright 2011 CHRONIOUS -- IMATI-CNR
    16. 16. Critical and open issues for future work User notifications • about changes in Enrichment Tool data (e.g. if new documents with extracted candidate concepts are available) •supporting the collaboration among clinicians and Ontology Engineers Re-indexing of documents •what happens when there is a new ontology version? • some incremental indexing should be provided20 October 2011 SWWS-OTM2011 Copyright 2011 CHRONIOUS -- IMATI-CNR

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