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Semantic integration of cervical cancer data repositories to facilitate multicenter association studies: the ASSIST approach.

Agorastos T, Koutkias V, Falelakis M, Lekka I, Mikos T, Delopoulos A, Mitkas PA, Tantsis A, Weyers S, Coorevits P, Kaufmann AM, Kurzeja R, Maglaveras N - Cancer Inform (2009)

Bottom Line: The project aims to facilitate the research for cervical precancer and cancer through a system that virtually unifies multiple patient record repositories, physically located in different medical centers/hospitals, thus, increasing flexibility by allowing the formation of study groups "on demand" and by recycling patient records in new studies.The current paper presents the knowledge elicitation approach followed, towards the definition and representation of the disease's medical concepts and rules that constitute the basis for the ASSIST Cervical Cancer Ontology.The proposed approach constitutes a paradigm for semantic integration of heterogeneous clinical data that may be applicable to other biomedical application domains.

View Article: PubMed Central - PubMed

Affiliation: Department of Obstetrics and Gynecology, Papageorgiou General Hospital, Aristotle University of Thessaloniki, Greece.

ABSTRACT
The current work addresses the unification of Electronic Health Records related to cervical cancer into a single medical knowledge source, in the context of the EU-funded ASSIST research project. The project aims to facilitate the research for cervical precancer and cancer through a system that virtually unifies multiple patient record repositories, physically located in different medical centers/hospitals, thus, increasing flexibility by allowing the formation of study groups "on demand" and by recycling patient records in new studies. To this end, ASSIST uses semantic technologies to translate all medical entities (such as patient examination results, history, habits, genetic profile) and represent them in a common form, encoded in the ASSIST Cervical Cancer Ontology. The current paper presents the knowledge elicitation approach followed, towards the definition and representation of the disease's medical concepts and rules that constitute the basis for the ASSIST Cervical Cancer Ontology. The proposed approach constitutes a paradigm for semantic integration of heterogeneous clinical data that may be applicable to other biomedical application domains.

No MeSH data available.


Related in: MedlinePlus

Viewing the distribution of MTHFR genotypes in patients with different cytology results: In the current example, the user has selected all patients with data for the MTHFR polymorphism. Then, he/she has selected to view the MTHFR distribution of the three MTHFR genotypes in patients with different cytology results. A preview of the current query is shown on the top of the page. The cytology results are expressed with the unified ASSIST cytology coding. As shown on the top of the screen, from the total of 2,032 patients the requested type of information exists for 975 patients.
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f6-cin-08-31: Viewing the distribution of MTHFR genotypes in patients with different cytology results: In the current example, the user has selected all patients with data for the MTHFR polymorphism. Then, he/she has selected to view the MTHFR distribution of the three MTHFR genotypes in patients with different cytology results. A preview of the current query is shown on the top of the page. The cytology results are expressed with the unified ASSIST cytology coding. As shown on the top of the screen, from the total of 2,032 patients the requested type of information exists for 975 patients.

Mentions: The user can express the severity of the disease through the results of cytology or colposcopy or histology or any combination of those. The results of those exams are expressed through the unified ASSIST coding. Using combined queries, the researcher asks for patients with genotypic data for the MTHFR polymorphism and for whom the staging of precancerous lesions is expressed through cytological results coded in the ASSIST unified cytology coding (Fig. 6). The graphical representation of the results indicates that the distribution of the MTHFR genotypes is different in the three stages of the disease. The user can continue with more queries involving additional patient parameters and further statistical tests on the extracted dataset. ASSIST offers a user friendly environment to express queries in a “language” easily understandable by the medical researcher and to also retrieve patient records that may use different internal coding schemes.


Semantic integration of cervical cancer data repositories to facilitate multicenter association studies: the ASSIST approach.

Agorastos T, Koutkias V, Falelakis M, Lekka I, Mikos T, Delopoulos A, Mitkas PA, Tantsis A, Weyers S, Coorevits P, Kaufmann AM, Kurzeja R, Maglaveras N - Cancer Inform (2009)

Viewing the distribution of MTHFR genotypes in patients with different cytology results: In the current example, the user has selected all patients with data for the MTHFR polymorphism. Then, he/she has selected to view the MTHFR distribution of the three MTHFR genotypes in patients with different cytology results. A preview of the current query is shown on the top of the page. The cytology results are expressed with the unified ASSIST cytology coding. As shown on the top of the screen, from the total of 2,032 patients the requested type of information exists for 975 patients.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC2664695&req=5

f6-cin-08-31: Viewing the distribution of MTHFR genotypes in patients with different cytology results: In the current example, the user has selected all patients with data for the MTHFR polymorphism. Then, he/she has selected to view the MTHFR distribution of the three MTHFR genotypes in patients with different cytology results. A preview of the current query is shown on the top of the page. The cytology results are expressed with the unified ASSIST cytology coding. As shown on the top of the screen, from the total of 2,032 patients the requested type of information exists for 975 patients.
Mentions: The user can express the severity of the disease through the results of cytology or colposcopy or histology or any combination of those. The results of those exams are expressed through the unified ASSIST coding. Using combined queries, the researcher asks for patients with genotypic data for the MTHFR polymorphism and for whom the staging of precancerous lesions is expressed through cytological results coded in the ASSIST unified cytology coding (Fig. 6). The graphical representation of the results indicates that the distribution of the MTHFR genotypes is different in the three stages of the disease. The user can continue with more queries involving additional patient parameters and further statistical tests on the extracted dataset. ASSIST offers a user friendly environment to express queries in a “language” easily understandable by the medical researcher and to also retrieve patient records that may use different internal coding schemes.

Bottom Line: The project aims to facilitate the research for cervical precancer and cancer through a system that virtually unifies multiple patient record repositories, physically located in different medical centers/hospitals, thus, increasing flexibility by allowing the formation of study groups "on demand" and by recycling patient records in new studies.The current paper presents the knowledge elicitation approach followed, towards the definition and representation of the disease's medical concepts and rules that constitute the basis for the ASSIST Cervical Cancer Ontology.The proposed approach constitutes a paradigm for semantic integration of heterogeneous clinical data that may be applicable to other biomedical application domains.

View Article: PubMed Central - PubMed

Affiliation: Department of Obstetrics and Gynecology, Papageorgiou General Hospital, Aristotle University of Thessaloniki, Greece.

ABSTRACT
The current work addresses the unification of Electronic Health Records related to cervical cancer into a single medical knowledge source, in the context of the EU-funded ASSIST research project. The project aims to facilitate the research for cervical precancer and cancer through a system that virtually unifies multiple patient record repositories, physically located in different medical centers/hospitals, thus, increasing flexibility by allowing the formation of study groups "on demand" and by recycling patient records in new studies. To this end, ASSIST uses semantic technologies to translate all medical entities (such as patient examination results, history, habits, genetic profile) and represent them in a common form, encoded in the ASSIST Cervical Cancer Ontology. The current paper presents the knowledge elicitation approach followed, towards the definition and representation of the disease's medical concepts and rules that constitute the basis for the ASSIST Cervical Cancer Ontology. The proposed approach constitutes a paradigm for semantic integration of heterogeneous clinical data that may be applicable to other biomedical application domains.

No MeSH data available.


Related in: MedlinePlus