Organizing Knowledge in a Semantic Web for Pathology

  title={Organizing Knowledge in a Semantic Web for Pathology},
  author={Robert Tolksdorf and Elena Paslaru Bontas Simperl},
Digital pathology and telepathology allow for the extended usage of electronic images for diagnostics, support or educational purposes in anatomical or clinical pathology. Current approaches have not found wide acceptance in routine pathology, mainly due to limitations in image retrieval. In this paper we propose a semantic retrieval system for the pathology domain. The system combines text and image information and offers advanced content-based retrieval services for diagnosis, differential… 
Experiences Using Semantic Web Technologies to Realize an Information Retrieval System for Pathology
This paper focuses on problems and experiences gained in the project ”A Semantic Web for Pathology”, a research project using domain ontologies and ontology-driven natural language processing to support a content-based storage and retrieval for text and image-based medical information.
Generation and Management of a Medical Ontology in a Semantic Web Retrieval System
This paper describes the generation, maintenance and evolution of aSemantic Web-based ontology in the context of an information system for pathology that combines Semantic Web and NLP techniques to support a content-based storage and retrieval of medical reports and digital images.
Practical Experiences in Building Ontology-based Retrieval Systems
This paper describes practical experiences and lessons learned in the project “A Semantic Web for Pathology”, a project using domain ontologies and ontology-driven natural language processing to
Creating Ontologies for Content Representation-The OntoSeed Suite
This paper presents an NLP-based method to aid ontology design in a specific setting, namely that of semantic annotation of text, and suggests ways to specify domain ontologies in a “linguistics-friendly” format in order to improve further ontology-based natural language processing tasks such as semantic annotation.
BioSEME: A Semantically-Integrated Content Management System for Cancer Research
In this project, we propose a paradigm shift from the use of relational databases and traditional web publishing tools to a Semantically-Integrated Research Content Management System augmented with
Ontology Engineering for the Semantic Annotation of Medical Data
A method to construct a semantic Web-based medical ontology is described, which is used for the semantic annotation of medical reports, and the engineering process is evaluated against a reuse-oriented approach.
Semantic Interoperability in the BRITE Project: Ontologies as a Tool for Collaboration, Cooperation and Knowledge Management
The paper defines the inter-relation among these components of BRITE, focuses on the domain ontology functionalities, and concludes with a critical reflection and valuable lessons learnt.


Feeding OWL: Extracting and Representing the Content of Pathology Reports
An ongoing project that combines NLP with semantic web technologies to support a content-based storage and retrieval of medical pathology reports provides a good example of how NLP techniques can be used to populate the Semantic Web.
Navigation in medical Internet image databases
  • T. Prokosch
  • Computer Science
    Medical informatics and the Internet in medicine
  • 2001
The techniques of navigation within WWW-databases and the semantic types of their queries have been analysed and UMLS especially shows that a well defined thesaurus can improve navigation.
Using the UMLS Semantic Network as a basis for constructing a terminological knowledge base: a preliminary report.
The preliminary results of the attempt to reuse the UMLS Semantic Network as an ontology for the knowledge base of a patient education system are described.
Pathfinder: multiresolution region-based searching of pathology images using IRM
The fast growth of digitized pathology slides has created great challenges in research on image database retrieval. The prevalent retrieval technique involves human-supplied text annotations to
Knowledge engineering the UMLS.
A four-step knowledge engineering approach to transform a major portion of the Unified Medical Language System into a formally sound description logics system and reports on experiments with a Loom knowledge base which consists of 164,000 concepts and 76,000 relations covering human anatomy and pathology.
Mapping the UMLS Semantic Network into general ontologies
In this study, we analyzed the compatibility between an ontology of the biomedical domain (the UMLS Semantic Network) and two other ontologies: the Upper Cyc Ontology (UCO) and WordNet. 1) We
Research Paper: PathMaster: Content-based Cell Image Retrieval Using Automated Feature Extraction
A method for automatically indexing images of individual cells and their associated diagnoses by computationally derived cell descriptors may serve to better index data contained in digital image databases, thereby enabling cytologists and pathologists to cross-reference cells of unknown etiology or nature.
Representing the UMLS as an OODB: Modeling Issues and Advantages
This work presents a representation to support the comprehension and navigation of the UMLS, the Metathesaurus and the Semantic Network, as a uniied system, and presents examples of how the intersection classes help expose omissions of concepts, highlight errors of semantic type classiication, and uncover ambiguities of concepts in the U MLS.