A cascaded approach to normalising gene mentions in biomedical literature

Linking gene and protein names mentioned in the literature to unique identifiers in referent genomic databases is an essential step in accessing and integrating knowledge in the biomedical domain. However, it remains a challenging task due to lexical and terminological variation, and ambiguity of gene name mentions in documents. We present a generic and effective rule-based approach to link gene mentions in the literature to referent genomic databases, where pre-processing of both gene synonyms in the databases and gene mentions in text are first applied. The mapping method employs a cascaded approach, which combines exact, exact-like and token-based approximate matching by using flexible representations of a gene synonym dictionary and gene mentions generated during the pre-processing phase. We also consider multi-gene name mentions and permutation of components in gene names. A systematic evaluation of the suggested methods has identified steps that are beneficial for improving either precision or recall in gene name identification. The results of the experiments on the BioCreAtIvE2 data sets (identification of human gene names) demonstrated that our methods achieved highly encouraging results with F-measure of up to 81.20%

Computerization of workflows, guidelines and care pathways: a review of implementation challenges for process-oriented health information systems

There is a need to integrate the various theoretical frameworks and formalisms for modeling clinical guidelines, workflows, and pathways, in order to move beyond providing support for individual clinical decisions and toward the provision of process-oriented, patient-centered, health information systems (HIS). In this review, we analyze the challenges in developing process-oriented HIS that formally model guidelines, workflows, and care pathways. A qualitative meta-synthesis was performed on studies published in English between 1995 and 2010 that addressed the modeling process and reported the exposition of a new methodology, model, system implementation, or system architecture. Thematic analysis, principal component analysis (PCA) and data visualisation techniques were used to identify and cluster the underlying implementation ‘challenge’ themes. One hundred and eight relevant studies were selected for review. Twenty-five underlying ‘challenge’ themes were identified. These were clustered into 10 distinct groups, from which a conceptual model of the implementation process was developed. We found that the development of systems supporting individual clinical decisions is evolving toward the implementation of adaptable care pathways on the semantic web, incorporating formal, clinical, and organizational ontologies, and the use of workflow management systems. These architectures now need to be implemented and evaluated on a wider scale within clinical settings

Utilizing RxNorm to Support Practical Computing Applications: Capturing Medication History in Live Electronic Health Records

RxNorm was utilized as the basis for direct-capture of medication history data in a live EHR system deployed in a large, multi-state outpatient behavioral healthcare provider in the United States serving over 75,000 distinct patients each year across 130 clinical locations. This tool incorporated auto-complete search functionality for medications and proper dosage identification assistance. The overarching goal was to understand if and how standardized terminologies like RxNorm can be used to support practical computing applications in live EHR systems. We describe the stages of implementation, approaches used to adapt RxNorm's data structure for the intended EHR application, and the challenges faced. We evaluate the implementation using a four-factor framework addressing flexibility, speed, data integrity, and medication coverage. RxNorm proved to be functional for the intended application, given appropriate adaptations to address high-speed input/output (I/O) requirements of a live EHR and the flexibility required for data entry in multiple potential clinical scenarios. Future research around search optimization for medication entry, user profiling, and linking RxNorm to drug classification schemes holds great potential for improving the user experience and utility of medication data in EHRs.Comment: Appendix (including SQL/DDL Code) available by author request. Keywords: RxNorm; Electronic Health Record; Medication History; Interoperability; Unified Medical Language System; Search Optimizatio

Enriching ontological user profiles with tagging history for multi-domain recommendations

Many advanced recommendation frameworks employ ontologies of various complexities to model individuals and items, providing a mechanism for the expression of user interests and the representation of item attributes. As a result, complex matching techniques can be applied to support individuals in the discovery of items according to explicit and implicit user preferences. Recently, the rapid adoption of Web2.0, and the proliferation of social networking sites, has resulted in more and more users providing an increasing amount of information about themselves that could be exploited for recommendation purposes. However, the unification of personal information with ontologies using the contemporary knowledge representation methods often associated with Web2.0 applications, such as community tagging, is a non-trivial task. In this paper, we propose a method for the unification of tags with ontologies by grounding tags to a shared representation in the form of Wordnet and Wikipedia. We incorporate individuals' tagging history into their ontological profiles by matching tags with ontology concepts. This approach is preliminary evaluated by extending an existing news recommendation system with user tagging histories harvested from popular social networking sites

Interchanging lexical resources on the Semantic Web

Lexica and terminology databases play a vital role in many NLP applications, but currently most such resources are published in application-specific formats, or with custom access interfaces, leading to the problem that much of this data is in ‘‘data silos’’ and hence difficult to access. The Semantic Web and in particular the Linked Data initiative provide effective solutions to this problem, as well as possibilities for data reuse by inter-lexicon linking, and incorporation of data categories by dereferencable URIs. The Semantic Web focuses on the use of ontologies to describe semantics on the Web, but currently there is no standard for providing complex lexical information for such ontologies and for describing the relationship between the lexicon and the ontology. We present our model, lemon, which aims to address these gap

Designing interoperable museum information systems

Museum collections are characterized by heterogeneity, since they usually host a plethora of objects of categories, while each of them requires different description policies and metadata standards. Moreover the museum records, which keep the history and evolution of the hosted collections, request proactive curation in order to preserve this rich and diverse information. In this paper, the architecture of an innovative museum information system, as well as its implementation details is presented. In particular the requirements and the system architecture are presented along with the problems that were encountered. The main directions of the system design are (a) to increase interoperability levels and therefore assist proactive curation and (b) to enhance navigation by the usage of handheld devices. The first direction is satisfied by the design of a rich metadata schema based on the CIDOC/CRM standard. The second direction is fulfilled by the implementation of a module, which integrates the museum database with a subsystem appropriate to support user navigation into the museum floors and rooms. The module is expressed as a navigation functionality, which is accessed through handheld devices and peripherals, such as PDAs and RFID tags. The proposed system is functional and operates into the Solomos Museum, situated in Zakynthos island, Greece