Information Extraction, Data Integration, and Uncertain Data Management: The State of The Art

Information Extraction, data Integration, and uncertain data management are different areas of research that got vast focus in the last two decades. Many researches tackled those areas of research individually. However, information extraction systems should have integrated with data integration methods to make use of the extracted information. Handling uncertainty in extraction and integration process is an important issue to enhance the quality of the data in such integrated systems. This article presents the state of the art of the mentioned areas of research and shows the common grounds and how to integrate information extraction and data integration under uncertainty management cover

Conceptual biology, hypothesis discovery, and text mining: Swanson's legacy

Innovative biomedical librarians and information specialists who want to expand their roles as expert searchers need to know about profound changes in biology and parallel trends in text mining. In recent years, conceptual biology has emerged as a complement to empirical biology. This is partly in response to the availability of massive digital resources such as the network of databases for molecular biologists at the National Center for Biotechnology Information. Developments in text mining and hypothesis discovery systems based on the early work of Swanson, a mathematician and information scientist, are coincident with the emergence of conceptual biology. Very little has been written to introduce biomedical digital librarians to these new trends. In this paper, background for data and text mining, as well as for knowledge discovery in databases (KDD) and in text (KDT) is presented, then a brief review of Swanson's ideas, followed by a discussion of recent approaches to hypothesis discovery and testing. 'Testing' in the context of text mining involves partially automated methods for finding evidence in the literature to support hypothetical relationships. Concluding remarks follow regarding (a) the limits of current strategies for evaluation of hypothesis discovery systems and (b) the role of literature-based discovery in concert with empirical research. Report of an informatics-driven literature review for biomarkers of systemic lupus erythematosus is mentioned. Swanson's vision of the hidden value in the literature of science and, by extension, in biomedical digital databases, is still remarkably generative for information scientists, biologists, and physicians. © 2006Bekhuis; licensee BioMed Central Ltd

Improving Term Extraction with Terminological Resources

Studies of different term extractors on a corpus of the biomedical domain revealed decreasing performances when applied to highly technical texts. The difficulty or impossibility of customising them to new domains is an additional limitation. In this paper, we propose to use external terminologies to influence generic linguistic data in order to augment the quality of the extraction. The tool we implemented exploits testified terms at different steps of the process: chunking, parsing and extraction of term candidates. Experiments reported here show that, using this method, more term candidates can be acquired with a higher level of reliability. We further describe the extraction process involving endogenous disambiguation implemented in the term extractor YaTeA

The Partial Evaluation Approach to Information Personalization

Information personalization refers to the automatic adjustment of information content, structure, and presentation tailored to an individual user. By reducing information overload and customizing information access, personalization systems have emerged as an important segment of the Internet economy. This paper presents a systematic modeling methodology - PIPE (`Personalization is Partial Evaluation') - for personalization. Personalization systems are designed and implemented in PIPE by modeling an information-seeking interaction in a programmatic representation. The representation supports the description of information-seeking activities as partial information and their subsequent realization by partial evaluation, a technique for specializing programs. We describe the modeling methodology at a conceptual level and outline representational choices. We present two application case studies that use PIPE for personalizing web sites and describe how PIPE suggests a novel evaluation criterion for information system designs. Finally, we mention several fundamental implications of adopting the PIPE model for personalization and when it is (and is not) applicable.Comment: Comprehensive overview of the PIPE model for personalizatio

Exploring The Value Of Folksonomies For Creating Semantic Metadata

Finding good keywords to describe resources is an on-going problem: typically we select such words manually from a thesaurus of terms, or they are created using automatic keyword extraction techniques. Folksonomies are an increasingly well populated source of unstructured tags describing web resources. This paper explores the value of the folksonomy tags as potential source of keyword metadata by examining the relationship between folksonomies, community produced annotations, and keywords extracted by machines. The experiment has been carried-out in two ways: subjectively, by asking two human indexers to evaluate the quality of the generated keywords from both systems; and automatically, by measuring the percentage of overlap between the folksonomy set and machine generated keywords set. The results of this experiment show that the folksonomy tags agree more closely with the human generated keywords than those automatically generated. The results also showed that the trained indexers preferred the semantics of folksonomy tags compared to keywords extracted automatically. These results can be considered as evidence for the strong relationship of folksonomies to the human indexer’s mindset, demonstrating that folksonomies used in the del.icio.us bookmarking service are a potential source for generating semantic metadata to annotate web resources