The rapidly increasing wealth of genomic data has driven the development of tools to assist in the task of representing and processing information about genes, their products and their functions. One of the most important of these tools is the Gene Ontology (GO), which is being developed in tandem with work on a variety of bioinformatics databases. An examination of the structure of GO, however, reveals a number of problems, which we believe can be resolved by taking account of certain (...) organizing principles drawn from philosophical ontology. We shall explore the results of applying such principles to GO with a view to improving GO’s consistency and coherence and thus its future applicability in the automated processing of biological data. (shrink)

In the course of the discussion, Professor Quine pinpoints the difficulties involved in translation, brings to light the anomalies and conflicts implicit in our ...

This is a copy of the Proceedings version of a paper presented at the Workshop on Computational Intelligence and Semiotics, organized by João Queiroz and Ricardo Gudwin, held at Itaú Cultural, São Paulo, Brazil, on 8-9 October, 2002. (This version contains material not actually delivered at the conference.) Queiroz and Gudwin will be releasing the Proceedings volume on a..

As an informational technology, the World Wide Web has enjoyed spectacular success. In just ten years it has transformed the way information is produced, stored, and shared in arenas as diverse as shopping, family photo albums, and high-level academic research. The “Semantic Web” was touted by its developers as equally revolutionary but has not yet achieved anything like the Web’s exponential uptake. This 17 000 word survey article explores why this might be so, from a perspective that bridges both philosophy (...) and IT. (*Also translated into Croatian and republished in Vjesnik bibliotekara Hrvatske 53, 1(2010), 155-206: See external link #2). (shrink)

Wikipedia is a free encyclopedia that is written and edited entirely by visitors to its website. I argue that we are misled when we think of it in the same epistemic category with traditional general encyclopedias. An empirical assessment of its reliability reveals that it varies widely from topic to topic. So any particular claim found in it cannot be relied on based on its source. I survey some methods that we use in assessing specific claims and argue that the (...) structure of the Wikipedia frustrates them. (shrink)

Wikipedia can be utilized as a controlled vocabulary for identifying the main topics in a document, with article titles serving as index terms and redirect titles as their synonyms. Wikipedia contains over 4M such titles covering the terminology of nearly any document collection. This permits controlled indexing in the absence of manually created vocabularies. We combine state-of-the-art strategies for automatic controlled indexing with Wikipedia’s unique property—a richly hyperlinked encyclopedia. We evaluate the scheme by comparing automatically assigned topics with those chosen (...) manually by human indexers. Analysis of indexing consistency shows that our algorithm performs as well as the average person. (shrink)

Integration of ontologies begins with establishing mappings between their concept entries. We map categories from the largest manually-built ontology, Cyc, onto Wikipedia articles describing corresponding concepts. Our method draws both on Wikipedia’s rich but chaotic hyperlink structure and Cyc’s carefully defined taxonomic and common-sense knowledge. On 9,333 manual alignments by one person, we achieve an F-measure of 90%; on 100 alignments by six human subjects the average agreement of the method with the subject is close to their agreement with each (...) other. We cover 62.8% of Cyc categories relating to common-sense knowledge and discuss what further information might be added to Cyc given this substantial new alignment. (shrink)