SOAP, cleaning multiple alignments from unstable blocks.

Multiple correspondence analysis (MCA) is a multivariate method for analyzing multidimensional contingency tables. General software procedures to perform MCA are available. Among them SAS Proc CORRESP, SPAD CORMU procedure and the mca function of the MASS library in S-PLUS are probably the most used. However, CORRESP and CORMU output is different from that of mca function. The aim of this short note is showing how to obtain from mca function results compatible with those achieved with SAS or SPAD. A modified code is proposed in order to obtain the same coordinate system computed by SAS and SPAD. Moreover, the computation of the contributions of the levels of the factors to the inertia explained by each axis, the squared cosine of each factor level and the re-evaluation of the inertia explained by each axis have been added in order to improve the interpretations of the results of the decomposition.

Programming Languages↗

PubMed2003

The UMLS Semantic Network and the Semantic Web.

The Unified Medical Language System is an extensive source of biomedical knowledge developed and maintained by the US National Library of Medicine (NLM) and is being currently used in a wide variety of biomedical applications. The Semantic Network, a component of the UMLS is a structured description of core biomedical knowledge consisting of well defined semantic types and relationships between them. We investigate the expressiveness of DAML+OIL, a markup language proposed for ontologies on the Semantic Web, for representing the knowledge contained in the Semantic Network. Requirements specific to the Semantic Network, such as polymorphic relationships and blocking relationship inheritance are discussed and approaches to represent these in DAML+OIL are presented. Finally, conclusions are presented along with a discussion of ongoing and future work.

Programming Languages↗

PubMed2002

Representing nested semantic information in a linear string of text using XML.

XML has been widely adopted as an important data interchange language. The structure of XML enables sharing of data elements with variable degrees of nesting as long as the elements are grouped in a strict tree-like fashion. This requirement potentially restricts the usefulness of XML for marking up written text, which often includes features that do not properly nest within other features. We encountered this problem while marking up medical text with structured semantic information from a Natural Language Processor. Traditional approaches to this problem separate the structured information from the actual text mark up. This paper introduces an alternative solution, which tightly integrates the semantic structure with the text. The resulting XML markup preserves the linearity of the medical texts and can therefore be easily expanded with additional types of information.

Programming Languages↗