Archive for » September, 2011 «

Monday, September 05th, 2011 | Author:

I wrote a position paper about a different approach towards development of information extractors, which I call Sherlock Holmes-style based on his famous quote “when you have eliminated the impossible, whatever remains, however improbable, must be the truth”. The idea is that we fundamentally treat annotations as uncertain. We even start with a “no knowledge”, i.e., “everything is possible” starting point and then interactively add more knowledge, apply the knowledge directly to the annotation state by removing possible annotations and recalculating the probabilities of the remaining ones. For example, “Paris Hilton”, “Paris”, and “Hilton” can all be interpreted as a City, Hotel or Person name. But adding knowledge like “If a phrase is interpreted as a Person Name, then its subphrases should not be interpreted as a City” makes the annotations <"Paris Hilton":Person Name> and <"Paris":City> mutually exclusive. Observe that initially all annotations were independent, and these two are now dependent. We argue in the paper that the main challenge in this approach lies in efficient storage and conditioning of probabilistic dependencies, because trivial approaches do not work.
Handling Uncertainty in Information Extraction.
Maurice van Keulen, Mena Badieh Habib
This position paper proposes an interactive approach for developing information extractors based on the ontology definition process with knowledge about possible (in)correctness of annotations. We discuss the problem of managing and manipulating probabilistic dependencies.

The paper will be presented at the URSW workshop co-located with ICSW 2011, 23 October 2011, Bonn, Germany [details]

Thursday, September 01st, 2011 | Author:

A master student performed a problem exploration for the PayDIBI project. This is the report he wrote.
Integration of Biological Sources – Exploring the Case of Protein Homology
Tjeerd W. Boerman, Maurice van Keulen, Paul van der Vet, Edouard I. Severing (Wageningen University)
Data integration is a key issue in the domain of bioin- formatics, which deals with huge amounts of heterogeneous biological data that grows and changes rapidly. This paper serves as an introduction in the field of bioinformatics and the biological concepts it deals with, and an exploration of the integration problems a bioinformatics scientist faces. We examine ProGMap, an integrated protein homology system used by bioinformatics scientists at Wageningen University, and several use cases related to protein homology. A key issue we identify is the huge manual effort required to unify source databases into a single resource. Uncertain databases are able to contain several possible worlds, and it has been proposed that they can be used to significantly reduce initial integration efforts. We propose several directions for future work where uncertain databases can be applied to bioinformatics, with the goal of furthering the cause of bioinformatics integration.
[details]