The DeepThought Core Architecture Framework

The research performed in the DeepThought project aims at demonstrating the potential of deep linguistic processing if combined with shallow methods for robustness. Classical information retrieval is extended by high precision concept indexing and relation detection. On the basis of this approach, the feasibility of three ambitious applications will be demonstrated, namely: precise information extraction for business intelligence; email response management for customer relationship management; creativity support for document production and collective brainstorming. Common to these applications, and the basis for their development is the XML-based, RMRS-enabled core architecture framework that will be described in detail in this paper. The framework is not limited to the applications envisaged in the DeepThought project, but can also be employed e.g. to generate and make use of XML standoff annotation of documents and linguistic corpora, and in general for a wide range of NLP-based applications and research purposes

Corpora and evaluation tools for multilingual named entity grammar development

We present an effort for the development of multilingual named entity grammars in a unification-based finite-state formalism (SProUT). Following an extended version of the MUC7 standard, we have developed Named Entity Recognition grammars for German, Chinese, Japanese, French, Spanish, English, and Czech. The grammars recognize person names, organizations, geographical locations, currency, time and date expressions. Subgrammars and gazetteers are shared as much as possible for the grammars of the different languages. Multilingual corpora from the business domain are used for grammar development and evaluation. The annotation format (named entity and other linguistic information) is described. We present an evaluation tool which provides detailed statistics and diagnostics, allows for partial matching of annotations, and supports user-defined mappings between different annotation and grammar output formats

A geo-temporal information extraction service for processing descriptive metadata in digital libraries

In the context of digital map libraries, resources are usually described according to metadata records that define the relevant subject, location, time-span, format and keywords. On what concerns locations and time-spans, metadata records are often incomplete or they provide information in a way that is not machine-understandable (e.g. textual descriptions). This paper presents techniques for extracting geotemporal information from text, using relatively simple text mining methods that leverage on a Web gazetteer service. The idea is to go from human-made geotemporal referencing (i.e. using place and period names in textual expressions) into geo-spatial coordinates and time-spans. A prototype system, implementing the proposed methods, is described in detail. Experimental results demonstrate the efficiency and accuracy of the proposed approaches

Large-scale event extraction from literature with multi-level gene normalization

Text mining for the life sciences aims to aid database curation, knowledge summarization and information retrieval through the automated processing of biomedical texts. To provide comprehensive coverage and enable full integration with existing biomolecular database records, it is crucial that text mining tools scale up to millions of articles and that their analyses can be unambiguously linked to information recorded in resources such as UniProt, KEGG, BioGRID and NCBI databases. In this study, we investigate how fully automated text mining of complex biomolecular events can be augmented with a normalization strategy that identifies biological concepts in text, mapping them to identifiers at varying levels of granularity, ranging from canonicalized symbols to unique gene and proteins and broad gene families. To this end, we have combined two state-of-the-art text mining components, previously evaluated on two community-wide challenges, and have extended and improved upon these methods by exploiting their complementary nature. Using these systems, we perform normalization and event extraction to create a large-scale resource that is publicly available, unique in semantic scope, and covers all 21.9 million PubMed abstracts and 460 thousand PubMed Central open access full-text articles. This dataset contains 40 million biomolecular events involving 76 million gene/protein mentions, linked to 122 thousand distinct genes from 5032 species across the full taxonomic tree. Detailed evaluations and analyses reveal promising results for application of this data in database and pathway curation efforts. The main software components used in this study are released under an open-source license. Further, the resulting dataset is freely accessible through a novel API, providing programmatic and customized access (http://www.evexdb.org/api/v001/). Finally, to allow for large-scale bioinformatic analyses, the entire resource is available for bulk download from http://evexdb.org/download/, under the Creative Commons -Attribution - Share Alike (CC BY-SA) license

Report of MIRACLE team for Geographical IR in CLEF 2006

The main objective of the designed experiments is testing the effects of geographical information retrieval from documents that contain geographical tags. In the designed experiments we try to isolate geographical retrieval from textual retrieval replacing all geo-entity textual references from topics with associated tags and splitting the retrieval process in two phases: textual retrieval from the textual part of the topic without geo-entity references and geographical retrieval from the tagged text generated by the topic tagger. Textual and geographical results are combined applying different techniques: union, intersection, difference, and external join based. Our geographic information retrieval system consists of a set of basics components organized in two categories: (i) linguistic tools oriented to textual analysis and retrieval and (ii) resources and tools oriented to geographical analysis. These tools are combined to carry out the different phases of the system: (i) documents and topics analysis, (ii) relevant documents retrieval and (iii) result combination. If we compare the results achieved to the last campaign’s results, we can assert that mean average precision gets worse when the textual geo-entity references are replaced with geographical tags. Part of this worsening is due to our experiments return cero pertinent documents if no documents satisfy de geographical sub-query. But if we only analyze the results of queries that satisfied both textual and geographical terms, we observe that the designed experiments recover pertinent documents quickly, improving R-Precision values. We conclude that the developed geographical information retrieval system is very sensible to textual georeference and therefore it is necessary to improve the name entity recognition module