Named Entity Extraction: la piattaforma Gate/Annie

In questo lavoro si introducono i concetti di base di Natural Language Processing, soffermandosi su Information Extraction e analizzandone gli ambiti applicativi, le attività principali e la differenza rispetto a Information Retrieval. Successivamente si analizza il processo di Named Entity Recognition, focalizzando l’attenzione sulle principali problematiche di annotazione di testi e sui metodi per la valutazione della qualità dell’estrazione di entità. Infine si fornisce una panoramica della piattaforma software open-source di language processing GATE/ANNIE, descrivendone l’architettura e i suoi componenti principali, con approfondimenti sugli strumenti che GATE offre per l'approccio rule-based a Named Entity Recognition.

OSIRISv1.2: a named entity recognition system for sequence variants of genes in biomedical literature

Background: Single Nucleotide Polymorphisms, among other type of sequence variants, constitute key elements in genetic epidemiology and pharmacogenomics. While sequence data about genetic variation is found at databases such as dbSNP, clues about the functional and phenotypic consequences of the variations are generally found in biomedical literature. The identification of the relevant documents and the extraction of the information from them are hampered by the large size of literature databases and the lack of widely accepted standard notation for biomedical entities. Thus, automatic systems for the identification of citations of allelic variants of genes in biomedical texts are required. Results: Our group has previously reported the development of OSIRIS, a system aimed at the retrieval of literature about allelic variants of genes http://ibi.imim.es/osirisform.html. Here we describe the development of a new version of OSIRIS (OSIRISv1.2, http://ibi.imim.es/OSIRISv1.2.html webcite) which incorporates a new entity recognition module and is built on top of a local mirror of the MEDLINE collection and HgenetInfoDB: a database that collects data on human gene sequence variations. The new entity recognition module is based on a pattern-based search algorithm for the identification of variation terms in the texts and their mapping to dbSNP identifiers. The performance of OSIRISv1.2 was evaluated on a manually annotated corpus, resulting in 99% precision, 82% recall, and an F-score of 0.89. As an example, the application of the system for collecting literature citations for the allelic variants of genes related to the diseases intracranial aneurysm and breast cancer is presented. Conclusion: OSIRISv1.2 can be used to link literature references to dbSNP database entries with high accuracy, and therefore is suitable for collecting current knowledge on gene sequence variations and supporting the functional annotation of variation databases. The application of OSIRISv1.2 in combination with controlled vocabularies like MeSH provides a way to identify associations of biomedical interest, such as those that relate SNPs with diseases.

Design And Development Of A Named Entity Based Question Answering System For Malayalam Language

This is a Named Entity Based Question Answering System for Malayalam Language. Although a vast amount of information is available today in digital form, no effective information access mechanism exists to provide humans with convenient information access. Information Retrieval and Question Answering systems are the two mechanisms available now for information access. Information systems typically return a long list of documents in response to a user’s query which are to be skimmed by the user to determine whether they contain an answer. But a Question Answering System allows the user to state his/her information need as a natural language question and receives most appropriate answer in a word or a sentence or a paragraph. This system is based on Named Entity Tagging and Question Classification. Document tagging extracts useful information from the documents which will be used in finding the answer to the question. Question Classification extracts useful information from the question to determine the type of the question and the way in which the question is to be answered. Various Machine Learning methods are used to tag the documents. Rule-Based Approach is used for Question Classification. Malayalam belongs to the Dravidian family of languages and is one of the four major languages of this family. It is one of the 22 Scheduled Languages of India with official language status in the state of Kerala. It is spoken by 40 million people. Malayalam is a morphologically rich agglutinative language and relatively of free word order. Also Malayalam has a productive morphology that allows the creation of complex words which are often highly ambiguous. Document tagging tools such as Parts-of-Speech Tagger, Phrase Chunker, Named Entity Tagger, and Compound Word Splitter are developed as a part of this research work. No such tools were available for Malayalam language. Finite State Transducer, High Order Conditional Random Field, Artificial Immunity System Principles, and Support Vector Machines are the techniques used for the design of these document preprocessing tools. This research work describes how the Named Entity is used to represent the documents. Single sentence questions are used to test the system. Overall Precision and Recall obtained are 88.5% and 85.9% respectively. This work can be extended in several directions. The coverage of non-factoid questions can be increased and also it can be extended to include open domain applications. Reference Resolution and Word Sense Disambiguation techniques are suggested as the future enhancements

Entity-based semantic search on conversational transcripts semantic

This paper describes the implementation of a semantic web search engine on conversation styled transcripts. Our choice of data is Hansard, a publicly available conversation style transcript of parliamentary debates. The current search engine implementation on Hansard is limited to running search queries based on keywords or phrases hence lacks the ability to make semantic inferences from user queries. By making use of knowledge such as the relationship between members of parliament, constituencies, terms of office, as well as topics of debates the search results can be improved in terms of both relevance and coverage. Our contribution is not algorithmic instead we describe how we exploit a collection of external data sources, ontologies, semantic web vocabularies and named entity extraction in the analysis of underlying semantics of user queries as well as the semantic enrichment of the search index thereby improving the quality of results.

Entity extraction e text classification come strumenti per la sentiment analysis di testi giornalistici

In this thesis we are going to talk about technologies which allow us to approach sentiment analysis on newspapers articles. The final goal of this work is to help social scholars to do content analysis on big corpora of texts in a faster way thanks to the support of automatic text classification.

OpeNER: open polarity enhanced named entity recognition

Actualmente existe una gran cantidad de empresas ofreciendo servicios para el análisis de contenido y minería de datos de las redes sociales con el objetivo de realizar análisis de opiniones y gestión de la reputación. Un alto porcentaje de pequeñas y medianas empresas (pymes) ofrecen soluciones específicas a un sector o dominio industrial. Sin embargo, la adquisición de la necesaria tecnología básica para ofrecer tales servicios es demasiado compleja y constituye un sobrecoste demasiado alto para sus limitados recursos. El objetivo del proyecto europeo OpeNER es la reutilización y desarrollo de componentes y recursos para el procesamiento lingüístico que proporcione la tecnología necesaria para su uso industrial y/o académico.

ESpotter : adaptive named entity recognition for web browsing

Browsing constitutes an important part of the user information searching process on the Web. In this paper, we present a browser plug-in called ESpotter, which recognizes entities of various types on Web pages and highlights them according to their types to assist user browsing. ESpotter uses a range of standard named entity recognition techniques. In addition, a key new feature of ESpotter is that it addresses the problem of multiple domains on the Web by adapting lexicon and patterns to these domains.

Cultural Knowledge for Named Entity Disambiguation: A Graph-Based Semantic Relatedness Approach

One of the ultimate aims of Natural Language Processing is to automate the analysis of the meaning of text. A fundamental step in that direction consists in enabling effective ways to automatically link textual references to their referents, that is, real world objects. The work presented in this paper addresses the problem of attributing a sense to proper names in a given text, i.e., automatically associating words representing Named Entities with their referents. The method for Named Entity Disambiguation proposed here is based on the concept of semantic relatedness, which in this work is obtained via a graph-based model over Wikipedia. We show that, without building the traditional bag of words representation of the text, but instead only considering named entities within the text, the proposed method achieves results competitive with the state-of-the-art on two different datasets.

Le repérage automatique des entités nommées dans la langue arabe : vers la création d'un système à base de règles

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal

Frame-driven Extraction of Linked Data and Ontologies from Text

Ontology design and population -core aspects of semantic technologies- re- cently have become fields of great interest due to the increasing need of domain-specific knowledge bases that can boost the use of Semantic Web. For building such knowledge resources, the state of the art tools for ontology design require a lot of human work. Producing meaningful schemas and populating them with domain-specific data is in fact a very difficult and time-consuming task. Even more if the task consists in modelling knowledge at a web scale. The primary aim of this work is to investigate a novel and flexible method- ology for automatically learning ontology from textual data, lightening the human workload required for conceptualizing domain-specific knowledge and populating an extracted schema with real data, speeding up the whole ontology production process. Here computational linguistics plays a fundamental role, from automati- cally identifying facts from natural language and extracting frame of relations among recognized entities, to producing linked data with which extending existing knowledge bases or creating new ones. In the state of the art, automatic ontology learning systems are mainly based on plain-pipelined linguistics classifiers performing tasks such as Named Entity recognition, Entity resolution, Taxonomy and Relation extraction [11]. These approaches present some weaknesses, specially in capturing struc- tures through which the meaning of complex concepts is expressed [24]. Humans, in fact, tend to organize knowledge in well-defined patterns, which include participant entities and meaningful relations linking entities with each other. In literature, these structures have been called Semantic Frames by Fill- 6 Introduction more [20], or more recently as Knowledge Patterns [23]. Some NLP studies has recently shown the possibility of performing more accurate deep parsing with the ability of logically understanding the structure of discourse [7]. In this work, some of these technologies have been investigated and em- ployed to produce accurate ontology schemas. The long-term goal is to collect large amounts of semantically structured information from the web of crowds, through an automated process, in order to identify and investigate the cognitive patterns used by human to organize their knowledge.

Ontology-based protein-protein interactions extraction from literature using the hidden vector state model

This paper proposes a novel framework of incorporating protein-protein interactions (PPI) ontology knowledge into PPI extraction from biomedical literature in order to address the emerging challenges of deep natural language understanding. It is built upon the existing work on relation extraction using the Hidden Vector State (HVS) model. The HVS model belongs to the category of statistical learning methods. It can be trained directly from un-annotated data in a constrained way whilst at the same time being able to capture the underlying named entity relationships. However, it is difficult to incorporate background knowledge or non-local information into the HVS model. This paper proposes to represent the HVS model as a conditionally trained undirected graphical model in which non-local features derived from PPI ontology through inference would be easily incorporated. The seamless fusion of ontology inference with statistical learning produces a new paradigm to information extraction.

Reconstructing transcriptional regulatory networks using data integration and text mining

Transcriptional Regulatory Networks (TRNs) are powerful tool for representing several interactions that occur within a cell. Recent studies have provided information to help researchers in the tasks of building and understanding these networks. One of the major sources of information to build TRNs is biomedical literature. However, due to the rapidly increasing number of scientific papers, it is quite difficult to analyse the large amount of papers that have been published about this subject. This fact has heightened the importance of Biomedical Text Mining approaches in this task. Also, owing to the lack of adequate standards, as the number of databases increases, several inconsistencies concerning gene and protein names and identifiers are common. In this work, we developed an integrated approach for the reconstruction of TRNs that retrieve the relevant information from important biological databases and insert it into a unique repository, named KREN. Also, we applied text mining techniques over this integrated repository to build TRNs. However, was necessary to create a dictionary of names and synonyms associated with these entities and also develop an approach that retrieves all the abstracts from the related scientific papers stored on PubMed, in order to create a corpora of data about genes. Furthermore, these tasks were integrated into @Note, a software system that allows to use some methods from the Biomedical Text Mining field, including an algorithms for Named Entity Recognition (NER), extraction of all relevant terms from publication abstracts, extraction relationships between biological entities (genes, proteins and transcription factors). And finally, extended this tool to allow the reconstruction Transcriptional Regulatory Networks through using scientific literature.

An anonymizable entity finder in judicial decisions

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal

Adapting Web content for low-literacy readers by using lexical elaboration and named entities labeling

This paper presents an approach for assisting low-literacy readers in accessing Web online information. The oEducational FACILITAo tool is a Web content adaptation tool that provides innovative features and follows more intuitive interaction models regarding accessibility concerns. Especially, we propose an interaction model and a Web application that explore the natural language processing tasks of lexical elaboration and named entity labeling for improving Web accessibility. We report on the results obtained from a pilot study on usability analysis carried out with low-literacy users. The preliminary results show that oEducational FACILITAo improves the comprehension of text elements, although the assistance mechanisms might also confuse users when word sense ambiguity is introduced, by gathering, for a complex word, a list of synonyms with multiple meanings. This fact evokes a future solution in which the correct sense for a complex word in a sentence is identified, solving this pervasive characteristic of natural languages. The pilot study also identified that experienced computer users find the tool to be more useful than novice computer users do.

Sentiment analysis on twitter for the portuguese language

Dissertação para obtenção do Grau de Mestre em Engenharia Informática