Collaborative text-annotation resource for disease-centered relation extraction from biomedical text

Agglomerating results from studies of individual biological components has shown the potential to produce biomedical discovery and the promise of therapeutic development. Such knowledge integration could be tremendously facilitated by automated text mining for relation extraction in the biomedical literature. Relation extraction systems cannot be developed without substantial datasets annotated with ground truth for benchmarking and training. The creation of such datasets is hampered by the absence of a resource for launching a distributed annotation effort, as well as by the lack of a standardized annotation schema. We have developed an annotation schema and an annotation tool which can be widely adopted so that the resulting annotated corpora from a multitude of disease studies could be assembled into a unified benchmark dataset. The contribution of this paper is threefold. First, we provide an overview of available benchmark corpora and derive a simple annotation schema for specific binary relation extraction problems such as protein–protein and gene–disease relation extraction. Second, we present BioNotate: an open source annotation resource for the distributed creation of a large corpus. Third, we present and make available the results of a pilot annotation effort of the autism disease networkP08-TIC-4299 of J. A., Sevilla and TIN2006-13177 of DGICT, MadridMilton foundationNational Science Foundation under Grant No. 054348

CellFinder: a cell data repository

CellFinder (http://www.cellfinder.org) is a comprehensive one-stop resource for molecular data characterizing mammalian cells in different tissues and in different development stages. It is built from carefully selected data sets stemming from other curated databases and the biomedical literature. To date, CellFinder describes 3394 cell types and 50 951 cell lines. The database currently contains 3055 microscopic and anatomical images, 205 whole-genome expression profiles of 194 cell/tissue types from RNA-seq and microarrays and 553 905 protein expressions for 535 cells/tissues. Text mining of a corpus of >2000 publications followed by manual curation confirmed expression information on ∼900 proteins and genes. CellFinder's data model is capable to seamlessly represent entities from single cells to the organ level, to incorporate mappings between homologous entities in different species and to describe processes of cell development and differentiation. Its ontological backbone currently consists of 204 741 ontology terms incorporated from 10 different ontologies unified under the novel CELDA ontology. CellFinder's web portal allows searching, browsing and comparing the stored data, interactive construction of developmental trees and navigating the partonomic hierarchy of cells and tissues through a unique body browser designed for life scientists and clinicians

Genotator: A disease-agnostic tool for genetic annotation of disease

<p>Abstract</p> <p>Background</p> <p>Disease-specific genetic information has been increasing at rapid rates as a consequence of recent improvements and massive cost reductions in sequencing technologies. Numerous systems designed to capture and organize this mounting sea of genetic data have emerged, but these resources differ dramatically in their disease coverage and genetic depth. With few exceptions, researchers must manually search a variety of sites to assemble a complete set of genetic evidence for a particular disease of interest, a process that is both time-consuming and error-prone.</p> <p>Methods</p> <p>We designed a real-time aggregation tool that provides both comprehensive coverage and reliable gene-to-disease rankings for any disease. Our tool, called Genotator, automatically integrates data from 11 externally accessible clinical genetics resources and uses these data in a straightforward formula to rank genes in order of disease relevance. We tested the accuracy of coverage of Genotator in three separate diseases for which there exist specialty curated databases, Autism Spectrum Disorder, Parkinson's Disease, and Alzheimer Disease. Genotator is freely available at <url>http://genotator.hms.harvard.edu</url>.</p> <p>Results</p> <p>Genotator demonstrated that most of the 11 selected databases contain unique information about the genetic composition of disease, with 2514 genes found in only one of the 11 databases. These findings confirm that the integration of these databases provides a more complete picture than would be possible from any one database alone. Genotator successfully identified at least 75% of the top ranked genes for all three of our use cases, including a 90% concordance with the top 40 ranked candidates for Alzheimer Disease.</p> <p>Conclusions</p> <p>As a meta-query engine, Genotator provides high coverage of both historical genetic research as well as recent advances in the genetic understanding of specific diseases. As such, Genotator provides a real-time aggregation of ranked data that remains current with the pace of research in the disease fields. Genotator's algorithm appropriately transforms query terms to match the input requirements of each targeted databases and accurately resolves named synonyms to ensure full coverage of the genetic results with official nomenclature. Genotator generates an excel-style output that is consistent across disease queries and readily importable to other applications.</p

Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts

Biomedical literature curation is the process of automatically and/or manually deriving knowledge from scientific publications and recording it into specialized databases for structured delivery to users. It is a slow, error-prone, complex, costly and, yet, highly important task. Previous experiences have proven that text mining can assist in its many phases, especially, in triage of relevant documents and extraction of named entities and biological events. Here, we present the curation pipeline of the CellFinder database, a repository of cell research, which includes data derived from literature curation and microarrays to identify cell types, cell lines, organs and so forth, and especially patterns in gene expression. The curation pipeline is based on freely available tools in all text mining steps, as well as the manual validation of extracted data. Preliminary results are presented for a data set of 2376 full texts from which >4500 gene expression events in cell or anatomical part have been extracted. Validation of half of this data resulted in a precision of ~50% of the extracted data, which indicates that we are on the right track with our pipeline for the proposed task. However, evaluation of the methods shows that there is still room for improvement in the named-entity recognition and that a larger and more robust corpus is needed to achieve a better performance for event extraction. Database URL: http://www.cellfinder.org

Dynamic OSINT System Sourcing from Social Networks

Nowadays, the World Wide Web (WWW) is simultaneously an accumulator and a provider of huge amounts of information, which is delivered to users through news, blogs, social networks, etc. The exponential growth of information is a major challenge for the community in general, since the frequent demand and correlation of news becomes a repetitive task, potentially tedious and prone to errors. Although information scrutiny is still performed manually and on a regular basis by most people, the emergence of Open-Source Intelligence (OSINT) systems in recent years for monitoring, selection and extraction of textual information from social networks and the Web promise to change the life of some of them. These systems are now very popular and useful tools for professionals from different areas, such as the cyber-security community, where being updated with the latest news and trends can lead to a direct impact on threat response. This work aims to address the previously motivated problem through the implementation of a dynamic OSINT system. For this system, two algorithms were developed: one to dynamically add, remove and rate user accounts with relevant tweets in the computer security area; and another one to classify the publications of those users. The relevance of a user depends not only on how frequently he publishes, but also on his importance (status) in the social network, as well as on the relevance of the information published by him. Text mining functions are proposed herein to achieve the objective of measuring the relevance of text segments. The proposed approach is innovative, involving dynamic management of the relevance of users and their publications, thus ensuring a more reliable and important source of information framework. Apart from the algorithms and functions on which they were build (which were also proposed in the scope of this work), this dissertation describes several experiments and tests used in their evaluation. The qualitative results are very interesting and demonstrate the practical usefulness of the approach. In terms of human-machine interface, a mural of information, generated dynamically and automatically from the social network Twitter, is provided to the end-user. In the current version of the system, the mural is presented in the form of a web page, highlighting the news by its relevancy (red for high relevance, yellow for moderate relevance, and green for low relevance). The main contributions of this work are the two proposed algorithms and their evaluation. A fully working prototype of a system with their implementation, along with a mural for showing selected news, is another important output of this work.Atualmente, a World Wide Web (WWW) fornece aos utilizadores enormes quantidades de informação sob os mais diversos formatos: notícias, blogs, nas redes sociais, entre outros. O crescimento exponencial desta informação representa um grande desafio para a comunidade em geral, uma vez que a procura e correlação frequente de notícias acaba por se tornar numa tarefa repetitiva, potencialmente aborrecida e sujeita a erros. Apesar da maioria das pessoas ainda fazer o escrutínio da informação de forma manual e regularmente, têm surgido, nos últimos anos, sistemas Open-Source Intelligence (OSINT) que efetuam a vigilância, seleção e extração de informação textual, a partir de redes sociais e da web em geral. Estes sistemas são hoje ferramentas muito populares e úteis aos profissionais de diversas áreas, como a da cibersegurança, onde estar atualizado com as notícias e as tendências mais recentes pode levar a um impacto direto na reação a ameaças. O objetivo deste trabalho passa pela tentativa de solucionar o problema motivado anteriormente, através da implementação de um sistema dinâmico OSINT. Para este sistema foram desenvolvidos dois algoritmos: um para adicionar, remover e classificar, dinamicamente, contas de utilizadores com tweets relevantes na área da segurança informática e outro para classificar as publicações desses utilizadores. A relevância de um utilizador depende não só da sua frequência de publicação mas também da sua importância (status) na rede social, bem como a relevância da informação publicada. Neste último ponto, são propostas funções de prospeção de texto que permitem medir a relevância de segmentos de texto. A abordagem proposta é inovadora, envolvendo gestão dinâmica da relevância dos utilizadores e das suas publicações, garantindo assim um quadro de fonte de informação mais fidedigna e importante. Para além dos algoritmos e das funções que os compõem (também propostas no contexto deste trabalho), esta dissertação descreve várias experiências e testes usados na sua avaliação. Os resultados qualitativos constatados são pertinentes, denotando uma elevada utilidade prática. Em termos de interface homem-máquina, é disponibilizado um mural de informação contínua que vai sendo gerado dinâmica e automaticamente, a partir da rede social Twitter, e apresentado sob a forma de uma página web, destacando as notícias apresentadas pelo grau de relevância que possuem (vermelho para relevância elevada, amarelo para relevância moderada e verde para relevância reduzida). As contribuições principais deste trabalho compreendem os dois algoritmos propostos e a sua avaliação. Um protótipo totalmente funcional de um sistema que os implementa, acompanhado pelo mural que mostra as notícias selecionadas, constituem outro resultado importante do trabalho

GeoAnnotator: A Collaborative Semi-Automatic Platform for Constructing Geo-Annotated Text Corpora

Ground-truth datasets are essential for the training and evaluation of any automated algorithm. As such, gold-standard annotated corpora underlie most advances in natural language processing (NLP). However, only a few relatively small (geo-)annotated datasets are available for geoparsing, i.e., the automatic recognition and geolocation of place references in unstructured text. The creation of geoparsing corpora that include both the recognition of place names in text and matching of those names to toponyms in a geographic gazetteer (a process we call geo-annotation), is a laborious, time-consuming and expensive task. The field lacks efficient geo-annotation tools to support corpus building and lacks design guidelines for the development of such tools. Here, we present the iterative design of GeoAnnotator, a web-based, semi-automatic and collaborative visual analytics platform for geo-annotation. GeoAnnotator facilitates collaborative, multi-annotator creation of large corpora of geo-annotated text by generating computationally-generated pre-annotations that can be improved by human-annotator users. The resulting corpora can be used in improving and benchmarking geoparsing algorithms as well as various other spatial language-related methods. Further, the iterative design process and the resulting design decisions can be used in annotation platforms tailored for other application domains of NLP

Semantic resources in pharmacovigilance: a corpus and an ontology for drug-drug interactions

Mención Internacional en el título de doctorNowadays, with the increasing use of several drugs for the treatment of one or more different diseases (polytherapy) in large populations, the risk for drugs combinations that have not been studied in pre-authorization clinical trials has increased. This provides a favourable setting for the occurrence of drug-drug interactions (DDIs), a common adverse drug reaction (ADR) representing an important risk to patients safety, and an increase in healthcare costs. Their early detection is, therefore, a main concern in the clinical setting. Although there are different databases supporting healthcare professionals in the detection of DDIs, the quality of these databases is very uneven, and the consistency of their content is limited. Furthermore, these databases do not scale well to the large and growing number of pharmacovigilance literature in recent years. In addition, large amounts of current and valuable information are hidden in published articles, scientific journals, books, and technical reports. Thus, the large number of DDI information sources has overwhelmed most healthcare professionals because it is not possible to remain up to date on everything published about DDIs. Computational methods can play a key role in the identification, explanation, and prediction of DDIs on a large scale, since they can be used to collect, analyze and manipulate large amounts of biological and pharmacological data. Natural language processing (NLP) techniques can be used to retrieve and extract DDI information from pharmacological texts, supporting researchers and healthcare professionals on the challenging task of searching DDI information among different and heterogeneous sources. However, these methods rely on the availability of specific resources providing the domain knowledge, such as databases, terminological vocabularies, corpora, ontologies, and so forth, which are necessary to address the Information Extraction (IE) tasks. In this thesis, we have developed two semantic resources for the DDI domain that make an important contribution to the research and development of IE systems for DDIs. We have reviewed and analyzed the existing corpora and ontologies relevant to this domain, based on their strengths and weaknesses, we have developed the DDI corpus and the ontology for drug-drug interactions (named DINTO). The DDI corpus has proven to fulfil the characteristics of a high-quality gold-standard, and has demonstrated its usefulness as a benchmark for the training and testing of different IE systems in the SemEval-2013 DDIExtraction shared task. Meanwhile, DINTO has been used and evaluated in two different applications. Firstly, it has been proven that the knowledge represented in the ontology can be used to infer DDIs and their different mechanisms. Secondly, we have provided a proof-of-concept of the contribution of DINTO to NLP, by providing the domain knowledge to be exploited by an IE pilot prototype. From these results, we believe that these two semantic resources will encourage further research into the application of computational methods to the early detection of DDIs. This work has been partially supported by the Regional Government of Madrid under the Research Network MA2VICMR [S2009/TIC-1542], by the Spanish Ministry of Education under the project MULTIMEDICA [TIN2010-20644-C03-01] and by the European Commission Seventh Framework Programme under TrendMiner project [FP7-ICT287863].Hoy en día ha habido un notable aumento del número de pacientes polimedicados que reciben simultáneamente varios fármacos para el tratamiento de una o varias enfermedades. Esta situación proporciona el escenario ideal para la prescripción de combinaciones de fármacos que no han sido estudiadas previamente en ensayos clínicos, y puede dar lugar a un aumento de interacciones farmacológicas (DDIs por sus siglas en inglés). Las interacciones entre fármacos son un tipo de reacción adversa que supone no sólo un riesgo para los pacientes, sino también una importante causa de aumento del gasto sanitario. Por lo tanto, su detección temprana es crucial en la práctica clínica. En la actualidad existen diversos recursos y bases de datos que pueden ayudar a los profesionales sanitarios en la detección de posibles interacciones farmacológicas. Sin embargo, la calidad de su información varía considerablemente de unos a otros, y la consistencia de sus contenidos es limitada. Además, la actualización de estos recursos es difícil debido al aumento que ha experimentado la literatura farmacológica en los últimos años. De hecho, mucha información sobre DDIs se encuentra dispersa en artículos, revistas científicas, libros o informes técnicos, lo que ha hecho que la mayoría de los profesionales sanitarios se hayan visto abrumados al intentar mantenerse actualizados en el dominio de las interacciones farmacológicas. La ingeniería informática puede representar un papel fundamental en este campo permitiendo la identificación, explicación y predicción de DDIs, ya que puede ayudar a recopilar, analizar y manipular grandes cantidades de datos biológicos y farmacológicos. En concreto, las técnicas del procesamiento del lenguaje natural (PLN) pueden ayudar a recuperar y extraer información sobre DDIs de textos farmacológicos, ayudando a los investigadores y profesionales sanitarios en la complicada tarea de buscar esta información en diversas fuentes. Sin embargo, el desarrollo de estos métodos depende de la disponibilidad de recursos específicos que proporcionen el conocimiento del dominio, como bases de datos, vocabularios terminológicos, corpora u ontologías, entre otros, que son necesarios para desarrollar las tareas de extracción de información (EI). En el marco de esta tesis hemos desarrollado dos recursos semánticos en el dominio de las interacciones farmacológicas que suponen una importante contribución a la investigación y al desarrollo de sistemas de EI sobre DDIs. En primer lugar hemos revisado y analizado los corpora y ontologías existentes relevantes para el dominio y, en base a sus potenciales y limitaciones, hemos desarrollado el corpus DDI y la ontología para interacciones farmacológicas DINTO. El corpus DDI ha demostrado cumplir con las características de un estándar de oro de gran calidad, así como su utilidad para el entrenamiento y evaluación de distintos sistemas en la tarea de extracción de información SemEval-2013 DDIExtraction Task. Por su parte, DINTO ha sido utilizada y evaluada en dos aplicaciones diferentes. En primer lugar, hemos demostrado que esta ontología puede ser utilizada para inferir interacciones entre fármacos y los mecanismos por los que ocurren. En segundo lugar, hemos obtenido una primera prueba de concepto de la contribución de DINTO al área del PLN al proporcionar el conocimiento del dominio necesario para ser explotado por un prototipo de un sistema de EI. En vista de estos resultados, creemos que estos dos recursos semánticos pueden estimular la investigación en el desarrollo de métodos computaciones para la detección temprana de DDIs. Este trabajo ha sido financiado parcialmente por el Gobierno Regional de Madrid a través de la red de investigación MA2VICMR [S2009/TIC-1542], por el Ministerio de Educación Español, a través del proyecto MULTIMEDICA [TIN2010-20644-C03-01], y por el Séptimo Programa Macro de la Comisión Europea a través del proyecto TrendMiner [FP7-ICT287863].This work has been partially supported by the Regional Government of Madrid under the Research Network MA2VICMR [S2009/TIC-1542], by the Spanish Ministry of Education under the project MULTIMEDICA [TIN2010-20644-C03-01] and by the European Commission Seventh Framework Programme under TrendMiner project [FP7-ICT287863].Programa Oficial de Doctorado en Ciencia y Tecnología InformáticaPresidente: Asunción Gómez Pérez.- Secretario: María Belén Ruiz Mezcua.- Vocal: Mariana Neve