UIMA in the Biocuration Workflow: A coherent framework for cooperation between biologists and computational linguists

As collaborating partners, Barcelona Media Innovation Centre and GRIB (Universitat Pompeu Fabra) seek to combine strengths from Computational Linguistics and Biomedicine to produce a robust Text Mining system to generate data that will help biocurators in their daily work. The first version of this system will focus on the discovery of relationships between genes, SNPs (Single Nucleotide Polymorphisms) and diseases from the literature.

A first challenge that we were faced with during the setup of this project is the fact that most current tools that support the curation workflow are complex, ad-hoc built applications which sometimes make difficult the interoperability and results sharing between research groups from different and unrelated expert fields. Often, biologists (even computer-savvy ones) are hard pressed to use and adapt sophisticated Natural Language Processing systems, and computational linguists are challenged by the intricacies of biology in applying their processing pipelines to elicit knowledge from texts. The flow of knowledge (needed to develop a usable, practical tool) to and from the parties involved in the development of such systems is not always easy or straightforward.

The modular and versatile architecture of UIMA (Unstructed Information Management Architecture) provides a framework to address these challenges. UIMA is a component architecture and software framework implementation (including a UIMA SDK) to develop applications that analyse large volumes of unstructured information, and has been increasingly adopted by a significant part of the BioNLP community that needs industrial-grade and robust applications to exploit the whole bibliome. The use of UIMA to develop Text Mining applications useful for curation purposes allows the combination of diverse expertises which is beyond the individual know-how of biologists, computer scientists or linguists in isolation. A good synergy and circulation of knowledge between these experts is fundamental to the development of a successful curation tool

Overview of the protein-protein interaction annotation extraction task of BioCreative II

© 2008 Krallinger et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution Licens

La imagen y la narrativa como herramientas para el abordaje psicosocial en escenarios de violencia. Ibagué, Bogotá, Plata Huila

En el presente trabajo se presenta un muestreo de casos de la situación social colombiana en las últimas décadas marcadas por el accionar violento de grupos armados que dejan como consecuencia afectaciones física y psicosociales. Estas afectaciones nos permiten como futuros psicólogos crear estrategias efectivas de intervención y acompañamiento psicosocial, para promover la reconstrucción de vidas y el logro de metas no alcanzadas por los episodios de violencia. Las diferentes temáticas desarrolladas en el Diplomado de Profundización Acompañamiento Psicosocial en Escenarios de Violencia, permite comprender y reflexionar críticamente sobre las consecuencias psicosociales que se producen desde la violencia , además visualizar y entender las diferentes estrategas psicosociales como la foto voz, el uso de prácticas narrativas entre algunas estrategias en la reconstrucción y resignificación de sentido y significado de los sucesos acontecidos en el desarrollo de la vida cotidiana de las diferentes comunidades afectada por el fenómeno violento. Se describe el relato seleccionado a nivel colaborativo relato # 5: Carlos Arturo un joven adolescente de 14 años víctima del conflicto armado, con una condición de discapacidad consecuencia de una granada, artefacto que no solo le causó daños físicos sino también psicológicos. Se diligencia un cuadro de formulación de preguntas de tipo estratégicas, circulares y reflexivas, las cuales serán justificadas desde el campo psicosocial. También realiza un análisis colaborativo del Caso de Peñas Coloradas, población ubicada en el departamento del Caquetá que sobreviven de los cultivos de hoja de coca, se encuentran entre el accionar de los grupos guerrillero y la acción descomunal del Estado, han sido desplazados y convertidos en víctimas del conflicto armado lo que los lleva a la situación de sufrir la mayoría de las afectaciones psicosociales descritas, para ello se plantean tres estrategias de abordaje psicosocial que permiten mitigar la crisis que genera la violencia. Finalmente, se presenta un informe analítico del trabajo colaborativo de la foto voz, donde se observan diferentes contextos de nuestro país, resumen que es plasmado en una página Wix.The present work makes a remembrance of the violent events present in our Colombian territory for many decades, this social problem extends to the collective and individual level. The emotional and physical affectations that violence leaves in its wake allow us as future mental health professionals to create effective intervention strategies and psychosocial support, which achieve the reconstruction of lives and the achievement of goals that were destroyed by the episodes of violence. . The different themes developed in the Diploma in Deepening Psychosocial Accompaniment in Scenarios of Violence, help us to identify from subjectivity the pain caused by violent events and lead us to critically reflect on the narrative of construction of historical memory developed by victims of violence. armed conflict. The story selected at the collaborative level is described. Story # 5: Carlos Arturo, a 14-year-old young adolescent victim of the armed conflict, with a disability condition resulting from a grenade, an artifact that not only caused him physical but also psychological damage. A table of formulation of strategic, circular and reflective questions is filled out, which will be justified from the psychosocial field. It also carries out a collaborative analysis of the Case of Peñas Coloradas, a population of settlers who are victims of the armed conflict who have been displaced, a situation that leads them to suffer hunger and violence, for this purpose, three psychosocial approach strategies are proposed to mitigate the crisis. that generates violence. Finally, an analytical report of the collaborative work of the photo voice is presented, where different contexts of our country are observed, a summary that is reflected in a wix page

Automatic reconstruction of a bacterial regulatory network using Natural Language Processing

<p>Abstract</p> <p>Background</p> <p>Manual curation of biological databases, an expensive and labor-intensive process, is essential for high quality integrated data. In this paper we report the implementation of a state-of-the-art Natural Language Processing system that creates computer-readable networks of regulatory interactions directly from different collections of abstracts and full-text papers. Our major aim is to understand how automatic annotation using Text-Mining techniques can complement manual curation of biological databases. We implemented a rule-based system to generate networks from different sets of documents dealing with regulation in <it>Escherichia coli </it>K-12.</p> <p>Results</p> <p>Performance evaluation is based on the most comprehensive transcriptional regulation database for any organism, the manually-curated RegulonDB, 45% of which we were able to recreate automatically. From our automated analysis we were also able to find some new interactions from papers not already curated, or that were missed in the manual filtering and review of the literature. We also put forward a novel Regulatory Interaction Markup Language better suited than SBML for simultaneously representing data of interest for biologists and text miners.</p> <p>Conclusion</p> <p>Manual curation of the output of automatic processing of text is a good way to complement a more detailed review of the literature, either for validating the results of what has been already annotated, or for discovering facts and information that might have been overlooked at the triage or curation stages.</p

Sublingual immunotherapy for asthma.

BACKGROUND: Asthma is a common long-term respiratory disease affecting approximately 300 million people worldwide. Approximately half of people with asthma have an important allergic component to their disease, which may provide an opportunity for targeted treatment. Sublingual immunotherapy (SLIT) aims to reduce asthma symptoms by delivering increasing doses of an allergen (e.g. house dust mite, pollen extract) under the tongue to induce immune tolerance. However, it is not clear whether the sublingual delivery route is safe and effective in asthma. OBJECTIVES: To assess the efficacy and safety of sublingual immunotherapy compared with placebo or standard care for adults and children with asthma. SEARCH METHODS: We identified trials from the Cochrane Airways Group Specialised Register (CAGR), ClinicalTrials.gov (www.ClinicalTrials.gov), the World Health Organization (WHO) trials portal (www.who.int/ictrp/en/) and reference lists of all primary studies and review articles. The search is up to date as of 25 March 2015. SELECTION CRITERIA: We included parallel randomised controlled trials (RCTs), irrespective of blinding or duration, that evaluated sublingual immunotherapy versus placebo or as an add-on to standard asthma management. We included both adults and children with asthma of any severity and with any allergen-sensitisation pattern. We included studies that recruited participants with asthma, rhinitis, or both, providing at least 80% of trial participants had a diagnosis of asthma. DATA COLLECTION AND ANALYSIS: Two review authors independently screened the search results for included trials, extracted numerical data and assessed risk of bias, all of which were cross-checked for accuracy. We resolved disagreements by discussion.We analysed dichotomous data as odds ratios (ORs) or risk differences (RDs) using study participants as the unit of analysis; we analysed continuous data as mean differences (MDs) or standardised mean differences (SMDs) using random-effects models. We rated all outcomes using GRADE (Grades of Recommendation, Assessment, Development and Evaluation) and presented results in the 'Summary of findings' table. MAIN RESULTS: Fifty-two studies met our inclusion criteria, randomly assigning 5077 participants to comparisons of interest. Most studies were double-blind and placebo-controlled, but studies varied in duration from one day to three years. Most participants had mild or intermittent asthma, often with co-morbid allergic rhinitis. Eighteen studies recruited only adults, 25 recruited only children and several recruited both or did not specify (n = 9).With the exception of adverse events, reporting of outcomes of interest to this review was infrequent, and selective reporting may have had a serious effect on the completeness of the evidence. Allocation procedures generally were not well described, about a quarter of the studies were at high risk of bias for performance or detection bias or both and participant attrition was high or unknown in around half of the studies.One short study reported exacerbations requiring a hospital visit and observed no adverse events. Five studies reported quality of life, but the data were not suitable for meta-analysis. Serious adverse events were infrequent, and analysis using risk differences suggests that no more than 1 in 100 are likely to suffer a serious adverse event as a result of treatment with SLIT (RD 0.0012, 95% confidence interval (CI) -0.0077 to 0.0102; participants = 2560; studies = 22; moderate-quality evidence).Within secondary outcomes, wide but varied reporting of largely unvalidated asthma symptom and medication scores precluded meaningful meta-analysis; a general trend suggested SLIT benefit over placebo, but variation in scales meant that results were difficult to interpret.Changes in inhaled corticosteroid use in micrograms per day (MD 35.10 mcg/d, 95% CI -50.21 to 120.42; low-quality evidence), exacerbations requiring oral steroids (studies = 2; no events) and bronchial provocation (SMD 0.69, 95% CI -0.04 to 1.43; very low-quality evidence) were not often reported. This led to many imprecise estimates with wide confidence intervals that included the possibility of both benefit and harm from SLIT.More people taking SLIT had adverse events of any kind compared with control (OR 1.70, 95% CI 1.21 to 2.38; low-quality evidence; participants = 1755; studies = 19), but events were usually reported to be transient and mild.Lack of data prevented most of the planned subgroup and sensitivity analyses. AUTHORS' CONCLUSIONS: Lack of data for important outcomes such as exacerbations and quality of life and use of different unvalidated symptom and medication scores have limited our ability to draw a clinically useful conclusion. Further research using validated scales and important outcomes for patients and decision makers is needed so that SLIT can be properly assessed as clinical treatment for asthma. Very few serious adverse events have been reported, but most studies have included patients with intermittent or mild asthma, so we cannot comment on the safety of SLIT for those with moderate or severe asthma. SLIT is associated with increased risk of all adverse events

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Referentes y reflexiones para la construcción de una propuesta pedagógica que fortalezca el programa de apoyo escolar en la fundación ZUÁ

Este informe es resultado del trabajo realizado por un Grupo de Docentes Pasantes de Práctica Social (en adelante G. D. P.) de la Facultad de Ciencias y Educación de la Universidad Distrital Francisco José de Caldas (En adelante U. D.), aspirantes al título de licenciados en Educación Básica con Énfasis en Humanidades y Lengua Castellana, en la FUNDACIÓN ZUÁ (en adelante F. Z.). Dicho trabajo se inscribe principalmente en el marco de las pasantías con carácter de práctica social que la U. D. pone a consideración de sus estudiantes como opción de grado. En este informe se exponen diversos aspectos sobre la comunidad en donde se desarrolla la pasantía, haciendo referencia a la localidad, el barrio, y la institución: su historia, su estructura organizacional y administrativa, su modelo de organización pedagógica y su impacto social. Además, se describe la comunidad específica de trabajo. Después se da a conocer el problema que pretende abordarse en este informe, y se explica la importancia y pertinencia de dicho planteamiento. En esta medida se expone la metodología de la investigación, la metodología pedagógica, los referentes teóricos, la sistematización, y las conclusiones a las que se dio lugar por medio de esta labor