BioCreative III interactive task: an overview

The BioCreative challenge evaluation is a community-wide effort for evaluating text mining and information extraction systems applied to the biological domain. The biocurator community, as an active user of biomedical literature, provides a diverse and engaged end user group for text mining tools. Earlier BioCreative challenges involved many text mining teams in developing basic capabilities relevant to biological curation, but they did not address the issues of system usage, insertion into the workflow and adoption by curators. Thus in BioCreative III (BC-III), the InterActive Task (IAT) was introduced to address the utility and usability of text mining tools for real-life biocuration tasks. To support the aims of the IAT in BC-III, involvement of both developers and end users was solicited, and the development of a user interface to address the tasks interactively was requested

You can't always sketch what you want: Understanding Sensemaking in Visual Query Systems

Visual query systems (VQSs) empower users to interactively search for line charts with desired visual patterns, typically specified using intuitive sketch-based interfaces. Despite decades of past work on VQSs, these efforts have not translated to adoption in practice, possibly because VQSs are largely evaluated in unrealistic lab-based settings. To remedy this gap in adoption, we collaborated with experts from three diverse domains---astronomy, genetics, and material science---via a year-long user-centered design process to develop a VQS that supports their workflow and analytical needs, and evaluate how VQSs can be used in practice. Our study results reveal that ad-hoc sketch-only querying is not as commonly used as prior work suggests, since analysts are often unable to precisely express their patterns of interest. In addition, we characterize three essential sensemaking processes supported by our enhanced VQS. We discover that participants employ all three processes, but in different proportions, depending on the analytical needs in each domain. Our findings suggest that all three sensemaking processes must be integrated in order to make future VQSs useful for a wide range of analytical inquiries.Comment: Accepted for presentation at IEEE VAST 2019, to be held October 20-25 in Vancouver, Canada. Paper will also be published in a special issue of IEEE Transactions on Visualization and Computer Graphics (TVCG) IEEE VIS (InfoVis/VAST/SciVis) 2019 ACM 2012 CCS - Human-centered computing, Visualization, Visualization design and evaluation method

The GA4GH Variation Representation Specification (VRS): a Computational Framework for the Precise Representation and Federated Identification of Molecular Variation

Maximizing the personal, public, research, and clinical value of genomic information will require that clinicians, researchers, and testing laboratories exchange genetic variation data reliably. Developed by a partnership among national information resource providers, public initiatives, and diagnostic testing laboratories under the auspices of the Global Alliance for Genomics and Health (GA4GH), the Variation Representation Specification (VRS, pronounced “verse”) is an extensible framework for the semantically precise and computable representation of variation that complements contemporary human-readable and flat file standards for variation representation. VRS objects are designed to be semantically precise representations of variation, and leverage this design to enable unique, federated identification of molecular variation. We describe the components of this framework, including the terminology and information model, schema, data sharing conventions, and a reference implementation, each of which is intended to be broadly useful and freely available for community use. The specification, documentation, examples, and community links are available at https://vrs.ga4gh.org/

Die Rolle der Zielnähe und der investierten Anstrengung für den erwarteten Wert einer Handlung

In human neuroscientific research, there has been an increasing interest in how the brain computes the value of an anticipated outcome. However, evidence is still missing about which valuation related brain regions are modulated by the proximity to an expected goal and the previously invested effort to reach a goal. The aim of this dissertation is to investigate the effects of goal proximity and invested effort on valuation related regions in the human brain. We addressed this question in two fMRI studies by integrating a commonly used reward anticipation task in differential versions of a Multitrial Reward Schedule Paradigm. In both experiments, subjects had to perform consecutive reward anticipation tasks under two different reward contingencies: in the delayed condition, participants received a monetary reward only after successful completion of multiple consecutive trials. In the immediate condition, money was earned after every successful trial. In the first study, we could demonstrate that the rostral cingulate zone of the posterior medial frontal cortex signals action value contingent to goal proximity, thereby replicating neurophysiological findings about goal proximity signals in a homologous region in non-human primates. The findings of the second study imply that brain regions associated with general cognitive control processes are modulated by previous effort investment. Furthermore, we found the posterior lateral prefrontal cortex and the orbitofrontal cortex to be involved in coding for the effort-based context of a situation. In sum, these results extend the role of the human rostral cingulate zone in outcome evaluation to the continuous updating of action values over a course of action steps based on the proximity to the expected reward. Furthermore, we tentatively suggest that previous effort investment invokes processes under the control of the executive system, and that posterior lateral prefrontal cortex and the orbitofrontal cortex are involved in an effort-based context representation that can be used for outcome evaluation that is dependent on the characteristics of the current situation.Derzeit besteht im Bereich der Neurowissenschaften ein großes Interesse daran aufzuklären, auf welche Weise verschiedene Variablen die Wertigkeit eines erwarteten Handlungsziels beeinflussen bzw. welche Hirnregionen an der Repräsentation der Wertigkeit eines Handlungsziels beteiligt sind. Die meisten Untersuchungen beziehen sich dabei auf Einflussgrößen wie die erwartete Belohnungshöhe, die Wahrscheinlichkeit, mit der ein bestimmtes Ereignis eintritt, oder die Dauer bis zum Erhalt einer Belohnung. Bisher liegen jedoch kaum Untersuchungen vor bezüglich zweier anderer Variablen, die ebenfalls den erwarteten Wert eines Handlungsergebnisses beeinflussen. Das sind (a) die Nähe zu dem erwarteten Ziel und (b) die bisher investierte Anstrengung, um ein Ziel zu erreichen. Das Ziel der vorliegenden Dissertation ist zu untersuchen, wie die Nähe zum Ziel und die bisher investierte Anstrengung Gehirnregionen beeinflussen, die mit der Repräsentation von Wertigkeit im Zusammenhang stehen. Dazu führten wir zwei fMRT-Studien durch, in denen wir eine klassische Belohnungs-Antizipationsaufgabe in unterschiedliche Versionen eines „Multitrial Reward Schedule“ Paradigmas integriert haben. Das bedeutet, dass die Probanden Belohnungs-Antizipationsaufgaben unter zwei unterschiedlichen Belohnungskontingenzen bearbeiteten: In der verzögerten Bedingung erhielten die Probanden einen Geldbetrag nach der erfolgreichen Bearbeitung von mehreren aufeinanderfolgenden Aufgaben, in der direkten Bedingung dagegen nach jeder korrekt ausgeführten Aufgabe. In der ersten Studie konnte eine sukzessiv ansteigende Aktivität in Abhängigkeit zur Zielnähe in der rostralen cingulären Zone identifiziert werden. Das deutet darauf hin, dass dieses Areal den Wert einer Handlung in Abhängigkeit zur Nähe zum Ziel kodiert. Die Ergebnisse der zweiten Studie zeigten, dass die bisher investierte Anstrengung kortikale Regionen moduliert, die klassischerweise mit kognitiven Kontrollfunktionen in Zusammenhang gebracht werden. Außerdem repräsentierten der posteriore laterale präfrontale Cortex und der orbitofrontale Cortex den motivationalen Kontext eines Trials anhand des Risikos des Verlustes von bisher investierter Anstrengung. Insgesamt weisen diese Befunde darauf hin, dass die rostrale cinguläre Zone eine entscheidende Rolle spielt für die Kontrolle sequenzieller Handlungsstufen, die auf eine verzögerte Belohnung ausgerichtet sind. Diese Kontrollfunktion scheint auf der kontinuierlichen Aktualisierung des Wertes einer Handlungsstufe zu basieren, der von der aktuellen Zielnähe bestimmt wird. Die Befunde der zweiten Studie lassen darauf schließen, dass sich die bisher investierte Anstrengung zur Erreichung eines Handlungsziels auf die Bereitstellung von allgemeinen kognitiven Ressourcen auswirkt. Das Risiko des Verlustes von bisher investierter Anstrengung kann außerdem ein kontextuelles Merkmal der Situation darstellen, das als Bezugsrahmen für die Evaluation des erwarteten Wertes dienen kann

Information retrieval and text mining technologies for chemistry

Efficient access to chemical information contained in scientific literature, patents, technical reports, or the web is a pressing need shared by researchers and patent attorneys from different chemical disciplines. Retrieval of important chemical information in most cases starts with finding relevant documents for a particular chemical compound or family. Targeted retrieval of chemical documents is closely connected to the automatic recognition of chemical entities in the text, which commonly involves the extraction of the entire list of chemicals mentioned in a document, including any associated information. In this Review, we provide a comprehensive and in-depth description of fundamental concepts, technical implementations, and current technologies for meeting these information demands. A strong focus is placed on community challenges addressing systems performance, more particularly CHEMDNER and CHEMDNER patents tasks of BioCreative IV and V, respectively. Considering the growing interest in the construction of automatically annotated chemical knowledge bases that integrate chemical information and biological data, cheminformatics approaches for mapping the extracted chemical names into chemical structures and their subsequent annotation together with text mining applications for linking chemistry with biological information are also presented. Finally, future trends and current challenges are highlighted as a roadmap proposal for research in this emerging field.A.V. and M.K. acknowledge funding from the European Community’s Horizon 2020 Program (project reference: 654021 - OpenMinted). M.K. additionally acknowledges the Encomienda MINETAD-CNIO as part of the Plan for the Advancement of Language Technology. O.R. and J.O. thank the Foundation for Applied Medical Research (FIMA), University of Navarra (Pamplona, Spain). This work was partially funded by Consellería de Cultura, Educación e Ordenación Universitaria (Xunta de Galicia), and FEDER (European Union), and the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684). We thank Iñigo Garciá -Yoldi for useful feedback and discussions during the preparation of the manuscript.info:eu-repo/semantics/publishedVersio

Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy

<p>Abstract</p> <p>Background</p> <p>Ontology term labels can be ambiguous and have multiple senses. While this is no problem for human annotators, it is a challenge to automated methods, which identify ontology terms in text. Classical approaches to word sense disambiguation use co-occurring words or terms. However, most treat ontologies as simple terminologies, without making use of the ontology structure or the semantic similarity between terms. Another useful source of information for disambiguation are metadata. Here, we systematically compare three approaches to word sense disambiguation, which use ontologies and metadata, respectively.</p> <p>Results</p> <p>The 'Closest Sense' method assumes that the ontology defines multiple senses of the term. It computes the shortest path of co-occurring terms in the document to one of these senses. The 'Term Cooc' method defines a log-odds ratio for co-occurring terms including co-occurrences inferred from the ontology structure. The 'MetaData' approach trains a classifier on metadata. It does not require any ontology, but requires training data, which the other methods do not. To evaluate these approaches we defined a manually curated training corpus of 2600 documents for seven ambiguous terms from the Gene Ontology and MeSH. All approaches over all conditions achieve 80% success rate on average. The 'MetaData' approach performed best with 96%, when trained on high-quality data. Its performance deteriorates as quality of the training data decreases. The 'Term Cooc' approach performs better on Gene Ontology (92% success) than on MeSH (73% success) as MeSH is not a strict is-a/part-of, but rather a loose is-related-to hierarchy. The 'Closest Sense' approach achieves on average 80% success rate.</p> <p>Conclusion</p> <p>Metadata is valuable for disambiguation, but requires high quality training data. Closest Sense requires no training, but a large, consistently modelled ontology, which are two opposing conditions. Term Cooc achieves greater 90% success given a consistently modelled ontology. Overall, the results show that well structured ontologies can play a very important role to improve disambiguation.</p> <p>Availability</p> <p>The three benchmark datasets created for the purpose of disambiguation are available in Additional file <supplr sid="S1">1</supplr>.</p> <suppl id="S1"> <title> <p>Additional file 1</p> </title> <text> <p><b>Benchmark datasets used in the experiments.</b> The three corpora (High quality/Low quantity corpus; Medium quality/Medium quantity corpus; Low quality/High quantity corpus) are given in the form of PubMed identifiers (PMID) for True/False cases for the 7 ambiguous terms examined (GO/MeSH/UMLS identifiers are also given).</p> </text> <file name="1471-2105-10-28-S1.txt"> <p>Click here for file</p> </file> </suppl

The coherent organization of mental life depends on mechanisms for context-sensitive gain-control that are impaired in schizophrenia

There is rapidly growing evidence that schizophrenia involves changes in context-sensitive gain-control and probabilistic inference. In addition to the well-known cognitive disorganization to which these changes lead, basic aspects of vision are also impaired, as discussed by other papers on this Frontiers Research Topic. The aim of this paper is to contribute to our understanding of such findings by examining five central hypotheses. First, context-sensitive gain-control is fundamental to brain function and mental life. Second, it occurs in many different regions of the cerebral cortex of many different mammalian species. Third, it has several computational functions, each with wide generality. Fourth, it is implemented by several neural mechanisms at cellular and circuit levels. Fifth, impairments of context-sensitive gain-control produce many of the well-known symptoms of schizophrenia and change basic processes of visual perception. These hypotheses suggest why disorders of vision in schizophrenia may provide insights into the nature and mechanisms of impaired reality testing and thought disorder in psychosis. They may also cast light on normal mental function and its neural bases. Limitations of these hypotheses, and ways in which they need further testing and development, are outlined

Language in genetics research informed consent: The language gap and unrecognized miscommunication

Informed choice is fundamentally a process of communication, reliant entirely on the tools of language. However, the meanings and understandings of words change with time, setting, and context, threatening the basis of consent. We conducted a qualitative content analysis of Canadian genetics research documents, exploring the impacts of language on informed consent. Numerous language usages were noted as potential barriers to informed consent, including language that was vague, variable, and unusually defined. Unique combinations of words were observed to generate novel concepts without clear meanings and definitions were absent or unclear. However, the ambiguity of the language was concealed by words that were simple and familiar. We conclude that a gap in communication may exist when discussing genetics, health, and disease, in that the same words, when used by different individuals, can have different meanings, and thus individuals may not fully understand each other despite using the same words

Semantic radical consistency and character transparency effects in Chinese: an ERP study

BACKGROUND: This event-related potential (ERP) study aims to investigate the representation and temporal dynamics of Chinese orthography-to-semantics mappings by simultaneously manipulating character transparency and semantic radical consistency. Character components, referred to as radicals, make up the building blocks used dur...postprin