6,506 research outputs found
Using Neural Networks for Relation Extraction from Biomedical Literature
Using different sources of information to support automated extracting of
relations between biomedical concepts contributes to the development of our
understanding of biological systems. The primary comprehensive source of these
relations is biomedical literature. Several relation extraction approaches have
been proposed to identify relations between concepts in biomedical literature,
namely, using neural networks algorithms. The use of multichannel architectures
composed of multiple data representations, as in deep neural networks, is
leading to state-of-the-art results. The right combination of data
representations can eventually lead us to even higher evaluation scores in
relation extraction tasks. Thus, biomedical ontologies play a fundamental role
by providing semantic and ancestry information about an entity. The
incorporation of biomedical ontologies has already been proved to enhance
previous state-of-the-art results.Comment: Artificial Neural Networks book (Springer) - Chapter 1
EXACT2: the semantics of biomedical protocols
© 2014 Soldatova et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.This article has been made available through the Brunel Open Access Publishing Fund.Background: The reliability and reproducibility of experimental procedures is a cornerstone of scientific practice. There is a pressing technological need for the better representation of biomedical protocols to enable other agents (human or machine) to better reproduce results. A framework that ensures that all information required for the replication of experimental protocols is essential to achieve reproducibility. Methods: We have developed the ontology EXACT2 (EXperimental ACTions) that is designed to capture the full semantics of biomedical protocols required for their reproducibility. To construct EXACT2 we manually inspected hundreds of published and commercial biomedical protocols from several areas of biomedicine. After establishing a clear pattern for extracting the required information we utilized text-mining tools to translate the protocols into a machine amenable format. We have verified the utility of EXACT2 through the successful processing of previously ‘unseen’ (not used for the construction of EXACT2) protocols. Results: The paper reports on a fundamentally new version EXACT2 that supports the semantically-defined representation of biomedical protocols. The ability of EXACT2 to capture the semantics of biomedical procedures was verified through a text mining use case. In this EXACT2 is used as a reference model for text mining tools to identify terms pertinent to experimental actions, and their properties, in biomedical protocols expressed in natural language. An EXACT2-based framework for the translation of biomedical protocols to a machine amenable format is proposed. Conclusions: The EXACT2 ontology is sufficient to record, in a machine processable form, the essential information about biomedical protocols. EXACT2 defines explicit semantics of experimental actions, and can be used by various computer applications. It can serve as a reference model for for the translation of biomedical protocols in natural language into a semantically-defined format.This work has been partially funded by the Brunel University BRIEF award and a grant from Occams Resources
OHMI: The Ontology of Host-Microbiome Interactions
Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following the OBO Foundry principles. OHMI leverages established ontologies to create logically structured representations of microbiomes, microbial taxonomy, host species, host anatomical entities, and HMIs under different conditions and associated study protocols and types of data analysis and experimental results
Ontology of core data mining entities
In this article, we present OntoDM-core, an ontology of core data mining
entities. OntoDM-core defines themost essential datamining entities in a three-layered
ontological structure comprising of a specification, an implementation and an application
layer. It provides a representational framework for the description of mining
structured data, and in addition provides taxonomies of datasets, data mining tasks,
generalizations, data mining algorithms and constraints, based on the type of data.
OntoDM-core is designed to support a wide range of applications/use cases, such as
semantic annotation of data mining algorithms, datasets and results; annotation of
QSAR studies in the context of drug discovery investigations; and disambiguation of
terms in text mining. The ontology has been thoroughly assessed following the practices
in ontology engineering, is fully interoperable with many domain resources and
is easy to extend
The Materials Science Procedural Text Corpus: Annotating Materials Synthesis Procedures with Shallow Semantic Structures
Materials science literature contains millions of materials synthesis
procedures described in unstructured natural language text. Large-scale
analysis of these synthesis procedures would facilitate deeper scientific
understanding of materials synthesis and enable automated synthesis planning.
Such analysis requires extracting structured representations of synthesis
procedures from the raw text as a first step. To facilitate the training and
evaluation of synthesis extraction models, we introduce a dataset of 230
synthesis procedures annotated by domain experts with labeled graphs that
express the semantics of the synthesis sentences. The nodes in this graph are
synthesis operations and their typed arguments, and labeled edges specify
relations between the nodes. We describe this new resource in detail and
highlight some specific challenges to annotating scientific text with shallow
semantic structure. We make the corpus available to the community to promote
further research and development of scientific information extraction systems.Comment: Accepted as a long paper at the Linguistic Annotation Workshop (LAW)
at ACL 201
What's unusual in online disease outbreak news?
Background: Accurate and timely detection of public health events of
international concern is necessary to help support risk assessment and response
and save lives. Novel event-based methods that use the World Wide Web as a
signal source offer potential to extend health surveillance into areas where
traditional indicator networks are lacking. In this paper we address the issue
of systematically evaluating online health news to support automatic alerting
using daily disease-country counts text mined from real world data using
BioCaster. For 18 data sets produced by BioCaster, we compare 5 aberration
detection algorithms (EARS C2, C3, W2, F-statistic and EWMA) for performance
against expert moderated ProMED-mail postings. Results: We report sensitivity,
specificity, positive predictive value (PPV), negative predictive value (NPV),
mean alerts/100 days and F1, at 95% confidence interval (CI) for 287
ProMED-mail postings on 18 outbreaks across 14 countries over a 366 day period.
Results indicate that W2 had the best F1 with a slight benefit for day of week
effect over C2. In drill down analysis we indicate issues arising from the
granular choice of country-level modeling, sudden drops in reporting due to day
of week effects and reporting bias. Automatic alerting has been implemented in
BioCaster available from http://born.nii.ac.jp. Conclusions: Online health news
alerts have the potential to enhance manual analytical methods by increasing
throughput, timeliness and detection rates. Systematic evaluation of health
news aberrations is necessary to push forward our understanding of the complex
relationship between news report volumes and case numbers and to select the
best performing features and algorithms
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