Semantic annotations

This article describes an ensembling system to automatically extract adverse drug events and drug related entities from clinical narratives, which was developed for the 2018 n2c2 Shared Task Track 2. Materials and Methods: We designed a neural model to tackle both nested (entities embedded in other entities) and polysemous entities (entities annotated with multiple semantic types) based on MIMIC III discharge summaries.

9p vighostrider 25-05-2023 3 2   Download

In this paper, we build a model to evaluate and select an effective and reasonable set of semantic labels from 3 commonly used sets of semantic labels: LLOCE (Longman Lexicon of Contemporary English), LDOCE (Longman Dictionary) of Contemporary English) and WordNet. And then, select the appropriate set of labels, apply it to automatic semantic labeling systems for Vietnamese, help eliminate semantic ambiguity, and support automatic translation, automatic question-and-answer systems efficiently.

13p vifalcon 18-05-2023 9 3   Download

Digitised monogenean images are usually stored in file system directories in an unstructured manner. In this paper we propose a semantic representation of these images in the form of a Monogenean Haptoral Bar Image (MHBI) ontology, which are annotated with taxonomic classification, diagnostic hard part and image properties.

11p viwyoming2711 16-12-2020 15 1   Download

Cilia are hairlike structures protruding from nearly every cell in the body. Diseases known as ciliopathies where cilia function is disrupted can result in a wide spectrum of diseases. However, most techniques for assessing ciliary motion rely on manual identification and tracking of cilia. This annotation is tedious and error-prone and more analytical techniques impose strong assumptions such as periodic motion of beating cilia.

8p vigeorgia2711 01-12-2020 9 1   Download

Gene Ontology (GO) has been used widely to study functional relationships between genes. The current semantic similarity measures rely only on GO annotations and GO structure. This limits the power of GO-based similarity because of the limited proportion of genes that are annotated to GO in most organisms.

14p vikentucky2711 26-11-2020 13 1   Download

Semantic approaches such as concept-based information retrieval rely on a corpus in which resources are indexed by concepts belonging to a domain ontology. In order to keep such applications up-to-date, new entities need to be frequently annotated to enrich the corpus.

10p vikentucky2711 24-11-2020 16 1   Download

In this paper, we evaluate the impact of different text representations of biomedical texts as features for reproducing the MeSH annotations of some of the most frequent MeSH headings. In addition to unigrams and bigrams, these features include noun phrases, citation meta-data, citation structure, and semantic annotation of the citations.

12p vikentucky2711 24-11-2020 9 3   Download

The amount of scientific information about MicroRNAs (miRNAs) is growing exponentially, making it difficult for researchers to interpret experimental results. In this study, we present an automated text mining approach using Latent Semantic Indexing (LSI) for prioritization, clustering and functional annotation of miRNAs.

12p vioklahoma2711 19-11-2020 7 1   Download

Scientific names in biology act as universal links. They allow us to cross-reference information about organisms globally. However variations in spelling of scientific names greatly diminish their ability to interconnect data. Such variations may include abbreviations, annotations, misspellings, etc.

14p viflorida2711 30-10-2020 9 1   Download

Consumers increasingly use online resources for their health information needs. While current search engines can address these needs to some extent, they generally do not take into account that most health information needs are complex and can only fully be expressed in natural language.

28p viconnecticut2711 28-10-2020 15 0   Download

Comparing and classifying functions of gene products are important in today’s biomedical research. The semantic similarity derived from the Gene Ontology (GO) annotation has been regarded as one of the most widely used indicators for protein interaction.

14p viconnecticut2711 28-10-2020 15 1   Download

Almost 16,000 human long non-coding RNA (lncRNA) genes have been identified in the GENCODE project. However, the function of most of them remains to be discovered. The function of lncRNAs and other novel genes can be predicted by identifying significantly enriched annotation terms in already annotated genes that are co-expressed with the lncRNAs.

12p vicoachella2711 27-10-2020 7 1   Download

Despite a wide adoption of English in science, a significant amount of biomedical data are produced in other languages, such as French. Yet a majority of natural language processing or semantic tools as well as domain terminologies or ontologies are only available in English, and cannot be readily applied to other languages, due to fundamental linguistic differences.

26p viconnecticut2711 28-10-2020 11 1   Download

Biological knowledge, and therefore Gene Ontology annotation sets, for human genes is incomplete. Recent studies have reported that biases in available GO annotations result in biased estimates of functional similarities of genes, but it is still unclear what the effect of incompleteness itself may be, even in the absence of bias.

15p vijisoo2711 27-10-2020 12 0   Download

Mathematics and Phy sics-based simulation models have the potential to help interpret and encapsulate biological phenomena in a computable and reproducible form. Similarly, comprehensive descriptions of such models help to ensure that such models are accessible, discoverable, and reusable.

10p vicolorado2711 23-10-2020 7 1   Download

Many disease causing genes have been identified through different methods, but there have been no uniform annotations of biomedical named entity (bio-NE) of the disease phenotypes of these genes yet. Furthermore, semantic similarity comparison between two bio-NE annotations has become important for data integration or system genetics analysis.

14p vicolorado2711 22-10-2020 10 0   Download

Understanding process design as open learning facility allows promoting organizational structures and change proposals in an informed and bottom-up way. In this work the constitutive elements and processes of such a participatory infrastructure are studied from an open educational resource and open access perspective on the individual and collective level. Besides providing OER the focus is on generating work process-relevant knowledge from an individual perspective, disseminating it for collective reflection, and propagating it to organizational practice.

24p kequaidan1 05-11-2019 20 1   Download

In this paper, we present a method for generating automatically semantic annotations of sport news items. It combines the results obtained through our continuous study of capturing different kinds of semantics which having from simple to more complex representation structure.

8p visasuke2711 25-04-2019 20 0   Download

In this project an approach based on Wikipedia link structure for word sense Disambiguation is presented and evaluated. This paper describes a method for creating sense tagged data using Wikipedia as a source of sense semantic annotations. Word sense disambiguation (WSD) is the ability to identify the meaning of words in context in a computational manner.

5p byphasse043256 24-03-2019 20 2   Download

In data-oriented language processing, an annotated language corpus is used as a stochastic grammar. The most probable analysis of a new sentence is constructed by combining fragments from the corpus in the most probable way. This approach has been successfully used for syntactic analysis, using corpora with syntactic annotations such as the Penn Tree-bank. If a corpus with semantically annotated sentences is used, the same approach can also generate the most probable semantic interpretation of an input sentence. The present paper explains this semantic interpretation method. ...

9p bunthai_1 06-05-2013 51 3   Download