16 papers · ranked by Valyu relevance
Anastasia Drozdova, Ekaterina Trofimova, Polina Guseva, Anna Scherbakova + 2 more
The use of program code as a data source is increasingly expanding among data scientists. The purpose of the usage varies from the semantic classification of code to the automatic generation of programs. However, the machine learning model application is somewhat limited without annotating the code snippets. To address…
Jian Wang, Tao Lin, Rongsen Zhao, Huiling Zhao + 1 more
The deep natural language translation models have been used for automatic code error correction and have demonstrated outstanding potential. However, a large and accurately annotated training dataset is essential for these models to perform well. The key to improving the performance of these models lies in…
Alexander Donath, Frank Jühling, Marwa Al-Arab, Stephan H Bernhart + 4 more
'Franziska Reinhardt' 'Peter F Stadler' 'Martin Middendorf' 'Matthias Bernt'] Title: Abstract With the rapid increase of sequenced metazoan mitochondrial genomes, a detailed manual annotation is becoming more and more infeasible. While it is easy to identify the approximate location of protein-coding genes within…
Kevin M Livingston, Michael Bada, Lawrence E Hunter, Karin Verspoor
Background Though the annotation of digital artifacts with metadata has a long history, the bulk of that work focuses on the association of single terms or concepts to single targets. As annotation efforts expand to capture more complex information, annotations will need to be able to refer to knowledge structures…
Piotr Minkiewicz, Małgorzata Darewicz, Anna Iwaniak, Marta Turło + 1 more
'Joanna Bojarska'] Phosphorylation represents one of the most important modifications of amino acids, peptides, and proteins. By modifying the latter, it is useful in improving the functional properties of foods. Although all these substances are broadly annotated in internet databases, there is no unified code for…
Jin-Dong Kim, Tomoko Ohta, Jun'ichi Tsujii
Background Advanced Text Mining (TM) such as semantic enrichment of papers, event or relation extraction, and intelligent Question Answering have increasingly attracted attention in the bio-medical domain. For such attempts to succeed, text annotation from the biological point of view is indispensable. However, due to…
Ehsan Abdekhodaie, Javad Hatami, Hadi Bahrami Ehsan, Reza Kormi-Nouri
'Reza Kormi-Nouri'] There is a lack of free software that provides a professional and smooth experience in text editing and markup for qualitative data analysis. Word processing software like Microsoft Word provides a good editing experience, allowing the researcher to effortlessly add comments to text portions.…
Samuel Dobbie, Huw Strafford, W. Owen Pickrell, Beata Fonferko-Shadrach + 4 more
'Beata Fonferko-Shadrach' 'Carys Jones' 'Ashley Akbari' 'Simon Thompson' 'Arron Lacey'] Across various domains, such as health and social care, law, news, and social media, there are increasing quantities of unstructured texts being produced. These potential data sources often contain rich information that could be…
Paolo Ciccarese, Marco Ocana, Leyla Jael Garcia Castro, Sudeshna Das + 1 more
'Tim Clark'] Background There is currently a gap between the rich and expressive collection of published biomedical ontologies, and the natural language expression of biomedical papers consumed on a daily basis by scientific researchers. The purpose of this paper is to provide an open, shareable structure for dynamic…
Christian O'Reilly, Elisabetta Iavarone, Sean L. Hill
Large models of complex neuronal circuits require specifying numerous parameters, with values that often need to be extracted from the literature, a tedious and error-prone process. To help establishing shareable curated corpora of annotations, we have developed a literature curation framework comprising an annotation…
Paolo Ciccarese, Marco Ocana, Tim Clark
Background Our group has developed a useful shared software framework for performing, versioning, sharing and viewing Web annotations of a number of kinds, using an open representation model. Methods The Domeo Annotation Tool was developed in tandem with this open model, the Annotation Ontology (AO). Development of…
Andon Tchechmedjiev, Amine Abdaoui, Vincent Emonet, Stella Zevio + 1 more
'Clement Jonquet'] Background 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…
L. Suhrbier, W.-H. Kusber, O. Tschöpe, A. Güntsch + 1 more
Biological research collections holding billions of specimens world-wide provide the most important baseline information for systematic biodiversity research. Increasingly, specimen data records become available in virtual herbaria and data portals. The traditional (physical) annotation procedure fails here, so that an…
Mohamed Jmaiel, Mounir Mokhtari, Bessam Abdulrazak, Hamdi Aloulou + 4 more
'Slim Kallel' 'Khalil Chehab' 'Anis Kalboussi' 'Ahmed Hadj Kacem'] The annotation practice is an almost daily activity; it is used by healthcare professionals (PHC) to analyze, collaborate, share knowledge and communicate, between them, information present in the healthcare record of patients. These annotations are…
Fabio Giachelle, Ornella Irrera, Gianmaria Silvello
Background Semantic annotators and Natural Language Processing (NLP) methods for Named Entity Recognition and Linking (NER+L) require plenty of training and test data, especially in the biomedical domain. Despite the abundance of unstructured biomedical data, the lack of richly annotated biomedical datasets poses…
Ornella Irrera, Stefano Marchesin, Gianmaria Silvello
Background The constant growth of biomedical data is accompanied by the need for new methodologies to effectively and efficiently extract machine-readable knowledge for training and testing purposes. A crucial aspect in this regard is creating large, often manually or semi-manually, annotated corpora vital for…