Featured videos
View featured videos from across the BMC-series journals
Page 4 of 29
The development of bioinformatics databases, algorithms, and tools throughout the last years has lead to a highly distributed world of bioinformatics services. Without adequate management and development suppo...
Information Extraction (IE) is a component of text mining that facilitates knowledge discovery by automatically locating instances of interesting biomedical events from huge document collections. As events are...
In this work we describe an approach that facilitates the automatic recognition of eight relationships defined between medical problems, treatments and tests. Unlike the traditional bag-of-words representation, i...
Small molecules are of increasing interest for bioinformatics in areas such as metabolomics and drug discovery. The recent release of large open access chemistry databases generates a demand for flexible tools...
Biological contextual information helps understand various phenomena occurring in the biological systems consisting of complex molecular relations. The construction of context-specific relational resources vas...
Lately, there has been a great interest in the application of information extraction methods to the biomedical domain, in particular, to the extraction of relationships of genes, proteins, and RNA from scienti...
Biomedical named entity recognition (BioNER) is a basic and important medical information extraction task to extract medical entities with special meaning from medical texts. In recent years, deep learning has...
A fundamental goal of the U.S. National Institute of Health (NIH) "Roadmap" is to strengthen Translational Research, defined as the movement of discoveries in basic research to application at the clinical level. ...
Elucidation of interactive relation between chemicals and genes is of key relevance not only for discovering new drug leads in drug development but also for repositioning existing drugs to novel therapeutic ta...
With advancements in omics technologies, the range of biological processes where long non-coding RNAs (lncRNAs) are involved, is expanding extensively, thereby generating the need to develop lncRNA annotation ...
As Twitter has become an active data source for health surveillance research, it is important that efficient and effective methods are developed to identify tweets related to personal health experience. Conven...
Making accurate patient care decision, as early as possible, is a constant challenge, especially for physicians in the emergency department. The increasing volumes of electronic medical records (EMRs) open new...
The Clinical E-Science Framework (CLEF) project has built a system to extract clinically significant information from the textual component of medical records in order to support clinical research, evidence-ba...
Scientific workflows improve the process of scientific experiments by making computations explicit, underscoring data flow, and emphasizing the participation of humans in the process when intuition and human r...
Mathematical and computational modelling of biochemical systems has seen a lot of effort devoted to the definition and implementation of high-performance mechanistic simulation frameworks. Within these framewo...
The limitations of traditional computer-aided detection (CAD) systems for mammography, the extreme importance of early detection of breast cancer and the high impact of the false diagnosis of patients drive re...
Taxonomic descriptions are traditionally composed in natural language and published in a format that cannot be directly used by computers. The Exploring Taxon Concepts (ETC) project has been developing a set o...
The classifier relies on the UMLS® knowledge source (Unified Medical Language System®) and on heuristic algorithms for ... clinical trial record and candidate GBD categories using natural language processing and ...
Two main achievements are described in this paper: (a) a system for document classification which crucially relies on the results of an advanced pipeline of natural language processing tools; (b) a system which i...
Currently, data about age-phenotype associations are not systematically organized and cannot be studied methodically. Searching for scientific articles describing phenotypic changes reported as occurring at a ...
Controlled vocabularies such as the Unified Medical Language System (UMLS®) and Medical Subject Headings ... (MeSH®) are widely used for biomedical natural language processing (NLP) tasks. However, the standard.....
With the development of e-Health, it plays a more and more important role in predicting whether a doctor’s answer can be accepted by a patient through online healthcare community. Unlike the previous work whic...
Although biomedical publications and literature are growing rapidly, there still lacks structured knowledge that can be easily processed by computer programs. In order to extract such knowledge from plain text...
Automatic signal-feature extraction algorithms are crucial for profile processing in bioinformatics. Both baseline drift and noise seriously affect the position and peak area of signals. An efficient algorithm...
The National Center for Biomedical Ontology (NCBO) is developing a system for automated, ontology-based access to online biomedical resources. The system's indexing workflow processes the text metadata of dive...
Visualization concerns the representation of data visually and is an important task in scientific research. Protein-protein interactions (PPI) are discovered using either wet lab techniques, such mass spectrom...
The bio-ontology community falls into two camps: first we have biology domain experts, who actually hold the knowledge we wish to capture in ontologies; second, we have ontology specialists, who hold knowledge...
Natural products are the source of various functional materials such as medicines, and understanding their biosynthetic pathways can provide information that is helpful for their effective production through t...
We participated, as Team 81, in the Article Classification and the Interaction Method subtasks (ACT and IMT, respectively) of the Protein-Protein Interaction...task of the BioCreative III Challenge. For the ACT, ...
Ontological concepts are useful for many different biomedical tasks. Concepts are difficult to recognize in text due to a disconnect between what is captured in an ontology and how the concepts are expressed i...
Word sense disambiguation (WSD) attempts to solve lexical ambiguities by identifying the correct meaning of a word based on its context. WSD has been demonstrated to be an important step in knowledge-based app...
In biomedical research, chemical and disease relation extraction from unstructured biomedical literature is an essential task. Effective context understanding and knowledge integration are two main research pr...
Based on the promising results obtained so far we suggest that the co-authorship information and the circumstances of the articles' release (like the title of the journal, the year of publication) can be a crucia...
With the growing availability of full-text articles online, scientists and other consumers of the life sciences literature now have the ability to go beyond searching bibliographic records (title, abstract, me...
The investigation of possible interactions between two proteins in intracellular signaling is an expensive and laborious procedure in the wet-lab, therefore, several in silico approaches have been implemented ...
The number of natural proteins represents a small fraction of all the possible protein sequences and there is an enormous number of proteins never sampled by nature, the so called "never born proteins" (NBPs)....
This paper describes the design of an event ontology being developed for application in the machine understanding of infectious disease-related events reported in natural language text. This event ontology is ...
The effective combination of texts and knowledge may improve performances of natural language processing tasks. For the recognition of chemical-induced...
Traditional genome annotation systems were developed in a very different computing era, one where the World Wide Web was just emerging. Consequently, these systems are built as centralized black boxes focused ...
Recent years have brought great progress in efforts to digitize the world’s biodiversity data, but integrating data from many different providers, and across research domains, remains challenging. Semantic Web...
We describe a prototype implementation of a platform that could underlie a Precision Oncology Rapid Learning system.
In pursuing personalized medicine, pharmacogenomic (PGx) knowledge may help guide prescribing drugs based on a person’s genotype. Here we evaluate the feasibility of incorporating PGx knowledge, combined with ...
The Pan-African bioinformatics network, H3ABioNet, comprises 27 research institutions in 17 African countries. H3ABioNet is part of the Human Health and Heredity in Africa program (H3Africa), an African-led re...
Examining the distribution of variation has proven an extremely profitable technique in the effort to identify sequences of biological significance. Most approaches in the field, however, evaluate only the con...
Extracting protein-protein interactions from biomedical literature is an important task in biomedical text mining. Supervised machine learning methods have been used with great success in this task but they te...
The package pyMeSHSim recognizes bio-NEs by using MetaMap which produces Unified Medical Language System (UMLS) concepts in natural language process. To map the UMLS concepts to Medical...> 0.94, precision > 0.56...
Functional annotation of proteins remains a challenging task. Currently the scientific literature serves as the main source for yet uncurated functional annotations, but curation work is slow and expensive. Au...
Topic detection is a task that automatically identifies topics (e.g., "biochemistry" and "protein structure") in scientific articles based on information content. Topic detection will benefit many other natural language
We propose MKEM, a Multi-level Knowledge Emergence Model, to discover implicit relationships using Natural Language Processing techniques such as Link Grammar and Ontologies such as Unified Medical Language Syste...
View featured videos from across the BMC-series journals
Speed
15 days to first decision for all manuscripts
70 days to first decision for reviewed manuscripts only
163 days from submission to acceptance
36 days from acceptance to publication
Citation Impact
3.169 - 2-year Impact Factor
3.629 - 5-year Impact Factor
1.276 - Source Normalized Impact per Paper (SNIP)
1.567 - SCImago Journal Rank (SJR)
Usage
6,337,109 Downloads (2021)
5089 Altmetric Mentions