A web-based NCBI-PubMed search application, which can analyze articles for selected biomedical verbs and give users relational information, such as subject, object, location, manner, time, etc. After receiving keyword query input, BWS retrieves matching PubMed abstracts and lists them along with snippets by order of relevancy to protein-protein interaction. Users can then select articles for further analysis, and BWS will find and mark up biomedical relations in the text. The analysis results can be viewed in the abstract text or in table form.
An automated method for determining which diseases are mentioned in biomedical text, the task of disease normalization. DNorm is a high-performing and mathematically principled framework for learning similarities between mentions and concept names directly from training data. DNorm is the first technique to use machine learning to normalize disease names and also the first method employing pairwise learning to rank in a normalization task.
Permits to recognize disease and chemical entities in text documents. D3NER is a named entity recognition (NER) application that uses entities recognition using conditional random fields (CRFs) and a bidirectional long short-term memory (biLSTM) network architect improved with embeddings of various informative linguistic information. It can be integrated as an alternative NER model into biomedical knowledge extracting systems.
A hybrid method integrating a machine-learning model with a pattern identification strategy to identify the individual components of each composite mention. SimConcept achieves high performance in identifying and resolving composite mentions for three key biological entities: genes (90.42% in F-measure), diseases (86.47% in F-measure), and chemicals (86.05% in F-measure). SimConcept is the first text mining tool to systematically handle many types of composite mentions. It could be useful to assist the bioconcept normalization task.
Exploits web-based data to highlight disease-related topics. DiTeX offers a platform allowing the visualization of disease-related topics, ranked by importance, based on a combined component approach (CCA) algorithm. This program uses multiple visualization techniques including disease-related trend graphs and a word cloud to give access to both real-time and long-term information related to disease and, subsequently, assist users in detecting emerging diseases.
A named entity recognition system intended primarily for biomedical text. BANNER uses conditional random fields as the primary recognition engine and includes a wide survey of the best techniques described in recent literature.
Utilizes simple yet effective linguistic features to extract relations with maximum entropy models. This chemical-induced disease (CID) relation extraction tool consisted of two specific subtasks: (i) the primary step for automatic Chemical Disease Relation (CDR) extraction is disease named entity recognition and normalization (DNER); (ii) CID relation extraction. Participants were provided with the same raw text as DNER, and asked to return a ranked list of chemical and disease entity pairs with normalized concept identifiers with which CIDs were associated in the abstract.
A system for disease mention recognition and normalization in biomedical texts. AuDis utilizes an order two conditional random fields model. To optimize the results, we customize several post-processing steps, including abbreviation resolution, consistency improvement and stopwords filtering. As the official evaluation on the chemical disease relation (CDR) task in BioCreative V, it obtained the best performance (86.46% of F-score) among 40 runs on disease normalization of the disease named entity recognition (DNER) sub task. These results suggest that AuDis is a high-performance recognition system.
Provides a comprehensive view of a patient. SemEHR is a semantic search and analytical system that provides a unified information extraction (IE) and semantic search system for obtaining clinical insight from unstructured clinical notes. It turns IE tasks into iterative ontology-based searches, which significantly lowers the barriers to secondary use of unstructured Electronic Health Records (EHRs) data.
Consists of a deep learning based disease named entity recognition (NER) architecture. ML-CNN is a program that treats NER as a simple word level classification problem in which only the context of a fixed-size window around the target word is considered as input. During the process, a conventional neural network (CNN)-based classifier model is built for recognizing the disease mentions in the texts.
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