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Citation: BMC Bioinformatics 2008 9(Suppl 11):S1
Manual curation of biological databases, an expensive and labor-intensive process, is essential for high quality integrated data ... the implementation of a state-of-the-art Natural Language Processing system tha...
Citation: BMC Bioinformatics 2007 8:293
Despite increasing interest in applying Natural Language Processing (NLP) to biomedical text, whether this...
Citation: BMC Bioinformatics 2008 9:193
Natural Language Processing (NLP) has been shown effective to...
Citation: BMC Bioinformatics 2014 15:266
The Enteropathogen Resource Integration Center (ERIC; http://www.ericbrc.org) has a goal of providing bioinformatics support for the scientific communi...
Citation: BMC Bioinformatics 2009 10:177
Many biomedical natural language processing systems demonstrated large differences between their previously...
Citation: BMC Bioinformatics 2012 13:207
We present an extension of the TM tool, which utilizes natural language processing (NLP) for analyzing the context of ... the global low-resolution docking scan was post-processed, separately, by constraints from...
Citation: BMC Bioinformatics 2018 19:84
Identifying local recurrences in breast cancer from patient data sets is important for clinical research and practice. Developing a model using natural language processing and machine learning to identify local r...
Citation: BMC Bioinformatics 2018 19(Suppl 17):498
We report the development and evaluation of Microbial Phenomics Information Extractor (MicroPIE, version 0.1.0). MicroPIE is a natural language processing application that uses a robust supervised classification....
Citation: BMC Bioinformatics 2016 17:528
Natural language processing (NLP) applications are increasingly important in...
Citation: BMC Bioinformatics 2016 17:32
Interest is growing in the application of syntactic parsers to natural language processing problems in biology, but assessing their performance...
Citation: BMC Bioinformatics 2007 8:24
Applications of Natural Language Processing (NLP) technology to biomedical texts have...subdomain variation within the biomedical domain, i.e., the extent to which different subject areas of biomedicine are chara...
Citation: BMC Bioinformatics 2011 12:212
Metabolic flux analysis has become an established method in systems biology and functional genomics. The most common approach for determining intracellular metabolic fluxes is to utilize mass spectrometry in c...
Citation: BMC Bioinformatics 2012 13:295
It has been suggested previously that genome and proteome sequences show characteristics typical of natural-language texts such as "signature-style" word ... , and that the algorithms originally developed for natural
Citation: BMC Bioinformatics 2011 12:12
Gas chromatography–mass spectrometry (GC-MS) is a technique frequently used in targeted and non-targeted measurements of metabolites. Most existing software tools for processing of raw instrument GC-MS data ti...
Citation: BMC Bioinformatics 2012 13:115
Many efforts exist to design and implement approaches and tools for data capture, integration and analysis in the life sciences. Challenges are not only the heterogeneity, size and distribution of information ...
Citation: BMC Bioinformatics 2014 15(Suppl 1):S2
Microarray data analysis has been the subject of extensive and ongoing pipeline development due to its complexity, the availability of several options at each analysis step, and the development of new analysis...
Citation: BMC Bioinformatics 2012 13:102
We introduced a novel way to represent protein sequences as continuous vectors (embeddings) by using the language model ELMo taken from natural language processing. By modeling protein sequences, ELMo effectively...
Citation: BMC Bioinformatics 2019 20:723
Liquid chromatography coupled to mass spectrometry (LC/MS) has been widely used in proteomics and metabolomics research. In this context, the technology has been increasingly used for differential profiling, i...
Citation: BMC Bioinformatics 2005 6:179
Information extraction (IE) efforts are widely acknowledged to be important in harnessing the rapid advance of biomedical knowledge, particularly in areas where important factual information is published in a ...
Citation: BMC Bioinformatics 2008 9:78
Due to the nature of scientific methodology, research articles are rich in speculative and tentative statements, also known as hedges. We explore a linguistically motivated approach to the problem of recognizi...
Citation: BMC Bioinformatics 2008 9(Suppl 11):S10
This article presents Neji, an open source framework optimized for biomedical concept recognition built around four key characteristics: modularity, scalability, speed, and usability. It integrates modules for bi...
Citation: BMC Bioinformatics 2013 14:281
Techniques from computational linguistics can provide new insights into the annotation process. GO annotations show similar statistical behaviours to those seen in natural language with measured exponents that pr...
Citation: BMC Bioinformatics 2012 13:127
We present a literature-driven workflow involving document delivery and natural language processing steps generating tagged sentences containing lipid, protein...bibliosphere. We illustrate the extent of the desc...
Citation: BMC Bioinformatics 2008 9(Suppl 1):S5
Calcium (Ca2+) propagates within tissues serving as an important information carrier. In particular, cilia beat frequency in oviduct cells is partially regulated by Ca2+ changes. Thus, measuring the calcium de...
Citation: BMC Bioinformatics 2013 14:162
During library construction polymerase chain reaction is used to enrich the DNA before sequencing. Typically, this process generates duplicate read sequences. Removal of these artifacts is mandatory, as they c...
Citation: BMC Bioinformatics 2016 17(Suppl 12):346
Coreference resolution is the task of finding strings in text that have the same referent as other strings. Failures of coreference resolution are a common cause of false negatives in information extraction fr...
Citation: BMC Bioinformatics 2017 18:372
One of the greatest challenges in Metabolic Engineering is to develop quantitative models and algorithms to identify a set of genetic manipulations that will result in a microbial strain with a desirable metab...
Citation: BMC Bioinformatics 2008 9:499
The resulting event-annotated corpus is the largest and one of the best in quality among similar annotation efforts. We expect it to become a valuable resource for NLP (Natural Language Processing)-based TM in th...
Citation: BMC Bioinformatics 2008 9:10
The knowledge of metabolic pathways and fluxes is important to understand the adaptation of organisms to their biotic and abiotic environment. The specific distribution of stable isotope labelled precursors in...
Citation: BMC Bioinformatics 2013 14:218
SPARQL query composition is difficult for the lay-person, and even the experienced bioinformatician in cases where the data model is unfamiliar. Moreover, established best-practices and internationalization co...
Citation: BMC Bioinformatics 2012 13(Suppl 1):S2
Genomic functional information is valuable for biomedical research. However, such information frequently needs to be extracted from the scientific literature and structured in order to be exploited by automatic s...
Citation: BMC Bioinformatics 2006 7:291
Citation: BMC Bioinformatics 2005 6(Suppl 3):P26
In the era of information overload, natural language processing (NLP) techniques are increasingly needed to...
Citation: BMC Bioinformatics 2020 21:188
Spectral processing and post-experimental data analysis are the major tasks in NMR-based metabonomics studies. While there are commercial and free licensed software tools available to assist these tasks, resea...
Citation: BMC Bioinformatics 2009 10:83
Data generated from liquid chromatography coupled to high-resolution mass spectrometry (LC-MS)-based studies of a biological sample can contain large amounts of biologically significant information in the form...
Citation: BMC Bioinformatics 2009 10:87
Tokenization is an important component of language processing yet there is no widely accepted tokenization method for English texts, including biomedical texts. Other than rule based techniques, tokenization i...
Citation: BMC Bioinformatics 2011 12(Suppl 3):S1
Our method allows efficient and complete search of OMIM phenotypes as well as improved data-mining of the OMIM phenome. Applying natural language processing, each phrase is tagged with additional semantic...
Citation: BMC Bioinformatics 2011 12:65
Here, we build an integrative platform, the E ncyclopedia of H epatocellular C arcinoma genes O nline, dubbed EHCO http://ehco.iis.sinica.edu.tw..., to...
Citation: BMC Bioinformatics 2007 8:66
We extracted semantic relations with the SemRep natural language processing system from 122,421,765 sentences, which ... organized in a relational database. The QA process is implemented as a search in this...
Citation: BMC Bioinformatics 2015 16:6
Syntactic analysis, or parsing, is a key task in natural language processing and a required component for many text...
Citation: BMC Bioinformatics 2020 21(Suppl 23):580
The evolving complexity of genome-scale experiments has increasingly centralized the role of a highly computable, accurate, and comprehensive resource spanning multiple biological scales and viewpoints. To provid...
Citation: BMC Bioinformatics 2009 10(Suppl 2):S8
Relation extraction is an essential procedure in literature mining. It focuses on extracting semantic relations between parts of text, called mentions. Biomedical literature includes an enormous amount of textual...
Citation: BMC Bioinformatics 2015 16(Suppl 16):S1
Within the emerging field of text mining and statistical natural language processing (NLP) applied to biomedical articles, a...
Citation: BMC Bioinformatics 2005 6(Suppl 1):S19
Current search engines are keyword-based. Semantic technologies promise a next generation of semantic search engines, which will be able to answer questions. Current approaches either apply natural language processing
Citation: BMC Bioinformatics 2009 10(Suppl 10):S7
Biomedical processes can provide essential information about the (mal-) functioning of an organism and are thus frequently represented in biomedical terminologies and ontologies, including the GO Biological Pr...
Citation: BMC Bioinformatics 2012 13:217
ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions f...
Citation: BMC Bioinformatics 2017 18:529
Hydrogen/deuterium exchange mass spectrometry (H/DX-MS) experiments implemented to characterize protein interaction and protein folding generate large quantities of data. Organizing, processing and visualizing...
Citation: BMC Bioinformatics 2009 10:162
We sketch our species identification tool for palm sized computers that helps knowledgeable observers with census activities. An algorithm turns an identification matrix into a minimal length series of questio...
Citation: BMC Bioinformatics 2008 9:150
Citation: BMC Bioinformatics 2008 9(Suppl 3):S1
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