AIMC Topic: Data Curation

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HPIDB 2.0: a curated database for host-pathogen interactions.

Database : the journal of biological databases and curation Jul 3, 2016
Identification and analysis of host-pathogen interactions (HPI) is essential to study infectious diseases. However, HPI data are sparse in existing molecular interaction databases, especially for agricultural host-pathogen systems. Therefore, resourc...
Gene Ontology Data Curation Humans Animals Host-Pathogen Interactions Databases, Factual
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Bi-convex Optimization to Learn Classifiers from Multiple Biomedical Annotations.

IEEE/ACM transactions on computational biology and bioinformatics Jun 7, 2016
The problem of constructing classifiers from multiple annotators who provide inconsistent training labels is important and occurs in many application domains. Many existing methods focus on the understanding and learning of the crowd behaviors. Sever...
Models, Theoretical Support Vector Machine Female Breast Neoplasms Medical Informatics Facial Expression Data Curation Artificial Intelligence Humans Databases, Factual Alzheimer Disease Image Interpretation, Computer-Assisted
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A study of the effectiveness of machine learning methods for classification of clinical interview fragments into a large number of categories.

Journal of biomedical informatics May 13, 2016
This study examines the effectiveness of state-of-the-art supervised machine learning methods in conjunction with different feature types for the task of automatic annotation of fragments of clinical text based on codebooks with a large number of cat...
Semantics Data Curation Decision Trees Bayes Theorem Machine Learning Support Vector Machine
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BELTracker: evidence sentence retrieval for BEL statements.

Database : the journal of biological databases and curation May 12, 2016
Biological expression language (BEL) is one of the main formal representation models of biological networks. The primary source of information for curating biological networks in BEL representation has been literature. It remains a challenge to ident...
Software Computational Biology Data Mining Semantics Data Curation Natural Language Processing Internet
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OntoStudyEdit: a new approach for ontology-based representation and management of metadata in clinical and epidemiological research.

Journal of biomedical semantics Dec 18, 2015
BACKGROUND: The specification of metadata in clinical and epidemiological study projects absorbs significant expense. The validity and quality of the collected data depend heavily on the precise and semantical correct representation of their metadata...
Data Curation Epidemiologic Studies Humans Biostatistics Biological Ontologies Software
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A Study of Neural Word Embeddings for Named Entity Recognition in Clinical Text.

AMIA ... Annual Symposium proceedings. AMIA Symposium Nov 5, 2015
Clinical Named Entity Recognition (NER) is a critical task for extracting important patient information from clinical text to support clinical and translational research. This study explored the neural word embeddings derived from a large unlabeled c...
Data Curation Pattern Recognition, Automated Algorithms Terminology as Topic Humans Natural Language Processing Semantics
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Finding Cervical Cancer Symptoms in Swedish Clinical Text using a Machine Learning Approach and NegEx.

AMIA ... Annual Symposium proceedings. AMIA Symposium Nov 5, 2015
Detection of early symptoms in cervical cancer is crucial for early treatment and survival. To find symptoms of cervical cancer in clinical text, Named Entity Recognition is needed. In this paper the Clinical Entity Finder, a machine-learning tool tr...
Machine Learning Electronic Health Records Sweden Uterine Cervical Neoplasms Female Humans Natural Language Processing Data Curation
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Scaling Out and Evaluation of OBSecAn, an Automated Section Annotator for Semi-Structured Clinical Documents, on a Large VA Clinical Corpus.

AMIA ... Annual Symposium proceedings. AMIA Symposium Nov 5, 2015
"Identifying and labeling" (annotating) sections improves the effectiveness of extracting information stored in the free text of clinical documents. OBSecAn, an automated ontology-based section annotator, was developed to identify and label sections ...
United States Natural Language Processing Humans Data Curation Reference Books, Medical Algorithms United States Department of Veterans Affairs
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SORTA: a system for ontology-based re-coding and technical annotation of biomedical phenotype data.

Database : the journal of biological databases and curation Sep 18, 2015
There is an urgent need to standardize the semantics of biomedical data values, such as phenotypes, to enable comparative and integrative analyses. However, it is unlikely that all studies will use the same data collection protocols. As a result, ret...
Knowledge Bases Humans Biological Ontologies Software Databases, Factual Data Curation Animals
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Using distant supervised learning to identify protein subcellular localizations from full-text scientific articles.

Journal of biomedical informatics Jul 26, 2015
Databases of curated biomedical knowledge, such as the protein-locations reflected in the UniProtKB database, provide an accurate and useful resource to researchers and decision makers. Our goal is to augment the manual efforts currently used to cura...
Data Curation Supervised Machine Learning Knowledge Bases Proteins Databases, Protein
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