AIMC Topic: Data Curation

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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...
Proteins Knowledge Bases Data Curation Databases, Protein Supervised Machine Learning
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Moving the mountain: analysis of the effort required to transform comparative anatomy into computable anatomy.

Database : the journal of biological databases and curation May 13, 2015
The diverse phenotypes of living organisms have been described for centuries, and though they may be digitized, they are not readily available in a computable form. Using over 100 morphological studies, the Phenoscape project has demonstrated that by...
Anatomy, Comparative Biological Ontologies Databases, Factual Humans Animals Natural Language Processing Data Curation Data Mining
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The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations.

Database : the journal of biological databases and curation May 9, 2015
Biocuration has become a cornerstone for analyses in biology, and to meet needs, the amount of annotations has considerably grown in recent years. However, the reliability of these annotations varies; it has thus become necessary to be able to assess...
Data Curation Congresses as Topic Biological Ontologies
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Ontology application and use at the ENCODE DCC.

Database : the journal of biological databases and curation Mar 16, 2015
The Encyclopedia of DNA elements (ENCODE) project is an ongoing collaborative effort to create a catalog of genomic annotations. To date, the project has generated over 4000 experiments across more than 350 cell lines and tissues using a wide array o...
Data Curation Gene Regulatory Networks Humans Mice Animals Transcription, Genetic Databases, Genetic Gene Ontology Molecular Sequence Annotation
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Shared resources, shared costs--leveraging biocuration resources.

Database : the journal of biological databases and curation Mar 16, 2015
The manual curation of the information in biomedical resources is an expensive task. This article argues the value of this approach in comparison with other apparently less costly options, such as automated annotation or text-mining, then discusses w...
Databases, Genetic Data Mining Gene Ontology Data Curation
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mycoCLAP, the database for characterized lignocellulose-active proteins of fungal origin: resource and text mining curation support.

Database : the journal of biological databases and curation Mar 8, 2015
Enzymes active on components of lignocellulosic biomass are used for industrial applications ranging from food processing to biofuels production. These include a diverse array of glycoside hydrolases, carbohydrate esterases, polysaccharide lyases and...
Enzymes Lignin Fungal Proteins Databases, Genetic Genes, Fungal Natural Language Processing Data Mining Data Curation
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Combining computational models, semantic annotations and simulation experiments in a graph database.

Database : the journal of biological databases and curation Mar 8, 2015
Model repositories such as the BioModels Database, the CellML Model Repository or JWS Online are frequently accessed to retrieve computational models of biological systems. However, their storage concepts support only restricted types of queries and ...
Biological Ontologies Data Curation Systems Biology Models, Biological Databases, Factual
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Regular expression-based learning to extract bodyweight values from clinical notes.

Journal of biomedical informatics Mar 5, 2015
BACKGROUND: Bodyweight related measures (weight, height, BMI, abdominal circumference) are extremely important for clinical care, research and quality improvement. These and other vitals signs data are frequently missing from structured tables of ele...
Data Curation Humans Body Weight Electronic Health Records Reproducibility of Results Data Mining Natural Language Processing
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Domain adaption of parsing for operative notes.

Journal of biomedical informatics Feb 7, 2015
BACKGROUND: Full syntactic parsing of clinical text as a part of clinical natural language processing (NLP) is critical for a wide range of applications. Several robust syntactic parsers are publicly available to produce linguistic representations fo...
Electronic Health Records Models, Statistical Humans Software Vocabulary, Controlled Natural Language Processing Data Curation Medical Informatics
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EcoliNet: a database of cofunctional gene network for Escherichia coli.

Database : the journal of biological databases and curation Feb 2, 2015
During the past several decades, Escherichia coli has been a treasure chest for molecular biology. The molecular mechanisms of many fundamental cellular processes have been discovered through research on this bacterium. Although much basic research n...
Genome, Bacterial Databases, Nucleic Acid Gene Ontology Data Curation Gene Regulatory Networks Escherichia coli
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