AIMC Topic: Data Curation

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RysannMD: A biomedical semantic annotator balancing speed and accuracy.

Journal of biomedical informatics May 26, 2017
Recently, both researchers and practitioners have explored the possibility of semantically annotating large and continuously evolving collections of biomedical texts such as research papers, medical reports, and physician notes in order to enable the...
Humans Natural Language Processing Semantics Data Mining Data Curation
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Semi-supervised medical entity recognition: A study on Spanish and Swedish clinical corpora.

Journal of biomedical informatics May 16, 2017
OBJECTIVE: The goal of this study is to investigate entity recognition within Electronic Health Records (EHRs) focusing on Spanish and Swedish. Of particular importance is a robust representation of the entities. In our case, we utilized unsupervised...
Humans Machine Learning Cluster Analysis Electronic Health Records Semantics Sweden Data Curation
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EHR-based phenotyping: Bulk learning and evaluation.

Journal of biomedical informatics Apr 12, 2017
In data-driven phenotyping, a core computational task is to identify medical concepts and their variations from sources of electronic health records (EHR) to stratify phenotypic cohorts. A conventional analytic framework for phenotyping largely uses ...
Models, Statistical Supervised Machine Learning Phenotype Electronic Health Records Data Curation Humans
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Building a comprehensive syntactic and semantic corpus of Chinese clinical texts.

Journal of biomedical informatics Apr 9, 2017
OBJECTIVE: To build a comprehensive corpus covering syntactic and semantic annotations of Chinese clinical texts with corresponding annotation guidelines and methods as well as to develop tools trained on the annotated corpus, which supplies baseline...
Language China Humans Data Curation Data Mining Semantics Narration Natural Language Processing
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NegAIT: A new parser for medical text simplification using morphological, sentential and double negation.

Journal of biomedical informatics Mar 22, 2017
Many different text features influence text readability and content comprehension. Negation is commonly suggested as one such feature, but few general-purpose tools exist to discover negation and studies of the impact of negation on text readability ...
Medical Informatics Comprehension Data Curation Natural Language Processing Bayes Theorem Software Language Humans
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Structuring Legacy Pathology Reports by openEHR Archetypes to Enable Semantic Querying.

Methods of information in medicine Feb 28, 2017
BACKGROUND: Clinical information is often stored as free text, e.g. in discharge summaries or pathology reports. These documents are semi-structured using section headers, numbered lists, items and classification strings. However, it is still challen...
Machine Learning Electronic Health Records Natural Language Processing Medical Record Linkage Vocabulary, Controlled Semantics Pathology Data Curation Guidelines as Topic Health Information Interoperability Information Storage and Retrieval
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Automatic query generation using word embeddings for retrieving passages describing experimental methods.

Database : the journal of biological databases and curation Jan 10, 2017
Information regarding the physical interactions among proteins is crucial, since protein-protein interactions (PPIs) are central for many biological processes. The experimental techniques used to verify PPIs are vital for characterizing and assessing...
Data Curation Data Mining Proteins Biological Ontologies Databases, Protein
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OntoBrowser: a collaborative tool for curation of ontologies by subject matter experts.

Bioinformatics (Oxford, England) Sep 6, 2016
UNLABELLED: The lack of controlled terminology and ontology usage leads to incomplete search results and poor interoperability between databases. One of the major underlying challenges of data integration is curating data to adhere to controlled term...
Software Databases, Factual Vocabulary, Controlled Data Curation Peer Review Biological Ontologies
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Training and evaluation corpora for the extraction of causal relationships encoded in biological expression language (BEL).

Database : the journal of biological databases and curation Aug 23, 2016
Success in extracting biological relationships is mainly dependent on the complexity of the task as well as the availability of high-quality training data. Here, we describe the new corpora in the systems biology modeling language BEL for training an...
Mice Humans Natural Language Processing Animals Data Mining Data Curation
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Crowdsourcing and curation: perspectives from biology and natural language processing.

Database : the journal of biological databases and curation Aug 7, 2016
Crowdsourcing is increasingly utilized for performing tasks in both natural language processing and biocuration. Although there have been many applications of crowdsourcing in these fields, there have been fewer high-level discussions of the methodol...
Data Curation Natural Language Processing Crowdsourcing Metadata
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