AIMC Topic: Data Curation

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Enumerating consistent sub-graphs of directed acyclic graphs: an insight into biomedical ontologies.

Bioinformatics (Oxford, England)
MOTIVATION: Modern problems of concept annotation associate an object of interest (gene, individual, text document) with a set of interrelated textual descriptors (functions, diseases, topics), often organized in concept hierarchies or ontologies. Mo...

miRandola 2017: a curated knowledge base of non-invasive biomarkers.

Nucleic acids research
miRandola (http://mirandola.iit.cnr.it/) is a database of extracellular non-coding RNAs (ncRNAs) that was initially published in 2012, foreseeing the relevance of ncRNAs as non-invasive biomarkers. An increasing amount of experimental evidence shows ...

Improving Clinical Named-Entity Recognition with Transfer Learning.

Studies in health technology and informatics
Transfer learning is a powerful machine learning technique that enables the internalizing and reuse of prior knowledge to new tasks. Transfer learning is currently the starting point for recognition tasks such as computer vision. However, in natural ...

Extracting chemical-protein relations with ensembles of SVM and deep learning models.

Database : the journal of biological databases and curation
Mining relations between chemicals and proteins from the biomedical literature is an increasingly important task. The CHEMPROT track at BioCreative VI aims to promote the development and evaluation of systems that can automatically detect the chemica...

Probabilistic and machine learning-based retrieval approaches for biomedical dataset retrieval.

Database : the journal of biological databases and curation
The bioCADDIE dataset retrieval challenge brought together different approaches to retrieval of biomedical datasets relevant to a user’s query, expressed as a text description of a needed dataset. We describe experiments in applying a data-driven, ma...

YummyData: providing high-quality open life science data.

Database : the journal of biological databases and curation
Many life science datasets are now available via Linked Data technologies, meaning that they are represented in a common format (the Resource Description Framework), and are accessible via standard APIs (SPARQL endpoints). While this is an important ...

Identification of errors in the IEDB using ontologies.

Database : the journal of biological databases and curation
The Immune Epitope Database (IEDB) is a free online resource that has manually curated over 18 500 references from the scientific literature. Our database presents experimental data relating to the recognition of immune epitopes by the adaptive immun...

FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability.

Database : the journal of biological databases and curation
The Immune Epitope Database (IEDB), at www.iedb.org, has the mission to make published experimental data relating to the recognition of immune epitopes easily available to the scientific public. By presenting curated data in a searchable database, we...