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Knowledge Bases

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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
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...

Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME.

Database : the journal of biological databases and curation
Today's large, public databases of protein-small molecule interaction data are creating important new opportunities for data mining and integration. At the same time, new graphical user interface-based workflow tools offer facile alternatives to cust...

APL: An angle probability list to improve knowledge-based metaheuristics for the three-dimensional protein structure prediction.

Computational biology and chemistry
Tertiary protein structure prediction is one of the most challenging problems in structural bioinformatics. Despite the advances in algorithm development and computational strategies, predicting the folded structure of a protein only from its amino a...

Expert system supporting an early prediction of the bronchopulmonary dysplasia.

Computers in biology and medicine
This work presents a decision support system which uses machine learning to support early prediction of bronchopulmonary dysplasia (BPD) for extremely premature infants after their first week of life. For that purpose a knowledge database was created...

Medication-indication knowledge bases: a systematic review and critical appraisal.

Journal of the American Medical Informatics Association : JAMIA
OBJECTIVE: Medication-indication information is a key part of the information needed for providing decision support for and promoting appropriate use of medications. However, this information is not readily available to end users, and a lot of the re...

Knowledge-Based Query Construction Using the CDSS Knowledge Base for Efficient Evidence Retrieval.

Sensors (Basel, Switzerland)
Finding appropriate evidence to support clinical practices is always challenging, and the construction of a query to retrieve such evidence is a fundamental step. Typically, evidence is found using manual or semi-automatic methods, which are time-con...

GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies.

PloS one
Cellular processes involve large numbers of RNA molecules. The functions of these RNA molecules and their binding to molecular machines are highly dependent on their 3D structures. One of the key challenges in RNA structure prediction and modeling is...

Network fingerprint: a knowledge-based characterization of biomedical networks.

Scientific reports
It can be difficult for biomedical researchers to understand complex molecular networks due to their unfamiliarity with the mathematical concepts employed. To represent molecular networks with clear meanings and familiar forms for biomedical research...

How to build up the actionable knowledge base: the role of 'best fit' framework synthesis for studies of improvement in healthcare.

BMJ quality & safety
Increasing recognition of the role and value of theory in improvement work in healthcare offers the prospect of capitalising upon, and consolidating, actionable lessons from synthesis of improvement projects and initiatives. We propose that informed ...