Artificial intelligence publications
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A Comparison of Microbial Genome Web Portals
This article compares the capabilities of the major microbial genome web portals to aid researchers in determining which portal(s) are best suited to their needs.
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Explanation to Avert Surprise
We present an explanation framework based on the notion of explanation drivers —i.e., the intent or purpose behind agent explanations. We focus on explanations meant to reconcile expectation violations and…
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Application of Text Analytics to Extract and Analyze Material–Application Pairs from a Large Scientific Corpus
In this work, we have successfully extracted material–application pairs and ranked them on their importance. This method provides a novel way to map scientific advances in a particular material to…
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The MetaCyc database of metabolic pathways and enzymes
This article provides an update on the developments in MetaCyc during the past two years, including the expansion of data and addition of new features.
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How accurate is automated gap filling of metabolic models?
Here we compare the results of applying an automated likelihood-based gap filler within the Pathway Tools software with the results of manually gap filling the same metabolic model.
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Evaluation of reaction gap-filling accuracy by randomization
We report on computational experiments of reaction gap filling in which we generated degraded versions of the EcoCyc-20.0-GEM model by randomly removing flux-carrying reactions from a growing model.
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The Omics Dashboard for interactive exploration of gene-expression data
The Omics Dashboard is a software tool for interactive exploration and analysis of gene-expression datasets.
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Semantic Instrumentation of Virtual Environments for Training
We discuss an approach in which the virtual environment is semantically instrumented in order to allow for the tracking of and reasoning about open-ended learner activity therein.
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An Ontology-Based Dialogue Management System for Virtual Personal Assistants
The features of OntoVPA are offered as potential solutions to core DM problems. We illustrate OntoVPA’s solutions to these problems by means of a running VPA example domain.
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Update notifications for the BioCyc collection of databases
The BioCyc update notifications service is a new mechanism to keep researchers informed of the latest developments in their areas of interest.
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The EcoCyc Database: Reflecting New Knowledge About Escherichia Coli K-12
New experimental discoveries about gene products, their function and regulation, new metabolic pathways, enzymes and cofactors are regularly added to EcoCyc.
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The BioCyc collection of microbial genomes and metabolic pathways
BioCyc.org is a microbial genome Web portal that combines thousands of genomes with additional information inferred by computer programs, imported from other databases and curated from the biomedical literature by…