Artificial intelligence publications
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VALET: Rule-Based Information Extraction for Rapid Deployment
We present VALET, a framework for rule-based information extraction written in Python. We show how a handful of rules suffices to implement sophisticated matching, and describe a user interface that…
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Pathway Tools Management of Pathway/Genome Data for Microbial Communities
The Pathway Tools software provides a suite of capabilities for storing and analyzing collections of genomic and metabolic information.
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An Ontology-Based Dialogue Management Framework for Virtual Personal Assistants in Common Lisp
We present a new approach to dialogue specification for Virtual Personal Assistants (VPAs) based on so-called dialogue workflow graphs. Our approach relies on Semantic Web technology (OWL), implemented in Common…
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Metabolic Modeling with MetaFlux
The MetaFlux software supports creating, executing, and solving quantitative metabolic flux models using flux balance analysis (FBA).
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The EcoCyc Database in 2021
This article highlights recent improvements to the curated data in the areas of metabolism, transport, DNA repair, and regulation of gene expression.
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What, Again? Automatic Deductive Synthesis of the Unification Algorithm
We describe work in progress towards deriving a unification algorithm automatically from a declarative specification using deductive methods.
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The BioCyc Metabolic Network Explorer
The Metabolic Network Explorer is a new addition to the BioCyc.org website and the Pathway Tools software suite that supports the interactive exploration of metabolic networks.
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Pathway Size Matters: The Influence of Pathway Granularity on Over-Representation (Enrichment) Statistics
We show that alternative pathway definitions can alter enrichment p -values by up to nine orders of magnitude, whereas statistical corrections typically alter enrichment p -values by only two orders…
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Leveraging Curation Among Escherichia coli Pathway/Genome Databases Using Ortholog-Based Annotation Propagation
We have developed a method to automatically propagate multiple types of curated knowledge from genes and proteins in one genome database to their orthologs in uncurated databases for related strains,…
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Prediction of Selected Biosynthetic Pathways for the Lipopolysaccharide Components in Porphyromonas gingivalis
We use bioinformatics tools to predict biosynthetic pathways for the production of the normal (O-type) lipopolysaccharide in the W50 strain Porphyromonas gingivalis and compare the pathway with other putative pathways…
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Pathway Tools Visualization of Organism-Scale Metabolic Networks
We have developed bioinformatics software tools that automatically generate a full metabolic-network diagram for an organism, and that enable searching and analyses of the network.
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Transformer Based Molecule Encoding for Property Prediction
We build a Transformer-based molecule encoder and property predictor network with novel input featurization that performs significantly better than existing methods.