Artificial intelligence publications
-
A Systematic Comparison of the MetaCyc and Kegg Pathway Databases
We present a comparison of the compound, reaction, and pathway content of MetaCyc version 16.0 and a KEGG version downloaded on Feb-27-2012...
-
Computing Minimal Nutrient Sets from Metabolic Networks Via Linear Constraint Solving
We present a method for computationally determining alternative growth media for an organism based on its metabolic network and transporter complement.
-
Sparse Conditional Mixture Model: Late Fusion with Missing Scores for Multimedia Event Detection
We present the Sparse Conditional Mixture Model (SCMM) which models only the observed detection scores for each example, thereby avoiding making any assumptions about the distributions of the scores that…
-
Automatic Strengthening of Graph-Structured Knowledge Bases
Keywords: Artificial Intelligence, Artificial Intelligence Center, AIC
-
Conceptual Models of Structure and Function
We report our achievements in creating conceptual, multidimensional models of biological structure and function out of the linear text of an introductory biology textbook.
-
Data Mining in the Metacyc Family of Pathway Databases
The MetaCyc family of pathway databases consists of thousands of databases that were derived through computational inference of metabolic pathways from the MetaCyc pathway/genome database (PGDB).
-
KB_Bio_101: A challenge for OWL Reasoners
We describe the axiomatic content of a biology knowledge base that poses both theoretical and empirical challenges for OWL reasoning.
-
Dead End Metabolites — Defining the Known Unknowns of the E. coli Metabolic Network
We have analysed the occurrence of dead end metabolites within the database – these are metabolites which lack the requisite reactions (either metabolic or transport) that would account for their…
-
A systematic comparison of the MetaCyc and KEGG pathway databases
We present a comparison of the compound, reaction, and pathway content of MetaCyc version 16.0 and a KEGG version downloaded on Feb-27-2012 to increase understanding of their relative sizes, their…
-
Groups: Knowledge Spreadsheets for symbolic biocomputing
Groups allows Pathway Tools users to define a group of objects (e.g. groups of genes or metabolites) from a Pathway/Genome Database.
-
Query Answering in Object Oriented Knowledge Bases in Logic Programming: Description and Challenge for ASP
We give a description of this KB and ASP programs for a suite of queries that have been of practical interest.
-
EcoCyc: Fusing Model Organism Databases with Systems Biology
Updates to EcoCyc content continue to improve the comprehensive picture of E. coli biology. The utility of EcoCyc is enhanced by new tools available on the EcoCyc web site, and…