Artificial intelligence publications
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Feature Derivation for Exploitation of Distant Annotation via Pattern Induction against Dependency Parses
We consider the use of distant supervision for biological information extraction, and introduce two understudied corpora of this form, the Biological Expression Language (BEL) Large Corpus and the Pathway Logic…
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Crowd-sourcing and author submission as alternatives to professional curation
This perspective considers the significant experience accumulated by the bioinformatics community with these two alternatives to professional curation in the last 20 years...
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How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications
We present a rationale for expanding the presence of the Lisp family of programming languages in bioinformatics and computational biology research.
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Solution Authoring via Demonstration and Annotation: An Empirical Study
This paper reports on a concept validation study that provides an empirical basis for the design of solution authoring frameworks based on end-user programming techniques.
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Representation and inference of cellular architecture for metabolic reconstruction and modeling
We developed a tool for inferring cellular architectures across many domains of life and extended our Cell Component Ontology to enable representation of the inferred architectures.
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The Time Is Right to Focus on Model Organism Metabolomes
We propose a grand challenge for metabolomics studies of model organisms: to identify and map all metabolites onto metabolic pathways, to develop quantitative metabolic models for model organisms, and to…
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Assessing Problem-Solving Process At Scale
This paper describes a hybrid approach to assessing process at scale in the context of the use of computational thinking practices during programming.
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The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
The MetaCyc database (MetaCyc.org) is a freely accessible comprehensive database describing metabolic pathways and enzymes from all domains of life.
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An Annotated Corpus and Method for Analysis of Ad-Hoc Structures Embedded in Text
We describe a method for identifying and performing functional analysis of structured regions that are embedded in natural language documents, such as tables or key-value lists.
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Can we replace curation with information extraction software?
Can we use programs for automated or semi-automated information extraction from scientific texts as practical alternatives to professional curation? I show that error rates of current information extraction programs are…
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Pathway collages: personalized multi-pathway diagrams
We define software for constructing personalized multi-pathway diagrams called pathway-collages using a combination of manual and automatic layouts.
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How Much Does Curation Cost?
Here we calculate the cost of biocuration of articles for the EcoCyc database as $219 per article over a 5-year period.