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The Gene Ontology resource: enriching a GOld mine
A historical archive covering the past 15 years of GO data with a consistent format and file structure for both the ontology and annotations is made available to maintain consistency with other ontologies.
Positional relationships between photoperiod response QTL and photoreceptor and vernalization genes in barley
The coincidence of photoperiod-responsive vernalization genes withPhotoperiod QTL suggests vernAlization genes should also be considered candidates for photoper period effects.
Finding Our Way through Phenotypes
Imagine if we could compute across phenotype data as easily as genomic data; this article calls for efforts to realize this vision and discusses the potential benefits.
The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses
This paper focuses on the plant anatomical entity branch of the Plant Ontology, describing the organizing principles, resources available to users and examples of how the PO is integrated into other plant genomics databases and web portals.
The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics
This work provides integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms, and provides access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world.
Ontologies as integrative tools for plant science.
Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding, and can advance plant science in four keys areas: comparative genetics, genomics, phenomics, and development; taxonomy and systematics; (3) semantic applications; and (4) education.
The Plant Ontology: A Tool for Plant Genomics.
This chapter introduces how the Plant Ontology and other related ontologies are constructed and organized, including languages and software used for ontology development, and provides an overview of the key features.
AISO: Annotation of Image Segments with Ontologies
- Nikhil Lingutla, Justin Preece, S. Todorovic, L. Cooper, Laura Moore, P. Jaiswal
- Biology, Computer ScienceJ. Biomed. Semant.
- 17 December 2014
A novel image segmentation and annotation software application, “Annotation of Image Segments with Ontologies” (AISO), which enables researchers and curators to delineate portions of an image into multiple highlighted segments and annotate them with an ontology-based controlled vocabulary.
An overview of the BioCreative 2012 Workshop Track III: interactive text mining task
- C. Arighi, Ben Carterette, Cathy H. Wu
- Computer ScienceDatabase J. Biol. Databases Curation
- 16 January 2013
An effort to bring together text mining tool developers and database biocurators to test the utility and usability of tools and indicates that some of the systems were able to improve efficiency of curation by speeding up the curation task significantly and improve annotation accuracy when compared with the performance on the manually curated set.
High-frequency Ds remobilization over multiple generations in barley facilitates gene tagging in large genome cereals
Observed remobilization frequencies of primary, secondary, tertiary, and quaternary TNPs, coupled with the tendency for localized Ds transposition, validates a saturation mutagenesis approach using Ds to tag and characterize genes linked to Ds in large genome cereals like barley and wheat.