
DOI . ORG {
}
Title[redir]:
Evaluating Computational Gene Ontology Annotations | SpringerLink
Description:
Two avenues to understanding gene function are complementary and often overlapping: experimental work and computational prediction. While experimental annotation generally produces high-quality annotations, it is low throughput. Conversely, computational annotations...
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Keywords {🔍}
annotations, computational, function, annotation, pubmed, gene, google, scholar, experimental, protein, methods, article, ontology, prediction, proteins, predictions, information, database, central, evaluation, number, cas, škunca, open, evidence, dessimoz, chapter, data, quality, biological, terms, evaluating, biology, databases, genes, biol, access, sequence, standard, handbook, molecular, evaluate, knowledge, set, combrex, bioinformatics, validation, functional, based, gold,
Topics {✒️}
mapping swiss-prot keywords c-type lectin mincle open access chapter general enzymatic screens open access charges existing high-quality annotations preclude high-quality predictions high-quality experimental annotations produce high-probability annotations open access license gene ontology handbook identifying membrane-bound proteins privacy choices/manage cookies activity-based proteomic approaches labor-intensive nature protein/protein interaction data thomas pd gene ontology annotations quick-fix solution activity-based protein profiling gene ontology consortium open world assumption function propagates annotations reference genome project existing experimental annotations full access high throughput screening open/closed world gene function status oma orthology database full function space predicted ontological annotations gold standard dataset gold standard dataset existing experimental information european economic area performing extensive experimentation controlled vocabulary established practical obstacles interfere major practical obstacle sonic hedgehog entry key maximally informative targets dramatic cost reductions cravatt bf text-mining systems street gower st assessing computational prediction specific gene families function prediction models
Questions {❓}
- Škunca N, Dessimoz C (2015) Phylogenetic profiling: how much input data is enough?
Schema {🗺️}
ScholarlyArticle:
headline:Evaluating Computational Gene Ontology Annotations
pageEnd:109
pageStart:97
image:https://media.springernature.com/w153/springer-static/cover/book/978-1-4939-3743-1.jpg
genre:
Springer Protocols
isPartOf:
name:The Gene Ontology Handbook
isbn:
978-1-4939-3743-1
978-1-4939-3741-7
type:Book
publisher:
name:Springer New York
logo:
url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
type:ImageObject
type:Organization
author:
name:Nives Škunca
affiliation:
name:ETH Zurich
address:
name:Department of Computer Science, ETH Zurich, Zurich, Switzerland
type:PostalAddress
type:Organization
name:SIB Swiss Institute of Bioinformatics
address:
name:SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
type:PostalAddress
type:Organization
name:University College London
address:
name:University College London, London, UK
type:PostalAddress
type:Organization
email:[email protected]
type:Person
name:Richard J. Roberts
affiliation:
name:New England Biolabs
address:
name:New England Biolabs, Ipswich, USA
type:PostalAddress
type:Organization
type:Person
name:Martin Steffen
affiliation:
name:Boston University
address:
name:Department of Biomedical Engineering, Boston University, Boston, USA
type:PostalAddress
type:Organization
name:Boston University School of Medicine
address:
name:Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, USA
type:PostalAddress
type:Organization
type:Person
keywords:Gene ontology, Evaluation, Tools, Prediction, Annotation, Function
description:Two avenues to understanding gene function are complementary and often overlapping: experimental work and computational prediction. While experimental annotation generally produces high-quality annotations, it is low throughput. Conversely, computational annotations have broad coverage, but the quality of annotations may be variable, and therefore evaluating the quality of computational annotations is a critical concern. In this chapter, we provide an overview of strategies to evaluate the quality of computational annotations. First, we discuss why evaluating quality in this setting is not trivial. We highlight the various issues that threaten to bias the evaluation of computational annotations, most of which stem from the incompleteness of biological databases. Second, we discuss solutions that address these issues, for example, targeted selection of new experimental annotations and leveraging the existing experimental annotations.
datePublished:2017
isAccessibleForFree:1
context:https://schema.org
Book:
name:The Gene Ontology Handbook
isbn:
978-1-4939-3743-1
978-1-4939-3741-7
Organization:
name:Springer New York
logo:
url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
type:ImageObject
name:ETH Zurich
address:
name:Department of Computer Science, ETH Zurich, Zurich, Switzerland
type:PostalAddress
name:SIB Swiss Institute of Bioinformatics
address:
name:SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
type:PostalAddress
name:University College London
address:
name:University College London, London, UK
type:PostalAddress
name:New England Biolabs
address:
name:New England Biolabs, Ipswich, USA
type:PostalAddress
name:Boston University
address:
name:Department of Biomedical Engineering, Boston University, Boston, USA
type:PostalAddress
name:Boston University School of Medicine
address:
name:Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, USA
type:PostalAddress
ImageObject:
url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
Person:
name:Nives Škunca
affiliation:
name:ETH Zurich
address:
name:Department of Computer Science, ETH Zurich, Zurich, Switzerland
type:PostalAddress
type:Organization
name:SIB Swiss Institute of Bioinformatics
address:
name:SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
type:PostalAddress
type:Organization
name:University College London
address:
name:University College London, London, UK
type:PostalAddress
type:Organization
email:[email protected]
name:Richard J. Roberts
affiliation:
name:New England Biolabs
address:
name:New England Biolabs, Ipswich, USA
type:PostalAddress
type:Organization
name:Martin Steffen
affiliation:
name:Boston University
address:
name:Department of Biomedical Engineering, Boston University, Boston, USA
type:PostalAddress
type:Organization
name:Boston University School of Medicine
address:
name:Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, USA
type:PostalAddress
type:Organization
PostalAddress:
name:Department of Computer Science, ETH Zurich, Zurich, Switzerland
name:SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
name:University College London, London, UK
name:New England Biolabs, Ipswich, USA
name:Department of Biomedical Engineering, Boston University, Boston, USA
name:Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, USA
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