Topic
Annotation
About: Annotation is a research topic. Over the lifetime, 6719 publications have been published within this topic receiving 203463 citations. The topic is also known as: note & markup.
Papers published on a yearly basis
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23 Dec 2005TL;DR: In this article, an active learning component trains an annotation model and proposes annotations to documents based on the annotation model, and a request handler conveys annotation requests from the graphical user interface to the active learning components.
Abstract: A document annotation system includes a graphical user interface used by an annotator to annotate documents. An active learning component trains an annotation model and proposes annotations to documents based on the annotation model. A request handler conveys annotation requests from the graphical user interface to the active learning component, conveys proposed annotations from the active learning component to the graphical user interface, and selectably conveys evaluation requests from the graphical user interface to a domain expert. During annotation, at least some low probability proposed annotations are presented to the annotator by the graphical user interface. The presented low probability proposed annotations enhance training of the annotation model by the active learning component.
134 citations
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TL;DR: Overall, it is found that electronic annotations have significantly improved in recent years, but also that their reliability now rivals that of annotations inferred by curators when they use evidence other than experiments from primary literature.
Abstract: Gene Ontology (GO) has established itself as the undisputed standard for protein function annotation. Most annotations are inferred electronically, i.e. without individual curator supervision, but they are widely considered unreliable. At the same time, we crucially depend on those automated annotations, as most newly sequenced genomes are non-model organisms. Here, we introduce a methodology to systematically and quantitatively evaluate electronic annotations. By exploiting changes in successive releases of the UniProt Gene Ontology Annotation database, we assessed the quality of electronic annotations in terms of specificity, reliability, and coverage. Overall, we not only found that electronic annotations have significantly improved in recent years, but also that their reliability now rivals that of annotations inferred by curators when they use evidence other than experiments from primary literature. This work provides the means to identify the subset of electronic annotations that can be relied upon—an important outcome given that >98% of all annotations are inferred without direct curation.
134 citations
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05 Jun 2003TL;DR: Embodiments provide a system, method, apparatus, means and computer program code that allow multiple annotations to a document to be created and that distinguish between the annotations made by different people as mentioned in this paper.
Abstract: Embodiments provide a system, method, apparatus, means, and computer program code that allow multiple annotations to a document to be created and that distinguish between the annotations made by different people. The people may view documents, exchange ideas and messages, etc. via a server or conference/collaboration system at different times and/or without being in direct communication with each other. In such an off-line collaboration mode, the people may want to add listen to, view, or add annotations regarding one or more documents. The methods and systems described herein allow users to follow the trail of annotations regarding a document and to distinguish between the voice or other audible annotations created by other people.
134 citations
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TL;DR: This unit addresses the issue of how GO vocabularies are constructed and related to genes and gene products and concludes with a discussion of how researchers can access, browse, and utilize the GO project in the course of their own research.
Abstract: Scientists wishing to utilize genomic data have quickly come to realize the benefit of standardizing descriptions of experimental procedures and results for computer-driven information retrieval systems. The focus of the Gene Ontology project is three-fold. First, the project goal is to compile the Gene Ontologies; structured vocabularies describing domains of molecular biology. Second, the project supports the use of these structured vocabularies in the annotation of gene products. Third, the gene product-to-GO annotation sets are provided by participating groups to the public through open access to the GO database and Web resource. This unit describes the current ontologies and what is beyond the scope of the Gene Ontology project. It addresses the issue of how GO vocabularies are constructed and related to genes and gene products. It concludes with a discussion of how researchers can access, browse, and utilize the GO project in the course of their own research.
133 citations
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TL;DR: The HAMAP project, or 'High-quality Automated and Manual Annotation of microbial Proteomes', aims to integrate manual and automatic annotation methods in order to enhance the speed of the curation process while preserving the quality of the database annotation.
132 citations