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.

Curation of the genome annotation of Pichia pastoris (Komagataella phaffii) CBS7435 from gene level to protein function

Abstract: As manually curated and non-automated BLAST analysis of the published Pichia pastoris genome sequences revealed many differences between the gene annotations of the strains GS115 and CBS7435, RNA-Seq analysis, supported by proteomics, was performed to improve the genome annotation. Detailed analysis of sequence alignment and protein domain predictions were made to extend the functional genome annotation to all P. pastoris sequences. This allowed the identification of 492 new ORFs, 4916 hypothetical UTRs and the correction of 341 incorrect ORF predictions, which were mainly due to the presence of upstream ATG or erroneous intron predictions. Moreover, 175 previously erroneously annotated ORFs need to be removed from the annotation. In total, we have annotated 5325 ORFs. Regarding the functionality of those genes, we improved all gene and protein descriptions. Thereby, the percentage of ORFs with functional annotation was increased from 48% to 73%. Furthermore, we defined functional groups, covering 25 biological cellular processes of interest, by grouping all genes that are part of the defined process. All data are presented in the newly launched genome browser and database available at [www.pichiagenome.org][1]. In summary, we present a wide spectrum of curation of the P. pastoris genome annotation from gene level to protein function. [1]: http://www.pichiagenome.org

GOAnnotator: linking protein GO annotations to evidence text

Abstract: Annotation of proteins with gene ontology (GO) terms is ongoing work and a complex task. Manual GO annotation is precise and precious, but it is time-consuming. Therefore, instead of curated annotations most of the proteins come with uncurated annotations, which have been generated automatically. Text-mining systems that use literature for automatic annotation have been proposed but they do not satisfy the high quality expectations of curators. In this paper we describe an approach that links uncurated annotations to text extracted from literature. The selection of the text is based on the similarity of the text to the term from the uncurated annotation. Besides substantiating the uncurated annotations, the extracted texts also lead to novel annotations. In addition, the approach uses the GO hierarchy to achieve high precision. Our approach is integrated into GOAnnotator, a tool that assists the curation process for GO annotation of UniProt proteins. The GO curators assessed GOAnnotator with a set of 66 distinct UniProt/SwissProt proteins with uncurated annotations. GOAnnotator provided correct evidence text at 93% precision. This high precision results from using the GO hierarchy to only select GO terms similar to GO terms from uncurated annotations in GOA. Our approach is the first one to achieve high precision, which is crucial for the efficient support of GO curators. GOAnnotator was implemented as a web tool that is freely available at http://xldb.di.fc.ul.pt/rebil/tools/goa/ .

Method of annotating timeline files

Abstract: The invention describes a method of annotating a timeline file (T) which method comprises identifying distinct key resources (K1, K2, K3, ..., Km) in the timeline file (T), and describing a number of annotations for one or more key resources (K1, K2, K3, ..., Km) in an annotation file (A) such that an annotation for a key resource (K1, K2, K3, ..., Km) is tied to the key resource (K1, K2, K3, ..., Km) corresponding to that annotation.

Proposal for an Extension of Traditional Named Entitites: from Guidelines to Evaluation, an Overview

Abstract: Within the framework of the construction of a fact database, we defined guidelines to extract named entities, using a taxonomy based on an extension of the usual named entities defini- tion. We thus defined new types of entities with broader coverage including substantive- based expressions. These extended named en- tities are hierarchical (with types and compo- nents) and compositional (with recursive type inclusion and metonymy annotation). Human annotators used these guidelines to annotate a 1.3M word broadcast news corpus in French. This article presents the definition and novelty of extended named entity annotation guide- lines, the human annotation of a global corpus and of a mini reference corpus, and the evalu- ation of annotations through the computation of inter-annotator agreement. Finally, we dis- cuss our approach and the computed results, and outline further work.

Video Annotation Through Search and Graph Reinforcement Mining

Abstract: Unlimited vocabulary annotation of multimedia documents remains elusive despite progress solving the problem in the case of a small, fixed lexicon. Taking advantage of the repetitive nature of modern information and online media databases with independent annotation instances, we present an approach to automatically annotate multimedia documents that uses mining techniques to discover new annotations from similar documents and to filter existing incorrect annotations. The annotation set is not limited to words that have training data or for which models have been created. It is limited only by the words in the collective annotation vocabulary of all the database documents. A graph reinforcement method driven by a particular modality (e.g., visual) is used to determine the contribution of a similar document to the annotation target. The graph supplies possible annotations of a different modality (e.g., text) that can be mined for annotations of the target. Experiments are performed using videos crawled from YouTube. A customized precision-recall metric shows that the annotations obtained using the proposed method are superior to those originally existing for the document. These extended, filtered tags are also superior to a state-of-the-art semi-supervised technique for graph reinforcement learning on the initial user-supplied annotations.