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.

The GOA database: Gene Ontology annotation updates for 2015

Abstract: The Gene Ontology Annotation (GOA) resource (http://www.ebi.ac.uk/GOA) provides evidence-based Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB). Manual annotations provided by UniProt curators are supplemented by manual and automatic annotations from model organism databases and specialist annotation groups. GOA currently supplies 368 million GO annotations to almost 54 million proteins in more than 480,000 taxonomic groups. The resource now provides annotations to five times the number of proteins it did 4 years ago. As a member of the GO Consortium, we adhere to the most up-to-date Consortium-agreed annotation guidelines via the use of quality control checks that ensures that the GOA resource supplies high-quality functional information to proteins from a wide range of species. Annotations from GOA are freely available and are accessible through a powerful web browser as well as a variety of annotation file formats.

Gene ontology annotations and resources

Abstract: The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new 'phylogenetic annotation' process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources.

Simultaneous image classification and annotation

Abstract: Image classification and annotation are important problems in computer vision, but rarely considered together. Intuitively, annotations provide evidence for the class label, and the class label provides evidence for annotations. For example, an image of class highway is more likely annotated with words “road,” “car,” and “traffic” than words “fish,” “boat,” and “scuba.” In this paper, we develop a new probabilistic model for jointly modeling the image, its class label, and its annotations. Our model treats the class label as a global description of the image, and treats annotation terms as local descriptions of parts of the image. Its underlying probabilistic assumptions naturally integrate these two sources of information. We derive an approximate inference and estimation algorithms based on variational methods, as well as efficient approximations for classifying and annotating new images. We examine the performance of our model on two real-world image data sets, illustrating that a single model provides competitive annotation performance, and superior classification performance.

Large scale image annotation: learning to rank with joint word-image embeddings

Abstract: Image annotation datasets are becoming larger and larger, with tens of millions of images and tens of thousands of possible annotations. We propose a strongly performing method that scales to such datasets by simultaneously learning to optimize precision at k of the ranked list of annotations for a given image and learning a low-dimensional joint embedding space for both images and annotations. Our method both outperforms several baseline methods and, in comparison to them, is faster and consumes less memory. We also demonstrate how our method learns an interpretable model, where annotations with alternate spellings or even languages are close in the embedding space. Hence, even when our model does not predict the exact annotation given by a human labeler, it often predicts similar annotations, a fact that we try to quantify by measuring the newly introduced "sibling" precision metric, where our method also obtains excellent results.

A New Baseline for Image Annotation

Abstract: Automatically assigning keywords to images is of great interest as it allows one to index, retrieve, and understand large collections of image data. Many techniques have been proposed for image annotation in the last decade that give reasonable performance on standard datasets. However, most of these works fail to compare their methods with simple baseline techniques to justify the need for complex models and subsequent training. In this work, we introduce a new baseline technique for image annotation that treats annotation as a retrieval problem. The proposed technique utilizes low-level image features and a simple combination of basic distances to find nearest neighbors of a given image. The keywords are then assigned using a greedy label transfer mechanism. The proposed baseline outperforms the current state-of-the-art methods on two standard and one large Web dataset. We believe that such a baseline measure will provide a strong platform to compare and better understand future annotation techniques.