Automatic Semantic Annotation of Music with Harmonic Structure

This paper presents an annotation model for harmonic structure of a piece of music, and a rule system that supports the automatic generation of harmonic annotations. Musical structure has so far received relatively little attention in the context of musical metadata and annotation, although it is highly relevant for musicians, musicologists and indirectly for music listeners. Activities in semantic annotation of music have so far mostly concentrated on features derived from audio data and file-level metadata. We have implemented a model and rule system for harmonic annotation as a starting point for semantic annotation of musical structure. Our model is for the musical style of Jazz, but the approach is not restricted to this style. The rule system describes a grammar that allows the fully automatic creation of an harmonic analysis as tree-structured annotations. We present a prototype ontology that defines the layers of harmonic analysis from chords symbols to the level of a complete piece. The annotation can be made on music in various formats, provided there is a way of addressing either chords or time points within the music. We argue that this approach, in connection with manual annotation, can support a number of application scenarios in music production, education, and retrieval and in musicology

A quick guide for student-driven community genome annotation

High quality gene models are necessary to expand the molecular and genetic tools available for a target organism, but these are available for only a handful of model organisms that have undergone extensive curation and experimental validation over the course of many years. The majority of gene models present in biological databases today have been identified in draft genome assemblies using automated annotation pipelines that are frequently based on orthologs from distantly related model organisms. Manual curation is time consuming and often requires substantial expertise, but is instrumental in improving gene model structure and identification. Manual annotation may seem to be a daunting and cost-prohibitive task for small research communities but involving undergraduates in community genome annotation consortiums can be mutually beneficial for both education and improved genomic resources. We outline a workflow for efficient manual annotation driven by a team of primarily undergraduate annotators. This model can be scaled to large teams and includes quality control processes through incremental evaluation. Moreover, it gives students an opportunity to increase their understanding of genome biology and to participate in scientific research in collaboration with peers and senior researchers at multiple institutions

Leveraging video annotations in video-based e-learning

The e-learning community has been producing and using video content for a long time, and in the last years, the advent of MOOCs greatly relied on video recordings of teacher courses. Video annotations are information pieces that can be anchored in the temporality of the video so as to sustain various processes ranging from active reading to rich media editing. In this position paper we study how video annotations can be used in an e-learning context - especially MOOCs - from the triple point of view of pedagogical processes, current technical platforms functionalities, and current challenges. Our analysis is that there is still plenty of room for leveraging video annotations in MOOCs beyond simple active reading, namely live annotation, performance annotation and annotation for assignment; and that new developments are needed to accompany this evolution.Comment: 7th International Conference on Computer Supported Education (CSEDU), Barcelone : Spain (2014

Foregrounding the Margins: A Dialogue about Literacy, Learning, and Social Annotation

Annotation, or the addition of a note to a text, enables readers-as-writers to make their thinking visible. This article, which is structured as a dialogue among four literacy educators, discusses the potential for social annotation to transform literacy learning, assessment, and teacher education. Collectively, the authors argue for social annotation as a vital and transformative practice in hybrid and post-pandemic education. The authors reflect on their personal and pedagogical uses of annotation, sharing related resources for educators across K-12 and higher education contexts

Annotation Graphs and Servers and Multi-Modal Resources: Infrastructure for Interdisciplinary Education, Research and Development

Annotation graphs and annotation servers offer infrastructure to support the analysis of human language resources in the form of time-series data such as text, audio and video. This paper outlines areas of common need among empirical linguists and computational linguists. After reviewing examples of data and tools used or under development for each of several areas, it proposes a common framework for future tool development, data annotation and resource sharing based upon annotation graphs and servers.Comment: 8 pages, 6 figure

Text as scene: discourse deixis and bridging relations

En este artículo se presenta un nuevo marco, “el texto como escena”, que establece las bases para la anotación de dos relaciones de correferencia: la deixis discursiva y las relaciones de bridging. La incorporación de lo que llamamos escenas textuales y contextuales proporciona unas directrices de anotación más flexibles, que diferencian claramente entre tipos de categorías generales. Un marco como éste, capaz de tratar la deixis discursiva y las relaciones de bridging desde una perspectiva común, tiene como objetivo mejorar el bajo grado de acuerdo entre anotadores obtenido por esquemas de anotación anteriores, que son incapaces de captar las referencias vagas inherentes a estos dos tipos de relaciones. Las directrices aquí presentadas completan el esquema de anotación diseñado para enriquecer el corpus español CESS-ECE con información correferencial y así construir el corpus CESS-Ancora.This paper presents a new framework, “text as scene”, which lays the foundations for the annotation of two coreferential links: discourse deixis and bridging relations. The incorporation of what we call textual and contextual scenes provides more flexible annotation guidelines, broad type categories being clearly differentiated. Such a framework that is capable of dealing with discourse deixis and bridging relations from a common perspective aims at improving the poor reliability scores obtained by previous annotation schemes, which fail to capture the vague references inherent in both these links. The guidelines presented here complete the annotation scheme designed to enrich the Spanish CESS-ECE corpus with coreference information, thus building the CESS-Ancora corpus.This paper has been supported by the FPU grant (AP2006-00994) from the Spanish Ministry of Education and Science. It is based on work supported by the CESS-ECE (HUM2004-21127), Lang2World (TIN2006- 15265-C06-06), and Praxem (HUM2006- 27378-E) projects

Community Outreach through Genomics Education Partnership

The J Craig Venter Institute (JCVI) has recently partnered with undergraduate university faculty to expand the scope of education and outreach program as part of the NIAID’s BRC initiative, by joining forces with faculty members participating in the Genomics Education Partnership (GEP). The goal of the GEP is to provide opportunities for undergraduate students to participate in genomics research and gain hands on experience. Faculty members trained on annotation methodologies and tools during the Prokaryotic Annotation Workshop conducted at JCVI, impart their knowledge in the classroom as part of the semester course. As a pilot project, we are currently collaborating with 3 groups lead by a faculty member, spread across 3 universities in the community curation of bacterial genomes. Each participating undergraduate group collectively annotates a specific bacterial genome that was sequenced at JCVI and run through the automatic annotation pipeline. Remote access to genome sequence data, pre-computed gene predictions, search results, automatic annotation and bioinformatics analysis is provided through our web-based manual annotation tool, MANATEE. The students log into JCVI genome databases with user specific ids and password and learn to annotate single genes, entire metabolic pathways leading to analysis of a question that may be unique to the genome being analyzed. Users of the genome data receive dedicated support and guidance from our in house annotation experts on the usage of JCVI’s tools and annotation methodologies. Through this exercise, the undergraduate students are introduced to concepts of genomics and bioinformatics and gain deeper understanding of the concepts of cellular metabolism and disease pathology, which may lead them to making scientific research their career path. Some groups are focusing on genome specific pathways and plan to conduct wet lab experiments to understand unique genome features. We are highly encouraged that this model of web based, remote access, community annotation has been successful and propose to leverage the community of annotators to update annotations of pathogen genomes in Pathema-BRC

Community annotation and bioinformatics workforce development in concert—Little Skate Genome Annotation Workshops and Jamborees

Recent advances in high-throughput DNA sequencing technologies have equipped biologists with a powerful new set of tools for advancing research goals. The resulting flood of sequence data has made it critically important to train the next generation of scientists to handle the inherent bioinformatic challenges. The North East Bioinformatics Collaborative (NEBC) is undertaking the genome sequencing and annotation of the little skate (Leucoraja erinacea) to promote advancement of bioinformatics infrastructure in our region, with an emphasis on practical education to create a critical mass of informatically savvy life scientists. In support of the Little Skate Genome Project, the NEBC members have developed several annotation workshops and jamborees to provide training in genome sequencing, annotation and analysis. Acting as a nexus for both curation activities and dissemination of project data, a project web portal, SkateBase (http://skatebase.org) has been developed. As a case study to illustrate effective coupling of community annotation with workforce development, we report the results of the Mitochondrial Genome Annotation Jamborees organized to annotate the first completely assembled element of the Little Skate Genome Project, as a culminating experience for participants from our three prior annotation workshops. We are applying the physical/virtual infrastructure and lessons learned from these activities to enhance and streamline the genome annotation workflow, as we look toward our continuing efforts for larger-scale functional and structural community annotation of the L. erinacea genome

The Use of Digital Video Annotation in Teacher Training: The Teachers’ Perspectives

The use of digital video offers interesting opportunities in teacher training, particularly the possibilities provided by video annotation, whereby people can add and share comments and opinions on the same videos, even from different places. This exploratory study aims to examine teachers’ perspectives of this technology, taking into account both their explicit and implicit evaluations. Different methods of using video annotation for training are compared, one based on its individual use, another supported by various types of tutorship. The data were collected and analysed first through a quantitative phase, followed by an in-depth qualitative phase. It is pointed out that to make this technology fully operational it is important to address the cultural and psychosocial aspects that control the emotional conditions which arise when one’s teaching behaviour is being observed and assessed

A participatory action research study on handwritten annotation feedback and its impact on staff and students

Annotation was introduced to a United Kingdom (UK) School of Nursing following an institutional audit within a UK University. Handwritten annotation (writing in the margins of student assignments) was introduced to the grading procedure to enhance the quality of student feedback and learning. Once in practice, annotation could be examined and an action research study facilitated the process. Post-qualifying essay scripts were examined for styles of annotation to identify its strengths and weaknesses. Five staff participated in action research to examine staff perceptions of annotation. Findings showed that words or telegraphic signs that stand alone in the margins of a student essay can be seen as abstract signs to the novitiate reader and need contextualising. If there is a negative tone in the markers’ annotation it can be detected by the student and interpreted as unhelpful or disparaging. There are a number of ways of improving annotation, and good practice guidelines are offered in the conclusion to this paper