bdbms -- A Database Management System for Biological Data

Biologists are increasingly using databases for storing and managing their data. Biological databases typically consist of a mixture of raw data, metadata, sequences, annotations, and related data obtained from various sources. Current database technology lacks several functionalities that are needed by biological databases. In this paper, we introduce bdbms, an extensible prototype database management system for supporting biological data. bdbms extends the functionalities of current DBMSs to include: (1) Annotation and provenance management including storage, indexing, manipulation, and querying of annotation and provenance as first class objects in bdbms, (2) Local dependency tracking to track the dependencies and derivations among data items, (3) Update authorization to support data curation via content-based authorization, in contrast to identity-based authorization, and (4) New access methods and their supporting operators that support pattern matching on various types of compressed biological data types. This paper presents the design of bdbms along with the techniques proposed to support these functionalities including an extension to SQL. We also outline some open issues in building bdbms.Comment: This article is published under a Creative Commons License Agreement (http://creativecommons.org/licenses/by/2.5/.) You may copy, distribute, display, and perform the work, make derivative works and make commercial use of the work, but, you must attribute the work to the author and CIDR 2007. 3rd Biennial Conference on Innovative Data Systems Research (CIDR) January 710, 2007, Asilomar, California, US

The CAMOMILE collaborative annotation platform for multi-modal, multi-lingual and multi-media documents

In this paper, we describe the organization and the implementation of the CAMOMILE collaborative annotation framework for multimodal, multimedia, multilingual (3M) data. Given the versatile nature of the analysis which can be performed on 3M data, the structure of the server was kept intentionally simple in order to preserve its genericity, relying on standard Web technologies. Layers of annotations, defined as data associated to a media fragment from the corpus, are stored in a database and can be managed through standard interfaces with authentication. Interfaces tailored specifically to the needed task can then be developed in an agile way, relying on simple but reliable services for the management of the centralized annotations. We then present our implementation of an active learning scenario for person annotation in video, relying on the CAMOMILE server; during a dry run experiment, the manual annotation of 716 speech segments was thus propagated to 3504 labeled tracks. The code of the CAMOMILE framework is distributed in open source.Peer ReviewedPostprint (author's final draft

Multi-Cue Structure Preserving MRF for Unconstrained Video Segmentation

Video segmentation is a stepping stone to understanding video context. Video segmentation enables one to represent a video by decomposing it into coherent regions which comprise whole or parts of objects. However, the challenge originates from the fact that most of the video segmentation algorithms are based on unsupervised learning due to expensive cost of pixelwise video annotation and intra-class variability within similar unconstrained video classes. We propose a Markov Random Field model for unconstrained video segmentation that relies on tight integration of multiple cues: vertices are defined from contour based superpixels, unary potentials from temporal smooth label likelihood and pairwise potentials from global structure of a video. Multi-cue structure is a breakthrough to extracting coherent object regions for unconstrained videos in absence of supervision. Our experiments on VSB100 dataset show that the proposed model significantly outperforms competing state-of-the-art algorithms. Qualitative analysis illustrates that video segmentation result of the proposed model is consistent with human perception of objects