The Distributed Annotation System

By R. Dowell, R. M. Jokerst, Allen Day, Sean R. Eddy, Lincoln D. Stein. BMC Bioinformatics, 2001

469 citations recorded by the source corpus.

BackgroundCurrently, most genome annotation is curated by centralized groups with limited resources. Efforts to share annotations transparently among multiple groups have not yet been satisfactory.ResultsHere we introduce a concept called the Distributed Annotation System (DAS). DAS allows sequence annotations to be decentralized among multiple third-party annotators and integrated on an as-needed basis by client-side software. The communication between client and servers in DAS is defined by the DAS XML specification. Annotations are displayed in layers, one per server. Any client or server adhering to the DAS XML specification can participate in the system; we describe a simple prototype client and server example.ConclusionsThe DAS specification is being used experimentally by Ensembl, WormBase, and the Berkeley Drosophila Genome Project. Continued success will depend on the readiness of the research community to adopt DAS and provide annotations. All components are freely available from the project website http://www.biodas.org/.

Subfields: Information Systems and Management, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1418d1b585ab94d4901562837df8b0d0b52217fd

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Citations in the corpus

NONCODE v3.0: integrative annotation of long noncoding RNAs (2011, unknown): “Distributed Annotation System (DAS) allows sequence annotations to be decentralized among multiple thirdparty annotators and integrated on an as-needed basis on the client side (29), which facilitates integration and collation of ncRNA annotations from multiple servers.”
The Bioperl toolkit: Perl modules for the life sciences. (2002, methodology): “server ( Dowell et al. 2001 ), and TFBS (Lenhard and Wasserman 2002) all use the Bioperl object model to describe”
UniProt Knowledgebase: a hub of integrated protein data (2011, methodology): “The UniProt DAS server (34), which is available at http:// www.ebi.ac.uk/das-srv/uniprot/das, provides access to sequences and annotation from both UniProtKB and the UniProt Archive (35), a comprehensive and non-redundant database that contains all of the protein sequences from the main publicly ava”
Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB (2013, methodology): “Pepper is a Java desktop application that combines 3D visualisation of overlaid maps and models with an interactive view of annotations of the molecules in the models, such as the model sequence, provided via the Distributed Annotation System (DAS; Dowell et al., 2001).”
The human genome browser at UCSC. (2002, methodology): “Most of the browser database also can be accessed via the Distributed Annotation Service (DAS) protocol (Dowell et al. 2001).”
The IntAct molecular interaction database in 2010 (2009, methodology): “Using the DAS protocol (22), this view shows protein features projected onto its sequence and, where available, its structure.”
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration (2012, methodology): “…the built-in file browser to select a file on the local file system, (ii) entering the URL of a file accessible over a network via HTTP or FTP, (iii) entering the URL of a Distributed Annotation System (DAS) feature source [18] or (iv) selecting entries from the ‘File > Load from Server’ menu.”
The generic genome browser: a building block for a model organism system database. (2002, background): “For this reason, an important near-term goal of the project is to complete an adaptor layer for the Distributed Annotation System (DAS; Dowell et al. 2001).”
Ensembl 2008 (2007, methodology): “Ensembl continues to make extensive use of the DAS protocol (23).”
Ensembl 2009 (2008, methodology): “– It allows its genome annotations, alignments, variation and functional genomics data to be dynamically federated with external data sources via the DAS protocol (3,4) and visualized through many of its website interfaces (http:// www.”
BioMOBY: An Open Source Biological Web Services Proposal (2002, background): “The response to this is twofold: (1) BioMOBY function requires ‘minimalist’ objects, and this necessitates the (relatively simple) task of creating our own lightweight object models and (2) BioMOBY is more concerned with data discovery and transport than standardisation or representation.”
The Pfam protein families database (2007, background): “Furthermore, we have adapted the features response so that it conforms to the ontology standards set out for DAS feature servers (23).”
COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer (2009, unknown): “org) via DAS [distributed annotation system, (5)].”
The Pfam protein families database (2011, background): “(DAS) ( 10 ) to aggregate multiple data sources in a single display.”
The PeptideAtlas project (2005, methodology): “Visualization of the results is achieved using the DAS in conjunction with the Ensembl genome brow-ser.”
Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser (2013, methodology): “In contrast to the extensible mark-up language format of DAS, which may be easier for a simple application to access, track data hubs present data in the native format of the data files with a rich set of options for controlling how that data should displayed.”
The UCSC Genome Browser Database (2003, methodology): “A large portion of the Genome Browser Database is accessible using the Distributed Annotation Service (DAS) protocol (12).”