Dasty2, an Ajax protein DAS client.
ABSTRACT Dasty2 is a highly interactive web client integrating protein sequence annotations from currently more than 40 sources, using the distributed annotation system (DAS). AVAILABILITY: Dasty2 is an open source tool freely available under the terms of the Apache License 2.0, publicly available at http://www.ebi.ac.uk/dasty/.
- SourceAvailable from: Alberto Labarga[Show abstract] [Hide abstract]
ABSTRACT: The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively deployed, end-user applications need to be aware of, and support, best practices and standards. Here, we report on an initiative in which software developers and genome biologists came together to explore and raise awareness of these issues: BioHackathon 2009. Developers in attendance came from diverse backgrounds, with experts in Web services, workflow tools, text mining and visualization. Genome biologists provided expertise and exemplar data from the domains of sequence and pathway analysis and glyco-informatics. One goal of the meeting was to evaluate the ability to address real world use cases in these domains using the tools that the developers represented. This resulted in i) a workflow to annotate 100,000 sequences from an invertebrate species; ii) an integrated system for analysis of the transcription factor binding sites (TFBSs) enriched based on differential gene expression data obtained from a microarray experiment; iii) a workflow to enumerate putative physical protein interactions among enzymes in a metabolic pathway using protein structure data; iv) a workflow to analyze glyco-gene-related diseases by searching for human homologs of glyco-genes in other species, such as fruit flies, and retrieving their phenotype-annotated SNPs. Beyond deriving prototype solutions for each use-case, a second major purpose of the BioHackathon was to highlight areas of insufficiency. We discuss the issues raised by our exploration of the problem/solution space, concluding that there are still problems with the way Web services are modeled and annotated, including: i) the absence of several useful data or analysis functions in the Web service "space"; ii) the lack of documentation of methods; iii) lack of compliance with the SOAP/WSDL specification among and between various programming-language libraries; and iv) incompatibility between various bioinformatics data formats. Although it was still difficult to solve real world problems posed to the developers by the biological researchers in attendance because of these problems, we note the promise of addressing these issues within a semantic framework.Journal of biomedical semantics. 08/2011; 2:4.
Article: InterPro protein classification.[Show abstract] [Hide abstract]
ABSTRACT: Improvements in nucleotide sequencing technology have resulted in an ever increasing number of nucleotide and protein sequences being deposited in databases. Unfortunately, the ability to manually classify and annotate these sequences cannot keep pace with their rapid generation, resulting in an increased bias toward unannotated sequence. Automatic annotation tools can help redress the balance. There are a number of different groups working to produce protein signatures that describe protein families, functional domains or conserved sites within related groups of proteins. Protein signature databases include CATH-Gene3D, HAMAP, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY, and TIGRFAMs. Their approaches range from characterising small conserved motifs that can identify members of a family or subfamily, to the use of hidden Markov models that describe the conservation of residues over entire domains or whole proteins. To increase their value as protein classification tools, protein signatures from these 11 databases have been combined into one, powerful annotation tool: the InterPro database (http://www.ebi.ac.uk/interpro/) (Hunter et al., Nucleic Acids Res 37:D211-D215, 2009). InterPro is an open-source protein resource used for the automatic annotation of proteins, and is scalable to the analysis of entire new genomes through the use of a downloadable version of InterProScan, which can be incorporated into an existing local pipeline. InterPro provides structural information from PDB (Kouranov et al., Nucleic Acids Res 34:D302-D305, 2006), its classification in CATH (Cuff et al., Nucleic Acids Res 37:D310-D314, 2009) and SCOP (Andreeva et al., Nucleic Acids Res 36:D419-D425, 2008), as well as homology models from ModBase (Pieper et al., Nucleic Acids Res 37:D347-D354, 2009) and SwissModel (Kiefer et al., Nucleic Acids Res 37:D387-D392, 2009), allowing a direct comparison of the protein signatures with the available structural information. This chapter reviews the signature methods found in the InterPro database, and provides an overview of the InterPro resource itself.Methods in molecular biology (Clifton, N.J.) 01/2011; 694:37-47. · 1.29 Impact Factor
Article: Dasty3, a WEB framework for DAS.[Show abstract] [Hide abstract]
ABSTRACT: MOTIVATION: Dasty3 is a highly interactive and extensible Web-based framework. It provides a rich Application Programming Interface upon which it is possible to develop specialized clients capable of retrieving information from DAS sources as well as from data providers not using the DAS protocol. Dasty3 provides significant improvements on previous Web-based frameworks and is implemented using the 1.6 DAS specification. AVAILABILITY: Dasty3 is an open-source tool freely available at http://www.ebi.ac.uk/dasty/ under the terms of the GNU General public license. Source and documentation can be found at http://code.google.com/p/dasty/. CONTACT: email@example.com.Bioinformatics 07/2011; 27(18):2616-7. · 5.47 Impact Factor
© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: firstname.lastname@example.org
Databases and Ontologies
Dasty2, an Ajax protein DAS client
Rafael C. Jimenez1,2,#, Antony F. Quinn1,#, Alexander Garcia3,# Alberto Labarga1,
Kieran O'Neill1,2, Fernando Martinez2, Gustavo A. Salazar2, Henning Hermjakob1,*
1Proteomics Services Team, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, UK.
2National Bioinformatics Network, NBN Central, Raapenberg Rd, Pinelands, 7405, Cape Town.
3Faculty of Linguistics and Literary Sciences, University of Bremen, Bremen, Germany
Associate Editor: Dr. Jonathan Wren
Summary: Dasty2 is a highly interactive web client integrating pro-
tein sequence annotations from currently more than 40 sources,
using the Distributed Annotation System (DAS).
Availability: Dasty2 is an open source tool freely available under
the terms of the Apache License 2.0, publicly available at
We have developed Dasty2, a lightweight, modular DAS client
for researchers who aim to visualise, share and compare protein
sequence annotations using the Distribution Annotation System
(DAS). DAS is a lightweight system for integrating data from mul-
tiple heterogeneous distributed databases (Dowell et al., 2001).
DAS provides a client-server communication protocol to exchange
biological annotation in XML format via HTTP requests. It allows
integrating DNA or protein annotations from multiple sources in a
web browser, rather than in large central databases. DAS allows
annotations to be visualised in the DAS client while control over
the original source remains with the data provider (Prlic et al.
2005). Unlike SPICE, a Desktop Java-based DAS client for protein
sequence and structure views (Prlic et al. 2005), Dasty2 is a web
application that only requires a web browser. Compared to other
web clients like Ensembl ProtView (Flicek et al. 2007), Dasty2
increases responsiveness and interactivity by providing a rich user
experience and mimics the efficiency of desktop applications.
Asynchronous loading and local caching of results enabled by
AJAX improves usability and system response time (Garrett et al.
Dasty2 retrieves, integrates and visualizes protein sequence infor-
mation and facilitates rapid searches to find, share and compare
annotations for the protein of interest. The graphical layout of
Dasty2 is composed of panels which display different related pro-
tein information such as sequence details, positional annotations,
literature references and the protein structure, if present in PDB.
Additionally it includes other panels which complement the user
interface by providing additional functionality such as protein ID
*To whom correspondence should be addressed.
#These authors contributed equally to this work.
search and ontology-based filtering. Panels are interconnected,
presenting an interactive display. For instance, the action of click-
ing on a positional feature highlights its coverage on the sequence
and on the protein structure and it shows a pop-up window with
more details about the feature. Dasty2 improves the rich user inter-
face allowing users to expand and collapse sections, zoom and
resize the graphic, display extra features, drag and drop feature
lines, as well as to highlight and sort features.
The modular architecture of Dasty2 allows the inclusion of fur-
ther panels to add functionality as well as the use of only selected
panels; for instance, OntoDas (O’Neill et al. 2007) allows users to
build conceptual queries using the Gene Ontology (GO). For this
purpose an additional panel displaying ontology annotations and
enabling query construction was created. As more modules are
added the number of panels will increase. Figure 1 illustrates how
the initial information is displayed. Some of the panels are:
- Search panel: Dasty2 provides a text box to search for proteins
using UniProt identifiers and accession numbers. The search can
be restricted to a certain number of DAS servers classified in the
DAS Registry by a specific label, for example a large, collabora-
tive annotation project like Biosapiens (Valencia 2005). The search
panel includes a drop-down list of registered labels.
- Status panel: Dasty2 typically queries dozens of servers in re-
sponse to a user query. To optimize the user experience, data will
be displayed as soon as the first server replies are received. A pro-
gress bar on the left shows the percentage of DAS servers that have
been processed, while status, error and warning messages are dis-
played under the “System information” section on the right. The
“Annotation Sources Loaded” section shows the status of each
DAS source being loaded, with links to the raw XML data.
- Sequence panel: Displays the protein identifier, amino acid se-
quence and length.
- Configuration panel: Contains options to control the display of
the positional features panel. Users can zoom into the sequence, or
show/hide columns and annotations from specific DAS sources.
- Positional features panel: Shows annotations which are located
on specific regions of the protein, for example signal sequences
and functional domains. Annotations are aligned against the pro-
tein sequence, allowing visual comparison of features, for example
predicted signal sequences from SignalP (Bendtsen at al. 2004)
versus experimentally determined signal sequences from UniProt.
The feature colours are defined by the UniProt DAS stylesheet
Bioinformatics Advance Access published August 11, 2008
by guest on January 31, 2013
Jimenez et al.
which provides details on how the annotations should be rendered.
Separate columns show the feature type and source of a feature. On
mouse-over, a popup window displays annotation details on the
individual feature, usually also containing a link back to the origi-
nal annotation source for additional detail. To support visual com-
parison, “drag and drop” can be used for manual reordering of
- Non-positional features panel: Displays annotations with no
positional coordinates, for example protein synonyms or literature
- Filtering panel: Presents three tree menus allowing customiza-
tion of the display by filtering positional and non-positional anno-
tations by type, server name and category. The hierarchical organi-
sation of feature types allows efficient focus on annotation types of
interest, by including/excluding whole annotation groups like
structural annotation with a single mouse click.
- Protein structure panel: Provides a 3D view of the protein
structure whenever PDB structures are available for the UniProt ID
requested. If Dasty2 finds more than one structure, it includes a
drop-down list to chose among them. Users can chose three de-
fined sizes to display the structure and have an option to view it in
a pop-up window.
Figure 1. A view of Dasty2 and its panels.
Technically, Dasty2 retrieves annotations mapped to protein se-
quence coordinates from remote DAS servers, taking as input Uni-
Prot identifiers or accession numbers (Apweiler et al. 2004). The
client establishes an initial connection to the DAS Registry (Prlic
et al. 2007) and retrieves a list of available DAS annotation serv-
ers. The client then connects to the UniProt DAS reference server
(Jones et al. 2005) to retrieve the protein sequence, and then re-
trieves feature annotation from each DAS annotation server.
Dasty2 merges the collected data from all these servers and pro-
vides the user with a unified, structured and interactive view of the
sequence and its annotated features.
Dasty2 is based on a client-server architecture. The retrieval
module on the server side combines annotations from multiple
DAS servers and makes them available to the visualisation module.
The visualisation module displays the information obtained from
the retrieval module. The visualisation module is based on Ajax
and runs on all major web browsers. It has been thoroughly tested
on Mozilla Firefox 1.5 and 2.0, and Windows® Internet Explorer
6.0 and 7.0. The retrieval module has been written in Perl (CGI)
and runs on a HTTP servers like Apache. Dasty2 can be accessed
at http://www.ebi.ac.uk/dasty, but can also be downloaded and
customised for third party web sites.
Dasty2 is not just a report of annotations but an interactive display
to conveniently manipulate and visualise protein sequence infor-
mation. This facilitates the interaction between the user and the
information stored in DAS servers. The use of Ajax technology
improves its efficiency when displaying information as it delivers a
richer user-experience; this technology also reduces the server
workloads and increases the responsiveness of the application.
As the recognition of the Distributed Annotation System for provi-
sion of protein information increases, the load on the Dasty2 client
increases through more DAS servers and more features per server.
Currently, filtering for relevant results is performed on the client
side after querying all available sources. Future versions of Dasty2
will include targeted querying facilities to reduce server and client
workload, and increase client responsiveness.
CONCLUSIONS AND FUTURE WORK
This work has been supported by the European Commission within
its FP6 Programme, contract number LSHG-CT-2003-503265
(BioSapiens); the European Bioinformatics Institute; the National
Bioinformatics Network of South Africa; and the Spanish Ministe-
rio de Educacion y Ciencia.
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Apweiler,R. et al. (2004). UniProt: the Universal Protein knowledgebase. Nucleic
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O’Neill,K. et al. (2007). OntoDas - integrating DAS with ontology-based queries. Bio-
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by guest on January 31, 2013