Pedro: a configurable data entry tool for XML

Garwood, Kevin; Taylor, Chris; Runte, Kai J.; Brass, Andy; Oliver, Stephen G.; Paton, Norman W.

doi:10.1093/bioinformatics/bth251

Cited by 23 publications

(13 citation statements)

References 2 publications

(2 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It is clear that tool support is required for this process to encourage either external service providers, or service consumers to generate their own semantic service descriptions. To this end, we use the PeDRo application [6]. This provides a GUI based interface which allows users to generate XML instance documents conformant to a given XML schema.…”

Section: Service Annotationmentioning

confidence: 99%

Feta: A Light-Weight Architecture for User Oriented Semantic Service Discovery

Lord

Alper

Wroe

et al. 2005

Lecture Notes in Computer Science

View full text Add to dashboard Cite

Abstract. Semantic Web Services offer the possibility of highly flexible web service architectures, where new services can be quickly discovered, orchestrated and composed into workflows. Most existing work has, however, focused on complex service descriptions for automated composition. In this paper, we describe the requirements from the bioinformatics domain which demand technically simpler descriptions, involving the user community at all levels. We describe our data model and lightweight semantic discovery architecture. We explain how this fits in the larger architecture of the my Grid project, which overall enables interoperability and composition across, disparate, autonomous, third-party services. Our contention is that such light-weight service discovery provides a good fit for user requirements of bioinformatics and possibly other domains.

show abstract

Section: Service Annotationmentioning

confidence: 99%

Feta: A Light-Weight Architecture for User Oriented Semantic Service Discovery

Lord

Alper

Wroe

et al. 2005

Lecture Notes in Computer Science

View full text Add to dashboard Cite

show abstract

“…It is crucial that software development is linked at an early stage through agreed documentation, XML-based definitions and controlled vocabularies that allow different tools to exchange primary data sets. First efforts are emerging regarding databases (Potter, 2001;Garwood et al, 2004b) and systems biology software infrastructure (ISB, http://www.systemsbiology.org/). There are not many Proteome Data Repository implementations in mySQL or Oracle available.…”

Section: Software…mentioning

confidence: 99%

A Bioinformatics Perspective on Proteomics: Data Storage, Analysis, and Integration

2005

View full text Add to dashboard Cite

The field of proteomics is advancing rapidly as a result of powerful new technologies and proteomics experiments yield a vast and increasing amount of information. Data regarding protein occurrence, abundance, identity, sequence, structure, properties, and interactions need to be stored. Currently, a common standard has not yet been established and open access to results is needed for further development of robust analysis algorithms. Databases for proteomics will evolve from pure storage into knowledge resources, providing a repository for information (meta-data) which is mainly not stored in simple flat files. This review will shed light on recent steps towards the generation of a common standard in proteomics data storage and integration, but is not meant to be a comprehensive overview of all available databases and tools in the proteomics community.

show abstract

“…As stated above, the consensus data model of the PPP pilot phase included only a limited representation of methods and results, to minimize the time commitment for participating experimentalists. Two methods for submitting were offered: (a) a combination of Microsoft Excel ™ , Microsoft Word ™ , and text forms, or (b) an XML (http://www.w3.org/XML) schema-based file format (PEDRO [5,6]). Those who chose the form-based submission were asked to fill out a set of preformatted Excel/ Word/text document templates, and submit them online using a web-based submission server at the University of Michigan.…”

Section: Data Submission Processmentioning

confidence: 99%

Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project

Adamski¹,

Blackwell²,

Menon³

et al. 2006

Exploring the Human Plasma Proteome

View full text Add to dashboard Cite

The pilot phase of the HUPO Plasma Proteome Project (PPP) is an international collaboration to catalog the protein composition of human blood plasma and serum by analyzing standardized aliquots of reference serum and plasma specimens using a variety of experimental techniques. Data management for this project included collection, integration, analysis, and dissemination of findings from participating organizations world-wide. Accomplishing this task required a communication and coordination infrastructure specific enough to support meaningful integration of results from all participants, but flexible enough to react to changing requirements and new insights gained during the course of the project and to allow participants with varying informatics capabilities to contribute. Challenges included integrating heterogeneous data, reducing redundant information to minimal identification sets, and data annotation. Our data integration workflow assembles a minimal and representative set of protein identifications, which account for the contributed data. It accommodates incomplete concordance of results from different laboratories, ambiguity and redundancy in contributed identifications, and redundancy in the protein sequence databases. Recommendations of the PPP for future largescale proteomics endeavors are described.

show abstract

Pedro: a configurable data entry tool for XML

Abstract: The application, source code, example models from several domains and tutorials can be downloaded from http://pedro.man.ac.uk/.

Cited by 23 publications

References 2 publications

Feta: A Light-Weight Architecture for User Oriented Semantic Service Discovery

Feta: A Light-Weight Architecture for User Oriented Semantic Service Discovery

A Bioinformatics Perspective on Proteomics: Data Storage, Analysis, and Integration

Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project

Contact Info

Product

Resources

About