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Biomoby Web Services -
Web Services and More

FAQ:
What are web services?
Common description:
Web services make it possible to get automated access to data from the internet without using a browser. The user can define a query with some kind of software (client) and, after it was send, will receive the result. If some web services from different institutions use the same format, the user can assemble larger networks from different web services using the provided data such that one web service gets as input the ouptut of one or more web services called before.
E.g.: Blast different Arabidopsis databases with one or more unknown nucleotide sequences (every blast job against a specific database is another web service). For finding all the phenotypes which resulted by a manipulation of the found genes, another web service can be used. The whole work can be done in one run.

Technical details:
A Web service is a software system designed to support interoperable machine-to-machine interaction over a network. Software applications written in various programming languages and running on various platforms can use web services to exchange data over computer networks like the Internet in a manner similar to inter-process communication on a single computer. This interoperability (for example, between Java and Python, or Microsoft Windows and Linux applications) is due to the use of open standards.
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What is BioMoby?
The MOBY system for interoperability between biological data hosts and analytical services. The MOBY-S system defines an ontology-based messaging standard through which a client will be able to automatically discover and interact with task-appropriate biological data and analytical service providers, without requiring manual manipulation of data formats as data flows from one provider to the next.
(http://biomoby.open-bio.org/index.php/what-is-moby/)
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Which web services do we provide?
We provide one BioMoby web service (number 1) in the scope of Arabidopsis web services (see below). Aditional web services can retrieve data from any species in GabiPD for which public data is available.

Web services:
workflow.png 1. GabiPDCheckMaterialByAGI
Input: AGI_LocusCode or AGI_SpliceVariant
Output: available clone(s) from ImaGenes GmbH (successor of RZPD)
Download the taverna workflow by clicking the right mouse button and choosing "Save Link As..."
workflow.png 2. GabiPDGetOrthologuesByAGI
Input: AGI_LocusCode or AGI_SpliceVariant or an alias (or part of them)
Output: Orthologous and co-orthologous gene pairs, identified by InParanoid
Download the taverna workflow by clicking the right mouse button and choosing "Save Link As..."
workflow.png 3. GabiPDGetRelatedDataByAGI
Input: AGI_LocusCode or AGI_SpliceVariant or an alias (or part of them)
Output: Related data objects found in GabiPD
Download the taverna workflow by clicking the right mouse button and choosing "Save Link As..."
workflow.png 4. GabiPDGetSequencesByAGI
Input: AGI_LocusCode or AGI_SpliceVariant or an alias (or part of them)
Output: Sequences associated with the given input
Download the taverna workflow by clicking the right mouse button and choosing "Save Link As..."
These services can be accessed by the BioMoby Dashboard, the Taverna client, by a selfmade Perl/Java client or command line.
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