BioMOBY
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Website | biomoby |
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BioMOBY is a registry of web services used in bioinformatics. It allows interoperability between biological data hosts and analytical services by annotating services with terms taken from standard ontologies. BioMOBY is released under the Artistic License.[1]
The BioMOBY project
The BioMoby project began at the Model Organism Bring Your own Database Interface Conference (MOBY-DIC), held in Emma Lake,
Funding for the BioMOBY project was subsequently adopted by Genome Prairie (2002-2005), Genome Alberta (2005-date), in part through Genome Canada, a not-for-profit institution leading the Canadian X-omic initiatives.
There are two main branches of the BioMOBY project. One is a web-service-based approach, while the other utilizes Semantic Web technologies. This article will refer only to the Web Service specifications. The other branch of the project, Semantic Moby, is described in a separate entry.
Moby
The Moby project defines three
The MOBY Namespace Ontology is derived from the Cross-Reference Abbreviations List of the Gene Ontology project. It is simply a list of abbreviations for the different types of identifiers that are used in bioinformatics. For example, Genbank has "gi" identifiers that are used to enumerate all of their sequence records - this is defined as "NCBI_gi" in the Namespace Ontology.
The MOBY Object Ontology is an ontology consisting of IS-A, HAS-A, and HAS relationships between data formats. For example, a DNASequence IS-A GenericSequence and HAS-A String representing the text of the sequence. All data in Moby must be represented as some type of MOBY Object. An XML serialization of this ontology is defined in the Moby API such that any given ontology node has a predictable XML structure.
Thus, between these two ontologies, a service provider and/or a client program can receive a piece of Moby XML, and immediately know both its structure, and its "intent" (semantics).
The final core component of Moby is the MOBY Central web service registry.[2] MOBY Central is aware of the Object, Namespace and Service ontologies, and thus can match consumers who have in-hand Moby data, with service providers who claim to consume that data-type (or some compatible ontological data-type) or to perform a particular operation on it. This "semantic matching" helps ensure that only relevant service providers are identified in a registry query, and moreover, ensures that the in-hand data can be passed to that service provider verbatim. As such, the interaction between a consumer and a service provider can be partially or fully automated, as shown in the Gbrowse Moby[3] and Ahab clients respectively.[4]
BioMOBY and RDF/OWL
BioMOBY does not, for its core operations, utilize the
Nevertheless, the BioMOBY system exhibits what can only be described as
However, BioMOBY does utilize the RDF/OWL standards, as of 2006, for the description of its Objects, Namespaces, Service, and Registry. Increasingly these ontologies are being used to govern the behaviour of all BioMOBY functions using DL reasoners.
BioMOBY clients
There are several
The Ahab client is a fully automated data mining tool.[4] Given a starting point, it will discover, and execute, every possible BioMOBY service and provide the results in a clickable interface.
See also
- Open Bioinformatics Foundation
- SADI the Semantic Automated Discovery and Integration Framework
References
- ^ "Getting the code – BioMoby".
- ^ "MOBY CentralRegistry". biomoby.open-bio.org. Archived from the original on 31 July 2021.
- ^ "MOBY-S Client Initialization". mobycentral.icapture.ubc.ca. Archived from the original on 10 November 2006.
- ^ a b "Ahab Deployments". bioinfo.icapture.ubc.ca. 17 June 2006. Archived from the original on 17 June 2006.
- ^ "The MOBY Data Class Ontology". biomoby.open-bio.org. Archived from the original on 31 July 2021.
- ^ "MOBY-S Client Initialization". moby.ucalgary.ca. Archived from the original on 4 June 2008.
- ^ "Seahawk Applet - A MOBY Web Services Browser". moby.ucalgary.ca. Archived from the original on 29 June 2007.
Funther reading
- Gordon, Paul MK; Sensen, Christoph W. (18 June 2007). "Seahawk: moving beyond HTML in Web-based bioinformatics analysis". BMC Bioinformatics. 8 (1): 208. PMID 17577405.