BioMOBY

From Wikipedia, the free encyclopedia

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.

1 The BioMOBY project
2 Moby
3 BioMOBY clients
4 See also
5 External links

[edit] The BioMOBY project

The BioMoby project began at the Model Organism Bring Your own Database Interface Conference (MOBY-DIC), held in Emma Lake, Saskatchewan on September 21, 2001. It stemmed from a conversation between Mark D Wilkinson and Suzanna Lewis during a [1] Gene Ontology developers meeting at the Carnegie Institute, Stanford, where the functionalities of the Genquire and Apollo genome annotation tools were being discussed and compared. The lack of a simple standard that would allow these tools to interact with the myriad of data-sources required to accurately annotate a genome was a critical need of both systems.

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 to these projects as Moby and [Semantic Moby], respectively, to clearly distinguish them.

[edit] Moby

The Moby project defines three Ontologies that describe biological data-types, biological data-formats, and bioinformatics analysis types. Most of the interoperable behaviours seen in Moby are achieved through the Object and Namespace ontologies.

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. MOBY Central is aware of the Object and Namespace 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). 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 and Ahab clients respectively.

[edit] BioMOBY clients

There are several client applications that can search and browse the BioMOBY registry of services. One of the most popular is the Taverna workbench built as part of the MyGrid project.