BioMOBY is a registry of web services used in

bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...

. 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 Artistic license (alongside more contextually-specific derivative terms such as poetic license, historical license, dramatic license, and narrative license) refers to deviation from fact or form for artistic purposes. It can include the alterat ...

The BioMOBY project

Th
BioMoby
project began at the Model Organism Bring Your own Database Interface Conference (MOBY-DIC), held i
Emma Lake

Saskatchewan Saskatchewan ( ; ) is a Provinces and territories of Canada, province in Western Canada, western Canada, bordered on the west by Alberta, on the north by the Northwest Territories, on the east by Manitoba, to the northeast by Nunavut, and on t ...

on September 21, 2001. It stemmed from a conversation betwee
Mark D Wilkinson
and

Suzanna Lewis Suzanna (Suzi) E. Lewis was a scientist and Principal investigator at the Berkeley Bioinformatics Open-source Project based at Lawrence Berkeley National Laboratory until her retirement in 2019. Lewis led the development of open standards and soft ...

during

Gene Ontology The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and ge ...

developers meeting at the Carnegie Institute,

Stanford Stanford University, officially Leland Stanford Junior University, is a Private university, private research university in Stanford, California. The campus occupies , among the largest in the United States, and enrolls over 17,000 students. S ...

, 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. Funding for the BioMOBY project was subsequently adopted by Genome Prairiebr>
(2002-2005), Genome Albertabr>
2005-date), in part through

Genome Canada Genome Canada is a non-profit organization that aims to use genomics-based technologies to improve the lives of Canadians. It is funded by the Government of Canada. Genome Canada provides large-scale investments that develop new technologies, conne ...

br>
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

Ontologies In computer science and information science, an ontology encompasses a representation, formal naming, and definition of the categories, properties, and relations between the concepts, data, and entities that substantiate one, many, or all domains ...

that describe biologica
data-types
biologica
data-formats
and bioinformatic
analysis types
Most of the interoperable behaviours seen in Moby are achieved through the Object (data-format) and Namespace (data-type) ontologies. The MOB
Namespace Ontology
is derived from the Cross-Reference Abbreviations List of th
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 MOB
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 th

web service registry.

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 Semantic matching is a technique used in computer science to identify information which is semantically related. Given any two graph-like structures, e.g. classifications, taxonomies database or XML schemas and ontologies, matching is an operat ...

" 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 th
Gbrowse Moby
an

clients respectively.

BioMOBY and RDF/OWL

BioMOBY does not, for its core operations, utilize the RDF or

OWL Owls are birds from the order Strigiformes (), which includes over 200 species of mostly solitary and nocturnal birds of prey typified by an upright stance, a large, broad head, binocular vision, binaural hearing, sharp talons, and feathers a ...

standards from the W3C. This is in part because neither of these standards were stable in 2001, when the project began, and in part because the library support for these standards were not "commodity" in any of the most common languages (i.e. Perl and Java) at that time. Nevertheless, the BioMOBY system exhibits what can only be described as Semantic Web-like behaviours. The BioMOB
Object Ontology
controls the valid data structures in exactly the same way as an

ontology defines an RDF data instance. BioMOBY Web Services consume and generat
BioMOBY XML
the structure of which is defined by th
BioMOBY Object Ontology
As such, BioMOBY Web Services have been acting as prototypical Semantic Web Services since 2001, despite not using the eventual RDF/OWL standards. However, BioMOBY does utilize the RDF/OWL standards, as of 2006, for the description of it
ObjectsNamespacesService
an
Registry
Increasingly these ontologies are being used to govern the behaviour of all BioMOBY functions using DL reasoners.

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 Apache Taverna was an open source software tool for designing and executing workflows, initially created by the myGrid project under the name ''Taverna Workbench'', then a project under the Apache incubator. Taverna allowed users to integrate many ...

built as part of the

MyGrid The myGrid consortium produces and uses a suite of tools design to “help e-Scientists get on with science and get on with scientists”. The tools support the creation of e-laboratories and have been used in domains as diverse as systems biol ...

project. The first BioMOBY client wa
Gbrowse Moby
written in 2001 to allow access to the prototype version of BioMoby Services. Gbrowse Mob

in addition to being a BioMoby browser, now works in tandem with the

to create SCUFL workflows reflecting the Gbrowse Moby browsing session that can then be run in a high-throughput environment. Th
Seahawk
applet also provides the ability to export a session history as a Taverna workflow, in what constitutes a

programming by example In computer science, programming by example (PbE), also termed programming by demonstration or more generally as demonstrational programming, is an end-user development technique for machine learning, teaching a computer new behavior by demonstratin ...

functionality. Th
Ahab
client is a fully automated data mining tool. Given a starting point, it will discover, and execute, every possible BioMOBY service and provide the results in a clickable interface.

References

{{reflist

External links

Official BioMOBY website

Publications about BioMOBY
tagged using

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