 | |
| Initial release | 21 September 2001 |
|---|---|
| Written in | Perl |
| Type | Bioinformatics |
| License | Artistic License and GPL |
| Website | biomoby |
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 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 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.
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.
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 (data-format) and Namespace (data-type) 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. [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 does not, for its core operations, utilize the RDF or OWL 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 BioMOBY Object Ontology controls the valid data structures in exactly the same way as an OWL ontology defines an RDF data instance. BioMOBY Web Services consume and generate BioMOBY XML, [5] the structure of which is defined by the 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 its Objects, Namespaces, Service, and Registry. Increasingly these ontologies are being used to govern the behaviour of all BioMOBY functions using DL reasoners.
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. The first BioMOBY client was Gbrowse Moby, [6] written in 2001 to allow access to the prototype version of BioMoby Services. Gbrowse Moby, in addition to being a BioMoby browser, now works in tandem with the Taverna workbench to create SCUFL workflows reflecting the Gbrowse Moby browsing session that can then be run in a high-throughput environment. The Seahawk applet also provides the ability to export a session history as a Taverna workflow, in what constitutes a programming by example functionality. [7]
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.
The Semantic Web, sometimes known as Web 3.0, is an extension of the World Wide Web through standards set by the World Wide Web Consortium (W3C). The goal of the Semantic Web is to make Internet data machine-readable.
In information science, an ontology encompasses a representation, formal naming, and definitions of the categories, properties, and relations between the concepts, data, or entities that pertain to one, many, or all domains of discourse. More simply, an ontology is a way of showing the properties of a subject area and how they are related, by defining a set of terms and relational expressions that represent the entities in that subject area. The field which studies ontologies so conceived is sometimes referred to as applied ontology.
The Resource Description Framework (RDF) is a World Wide Web Consortium (W3C) standard originally designed as a data model for metadata. It has come to be used as a general method for description and exchange of graph data. RDF provides a variety of syntax notations and data serialization formats, with Turtle currently being the most widely used notation.
The Web Ontology Language (OWL) is a family of knowledge representation languages for authoring ontologies. Ontologies are a formal way to describe taxonomies and classification networks, essentially defining the structure of knowledge for various domains: the nouns representing classes of objects and the verbs representing relations between the objects.
The Industry Foundation Classes (IFC) is a CAD data exchange data schema intended for description of architectural, building and construction industry data.
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A web resource is any identifiable resource present on or connected to the World Wide Web. Resources are identified using Uniform Resource Identifiers (URIs). In the Semantic Web, web resources and their semantic properties are described using the Resource Description Framework (RDF).
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A semantic web service, like conventional web services, is the server end of a client–server system for machine-to-machine interaction via the World Wide Web. Semantic services are a component of the semantic web because they use markup which makes data machine-readable in a detailed and sophisticated way.
The Open Biological and Biomedical Ontologies (OBO) Foundry is a group of people dedicated to build and maintain ontologies related to the life sciences. The OBO Foundry establishes a set of principles for ontology development for creating a suite of interoperable reference ontologies in the biomedical domain. Currently, there are more than a hundred ontologies that follow the OBO Foundry principles.
Semantic publishing on the Web, or semantic web publishing, refers to publishing information on the web as documents accompanied by semantic markup. Semantic publication provides a way for computers to understand the structure and even the meaning of the published information, making information search and data integration more efficient.
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In computer science, information science and systems engineering, ontology engineering is a field which studies the methods and methodologies for building ontologies, which encompasses a representation, formal naming and definition of the categories, properties and relations between the concepts, data and entities of a given domain of interest. In a broader sense, this field also includes a knowledge construction of the domain using formal ontology representations such as OWL/RDF. A large-scale representation of abstract concepts such as actions, time, physical objects and beliefs would be an example of ontological engineering. Ontology engineering is one of the areas of applied ontology, and can be seen as an application of philosophical ontology. Core ideas and objectives of ontology engineering are also central in conceptual modeling.
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