Representing, storing and accessing molecular interaction data: a review of models and tools

Strömbäck, Lena; Jakoniené, Vaida; Tan, He; Lambrix, Patrick

doi:10.1093/bib/bbl039

Cited by 33 publications

(17 citation statements)

References 26 publications

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“…However it is not our intention to comparatively evaluate these ontologies, as has been done recently [17,18]. Briefly, BioPax is designed to describe pathway rather than specific molecular interaction data.…”

Section: Resultsmentioning

confidence: 99%

Integrating Hierarchical Controlled Vocabularies With Owl Ontology: A Case Study From the Domain of Molecular Interactions

Davis¹,

Newman²,

Khan³

et al. 2007

Proceedings of the 6th Asia-Pacific Bioinformatics Conference

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Many efforts at standardising terminologies within the biological domain have resulted in the construction of hierarchical controlled vocabularies that capture domain knowledge. Vocabularies, such as the PSI-MI vocabulary, capture both deep and extensive domain knowledge, in the OBO (Open Biomedical Ontologies) format. However hierarchical vocabularies, such as PSI-MI which are represented in OBO, only represent simple parent-child relationships between terms. By contrast, ontologies constructed using the Web Ontology Language (OWL), such as BioPax, define many richer types of relationships between terms. OWL provides a semantically rich structured language for describing classes and sub-classes of entities and properties, relationships between them and expressing domain-specific rules or axioms that can be applied to extract new information through semantic inference. In order to fully exploit the domain knowledge inherent in domain-specific controlled vocabularies, they need to be represented as OWL-DL ontologies, rather than in formats such as OBO. In this paper, we describe a method for converting OBO vocabularies into OWL and * This work has been performed as part of a collaborative research and development project with Pfizer Global R&D and is partially supported by ARC grand CEO348221. 2 class instances represented as OWL-RDF triples. This approach preserves the hierarchical arrangement of the domain knowledge whilst also making the underlying parent-child relationships available to inference engines. This approach also has clear advantages over existing methods which incorporate terms from external controlled vocabularies as literals stripped of the context associated with their place in the hierarchy. By preserving this context, we enable machine inference over the ordered domain knowledge captured in OBO controlled vocabularies.

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Section: Resultsmentioning

confidence: 99%

Integrating Hierarchical Controlled Vocabularies With Owl Ontology: A Case Study From the Domain of Molecular Interactions

Davis¹,

Newman²,

Khan³

et al. 2007

Proceedings of the 6th Asia-Pacific Bioinformatics Conference

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show abstract

“…The choice of representation is important when passing complex objects as arguments between web services, but also to enable an understanding of the semantics of the services. In our case we have chosen to use available XML standards for bioinformatics [3], [4], such as SBML and UniPROT formats. This is a benefit, as it makes the functionality of the service transparent to anyone familiar with the standard, e. g. in our case the naming and the functionality of the SBML services have a direct relationship to the entities defined by SBML.…”

Section: Data Representationmentioning

confidence: 99%

“…These databases are being maintained and hosted by a large number of autonomous service providers, many of which are only concerned with a single database and its tools. Regarding how data should be represented and formatted and how its corresponding tools and algorithms should be interfaced, there exists a large number of standards [3] [4]. As an example, P. Lord et al say in [5] that "there are at least 20 different formats for representing DNA sequences, most of which have no formal specification".…”

Section: Introductionmentioning

confidence: 99%

Interoperable and Easy-to-Use Web Services for the Bioinformatics Community - A Case Study

Åsberg

Strömbäck

2010

2010 Second International Conference on Advances in Databases, Knowledge, and Data Applications

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In the field of bioinformatics, there exists a large number of web service providers and many competing standards regarding how data should be represented and interfaced. However, these web services are often hard to use for a non-expert programmer and it can be especially hard to see how different services can be used together to create scientific workflows. In this paper we have performed a literature study to identify problems involved in developing interoperable web services for the bioinformatics community and steps taken by other projects to, at least in part, address them. We have also conducted a case study by developing our own bioinformatic web service to further investigate these problems.

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“…OWL provides a framework for controlled vocabulary along with a formal semantics. BioPAX concepts, unlike generic XML concepts, have relationships to each other that can be processed automatically (see [11,12] for more information on using BioPAX vs. SBML). An automatic reasoner can infer that if B is a kind of A, then B inherits all of A's property definitions.…”

Section: Biopax Sbml and Sbomentioning

confidence: 99%

Kinetic Modeling Using BioPAX Ontology

Ruebenacker

Moraru

Schaff

et al. 2007

2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007)

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Thousands of biochemical interactions are available for download from curated databases such as Reactome, Pathway Interaction Database and other sources in the Biological Pathways Exchange (BioPAX) format. However, the BioPAX ontology does not encode the necessary information for kinetic modeling and simulation. The current standard for kinetic modeling is the System Biology Markup Language (SBML), but only a small number of models are available in SBML format in public repositories. Additionally, reusing and merging SBML models presents a significant challenge, because often each element has a value only in the context of the given model, and information encoding biological meaning is absent. We describe a software system that enables a variety of operations facilitating the use of BioPAX data to create kinetic models that can be visualized, edited, and simulated using the Virtual Cell (VCell), including improved conversion to SBML (for use with other simulation tools that support this format).

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Representing, storing and accessing molecular interaction data: a review of models and tools

Cited by 33 publications

References 26 publications

Integrating Hierarchical Controlled Vocabularies With Owl Ontology: A Case Study From the Domain of Molecular Interactions

Integrating Hierarchical Controlled Vocabularies With Owl Ontology: A Case Study From the Domain of Molecular Interactions

Interoperable and Easy-to-Use Web Services for the Bioinformatics Community - A Case Study

Kinetic Modeling Using BioPAX Ontology

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