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Article
Open AccessHaplogroup Context is Less Important in the Penetrance of Mitochondrial DNA Complex I Mutations Compared to mt-tRNA Mutations
Mitochondrial diseases are a highly complex, heterogeneous group of disorders. Mitochondrial DNA variants that are linked to disease can exhibit variable expression and penetrance. This has an implication for ...
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Reference Work Entry In depth
Ontologies and Life Science Data Management
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Article
Open AccessA document-centric approach for develo** the tolAPC ontology
There are many challenges associated with ontology building, as the process often touches on many different subject areas; it needs knowledge of the problem domain, an understanding of the ontology formalism, ...
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Living Reference Work Entry In depth
Ontologies and Life Science Data Management
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Chapter and Conference Paper
Lost in Translation: Data Integration Tools Meet the Semantic Web (Experiences from the Ondex Project)
More information is now being published in machine processable form on the web and, as de-facto distributed knowledge bases are materializing, partly encouraged by the vision of the Semantic Web, the focus is shi...
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Article
Open AccessModeling biomedical experimental processes with OBI
Experimental descriptions are typically stored as free text without using standardized terminology, creating challenges in comparison, reproduction and analysis. These difficulties impose limitations on data e...
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Article
Open AccessAn evolutionary approach to Function
Understanding the distinction between function and role is vexing and difficult. While it appears to be useful, in practice this distinction is hard to apply, particularly within biology.
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Article
Open AccessSelected papers from the 12th annual Bio-Ontologies meeting
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Article
Open AccessAnnotation of SBML models through rule-based semantic integration
The creation of accurate quantitative Systems Biology Markup Language (SBML) models is a time-intensive, manual process often complicated by the many data sources and formats required to annotate even a small ...
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Chapter
Develo** Ontologies within Decentralised Settings
This chapter addresses two research questions: “How should a well-engineered methodology facilitate the development of ontologies within communities of practice?” and “What methodology should be used?” If onto...
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Reference Work Entry In depth
Ontologies and Life Science Data Management
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Chapter
Application of Ontologies in Bioinformatics
The use of ontologies has become a mainstream activity within bioinformatics. In a largely descriptive science such as biology, the need to have a common understanding of things described is obvious. The need ...
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Article
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project
The Minimum Information for Biological and Biomedical Investigations (MIBBI) project aims to foster the coordinated development of minimum-information checklists and provide a resource for those exploring the ...
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Article
The minimum information about a genome sequence (MIGS) specification
With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspic...
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Article
Open AccessUnderstanding and using the meaning of statements in a bio-ontology: recasting the Gene Ontology in OWL
The bio-ontology community falls into two camps: first we have biology domain experts, who actually hold the knowledge we wish to capture in ontologies; second, we have ontology specialists, who hold knowledge...
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Chapter
Knowledge Discovery for Biology with Taverna
Life Science research has extended beyond in vivo and in vitro bench-bound science to incorporate in silico knowledge discovery, using resources that have been developed over time by different teams for different...
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Chapter and Conference Paper
Pedro Ontology Services: A Framework for Rapid Ontology Markup
Semantic Web technologies offer the possibility of increased accuracy and completeness in search and retrieval operations. In recent years, curators of data resources have begun favouring the use of ontologies...
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Chapter and Conference Paper
Seven Bottlenecks to Workflow Reuse and Repurposing
To date on-line processes (i.e. workflows) built in e-Science have been the result of collaborative team efforts. As more of these workflows are built, scientists start sharing and reusing stand-alone composition...
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Chapter and Conference Paper
Feta: A Light-Weight Architecture for User Oriented Semantic Service Discovery
Semantic Web Services offer the possibility of highly flexible web service architectures, where new services can be quickly discovered, orchestrated and composed into workflows. Most existing work has, however...
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Chapter and Conference Paper
Applying Semantic Web Services to Bioinformatics: Experiences Gained, Lessons Learnt
We have seen an increasing amount of interest in the application of Semantic Web technologies to Web services. The aim is to support automated discovery and composition of the services allowing seamless and tr...
