Deploying mutation impact text-mining software with the SADI Semantic Web Services framework

Riazanov, Alexandre; Laurila, Jonas Bergman; Baker, Christopher J. O.

doi:10.1186/1471-2105-12-s4-s6

Cited by 13 publications

(15 citation statements)

References 22 publications

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“…Because experimental findings are rarely reported to databases in a standardized form, metaresources, such as the Protein Mutant Database (PMD) (4) and Swiss-Prot/UniProt (5), manually curate publications to map variants to diseases. Natural language processing automates this mapping (6).…”

mentioning

confidence: 99%

Neutral and weakly nonneutral sequence variants may define individuality

Bromberg

Kahn

Rost

2013

Proc. Natl. Acad. Sci. U.S.A.

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Large-scale computational analyses of the growing wealth of genome-variation data consistently tell two distinct stories. The first is expected: coding variants reported in disease-related databases significantly alter the function of affected proteins. The second is surprising: the genomes of healthy individuals appear to carry many variants that are predicted to have some effect on function. As long as the complete experimental analysis of all human genome variants remains impossible, computational methods, such as PolyPhen, SNAP, and SIFT, might provide important insights. These methods capture the effects of particular variants very well and can highlight trends in populations of variants. Diseases are, arguably, extreme phenotypic variations and are often attributable to one or a few severely functionally disruptive variants. Our findings suggest a genomic basis of the different nondisease phenotypes. Prediction methods indicate that variants in seemingly healthy individuals tend to be neutral or weakly disruptive for protein molecular function. These variant effects are predicted to be largely either experimentally undetectable or are not deemed significant enough to be published. This may suggest that nondisease phenotypes arise through combinations of many variants whose effects are weakly nonneutral (damaging or enhancing) to the molecular protein function but fall within the wild-type range of overall physiological function.nsSNP | coding SNV | variome analysis | genomic variant burden | evolution

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mentioning

confidence: 99%

Neutral and weakly nonneutral sequence variants may define individuality

Bromberg

Kahn

Rost

2013

Proc. Natl. Acad. Sci. U.S.A.

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“…A general purpose solution can be adapted for use in a TM context by using TM resources if they are available, e.g. see a case study for SADI (89). Although general purpose workflow engines create an internal form of interoperability at the level of the process model, where all components within a workflow will work together, workflow engines from different providers cannot typically be expected to interact.…”

Section: Tools and Servicesmentioning

confidence: 99%

Text mining resources for the life sciences

Przybyła¹,

Shardlow²,

Aubin³

et al. 2016

Database

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Text mining is a powerful technology for quickly distilling key information from vast quantities of biomedical literature. However, to harness this power the researcher must be well versed in the availability, suitability, adaptability, interoperability and comparative accuracy of current text mining resources. In this survey, we give an overview of the text mining resources that exist in the life sciences to help researchers, especially those employed in biocuration, to engage with text mining in their own work. We categorize the various resources under three sections: Content Discovery looks at where and how to find biomedical publications for text mining; Knowledge Encoding describes the formats used to represent the different levels of information associated with content that enable text mining, including those formats used to carry such information between processes; Tools and Services gives an overview of workflow management systems that can be used to rapidly configure and compare domain- and task-specific processes, via access to a wide range of pre-built tools. We also provide links to relevant repositories in each section to enable the reader to find resources relevant to their own area of interest. Throughout this work we give a special focus to resources that are interoperable—those that have the crucial ability to share information, enabling smooth integration and reusability.

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“…For more technical details on SADI and SHARE, the reader is referred to [13], and Bioinformatics- and Chemoinformatics-related case studies can be found in [15-18]. …”

Section: Introductionmentioning

confidence: 99%

Semantic querying of relational data for clinical intelligence: a semantic web services-based approach

et al. 2013

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BackgroundClinical Intelligence, as a research and engineering discipline, is dedicated to the development of tools for data analysis for the purposes of clinical research, surveillance, and effective health care management. Self-service ad hoc querying of clinical data is one desirable type of functionality. Since most of the data are currently stored in relational or similar form, ad hoc querying is problematic as it requires specialised technical skills and the knowledge of particular data schemas.ResultsA possible solution is semantic querying where the user formulates queries in terms of domain ontologies that are much easier to navigate and comprehend than data schemas. In this article, we are exploring the possibility of using SADI Semantic Web services for semantic querying of clinical data. We have developed a prototype of a semantic querying infrastructure for the surveillance of, and research on, hospital-acquired infections.ConclusionsOur results suggest that SADI can support ad-hoc, self-service, semantic queries of relational data in a Clinical Intelligence context. The use of SADI compares favourably with approaches based on declarative semantic mappings from data schemas to ontologies, such as query rewriting and RDFizing by materialisation, because it can easily cope with situations when (i) some computation is required to turn relational data into RDF or OWL, e.g., to implement temporal reasoning, or (ii) integration with external data sources is necessary.

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Deploying mutation impact text-mining software with the SADI Semantic Web Services framework

Cited by 13 publications

References 22 publications

Neutral and weakly nonneutral sequence variants may define individuality

Neutral and weakly nonneutral sequence variants may define individuality

Text mining resources for the life sciences

Semantic querying of relational data for clinical intelligence: a semantic web services-based approach

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