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SORTA specifications

Information


Unique identifier OMICS_25577
Name SORTA
Alternative name System for Ontology-based Re-coding and Technical Annotation
Interface Web user interface
Restrictions to use None
Programming languages Java
License GNU General Public License version 3.0
Computer skills Basic
Version 1.1.2
Stability Stable
Maintained Yes

Maintainer


  • person_outline Morris Swertz

Additional information


https://molgenis.gitbooks.io/molgenis/quickstart/guide-quickstart.html

Publication for System for Ontology-based Re-coding and Technical Annotation

SORTA citations

 (3)
library_books

Linked Registries: Connecting Rare Diseases Patient Registries through a Semantic Web Layer

2017
Biomed Res Int
PMCID: 5682045
PMID: 29214177
DOI: 10.1155/2017/8327980

[…] e mapped to terms from more than one ontology, optimising its expressiveness and enriching the way it can be used in future research environments. In this step, semiautomated annotation tools such as SORTA [] and EGAS [] along human curation experts play an important role for the annotation of biomedical data (e.g., phenotypes, diseases).The second step of the pipeline consists in the configuratio […]

library_books

MetaSRA: normalized human sample specific metadata for the Sequence Read Archive

2017
Bioinformatics
PMCID: 5870770
PMID: 28535296
DOI: 10.1093/bioinformatics/btx334

[…] rms that incorrectly describe the sample. We note that the error rate is simply 1−precision. The metrics are demonstrated in . With these metrics, we compared our pipeline to the BioPortal Annotator, SORTA and ZOOMA across all ontologies (). Compared to these methods, our pipeline has a low error rate while maintaining a competitive recall. For example, although the ZOOMA pipeline scores a slightl […]

library_books

MOLGENIS/connect: a system for semi automatic integration of heterogeneous phenotype data with applications in biobanks

2016
Bioinformatics
PMCID: 4937195
PMID: 27153686
DOI: 10.1093/bioinformatics/btw155

[…] al cases that require us to add new rules. We would like to allow users to define custom rules for matching categories in the database. For matching string-type data values, we have developed a tool (SORTA) to semi-automatically recode the values based on the selected coding systems or ontologies, which we plan to incorporate in the near future (). […]

Citations

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SORTA institution(s)
University of Groningen, University Medical Centre Groningen, Genomics Coordination Centre, Department of Genetics, Groningen, the Netherlands; University of Groningen, University Medical Centre Groningen, Department of Genetics, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands; LifeLines Cohort Study and Biobank, Groningen, The Netherlands
SORTA funding source(s)
Supported by the European Union Seventh Framework Programme (FP7/2007-2013) grant number 261433 (Biobank Standardisation and Harmonisation forResearch Excellence in the European Union - BioSHaRE-EU) and grant number 284209 (BioMedBridges) and by BBMRI-NL, a research infrastructure financed by the Netherlands Organization for Scientific Research, grant number 184.021.007.

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