dc.contributor.author | Lacson, Ronilda C. | |
dc.contributor.author | Pitzer, Erik | |
dc.contributor.author | Hinske, Christian | |
dc.contributor.author | Galante, Pedro | |
dc.contributor.author | Ohno-Machado, Lucila | |
dc.date.accessioned | 2011-07-01T13:37:02Z | |
dc.date.issued | 2009 | |
dc.identifier.citation | Lacson, Ronilda, Erik Pitzer, Christian Hinske, Pedro Galante, and Lucila Ohno-Machado. 2009. Evaluation of a large-scale biomedical data annotation initiative. BMC Bioinformatics 10(Suppl 9): S10. | en_US |
dc.identifier.issn | 1471-2105 | en_US |
dc.identifier.uri | http://nrs.harvard.edu/urn-3:HUL.InstRepos:4931095 | |
dc.description.abstract | Background: This study describes a large-scale manual re-annotation of data samples in the Gene Expression Omnibus (GEO), using variables and values derived from the National Cancer Institute thesaurus. A framework is described for creating an annotation scheme for various diseases that is flexible, comprehensive, and scalable. The annotation structure is evaluated by measuring coverage and agreement between annotators. Results: There were 12,500 samples annotated with approximately 30 variables, in each of six disease categories – breast cancer, colon cancer, inflammatory bowel disease (IBD), rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), and Type 1 diabetes mellitus (DM). The annotators provided excellent variable coverage, with known values for over 98% of three critical variables: disease state, tissue, and sample type. There was 89% strict inter-annotator agreement and 92% agreement when using semantic and partial similarity measures. Conclusion: We show that it is possible to perform manual re-annotation of a large repository in a reliable manner. | en_US |
dc.language.iso | en_US | en_US |
dc.publisher | BioMed Central | en_US |
dc.relation.isversionof | doi:10.1186/1471-2105-10-S9-S10 | en_US |
dc.relation.hasversion | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2745681/pdf/ | en_US |
dash.license | LAA | |
dc.title | Evaluation of a Large-Scale Biomedical Data Annotation Initiative | en_US |
dc.type | Journal Article | en_US |
dc.description.version | Version of Record | en_US |
dc.relation.journal | BMC Bioinformatics | en_US |
dash.depositing.author | Lacson, Ronilda C. | |
dc.date.available | 2011-07-01T13:37:02Z | |
dash.affiliation.other | HMS^Radiology-Brigham and Women's Hospital | en_US |
dc.identifier.doi | 10.1186/1471-2105-10-S9-S10 | * |
dash.contributor.affiliated | Lacson, Ronilda | |