Assessing the quality of annotations in asthma gene expression experiments

Persistent Link:
http://hdl.handle.net/10150/610165
Title:
Assessing the quality of annotations in asthma gene expression experiments
Author:
Lacson, Ronilda; Mbagwu, Michael; Yousif, Hisham; Ohno-Machado, Lucila
Affiliation:
Decision Systems Group, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA, USA; Ohio State University, Columbus, OH, USA; University of Arizona, Tucson, AZ, USA; Division of Biomedical Informatics, University of California San Diego, La Jolla, CA, USA
Issue Date:
2010
Publisher:
BioMed Central
Citation:
Lacson et al. BMC Bioinformatics 2010, 11(Suppl 9):S8 http://www.biomedcentral.com/1471-2105/11/S9/S8
Journal:
BMC Bioinformatics
Rights:
© 2010 Lacson et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
Abstract:
BACKGROUND:The amount of data deposited in the Gene Expression Omnibus (GEO) has expanded significantly. It is important to ensure that these data are properly annotated with clinical data and descriptions of experimental conditions so that they can be useful for future analysis. This study assesses the adequacy of documented asthma markers in GEO. Three objective measures (coverage, consistency and association) were used for evaluation of annotations contained in 17 asthma studies.RESULTS:There were 918 asthma samples with 20,640 annotated markers. Of these markers, only 10,419 had documented values (50% coverage). In one study carefully examined for consistency, there were discrepancies in drug name usage, with brand name and generic name used in different sections to refer to the same drug. Annotated markers showed adequate association with other relevant variables (i.e. the use of medication only when its corresponding disease state was present).CONCLUSIONS:There is inadequate variable coverage within GEO and usage of terms lacks consistency. Association between relevant variables, however, was adequate.
EISSN:
1471-2105
DOI:
10.1186/1471-2105-11-S9-S8
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2105/11/S9/S8

Full metadata record

DC FieldValue Language
dc.contributor.authorLacson, Ronildaen
dc.contributor.authorMbagwu, Michaelen
dc.contributor.authorYousif, Hishamen
dc.contributor.authorOhno-Machado, Lucilaen
dc.date.accessioned2016-05-20T09:00:07Z-
dc.date.available2016-05-20T09:00:07Z-
dc.date.issued2010en
dc.identifier.citationLacson et al. BMC Bioinformatics 2010, 11(Suppl 9):S8 http://www.biomedcentral.com/1471-2105/11/S9/S8en
dc.identifier.doi10.1186/1471-2105-11-S9-S8en
dc.identifier.urihttp://hdl.handle.net/10150/610165-
dc.description.abstractBACKGROUND:The amount of data deposited in the Gene Expression Omnibus (GEO) has expanded significantly. It is important to ensure that these data are properly annotated with clinical data and descriptions of experimental conditions so that they can be useful for future analysis. This study assesses the adequacy of documented asthma markers in GEO. Three objective measures (coverage, consistency and association) were used for evaluation of annotations contained in 17 asthma studies.RESULTS:There were 918 asthma samples with 20,640 annotated markers. Of these markers, only 10,419 had documented values (50% coverage). In one study carefully examined for consistency, there were discrepancies in drug name usage, with brand name and generic name used in different sections to refer to the same drug. Annotated markers showed adequate association with other relevant variables (i.e. the use of medication only when its corresponding disease state was present).CONCLUSIONS:There is inadequate variable coverage within GEO and usage of terms lacks consistency. Association between relevant variables, however, was adequate.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2105/11/S9/S8en
dc.rights© 2010 Lacson et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)en
dc.titleAssessing the quality of annotations in asthma gene expression experimentsen
dc.typeArticleen
dc.identifier.eissn1471-2105en
dc.contributor.departmentDecision Systems Group, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA, USAen
dc.contributor.departmentOhio State University, Columbus, OH, USAen
dc.contributor.departmentUniversity of Arizona, Tucson, AZ, USAen
dc.contributor.departmentDivision of Biomedical Informatics, University of California San Diego, La Jolla, CA, USAen
dc.identifier.journalBMC Bioinformaticsen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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