title: NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases.
abstract: Neurodegenerative diseases are chronic debilitating conditions, characterized by progressive loss of neurons that represent a significant health care burden as the global elderly population continues to grow. Over the past decade, high-throughput technologies such as the Affymetrix GeneChip microarrays have provided new perspectives into the pathomechanisms underlying neurodegeneration. Public transcriptomic data repositories, namely Gene Expression Omnibus and curated ArrayExpress, enable researchers to conduct integrative meta-analysis; increasing the power to detect differentially regulated genes in disease and explore patterns of gene dysregulation across biologically related studies. The reliability of retrospective, large-scale integrative analyses depends on an appropriate combination of related datasets, in turn requiring detailed meta-annotations capturing the experimental setup. In most cases, we observe huge variation in compliance to defined standards for submitted metadata in public databases. Much of the information to complete, or refine meta-annotations are distributed in the associated publications. For example, tissue preparation or comorbidity information is frequently described in an article's supplementary tables. Several value-added databases have employed additional manual efforts to overcome this limitation. However, none of these databases explicate annotations that distinguish human and animal models in neurodegeneration context. Therefore, adopting a more specific disease focus, in combination with dedicated disease ontologies, will better empower the selection of comparable studies with refined annotations to address the research question at hand. In this article, we describe the detailed development of NeuroTransDB, a manually curated database containing metadata annotations for neurodegenerative studies. The database contains more than 20 dimensions of metadata annotations within 31 mouse, 5 rat and 45 human studies, defined in collaboration with domain disease experts. We elucidate the step-by-step guidelines used to critically prioritize studies from public archives and their metadata curation and discuss the key challenges encountered. Curated metadata for Alzheimer's disease gene expression studies are available for download. Database URL: www.scai.fraunhofer.de/NeuroTransDB.html.
authors.affiliation: Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53754 Sankt Augustin, Germany, Rheinische Friedrich-Wilhelms-Universitaet Bonn, Bonn-Aachen International Center for Information Technology, 53113, Bonn, Germany, shweta.bagewadi@scai.fraunhofer.de.
authors.forename: Shweta
authors.initials: S
authors.lastname: Bagewadi
authors.affiliation: Department of Chemistry, South University of Science and Technology of China, No 1088, Xueyuan Road, Xili, Shenzhen, China.
authors.forename: Subash
authors.initials: S
authors.lastname: Adhikari
authors.affiliation: Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53754 Sankt Augustin, Germany, Rheinische Friedrich-Wilhelms-Universitaet Bonn, Bonn-Aachen International Center for Information Technology, 53113, Bonn, Germany.
authors.forename: Anjani
authors.initials: A
authors.lastname: Dhrangadhariya
authors.affiliation: Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53754 Sankt Augustin, Germany, Rheinische Friedrich-Wilhelms-Universitaet Bonn, Bonn-Aachen International Center for Information Technology, 53113, Bonn, Germany.
authors.forename: Afroza Khanam
authors.initials: AK
authors.lastname: Irin
authors.affiliation: Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53754 Sankt Augustin, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Ebeling
authors.affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg and.
authors.forename: Aishwarya Alex
authors.initials: AA
authors.lastname: Namasivayam
authors.affiliation: Translational Bioinformatics, UCB Pharma, 216 Bath Rd, Slough SL1 3WE, United Kingdom.
authors.forename: Matthew
authors.initials: M
authors.lastname: Page
authors.affiliation: Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53754 Sankt Augustin, Germany, Rheinische Friedrich-Wilhelms-Universitaet Bonn, Bonn-Aachen International Center for Information Technology, 53113, Bonn, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Hofmann-Apitius
authors.affiliation: Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53754 Sankt Augustin, Germany, shweta.bagewadi@scai.fraunhofer.de philipp.senger@scai.fraunhofer.de.
authors.forename: Philipp
authors.initials: P
authors.lastname: Senger
mesh_terms: D000818:Animals; D066289:Data Curation; D030541:Databases, Genetic; D004195:Disease Models, Animal; D005786:Gene Expression Regulation; D006801:Humans; D051379:Mice; D019636:Neurodegenerative Diseases / Q000235:genetics / Q000378:metabolism; D051381:Rats; D059467:Transcriptome