The phenotype and genotype experiment object model (PaGE-OM): a robust data structure for information related to DNA variation

Brookes, Anthony J.; Lehväslaiho, Heikki; Muilu, Juha; Shigemoto, Yasumasa; Oroguchi, Takashige; Tomiki, Takeshi; Mukaiyama, Atsuhiro; Konagaya, Akihiko; Kojima, Toshio; Inoue, Ituro; Kuroda, Masako; Mizushima, Hiroshi; Þórisson, Guðmundur Á.; Dash, Debasis; Rajeevan, Haseena; Darlison, Matthew; Woon, Mark; Fredman, David; Smith, Albert V.; Senger, Martin; Naito, Kimitoshi; Sugawara, Hideaki

doi:10.1002/humu.20973

Cited by 16 publications

(13 citation statements)

References 18 publications

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“…It was approved as a standard by the OMG in March 2008. PaGE-OM defines a generic, platform-independent representation for entities such as alleles, genotypes, phenotype values, and relationships between these entities with the goal of enabling the capture of the minimum amount of information required to properly report most genetic experiments involving genotype and/or phenotype information (28). Further refinements of the PaGE-OM object model, harmonization with object models from other domains, and generation of exchange formats are underway at the time of writing.…”

Section: Methodsmentioning

confidence: 99%

Data Standards for Omics Data: The Basis of Data Sharing and Reuse

Chervitz¹,

Deutsch

Field

et al. 2011

Methods in Molecular Biology

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To facilitate sharing of Omics data, many groups of scientists have been working to establish the relevant data standards. The main components of data sharing standards are experiment description standards, data exchange standards, terminology standards, and experiment execution standards. Here we provide a survey of existing and emerging standards that are intended to assist the free and open exchange of large-format data.

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Section: Methodsmentioning

confidence: 99%

Data Standards for Omics Data: The Basis of Data Sharing and Reuse

Chervitz¹,

Deutsch

Field

et al. 2011

Methods in Molecular Biology

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“…The Phenotype and Genotype Experiment Object Model (PaGE-OM) [Brookes et al, 2009] (http://www.pageom. org/Home.html) has been developed and is currently being developed further by the GEN2PHEN project as Phenotype Object Model (Pheno-OM).…”

Section: Use Of Ontologiesmentioning

confidence: 99%

Guidelines for establishing locus specific databases

et al. 2011

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Information about genetic variation has been collected for some 20 years into registries, known as locus specific databases (LSDBs), which nowadays often contain information in addition to the actual genetic variation. Several issues have to be taken into account when considering establishing and maintaining LSDBs and these have been discussed previously in a number of articles describing guidelines and recommendations. This information is widely scattered and, for a newcomer, it would be difficult to obtain the latest information and guidance. Here, a sequence of steps essential for establishing an LSDB is discussed together with guidelines for each step. Curators need to collect information from various sources, code it in systematic way, and distribute to the research and clinical communities. In doing this, ethical issues have to be taken into account. To facilitate integration of information to, for example, analyze genotype-phenotype correlations, systematic data representation using established nomenclatures, data models, and ontologies is essential. LSDB curation and maintenance comprises a number of tasks that can be managed by following logical steps. These resources are becoming ever more important and new curators are essential to ensure that we will have expertly curated databases for all disease-related genes in the near future.

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“…Examples that embody GEN2PHEN's collaborative approach and success in the area of standards development include close partnering with the groups behind the PaGE-OM for G2P data [Brookes et al, 2009] (http://www.pageom.org), imminent publication of new core data models for phenotype data and locus-specific database (LSDB) content, and a joint effort with the NCBI that has produced the Locus Reference Genomic (LRG: http://www.lrg-sequence.org) framework for standardized reporting of gene variants [Dalgleish et al, 2010] …”

Section: Standards Developmentmentioning

confidence: 99%