For storing and managing data and metadata we use the open Biology Information System (openBIS) [ 20]. openBIS offers a structured data model for projects, experiments, samples, and datasets including the ability to apply user permission rules to collect and share experimental data in a secure way.
Aiming to increase efficiency and accuracy in searching LO Learning Objectt) metadata data, we used Lucene index search.
One example is the grid-inspector, a utilitarian metadata explorer, which we used as an opportunity to experiment with a new approach to build interactive applications using reactive programming and Virtual DOM (see The Reactive Loop).
Our methodology for the generation of each dataset is to assess the primary use cases, and relate each use case to one or more preexisting vocabularies, e.g., if a dataset relies on the assertion of bibliographic metadata, then we use DCMI Metadata Terms; or, if a dataset requires the aggregation of resources, then we use OAI-ORE.
We used additional metadata from the database to effectively predict SNPs and infer levels of polymorphism in coding versus noncoding regions and in gene families.
To quantify how different experimental approaches between the four studies contribute to the overall differences in expression profiles, we used the metadata accompanying the data sets and performed ANOVA analysis after fitting a set of linear models to the data.
To combine the geographic and temporal metadata with the genomic information, we used Bayesian evolutionary analysis by sampling trees (BEAST) (Drummond and Rambaut, 2007) to reconstruct the temporal and geographical history of the major PGs.
What metadata scheme should we use and how do we capture it?
From there I worked with the project team to begin thinking about what kinds of fields they would want to capture, and determine whether or how those fields could map to the existing metadata application profile that we use in the DDR.
Under the first approach for data integration, we use administrative metadata [ 26, 27] from the financial system and the medication dispensing system, to create automated crosswalks between systems.
