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By making the experimental metadata available as linked data, NIDM-Experiment will enable querying across the full neuroimaging data lifecycle, interrogating data possibly hosted on distributed resources.
However, the MAX IV data catalog will permanently store the experimental metadata and provide a persistent identifier for each data collection.
Using an SDRF file prepared according to the MIAME regulations, the user uploads both the preprocessed data and the experimental metadata to the system.
To address this issue, the DCC, like many other biological databases, is using terms from the ontologies to describe the experimental metadata.
Authors tend to provide minimum information as required by the guidelines in archives; publishing major part of the experimental metadata annotations in associated publication.
The major benefit from using ontologies to annotate the experimental metadata is an increased ability of search queries to return related experiments (https://www.encodeproject.org/help/getting-started search).org/help/getting-started search
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The recording of the microarray experimental metadata complies with Minimum Information About a Microarray Experiment (MIAME) guidelines.
We chose the Chado database to store the modENCODE experimental metadata and genomic features because of familiarity, availability of tools, nominal compatibility with FB and WB and browser neutrality.
Data analysis begins by obtaining the input raw read files and the corresponding experimental metadata.
This simplified system of storing free text and reserved tag and value pairs hence provides a consistent way to summarize the associated experimental metadata for each data file, and give sufficient details for any user to understand the enclosed data.
The latter manages the storage of experimental metadata, which can be collectively searched and browsed via a query interface or web services; the destination for associated data files, and their protocol for transfer, is custom defined by the local administrator on installation.
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