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Summary: The first open source software suite for experimentalists and curators that (i) assists in the annotation and local management of experimental metadata from high-throughput studies employing one or a combination of omics and other technologies; (ii) empowers users to uptake community-defined checklists and ontologies; and (iii) facilitates submission to international public repositories.
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See the section below on "Submitting experimental metadata" for more information.
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.
To address this issue, the DCC, like many other biological databases, is using terms from the ontologies to describe the experimental metadata.
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
The recording of the microarray experimental metadata complies with Minimum Information About a Microarray Experiment (MIAME) guidelines.
Metadata itself could be quite broad; from provenance of a study material, biological and experimental metadata, to technology based information settings, protocols and parameters [ 1, 2].
Improved incorporation of experimental "metadata" will increase annotation successes further, especially for large candidate sets.
Raw data and experimental metadata are maintained in other excellent platforms and are therefore linked for all public data mainly from GEO.
The lack of a data producer-driven submission step from yeast projects places the onus on SGD to collect, format and store all experimental metadata in a manner that enables easy search and retrieval for users.
Here, we describe the ENCODE DCC's use of ontologies to standardize experimental metadata.
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