Metadata searching

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One of the primary systems in ZENBU is that of metadata and metadata searching.

Search is modeled on the google/yahoo approach of prefix-based multiple-keyword searching. ZENBU also provides additional logic elements to fine tune one's queries.

  • and : by default space separating keywords in a search is interpreted as an and operation. This operates in the same way as set intersection [1]
  • or : is used for combining queries in the same way as set unioning [2]
  • not <keyword or ()phrase> : will exclude any items which match the phrase for the results. For example "not spliced" will return experiments which do not have the keyword spliced.
  •  !  : short hand for not
  • ( )  : nesting of parenthesis logic are supported.

It is good practice to always give a good description when saving configurations (view/track/script) or uploading data. ZENBU performs automatic keyword extraction from all metadata providing a wealth of ways to search the system.

Here is a complex example searching the Encode hg19 datasets in the Data Explorer experiment interface section.

encode hg19 (rnaseq hepg2 !spliced) or (chip-seq)

http://fantom.gsc.riken.jp/zenbu/dex/#section=Experiments;search=encode%20hg19%20(rnaseq%20hepg2%20!spliced)%20or%20(chip-seq)

Other general comments to help users with searching:

  • If a search is performed with too many terms, it may fail to return any results. This is the same behavior that google or yahoo has.
  • keywords are generally extracted from free-form metadata like names and descriptions but also controlled metadata like the genome assembly, controlled vocabulary, and ontology metadata.
  • for OSCtable files, keywords are extracted from the ParameterValue and ExperimentMetadata sections.
  • any metadata added into the system via the Metadata editing system becomes immediately available for searching