Advanced search functions

You might notice that the results of your cancer search (from the previous page) are not very specific yet. By default, all experimental fields which include this search term are listed, including the experiment description, sample annotation, publication title, submitter's email address, protocol description, etc.

If you want to search for experiments with a specific design, you can limit your search to certain fields. This can be done by writing the query in the format of

fieldname:value

Common "fields" that can be queried directly include:

  • the organism of the source material with organism:
  • the experimental factor (experimental variable) with ef:
  • the value of an experimental factor with efv:
  • the assay technology with exptype:
  • any attribute of the biological sample with sa:

(See the full list of field names).

Help

Let's look at an example:

Question: "I would like to find transcriptomics experiments which compare patients with diabetes mellitus to healthy individuals."

  • Use the fieldname "efv:" for experimental factor value to specify the disease: efv:diabetes AND efv:normal
  • To make sure you will find transcription profiling data from human samples with you can add: organism:"Homo sapiens" AND exptype:"Transcription profiling"

So the complete query would be:

efv:diabetes AND efv:normal AND organism:"Homo sapiens" AND exptype: "Transcription profiling"

Not constraining the search terms in the above example could result in false matches, e.g. experiments merely mentioning "diabetes" in the description field, when in fact they are studying a different disease (e.g. hypertension).

To search for a certain experiment type, the field code "exptype:" is very useful. The search term that follows should be from the list of experiment types. The exact terms (in quotations) can be used or parts of them, e.g. "exptype:ChIP" will find array- and sequencing-based ChIP assays.