Last Updated: 2018-11-28 12:15:08

An explanation of how to read a datum and sample queries can be found here.

Datum Search Engine

The search engine can be used by either typing a query directly into the search box or by using the query builder which can be accessed by clicking on "Show Query Builder" under the search box.

Using the Search Box

A query is one or more terms, separated by spaces. A datum will match only if it matches every query term. A term may have the following properties:

  • A term prefixed with a minus sign is negated, and will only match datums where that term is not found.
  • A term in quotes will match any string component of a datum, but only in its entirety. For example, "Erk" will not match "Erks" or "Erk1", but Erk (without quotes) will match both.
  • A term may take the form tag:term (or -tag:term, tag:"term", -tag:"term", etc.). If so, it only searches specific fields as constrained by the tag.
  • A term with no tag and no quotes will search the full text of the datum.
  • Terms may include * to match any number of any characters including none.

After a tag is typed into the search box, the next letter or letters entered will cause a drop-down list to appear which contains the first 20 elements in the field starting with that letter or letters. You can either select an item from the list or continue typing.

The list of Tags includes:

  • assay
  • assaytype
  • cells
  • change
  • chemical
  • extratype
  • gene
  • cellperturbation
  • protein
  • subject
  • treatment
  • treatmenttype
  • viral (looks for protein fields with the extra stipulation that the protein must be a viral protein)

Using the Query Builder

If you click on "Show Query Builder" under the search box, the query builder will appear. The first drop-down menu contains a list of the available tags.

The second menu allows you to refine your search using the verbs:

  • exists
  • does NOT exist
  • contains
  • does NOT contain
  • is exactly
  • is NOT exactly

Some tags have a limited choice of terms. For those tags, a third menu containing a list of choices will appear.

Additional terms can be added using the button.

When you are satisfied with your query, click on Search.

Displaying the Results

The found datums can be displayed in three different ways.

The Card format displays the first line, the environment line, a line containing the treatment times if applicable, the source line, and any extras comments. Any item colored blue can be clicked on for more information. Clicking a protein will bring up a box containing the Uniprot ID with a link to the Uniprot protein record, the HGNC symbol with a link to the HGNC record, and synonyms. Clicking on a chemical will bring up a box containing synonyms, a putative activity, and a link to the PubChem record. Clicking on the PubMed ID in the source field opens the PubMed record.

The Text format displays the entire datum in the original shorthand language.

The JSON format shows the datum parsed into JSON.

The last two formats can be downloaded for computational use.