Refining your search
Most of the time you are interested in finding experiments matching certain criteria. Two options are available for searching and filtering the experiment list: the filter box and the search box (Figure 10).
The option you choose depends on what kind of criteria you would like to use to find interesting experiments. The two methods can of course be combined. As a general rule, use the search box for attributes not listed in the filter box. For example, use the filters to select data sets from one species, and use the search box so specify the experimental variable(s) you are interested in. Examples are shown in Figure 10, below.
Figure 10 The filter and free-text search in ArrayExpress.
The filter box lets you select experiments by:
- species, e.g. only human material, or only Drosophila
- the type of analysed material: DNA, RNA, protein, metabolite
- technology type: microarray, sequencing, mass spectrometry
- array: the specific name of the array
Ticking the box "ArrayExpress data only" shows only curated experiments that were directly submitted to ArrayExpress.
In the free-text search box, you can enter keywords to start a query or enter an accession number (e.g. E-MTAB-3682) to go directly to the desired experiment page.
Put quotes around multiple keywords if you want to find experiments where these words are found next to each other e.g. "breast cancer". Entering multiple words without quotes will retrieve experiments where both keywords are found but they are not necessarily adjacent e.g. mouse leukemia.
Ontologies in ArrayExpress
Experiments in ArrayExpress are annotated with ontology terms from the Experimental Factor Ontology (EFO) (8). When you start typing in the search field, you will be shown suggestions of matching or similar terms from the EFO (Figure 10).
Ontologies help to make the experimental metadata clearer and bring them into a standardised form. Ontologies facilitate searching by matching synonyms (e.g. "human" = "Homo sapiens") and expanding the search to include "child terms" (e.g. "cancer cell line" will find "HeLa", "MCF7" and other related terms). In the free-text search drop-down list, you can reveal child terms by clicking the "+" sign and select a more specific term for your search.