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Programmatic Access
1. Updates to programmatic access1.1 Recent changes to programmatic accessSeptember 2010
1.2 Subscribe to the announcment listTo be notified of any future changes and extensions to the programmatic access please subscribe to the announcement list using the form below. ArrayExpress announcements and important news
2. Programmatic access of the Experiments ArchiveExperiment search results can be retrieved either in parsable XML format or JSON. 2.1 REST-style queries to retrieve results in XML formatExperiments and files linked to experiments can by searched for using keywords, by searching specific fields (e.g. sample attributes or experiment types), or by selecting experiments that have fulfill certain conditions such as the number of assays (hybridizations) or were released on a particular date. 2.1.1 Keyword searches for experiments and files associated with experimentsKey word searches of all fields for experiments and files linked to experiments can be made using the following format of URLs:
2.1.2 Specifing particular fields for searchingThe following terms can be used to specify the field in which a term is searched for. Either experiments or files can be searched for in all cases by using the 'experiments' or 'files' term in the URL.
To link different search criteria together use the '&' symbol. E.g.
2.1.3 Expanding searches using the Experimental Factor OntologyThe Experimental Factor Ontology is an application-focused ontology modelling the experimental factors in ArrayExpress. If the term expandefo=true is included in the URL then the search will be for occurrences of your term, and for synonyms and child terms in the Experimental Factor Ontology. E.g. if 'cancer' is entered the search will be for the term cancer, for synonyms of cancer and sub types of cancer such as lymphoma.
Some specific fields have EFO expansion on always: experimental factor value, experiment type, sample attribute and species.
2.1.4 Construction of queries using AND, OR and NOT operatorsMore complex queries can be constructed using the operators AND, OR or NOT. AND is the default if no operator is specified. Again, either experiments or files can be searched for in all cases by using the 'experiments' or 'files' term in the URL.
2.1.5 Filtering to get ArrayExpress direct submission dataSearches can be limited to experiments submitted directly to ArrayExpress (this is excludes data imported from the Gene Expression Omnibus (GEO, www.ncbi.nlm.nih.gov/geo/)) or to only the imported data. To do this use the following syntax:
For more information about how we import data from GEO see the GEO data help page.
2.1.6 Filtering by countsExperiments fulfilling certain count critera can also be searched for e.g. having more than 10 assays (hybridizations). These searches use the following syntax:
2.1.7 SortingThe results of a query can be sorted on several fields in ascending or descending order using sortby=xxx and sortorder=ascending/descending. The fields that can be used for sorting are:
Examples
2.1.8 Old-style queriesThe URL format for archive searches was changed in September 2010 to allow searching of specific fields, use of AND, OR, NOT, counts of attributes and ordering of results. The old-style URLs are still fully functional however. The format of the pre-September 2010 URL is described below.
Top2.1.8.1. Keyword searchesKeywords can be used to search for specific experiments, with the results returned in an XML document, using URLs with the experiments term and keywords=X format. E.g.
To narrow the search by using more than one keyword, separate terms by + e.g.
2.1.8.2 Species searchesTo narrow search to experiments with samples of a particular species include the 'species' term
2.1.8.3 Retrieving filesTo retrieve the list of files associated with a set of experiments use the 'files' term in the URL
To retrieve a list of files for a particular experiment format the query as follows:
Also note:
2.1.9 Accessing private data
2.1.10 Retrieve information about all public experimentsTo retrieve an xml file with information about all public experiments remove the keyword part of the search.
2.1.11 Format of XML resultsThe XML documents returned from a search lists how many experiments were retrieved and then either information about the experiment or lists the files associated with an experiment depending on the search made. In both cases information about each experiment is in an <experiment></experiment> element. 2.1.11.1 Searches for experimentsExample 
2.1.11.2 Searches for filesExample
Top2.2 JSON web services formatTo retrieve the results of queries in JSON format, the base URL changes from http://www.ebi.ac.uk/arrayexpress/xml/v2/ to http://www.ebi.ac.uk/arrayexpress/json/v2/. All queries described above can be carried out and will produce a JSON-format file while can by downloaded. E.g. experiment queriesTop
E.g. file queriesTop
There is one extra parameter 'jsonp' - Enable JSONP; the JSON output will be prepended with the value of the jsonp parameter and wrapped in parentheses. E.g.Top
3. Programmatic access of the Atlas of Gene ExpressionFor information about programmatic access of the Atlas of Gene Expression see the Atlas API help page. TopAny further questions, please see our FAQ. |
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