private static EBISearchService ebiSearchService = new EBISearchService_Service().getEBISearchServiceHttpPort();
Then, if you only need a list of identifiers which satisfy your search term you can do it in one single step:
ArrayOfString resultsIds = ebiSearchService.getAllResultsIds(domain, query);
domain being one of the available indexed databases (see listDomains method). However this is discouraged as it can return a huge list. It is suggested to do it in two steps:
int numOfResults = ebiSearchService.getNumberOfResults(domain, query); // and then page through numOfResults: ArrayOfStrings resultsIds = ebiSearchService.getResultsIds(domain, query, start, size);
If you need more info from the search engine you will have to send more than one query, starting with getting the resultsIds (see above) and then:
ArrayOfArrayOfString entries = ebiSearchService.getEntries(domain, resultsIds, fields);
The fields will depend on the queried domain (there is a listFields method to know which fields are available) .
The EB-Eye offers more methods, including searching cross references from one domain to another one.