API

The first step to using the ISAcreator API is to either include the ISAcreator jar in your class path or to import ISAcreator as a dependency.

<dependency>
    <groupId>org.isatools</groupId>
    <artifactId>ISAcreator</artifactId>
    <version>1.6.0</version>
</dependency>

You should also include the ISA tools repository, which can be done through insertion of this fragment of XML.

<repositories>
    <repository>
        <id>oerc</id>
        <url>http://frog.oerc.ox.ac.uk:8080/artifactory/repo/</url>
    </repository>
</repositories>

###Searching for publications from ISAcreator

Publication searching is provided by CiteXplore from the EBI. To call the publication searcher from ISAcreator, the following code will get you there.

 public List<CiteExploreResult> searchForPublicationByTitle(SearchOption searchOption, String query) {
        CiteExploreClient publicationSearcher = new CiteExploreClient();

        try {
            return publicationSearcher.searchForPublication(searchOption, query);
        } catch (QueryException_Exception qex) {
            System.out.printf("Caught QueryException_Exception: %s\n", qex.getFaultInfo().getMessage());
        } catch (NoPublicationFoundException e) {
            System.out.println("No publication found");
        }

        return new ArrayList<CiteExploreResult>();
    }

Searching for Ontologies from from ISAcreator

Get all ontologies from BioPortal

public List<Ontology> getAllOntologies() {
        BioPortalClient client = new BioPortalClient();

        return client.getAllOntologies(true);
    }

###Using the NCBO Annotator from ISAcreator

The following fragment of code will take a Set of Strings and find the ontology equivalents in BioPortal. The returned Map is a map from the free text term to it's equivalents.

public  Map<String, Map<String, AnnotatorResult>> searchForMatches(Set<String> freeText) {
        AnnotatorSearchClient sc = new AnnotatorSearchClient();

        Map<String, Map<String, AnnotatorResult>> result = sc.searchForTerms(freeText, "", true);

        int termsWithMatches = 0;
        for (String key : result.keySet()) {
            if(result.get(key).size() > 0) {
                termsWithMatches++;
            }
        }

        System.out.println(termsWithMatches+ "/" + freeText.size() + " terms have matches.");

        return result;
    }