String cloneId = array[4];
String cloneId = array[5];
    public void process(Reader reader) throws Exception {        BufferedReader br = new BufferedReader(reader);        //intentionally throw away first line        String line = br.readLine();        while ((line = br.readLine()) != null) {            String[] array = line.split("\t", -1); //keep trailing empty Strings            if (line.length() == 0 || line.startsWith("#")) {                continue;            }            String geneId = array[16].trim();            Item gene = createGene("Gene", geneId, organism.getIdentifier());            writer.store(ItemHelper.convert(gene));            String cloneId = array[4];            Item clone = createBioEntity("CDNAClone", cloneId, organism.getIdentifier());            clone.setReference("gene", gene.getIdentifier());            Item synonym = createItem("Synonym");            synonym.setAttribute("type", "identifier");            synonym.setAttribute("value", cloneId);            synonym.setReference("source", db.getIdentifier());            synonym.setReference("subject", clone.getIdentifier());            writer.store(ItemHelper.convert(synonym));            clone.addCollection(new ReferenceList("evidence",                    new ArrayList(Collections.singleton(db.getIdentifier()))));            writer.store(ItemHelper.convert(clone));        }    }