result.add(pub);
    protected Collection translateItem(Item srcItem)        throws ObjectStoreException, InterMineException {        Collection result = new HashSet();        String srcNs = OntologyUtil.getNamespaceFromURI(srcItem.getClassName());        String className = OntologyUtil.getFragmentFromURI(srcItem.getClassName());        Collection translated = super.translateItem(srcItem);        if (translated != null) {            for (Iterator i = translated.iterator(); i.hasNext();) {                boolean storeTgtItem = true;                Item tgtItem = (Item) i.next();                if ("ExperimentType".equals(className)) {                    Item pub = createPublication(srcItem);                    if (pub != null) {                        tgtItem.addReference(new Reference("publication", pub.getIdentifier()));                    }                    result.add(pub);                    // no confidence values in current data set                } else if ("InteractionElementType".equals(className)) {                    // create ProteinInteraction relation                    Item interaction = createProteinInteraction(srcItem, tgtItem);                    addReferencedItem(tgtItem, interaction, "relations", true, "evidence", true);                    // reference source database                    addReferencedItem(tgtItem, getDb(), "source", false, "", false);                    // ExperimentalResult need to reference ProteinInteractionExperiment                    promoteField(tgtItem, srcItem, "analysis", "experimentList", "experimentRef");                    // set confidence from attributeList                    Iterator iter = ItemHelper.convert(srcItemReader                                 .getItemById(srcItem.getReference("attributeList").getRefId()))                        .getCollection("attributes").getRefIds().iterator();                    while (iter.hasNext()) {                        Item attribute = ItemHelper.convert(srcItemReader                                                            .getItemById((String) iter.next()));                        String value = attribute.getAttribute("attribute").getValue().trim();                        String name = attribute.getAttribute("name").getValue().trim();                        if (Character.isDigit(value.charAt(0))                            && name.equals("author-confidence")) {                            tgtItem.addAttribute(new Attribute("confidence", value));                        }                    }                    result.add(interaction);                } else if ("ProteinInteractorType".equals(className)) {                    // protein needs swissport id set and synonym to swissprot                    Item xref = ItemHelper.convert(srcItemReader                                  .getItemById(srcItem.getReference("xref").getRefId()));                    Item dbXref = ItemHelper.convert(srcItemReader                                    .getItemById(xref.getReference("primaryRef").getRefId()));                    if (dbXref.getAttribute("db").getValue().equals("uniprot")) {                        String value = dbXref.getAttribute("id").getValue();                        tgtItem.addAttribute(new Attribute("swissProtId", value));                        //tgtItem.addAttribute(new Attribute("identifer", value));                        Item synonym = createItem(tgtNs + "Synonym", "");                        addReferencedItem(synonym, getSwissProt(), "source", false, "", false);                        synonym.addAttribute(new Attribute("synonym", value));                        addReferencedItem(tgtItem, synonym, "synonyms", true, "subject", false);                        result.add(synonym);                    }                } else if ("Source_Entry_EntrySet".equals(className)) {                    tgtItem.setIdentifier(getDb().getIdentifier());                    tgtItem.addAttribute(new Attribute("title",                            ItemHelper.convert(srcItemReader                                 .getItemById(srcItem.getReference("names").getRefId()))                                                 .getAttribute("shortLabel").getValue()));                }                result.add(tgtItem);            }        }        return result;    }