private BiologicalEntity guessEntity(String key) { String sql; if (key.endsWith("_HUMAN")) { sql = "SELECT * FROM proteinGene WHERE pname='" + key + "'"; HashMap<String, String> line = DBUtil.fillFirstRow(sql); if (line != null) { BiologicalEntity be = new BiologicalEntity(); be.setId(line.get("geneid")); be.setId_src(BiologicalEntity.ENTREZ); be.setType(BiologicalEntity.GENE); be.setName(key); // line.get("pname")); return be; } } sql = "SELECT geneid FROM gene WHERE symbol='" + key + "' AND taxid=9606"; String s = DBUtil.querySingle(sql); if (s != null) { BiologicalEntity be = new BiologicalEntity(); be.setId(s); be.setName(key); be.setId_src(BiologicalEntity.ENTREZ); be.setType(BiologicalEntity.GENE); return be; } sql = "SELECT geneid FROM geneAlias, gene WHERE gene.taxid=9606 AND geneAlias.alias='" + key + "' AND geneAlias.id_list=geneid"; s = DBUtil.querySingle(sql); if (s != null) { BiologicalEntity be = new BiologicalEntity(); be.setId(s); be.setName(key); be.setId_src(BiologicalEntity.ENTREZ); be.setType(BiologicalEntity.GENE); return be; } System.err.println("Cannot find an entry for " + key); return null; }