@Test
public final void testNormalizeInoh() {
// there're two Protein objects that have entityReference
// rdf:ID="IMR_0100366_G_alpha_s_Canonical" (in fact a generic ProteinReference inproperly
// defined);
// and that PR has two UniProt UnificationXref: P63092 (human), P63095 (rat).
// Identifiers.org URI for the PR should NOT be generated.
//
// Also, there was a bug when replacing the PR's URI (warning: IllegalBioPAXArgumentException:
// Incompatible type!..)
// The cause is that there was a (weird, invalid) PublicationXref having db:id as UniProt:P63092
// that gets the same URI!
// To avoid such issues altogether (despite illegal pub. xrefs), the Normalizer won't use
// Identifiers.org for PublicationXrefs anymore.
Model model = simpleIO.convertFromOWL(getClass().getResourceAsStream("/test-inoh.owl"));
Normalizer normalizer = new Normalizer();
normalizer.setXmlBase("");
normalizer.normalize(model);
// A weird PublicationXref that uses a UniProt ID won't be normalized:
assertFalse(model.containsID("http://identifiers.org/uniprot/P63092"));
// A PR with two UniProt IDs/unif.xrefs - human, rat - won't be normalized!
assertTrue(model.containsID(model.getXmlBase() + "IMR_0100366_G_alpha_s_Canonical"));
assertEquals(
"ProteinReference",
model
.getByID(model.getXmlBase() + "IMR_0100366_G_alpha_s_Canonical")
.getModelInterface()
.getSimpleName());
}
@Test
public final void testNormalize2() {
Model model = BioPAXLevel.L3.getDefaultFactory().createModel();
Xref ref = model.addNew(UnificationXref.class, "Xref1");
ref.setDb("uniprotkb"); // will be converted to 'uniprot'
ref.setId("Q0VCL1");
Xref uniprotX = ref;
ProteinReference pr = model.addNew(ProteinReference.class, "ProteinReference");
pr.setDisplayName("ProteinReference");
pr.addXref(uniprotX);
ref = model.addNew(RelationshipXref.class, "Xref2");
ref.setDb("refseq");
ref.setId("NP_001734");
pr.addXref(ref);
// normalizer won't merge diff. types of xref with the same db:id
ref = model.addNew(PublicationXref.class, "Xref3");
ref.setDb("pubmed");
ref.setId("2549346"); // the same id
pr.addXref(ref);
ref = model.addNew(RelationshipXref.class, "Xref4");
ref.setDb("pubmed");
ref.setId("2549346"); // the same id
pr.addXref(ref);
Normalizer normalizer = new Normalizer();
normalizer.normalize(model);
ProteinReference e = (ProteinReference) model.getByID("http://identifiers.org/uniprot/Q0VCL1");
assertNotNull(e);
assertEquals(4, e.getXref().size());
// print(e, model);
}
private void check(String input, Normalizer.Status status, String output, String rest)
throws ParserException {
Normalizer normalizer = new Normalizer(input);
Assert.assertEquals(normalizer.normalize(), status);
Assert.assertEquals(normalizer.getNormalized(), output);
Assert.assertEquals(normalizer.getUnparsed(), rest);
}
private void check(String input, Normalizer.Status status, String output) throws ParserException {
Normalizer normalizer = new Normalizer(input);
Assert.assertEquals(normalizer.normalize(), status);
if (status != Normalizer.Status.NEEDMORE) {
Assert.assertEquals(normalizer.getNormalized(), output);
}
}
@Test
public final void testAutoName() {
Model model = BioPAXLevel.L3.getDefaultFactory().createModel();
Provenance pro = model.addNew(Provenance.class, "http://identifiers.org/pid.pathway/");
pro.setStandardName("foo");
Normalizer.autoName(pro);
assertNotNull(pro.getStandardName());
assertTrue(pro.getName().contains("PID"));
assertTrue(pro.getName().contains("NCI_Nature curated"));
assertFalse(pro.getStandardName().equals("foo"));
}
@Test
public final void testNormalize3() {
Model model = BioPAXLevel.L3.getDefaultFactory().createModel();
Xref ref = model.addNew(UnificationXref.class, "Xref1");
ref.setDb("uniprotkb"); // will be converted to 'uniprot'
ref.setId("Q0VCL1");
ProteinReference pr = model.addNew(ProteinReference.class, "ProteinReference1");
pr.setDisplayName("A ProteinReference");
pr.addXref(ref);
assertEquals(1, ref.getXrefOf().size());
// System.out.println("Before the model is normalized - ");
// print(pr, model);
// go normalize!
Normalizer normalizer = new Normalizer();
normalizer.normalize(model);
// System.out.println("After the model is normalized - ");
// print(pr, model);
assertFalse(model.contains(pr)); // replaced by new norm. PR in the model
assertFalse(model.contains(ref)); // replaced by new norm. xref in the model
// now xrefOf is consistent with xref for all objects inn the model (since after some paxtools
// 4.1.3 snapshot)
assertEquals(0, pr.getXref().size()); // old PR has xref removed!
assertEquals(
0, ref.getXrefOf().size()); // because the old xref was replaced in all parent elements!
ProteinReference e = (ProteinReference) model.getByID("http://identifiers.org/uniprot/Q0VCL1");
assertNotNull(e);
assertEquals(1, e.getXref().size());
String normUri = Normalizer.uri(model.getXmlBase(), "UNIPROT", "Q0VCL1", UnificationXref.class);
ref = (UnificationXref) model.getByID(normUri);
assertNotNull(ref);
assertEquals(1, ref.getXrefOf().size());
// print(e, model);
}
/**
* Decomposes Diacritic characters to their combining forms.
*
* @param str String to be Normalized
* @return A Normalized String
*/
public String normalizeDiac(String str) {
StringBuilder retStr = new StringBuilder();
int strLength = str.length();
for (int i = 0; i < strLength; i++) {
char c = str.charAt(i);
int type = Character.getType(c);
if (type == Character.NON_SPACING_MARK
|| type == Character.MODIFIER_SYMBOL
|| type == Character.MODIFIER_LETTER) {
/*
* Trim because some decompositions have an extra space, such as
* U+00B4
*/
retStr.append(Normalizer.normalize(c, Normalizer.NFKC).trim());
} else {
retStr.append(str.charAt(i));
}
}
return retStr.toString();
}
/**
* Normalize presentation forms of characters to the separate parts.
*
* @see TextNormalize.normalizePres(String)
* @param str String to normalize
* @return Normalized form
*/
public String normalizePres(String str) {
StringBuilder builder = null;
int p = 0;
int q = 0;
int strLength = str.length();
for (; q < strLength; q++) {
// We only normalize if the codepoint is in a given range.
// Otherwise, NFKC converts too many things that would cause
// confusion. For example, it converts the micro symbol in
// extended Latin to the value in the Greek script. We normalize
// the Unicode Alphabetic and Arabic A&B Presentation forms.
char c = str.charAt(q);
if ((0xFB00 <= c && c <= 0xFDFF) || (0xFE70 <= c && c <= 0xFEFF)) {
if (builder == null) {
builder = new StringBuilder(strLength * 2);
}
builder.append(str.substring(p, q));
// Some fonts map U+FDF2 differently than the Unicode spec.
// They add an extra U+0627 character to compensate.
// This removes the extra character for those fonts.
if (c == 0xFDF2 && q > 0 && (str.charAt(q - 1) == 0x0627 || str.charAt(q - 1) == 0xFE8D)) {
builder.append("\u0644\u0644\u0647");
} else {
// Trim because some decompositions have an extra space,
// such as U+FC5E
builder.append(Normalizer.normalize(c, Normalizer.NFKC).trim());
}
p = q + 1;
}
}
if (builder == null) {
return str;
} else {
builder.append(str.substring(p, q));
return builder.toString();
}
}
/**
* Set the uriStartString attribute.
*
* @param uriStartString The uriStartString attribute value.
*/
public void setURIStartString(String uriStartString) {
CatalogMessages.reportNPEOnNull("uriStartString", uriStartString);
this.uriStartString = Normalizer.normalizeURI(uriStartString);
setMatchId(this.uriStartString);
}
@Test
public final void testUri() {
// using null or non-standard db
assertEquals(
Normalizer.uri("test/", "foo", "bar", UnificationXref.class),
Normalizer.uri("test/", "FOo", "bar", UnificationXref.class));
// 'pubchem' is a ambigous synonym (correct ones are: pubchem-substance, pubchem-compound, etc.)
assertEquals(
Normalizer.uri("", "pubchem", "bar", UnificationXref.class),
Normalizer.uri("", "PubChem", "bar", UnificationXref.class));
assertEquals(
Normalizer.uri("", null, "bar", UnificationXref.class),
Normalizer.uri(null, null, "bar", UnificationXref.class));
assertFalse(
Normalizer.uri(null, "foo", "bar", UnificationXref.class)
.equals(Normalizer.uri(null, "foo", "BAR", UnificationXref.class)));
assertFalse(
Normalizer.uri(null, "foo", "bar", UnificationXref.class)
.equals(Normalizer.uri(null, "foo", "bar", PublicationXref.class)));
// using standard db names (Miriam is used to normalize name and/or get identifiers.org URI) -
assertEquals(
Normalizer.uri("test/", "pubmed", "12345", PublicationXref.class),
Normalizer.uri("test/", "PubMED", "12345", PublicationXref.class));
assertEquals(
"http://identifiers.org/pubmed/12345",
Normalizer.uri("test/", "PubMED", "12345", PublicationXref.class));
assertFalse(
"http://identifiers.org/pubmed/12345"
.equals(
Normalizer.uri(
null, "PubMED", "12345", RelationshipXref.class))); // - not PublicationXref
assertEquals(
"http://identifiers.org/chebi/CHEBI:12345",
Normalizer.uri("", "chebi", "CHEBI:12345", SmallMoleculeReference.class));
assertEquals(
"http://identifiers.org/pubchem.substance/12345",
Normalizer.uri("", "pubchem-substance", "12345", SmallMoleculeReference.class));
System.setProperty(
"biopax.normalizer.uri.strategy", Normalizer.VALUE_NORMALIZER_URI_STRATEGY_SIMPLE);
assertEquals(
"SequenceModificationVocabulary_protein_modification_ontology_MOD_12345",
Normalizer.uri("", "PSI-mod", "MOD:12345", SequenceModificationVocabulary.class));
assertEquals(
"ControlledVocabulary_protein_modification_ontology_MOD_12345",
Normalizer.uri("", "MOD", "MOD:12345", ControlledVocabulary.class));
System.setProperty(
"biopax.normalizer.uri.strategy", Normalizer.VALUE_NORMALIZER_URI_STRATEGY_MD5);
// wrong id (case-sens.)
assertFalse(
"http://identifiers.org/chebi/CHEBI:12345"
.equals(Normalizer.uri("", "chebi", "chebi:12345", SmallMoleculeReference.class)));
// no 'pubchem' namespace there
assertFalse(
"http://identifiers.org/pubchem/12345"
.equals(Normalizer.uri("", "pubchem-substance", "12345", UnificationXref.class)));
// when there're special symbols, spaces in the 'id' part
assertEquals(
"UnificationXref_foo_bar", Normalizer.uri(null, null, "foo bar", UnificationXref.class));
assertEquals(
"http://identifiers.org/taxonomy/9606",
Normalizer.uri(null, "taxonomy", "9606", BioSource.class));
assertEquals(
"http://identifiers.org/taxonomy/9606",
Normalizer.uri(null, "NCBI Taxonomy", "9606", BioSource.class));
assertEquals(
"http://identifiers.org/taxonomy/9606",
Normalizer.uri(null, "NEWT", "9606", BioSource.class));
// when organism's id is not taxID (e.g., if the BioSource has tissue, cellType CVs...)
assertNotSame(
"http://identifiers.org/taxonomy/9606",
Normalizer.uri(null, "taxonomy", "9606_blah_blah", BioSource.class));
String uri = Normalizer.uri("", "UniProt", "W0C7J9", UnificationXref.class);
assertEquals("UnificationXref_uniprot_knowledgebase_W0C7J9", uri);
}
@Test
public final void testNormalize() throws UnsupportedEncodingException {
// Note: a UniProt AC version (e.g. P68250.1 .. P68250.94) is not the same thing as isoform ID!
Model model = BioPAXLevel.L3.getDefaultFactory().createModel();
Xref ref = model.addNew(UnificationXref.class, "Xref1");
ref.setDb("uniprotkb");
ref.setId("P68250");
ProteinReference pr = model.addNew(ProteinReference.class, "ProteinReference1");
pr.setDisplayName("ProteinReference1");
pr.addXref(ref);
ref = model.addNew(RelationshipXref.class, "Xref2");
ref.setDb("refseq");
ref.setId("NP_001734");
ref.setIdVersion(
"1"); // this xref won't be removed by norm. (version matters in xrefs comparing!)
pr.addXref(ref);
ref = model.addNew(UnificationXref.class, "Xref3");
ref.setDb("uniprotkb"); // will be converted to 'uniprot knowledgebase'
/* The following ID is the secondary accession of P68250,
* but Normalizer won't complain (it's Validator's and - later - Merger's job)!
* However, if it were P68250, the normalize(model) would throw exception
* (because ProteinReference1 becomes ProteinReference2, both get RDFId= urn:miriam:uniprot:P68250!)
*/
ref.setId("Q0VCL1");
Xref uniprotX = ref;
pr = model.addNew(ProteinReference.class, "ProteinReference2");
pr.setDisplayName("ProteinReference2");
pr.addXref(uniprotX);
ref = model.addNew(RelationshipXref.class, "Xref4");
ref.setDb("refseq");
ref.setId("NP_001734");
pr.addXref(ref);
// this ER is duplicate (same uniprot xref as ProteinReference2's) and must be removed by
// normalizer
pr = model.addNew(ProteinReference.class, "ProteinReference3");
pr.setDisplayName("ProteinReference3");
pr.addXref(uniprotX);
ref = model.addNew(RelationshipXref.class, "Xref5");
ref.setDb("refseq");
ref.setId("NP_001734");
pr.addXref(ref);
// normalizer won't merge diff. types of xref with the same db:id
ref = model.addNew(PublicationXref.class, "Xref6");
ref.setDb("pubmed");
ref.setId("2549346"); // the same id
pr.addXref(ref);
ref = model.addNew(RelationshipXref.class, "Xref7");
ref.setDb("pubmed");
ref.setId("2549346"); // the same id
pr.addXref(ref);
// add biosource
ref = model.addNew(UnificationXref.class, "Xref8");
ref.setDb("taxonomy");
ref.setId("10090"); // the same id
BioSource bioSource = model.addNew(BioSource.class, "BioSource_Mouse_Tissue");
bioSource.addXref((UnificationXref) ref);
// Provenance (must set ID and standard names from a name)
Provenance pro1 = model.addNew(Provenance.class, "pid");
pro1.addName("nci_nature"); // must be case insensitive (recognized)
pro1.setStandardName("foo"); // must be replaced
// Provenance (must create names from urn)
Provenance pro2 = model.addNew(Provenance.class, "http://identifiers.org/signaling-gateway/");
// add some entities with props
Pathway pw1 = model.addNew(Pathway.class, "pathway");
pw1.addDataSource(pro1);
pw1.setStandardName("Pathway");
Pathway pw2 = model.addNew(Pathway.class, "sub_pathway");
pw2.setStandardName("Sub-Pathway");
pw2.addDataSource(pro2);
pw1.addPathwayComponent(pw2);
// add data to test uniprot isoform xref and PR normalization
ref = model.addNew(UnificationXref.class, "Xref9");
ref.setDb("UniProt"); // normalizer will change it to "uniprot isoform"
ref.setId("P68250-2");
pr = model.addNew(ProteinReference.class, "ProteinReference4");
pr.setDisplayName("ProteinReference1isoformA");
pr.addXref(ref);
// next ones are to test normalizer can auto-fix 'uniprot' to 'uniprot isoform' xref,
// and also merge xrefs #9,#10 and PRs #4,#5 into one PR with one xref
// below, uniprot xref's idVersion='2' will be moved back to the id value, and db set to
// "UniProt Isoform" -
ref = model.addNew(UnificationXref.class, "Xref10");
ref.setDb(
"UniProtKb"); // NOT to be replaced with "UniProt Isoform" (version and isoform # are not
// the same thing)
ref.setId("P68250");
ref.setIdVersion("2"); // may be lost after merging with two other P68250 xrefs
// (version is not the same as isoform, unless db name is 'uniprot isoform')
pr = model.addNew(ProteinReference.class, "ProteinReference5");
pr.setDisplayName("ProteinReference1isoformB");
pr.addXref(ref);
// Following three Xrefs and PRs will be normalized to uniprot.isoform:P68250-1 and merged into
// one
ref = model.addNew(UnificationXref.class, "Xref11");
ref.setDb("UniProtKb"); // will be replaced with "uniprot isoform"
ref.setId("P68250-1");
pr = model.addNew(ProteinReference.class, "ProteinReference6");
pr.addXref(ref);
ref = model.addNew(UnificationXref.class, "Xref12");
ref.setDb("UniProt Isoform"); // because this is standard (isoform) db name (special case) ->
ref.setId("P68250"); // - this id will set to "P68250-1",
ref.setIdVersion("1"); // - and idVersion will be cleared!
pr = model.addNew(ProteinReference.class, "ProteinReference7");
pr.addXref(ref);
ref = model.addNew(UnificationXref.class, "Xref13");
ref.setDb("UniProt Isoform");
ref.setId("P68250-1");
pr = model.addNew(ProteinReference.class, "ProteinReference8");
pr.addXref(ref);
// special dangling UXs to test/catch a weird bug that accidentally makes db='uniprot
// isoform'...
UnificationXref ux = model.addNew(UnificationXref.class, "UniprotUX1");
ux.setDb("uniprot");
ux.setId("W0C7J9");
ux = model.addNew(UnificationXref.class, "UniprotUX2");
ux.setDb("uniprot");
ux.setId("W0C7J9.1"); // NOT to be changed to 'uniprot isoform'
ux = model.addNew(UnificationXref.class, "UniprotUX3");
ux.setDb("uniprot");
ux.setId("W0C7J9"); // NOT to be changed to 'uniprot isoform'
ux.setIdVersion("1");
ux = model.addNew(UnificationXref.class, "UniprotUX4");
ux.setDb("uniprot"); // will be changed to 'uniprot isoform'
ux.setId("W0C7J9-1");
ux = model.addNew(UnificationXref.class, "UniprotUX5");
ux.setDb("uniprot"); // will be changed to 'uniprot isoform'
ux.setId("P68250-3");
// go normalize!
Normalizer normalizer = new Normalizer();
normalizer.normalize(model);
// //tmp test print
// ByteArrayOutputStream out = new ByteArrayOutputStream();
// simpleIO.convertToOWL(model, out);
// System.out.println(out.toString());
// test for a bug that causes db='uniprot' become 'uniprot isoform' (the id matches both
// patterns)
assertTrue(model.containsID("UnificationXref_uniprot_knowledgebase_W0C7J9"));
assertFalse(model.containsID("UnificationXref_uniprot_isoform_W0C7J9"));
assertTrue(model.containsID("UnificationXref_uniprot_knowledgebase_W0C7J9_1"));
assertTrue(model.containsID("UnificationXref_uniprot_isoform_W0C7J9-1"));
assertTrue(model.containsID("UnificationXref_uniprot_isoform_P68250-3"));
assertTrue(model.containsID("UnificationXref_uniprot_knowledgebase_W0C7J9"));
// check Xref
String normUri = Normalizer.uri(model.getXmlBase(), "uniprot", "P68250", UnificationXref.class);
BioPAXElement bpe = model.getByID(normUri);
assertTrue(bpe instanceof UnificationXref);
// check PR
bpe = model.getByID("http://identifiers.org/uniprot/Q0VCL1");
assertTrue(bpe instanceof ProteinReference);
assertTrue(
model.containsID(
"Xref7")); // RX is not normalized unless (by mistake) it has identifiers.org uri
// test BioSource
assertFalse(model.containsID("BioSource_Mouse_Tissue"));
bpe =
model.getByID(
Normalizer.uri(
model.getXmlBase(),
"taxonomy",
"10090",
BioSource.class)); // "taxonomy" - capitalization can be any
assertTrue(bpe instanceof BioSource);
normUri = Normalizer.uri(model.getXmlBase(), "taxonomy", "10090", UnificationXref.class);
bpe = model.getByID(normUri);
assertTrue(bpe instanceof UnificationXref);
// test that one of each pair ProteinReference, 2nd,3rd and 4th,5th is removed/merged:
assertEquals(4, model.getObjects(ProteinReference.class).size());
// Provenance is no more normalized (Miriam is not enough for this task)!
assertEquals(2, model.getObjects(Provenance.class).size());
// dataSource property is not inferred/inherited from pw1 anymore (prop. inference feature was
// removed)
pw2 = (Pathway) model.getByID("sub_pathway");
assertEquals(1, pw2.getDataSource().size());
pw1 = (Pathway) model.getByID("pathway");
assertEquals(1, pw1.getDataSource().size());
// test uniprot isoform xrefs are detected and normalized the same way
// get the expected xref URI first
normUri =
Normalizer.uri(model.getXmlBase(), "uniprot isoform", "P68250-2", UnificationXref.class);
bpe = model.getByID(normUri);
assertNotNull(bpe);
assertEquals(1, ((Xref) bpe).getXrefOf().size());
}