diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java
index 2ac0d8b89c35145bba24a4f73149494543eaaf46..484eb23d2fe1900bcd21da7768e38b924430576f 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java
@@ -85,17 +85,17 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
/**
* Url used for accessing information about target synonyms.
*/
- static final String URLPEP = "https://www.drugbank.ca/biodb/polypeptides/";
+ static final String URLPEP = "https://www.drugbank.ca/polypeptides/";
/**
* Url that allows to search for drugs using target hgnc name.
*/
- static final String URL_TARGETS = "https://www.drugbank.ca/search?utf8=%E2%9C%93&searcher=targets&query=";
+ static final String URL_TARGETS = "https://www.drugbank.ca/search?utf8=%E2%9C%93&searcher=bio_entities&query=";
/**
* Url that helps finding drug name for given target identifier.
*/
- static final String URL_TARGET_DETAIL = "https://www.drugbank.ca/biodb/bio_entities/";
+ static final String URL_TARGET_DETAIL = "https://www.drugbank.ca/bio_entities/";
/**
* Pattern used to get information about {@link Drug#bloodBrainBarrier blood
@@ -107,7 +107,7 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
* Pattern that extract information about target identifier when searching for
* targets with given set of HGNC names.
*/
- private Pattern targetPattern = Pattern.compile("(?<=\"/biodb/bio_entities/)([\\s\\S]*?)(?=\")");
+ private Pattern targetPattern = Pattern.compile("(?<=\"/bio_entities/)([\\s\\S]*?)(?=\")");
/**
* Default constructor.
@@ -372,7 +372,7 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
type = htmlPage.substring(kindIndex, endKindIndex);
}
if (type.trim().equalsIgnoreCase("Protein")) {
- int uniprotIdStart = htmlPage.indexOf("/biodb/polypeptides/") + "/biodb/polypeptides/".length();
+ int uniprotIdStart = htmlPage.indexOf("\"/polypeptides/") + "\"/polypeptides/".length();
Target result = new Target();
result.setType(TargetType.SINGLE_PROTEIN);
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/TaxonomyBackend.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/TaxonomyBackend.java
index 5ab139112cd4630eb1ea13dcd46443ab1829a8ef..14fd467ed303f52aedad3ac2cd81f3eb8acbe20b 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/TaxonomyBackend.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/TaxonomyBackend.java
@@ -82,6 +82,10 @@ public class TaxonomyBackend extends CachableInterface implements IExternalServi
if (term == null || "".equals(term.trim())) {
return null;
}
+
+ if (term.equalsIgnoreCase("Humans")) {
+ term="Human";
+ }
String res = getCacheValue(TAXONOMY_CACHE_PREFIX + term);
if (res != null) {
return new MiriamData(MiriamType.TAXONOMY, res);
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java
index d17d83c79ae90e9e771607b0948a913171ccf75e..e9d6e92c0e66f38a0704c4511eb8e51801b6db6c 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java
@@ -81,8 +81,9 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
assertEquals("Diazoxide", test.getName());
assertEquals("DB01119", test.getSources().get(0).getResource());
assertTrue(test.getBloodBrainBarrier().equalsIgnoreCase("YES"));
+ logger.debug(test.getDescription());
boolean res = test.getDescription().contains(
- "A benzothiadiazine derivative that is a peripheral vasodilator used for hypertensive emergencies. It lacks diuretic effect, apparently because it lacks a sulfonamide group. [PubChem]");
+ "A benzothiadiazine derivative that is a peripheral vasodilator used for hypertensive emergencies. It lacks diuretic effect, apparently because it lacks a sulfonamide group.");
assertTrue(res);
assertEquals(6, test.getTargets().size());
assertTrue(test.getApproved());
@@ -159,9 +160,9 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
assertEquals("Amantadine", amantadineDrug.getName());
assertEquals("DB00915", amantadineDrug.getSources().get(0).getResource());
boolean res = amantadineDrug.getDescription().contains(
- "An antiviral that is used in the prophylactic or symptomatic treatment of influenza A. It is also used as an antiparkinsonian agent, to treat extrapyramidal reactions, and for postherpetic neuralgia. The mechanisms of its effects in movement disorders are not well understood but probably reflect an increase in synthesis and release of dopamine, with perhaps some inhibition of dopamine uptake. [PubChem]");
+ "An antiviral that is used in the prophylactic or symptomatic treatment of influenza A. It is also used as an antiparkinsonian agent, to treat extrapyramidal reactions, and for postherpetic neuralgia. The mechanisms of its effects in movement disorders are not well understood but probably reflect an increase in synthesis and release of dopamine, with perhaps some inhibition of dopamine uptake.");
assertTrue(res);
- assertEquals(3, amantadineDrug.getTargets().size());
+ assertTrue(amantadineDrug.getTargets().size() >= 3);
} catch (Exception e) {
e.printStackTrace();
@@ -280,7 +281,7 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
try {
List<Drug> drugs = drugBankHTMLParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "NFKB2"));
assertNotNull(drugs);
- assertTrue("Only " + drugs.size() + " drugs were found, but at least 8 were expected", drugs.size() >= 8);
+ assertTrue("Only " + drugs.size() + " drugs were found, but at least 5 were expected", drugs.size() >= 5);
drugBankHTMLParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "NFKB2"));
@@ -828,12 +829,12 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
}
}
-
+
@Test
public void testExtractTargetsFromPageContent() throws Exception {
try {
String pageContent = " Details</a>blablablablabla Details</a>";
- List<Target> result = drugBankHTMLParser.extractTargetsFromPageContent(pageContent,2,3);
+ List<Target> result = drugBankHTMLParser.extractTargetsFromPageContent(pageContent, 2, 3);
assertEquals(0, result.size());
@@ -843,7 +844,5 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
}
}
-
-
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/TaxonomyBackendTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/TaxonomyBackendTest.java
index 1feb63abcecca26c64dca2735350f11464c9feab..c94155996551a43242fe8b4022dba9aa42942d8f 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/TaxonomyBackendTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/TaxonomyBackendTest.java
@@ -57,6 +57,17 @@ public class TaxonomyBackendTest extends AnnotationTestFunctions {
}
}
+ @Test
+ public void testByHumansName() throws Exception {
+ try {
+ MiriamData md = taxonomyBackend.getByName("Humans");
+ assertTrue(md.equals(TaxonomyBackend.HUMAN_TAXONOMY));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testByComplexName() throws Exception {
try {
diff --git a/annotation/testFiles/drugbank/target-html-part.html b/annotation/testFiles/drugbank/target-html-part.html
index 6390aa9d5e41cd8b3eda80072cd06388eb404c49..85ec8534b49c5123e1ddc9078445d5e07225e7ac 100644
--- a/annotation/testFiles/drugbank/target-html-part.html
+++ b/annotation/testFiles/drugbank/target-html-part.html
@@ -1 +1 @@
- Details</a><strong>1. <a href="/biodb/polypeptides/P21430">Matrix protein 2</a></strong></div><div class="card-body"><div class="row"><div class="col-sm-12 col-lg-5"><dl><dt class="col-md-5 col-sm-6">Kind</dt><dd class="col-md-7 col-sm-6">Protein</dd><dt class="col-md-5 col-sm-6">Organism</dt><dd class="col-md-7 col-sm-6">Influenza A virus (strain A/Ann Arbor/6/1960 H2N2)</dd><dt class="col-md-5 col-sm-6">Pharmacological action</dt><dd class="col-md-7 col-sm-6"><div class="badge badge badge-yes">Yes</div></dd><dt class="col-md-5 col-sm-6">Actions</dt><dd class="col-md-7 col-sm-6"><div class="badge badge-pill badge-action">Inhibitor</div></dd></dl></div><div class="col-sm-12 col-lg-7"><dl><dt class="col-md-5 col-sm-6">General Function</dt><dd class="col-md-7 col-sm-6">Ion channel activity</dd><dt class="col-md-5 col-sm-6">Specific Function</dt><dd class="col-md-7 col-sm-6">Forms a proton-selective ion channel that is necessary for the efficient release of the viral genome during virus entry. After attaching to the cell surface, the virion enters the cell by endocytos...</dd><dt class="col-md-5 col-sm-6">Gene Name</dt><dd class="col-md-7 col-sm-6">M</dd><dt class="col-md-5 col-sm-6">Uniprot ID</dt><dd class="col-md-7 col-sm-6"><a target="_blank" href="http://www.uniprot.org/uniprot/P21430">P21430</a></dd><dt class="col-md-5 col-sm-6">Uniprot Name</dt><dd class="col-md-7 col-sm-6">Matrix protein 2</dd><dt class="col-md-5 col-sm-6">Molecular Weight</dt><dd class="col-md-7 col-sm-6">11165.62 Da</dd></dl></div></div><h5>References</h5><div class="references"><ol class="cite-this-references"><li id="reference-A10951">Wang C, Takeuchi K, Pinto LH, Lamb RA: Ion channel activity of influenza A virus M2 protein: characterization of the amantadine block. J Virol. 1993 Sep;67(9):5585-94. [<a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed/7688826">PubMed:7688826</a>] </li><li id="reference-A4968">Jing X, Ma C, Ohigashi Y, Oliveira FA, Jardetzky TS, Pinto LH, Lamb RA: Functional studies indicate amantadine binds to the pore of the influenza A virus M2 proton-selective ion channel. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10967-72. doi: 10.1073/pnas.0804958105. Epub 2008 Jul 31. [<a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed/18669647">PubMed:18669647</a>] </li><li id="reference-A10952">Wang J, Cady SD, Balannik V, Pinto LH, DeGrado WF, Hong M: Discovery of spiro-piperidine inhibitors and their modulation of the dynamics of the M2 proton channel from influenza A virus. J Am Chem Soc. 2009 Jun 17;131(23):8066-76. doi: 10.1021/ja900063s. [<a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed/19469531">PubMed:19469531</a>] </li><li id="reference-A3946">Beigel J, Bray M: Current and future antiviral therapy of severe seasonal and avian influenza. Antiviral Res. 2008 Apr;78(1):91-102. doi: 10.1016/j.antiviral.2008.01.003. Epub 2008 Feb 4. [<a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed/18328578">PubMed:18328578</a>] </li><li id="reference-A10953">Lear JD: Proton conduction through the M2 protein of the influenza A virus; a quantitative, mechanistic analysis of experimental data. FEBS Lett. 2003 Sep 18;552(1):17-22. [<a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed/12972146">PubMed:12972146</a>] </li><li id="reference-A10954">Salom D, Hill BR, Lear JD, DeGrado WF: pH-dependent tetramerization and amantadine binding of the transmembrane helix of M2 from the influenza A virus. Biochemistry. 2000 Nov 21;39(46):14160-70. [<a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed/11087364">PubMed:11087364</a>] </li></ol></div></div></div><div class="bond card" id="BE0000641"><div class="card-header"><a class="btn btn-drugbank-secondary btn-sm bond-details-link ml-3" href="/biodb/polypeptides/Q8TCU5">
\ No newline at end of file
+ Details</a><strong>1. <a href="/polypeptides/P21430">Matrix protein 2</a></strong></div><div class="card-body"><div class="row"><div class="col-sm-12 col-lg-5"><dl><dt class="col-md-5 col-sm-6">Kind</dt><dd class="col-md-7 col-sm-6">Protein</dd><dt class="col-md-5 col-sm-6">Organism</dt><dd class="col-md-7 col-sm-6">Influenza A virus (strain A/Ann Arbor/6/1960 H2N2)</dd><dt class="col-md-5 col-sm-6">Pharmacological action</dt><dd class="col-md-7 col-sm-6"><div class="badge badge badge-yes">Yes</div></dd><dt class="col-md-5 col-sm-6">Actions</dt><dd class="col-md-7 col-sm-6"><div class="badge badge-pill badge-action">Inhibitor</div></dd></dl></div><div class="col-sm-12 col-lg-7"><dl><dt class="col-md-5 col-sm-6">General Function</dt><dd class="col-md-7 col-sm-6">Ion channel activity</dd><dt class="col-md-5 col-sm-6">Specific Function</dt><dd class="col-md-7 col-sm-6">Forms a proton-selective ion channel that is necessary for the efficient release of the viral genome during virus entry. After attaching to the cell surface, the virion enters the cell by endocytos...</dd><dt class="col-md-5 col-sm-6">Gene Name</dt><dd class="col-md-7 col-sm-6">M</dd><dt class="col-md-5 col-sm-6">Uniprot ID</dt><dd class="col-md-7 col-sm-6"><a target="_blank" href="http://www.uniprot.org/uniprot/P21430">P21430</a></dd><dt class="col-md-5 col-sm-6">Uniprot Name</dt><dd class="col-md-7 col-sm-6">Matrix protein 2</dd><dt class="col-md-5 col-sm-6">Molecular Weight</dt><dd class="col-md-7 col-sm-6">11165.62 Da</dd></dl></div></div><h5>References</h5><div class="references"><ol class="cite-this-references"><li id="reference-A10951">Wang C, Takeuchi K, Pinto LH, Lamb RA: Ion channel activity of influenza A virus M2 protein: characterization of the amantadine block. J Virol. 1993 Sep;67(9):5585-94. [<a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed/7688826">PubMed:7688826</a>] </li><li id="reference-A4968">Jing X, Ma C, Ohigashi Y, Oliveira FA, Jardetzky TS, Pinto LH, Lamb RA: Functional studies indicate amantadine binds to the pore of the influenza A virus M2 proton-selective ion channel. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10967-72. doi: 10.1073/pnas.0804958105. Epub 2008 Jul 31. [<a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed/18669647">PubMed:18669647</a>] </li><li id="reference-A10952">Wang J, Cady SD, Balannik V, Pinto LH, DeGrado WF, Hong M: Discovery of spiro-piperidine inhibitors and their modulation of the dynamics of the M2 proton channel from influenza A virus. J Am Chem Soc. 2009 Jun 17;131(23):8066-76. doi: 10.1021/ja900063s. [<a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed/19469531">PubMed:19469531</a>] </li><li id="reference-A3946">Beigel J, Bray M: Current and future antiviral therapy of severe seasonal and avian influenza. Antiviral Res. 2008 Apr;78(1):91-102. doi: 10.1016/j.antiviral.2008.01.003. Epub 2008 Feb 4. [<a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed/18328578">PubMed:18328578</a>] </li><li id="reference-A10953">Lear JD: Proton conduction through the M2 protein of the influenza A virus; a quantitative, mechanistic analysis of experimental data. FEBS Lett. 2003 Sep 18;552(1):17-22. [<a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed/12972146">PubMed:12972146</a>] </li><li id="reference-A10954">Salom D, Hill BR, Lear JD, DeGrado WF: pH-dependent tetramerization and amantadine binding of the transmembrane helix of M2 from the influenza A virus. Biochemistry. 2000 Nov 21;39(46):14160-70. [<a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed/11087364">PubMed:11087364</a>] </li></ol></div></div></div><div class="bond card" id="BE0000641"><div class="card-header"><a class="btn btn-drugbank-secondary btn-sm bond-details-link ml-3" href="/polypeptides/Q8TCU5">
\ No newline at end of file