From 83ec09a7ac1410486035de9d91f80c5ce2ca7149 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 15 May 2019 18:46:44 +0200
Subject: [PATCH] new implementation of miriam connector (using identifiers.org
API)
---
.../annotation/services/MiriamConnector.java | 89 +++--
.../services/MiriamConnectorTest.java | 19 +-
.../lcsb/mapviewer/model/map/MiriamType.java | 355 +++++++++++++-----
.../V14.0.0.20190514__old_miriam_queries.sql | 1 +
4 files changed, 323 insertions(+), 141 deletions(-)
create mode 100644 persist/src/main/resources/db/migration/14.0.0~alpha.0/V14.0.0.20190514__old_miriam_queries.sql
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnector.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnector.java
index c7f2ae3e65..7ee9e02149 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnector.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnector.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.annotation.services;
import java.io.IOException;
+import java.util.Map;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -9,13 +10,14 @@ import org.springframework.stereotype.Service;
import org.w3c.dom.Document;
import org.w3c.dom.Node;
+import com.google.gson.Gson;
+
import lcsb.mapviewer.annotation.cache.CachableInterface;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.annotation.cache.WebPageDownloader;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
@@ -35,11 +37,6 @@ public final class MiriamConnector extends CachableInterface implements IExterna
*/
static final String LINK_DB_PREFIX = "Link: ";
- /**
- * String used to distinguish cached data for checking if uri is valid.
- */
- protected static final String VALID_URI_PREFIX = "Validity: ";
-
/**
* String describing invalid miriam entries that will be put into db (instead of
* null).
@@ -79,23 +76,43 @@ public final class MiriamConnector extends CachableInterface implements IExterna
}
return result;
}
- String uri = miriamData.getDataType().getUris().get(0) + ":" + miriamData.getResource();
- throw new NotImplementedException();
-// String[] urls = getLink().getLocations(uri);
-// if (urls == null) {
-// result = null;
-// } else if (urls.length > 0) {
-// result = urls[0];
-// }
-// if (result != null) {
-// setCacheValue(query, result);
-// return result;
-// } else {
-// logger.warn("Cannot find url for miriam: " + miriamData);
-// // if url cannot be found then mark miriam data as invalid for one day
-// setCacheValue(query, INVALID_LINK, 1);
-// return null;
-// }
+ String id;
+ if (miriamData.getDataType().getNamespace().isEmpty()) {
+ id = miriamData.getResource();
+ } else {
+ id = miriamData.getDataType().getNamespace() + ":" + miriamData.getResource();
+ }
+
+ query = "https://identifiers.org/rest/identifiers/validate/" + id;
+ String page;
+ try {
+ page = getWebPageContent(query);
+ Gson gson = new Gson();
+ Map<?, ?> map = gson.fromJson(page, Map.class);
+ return (String) map.get("url");
+
+ } catch (Exception e) {
+ throw new AnnotationException("Problem with accessing identifiers.org", e);
+ }
+ // Document document = XmlParser.getXmlDocumentFromString(page);
+ // Node uri = XmlParser.getNode("uri", document.getChildNodes());
+ // return XmlParser.getNodeValue(uri);
+
+ // String[] urls = getLink().getLocations(uri);
+ // if (urls == null) {
+ // result = null;
+ // } else if (urls.length > 0) {
+ // result = urls[0];
+ // }
+ // if (result != null) {
+ // setCacheValue(query, result);
+ // return result;
+ // } else {
+ // logger.warn("Cannot find url for miriam: " + miriamData);
+ // // if url cannot be found then mark miriam data as invalid for one day
+ // setCacheValue(query, INVALID_LINK, 1);
+ // return null;
+ // }
}
@Override
@@ -151,9 +168,6 @@ public final class MiriamConnector extends CachableInterface implements IExterna
MiriamType dataType = MiriamType.getTypeByUri(rows[0]);
String resource = rows[1];
result = getUrlString(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, dataType, resource));
- } else if (name.startsWith(VALID_URI_PREFIX)) {
- String tmp = name.substring(VALID_URI_PREFIX.length());
- result = "" + isValid(tmp);
} else if (name.startsWith("http")) {
try {
result = getWebPageContent(name);
@@ -171,23 +185,18 @@ public final class MiriamConnector extends CachableInterface implements IExterna
}
/**
- * Checks if uri (like the one defined in {@link MiriamType#getUris()}) is valid.
+ * Checks if {@link MiriamType} is valid.
*
- * @param uri
- * uri to check
- * @return <code>true</code> if uri in parameter is valid, <code>false</code>
+ * @param type
+ * type to be checked
+ * @return <code>true</code> if {@link MiriamType} is valid, <code>false</code>
* otherwise
*/
- public boolean isValid(String uri) {
- throw new NotImplementedException();
-// boolean result = false;
-// String name = getLink().getName(uri);
-// if (name == null) {
-// result = false;
-// } else {
-// result = !name.isEmpty();
-// }
-// return result;
+ public boolean isValidMiriamType(MiriamType type) {
+ if (type.getNamespace() == null || type.getExampleIdentifier() == null) {
+ return false;
+ }
+ return getUrlString(new MiriamData(type, type.getExampleIdentifier())) != null;
}
/**
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java
index 0559af7dbf..3e4f83bfc3 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java
@@ -136,8 +136,7 @@ public class MiriamConnectorTest extends AnnotationTestFunctions {
try {
for (MiriamType mt : MiriamType.values()) {
if (!MiriamType.UNKNOWN.equals(mt)) {
- String uri = mt.getUris().get(0);
- assertTrue("Invalid URI (" + uri + ") for MiriamType: " + mt, miriamConnector.isValid(mt.getUris().get(0)));
+ assertTrue("Invalid MiriamType (" + mt + ") for MiriamType: " + mt, miriamConnector.isValidMiriamType(mt));
}
}
@@ -147,18 +146,6 @@ public class MiriamConnectorTest extends AnnotationTestFunctions {
}
}
- @Test
- public void testRefresh() throws Exception {
- String query = MiriamConnector.VALID_URI_PREFIX + MiriamType.HGNC.getUris().get(0);
- try {
- String res = miriamConnector.refreshCacheQuery(query);
- assertNotNull(res);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
@Test
public void testRefresh2() throws Exception {
MiriamData md = TaxonomyBackend.HUMAN_TAXONOMY;
@@ -306,10 +293,10 @@ public class MiriamConnectorTest extends AnnotationTestFunctions {
}
@Test
- public void testCheckValidyOfEmptyUri() throws Exception {
+ public void testCheckValidyOfUnknownMiriamType() throws Exception {
try {
// user connector without cache
- boolean value = new MiriamConnector().isValid("");
+ boolean value = miriamConnector.isValidMiriamType(MiriamType.UNKNOWN);
assertFalse(value);
} catch (Exception e) {
e.printStackTrace();
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
index 5ffc194171..1aa56f17b4 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
@@ -26,22 +26,35 @@ public enum MiriamType {
BiGG_COMPARTMENT("BiGG Compartment",
"http://bigg.ucsd.edu/compartments/",
new String[] { "urn:miriam:bigg.compartment" },
- new Class<?>[] {}, "MIR:00000555"),
+ new Class<?>[] {},
+ "MIR:00000555",
+ new Class<?>[] {},
+ "bigg.compartment",
+ "c"),
BiGG_METABOLITE("BiGG Metabolite",
"http://bigg.ucsd.edu/universal/metabolites",
new String[] { "urn:miriam:bigg.metabolite" },
- new Class<?>[] {}, "MIR:00000556"),
+ new Class<?>[] {}, "MIR:00000556",
+ new Class<?>[] {},
+ "bigg.metabolite",
+ "12dgr161"),
BiGG_REACTIONS("BiGG Reaction",
"http://bigg.ucsd.edu/universal/reactions",
new String[] { "urn:miriam:bigg.reaction" },
- new Class<?>[] {}, "MIR:00000557"),
+ new Class<?>[] {}, "MIR:00000557",
+ new Class<?>[] {},
+ "bigg.reaction",
+ "13GS"),
BIOMODELS_DATABASE("BioModels Database",
"https://www.ebi.ac.uk/biomodels/",
new String[] { "urn:miriam:biomodels.db", "http://identifiers.org/biomodels.db/" },
- new Class<?>[] {}, "MIR:00000007"),
+ new Class<?>[] {}, "MIR:00000007",
+ new Class<?>[] {},
+ "biomodels.db",
+ "BIOMD0000000048"),
/**
* Brenda enzyme database: http://www.brenda-enzymes.org.
@@ -49,7 +62,10 @@ public enum MiriamType {
BRENDA("BRENDA",
"http://www.brenda-enzymes.org",
new String[] { "urn:miriam:brenda" },
- new Class<?>[] {}, "MIR:00100101"),
+ new Class<?>[] {}, "MIR:00000071",
+ new Class<?>[] {},
+ "brenda",
+ "1.1.1.1"),
/**
* Chemical Abstracts Service database: http://commonchemistry.org.
@@ -57,7 +73,10 @@ public enum MiriamType {
CAS("Chemical Abstracts Service",
"http://commonchemistry.org",
new String[] { "urn:miriam:cas" },
- new Class<?>[] {}, "MIR:00000237"),
+ new Class<?>[] {}, "MIR:00000237",
+ new Class<?>[] {},
+ "cas",
+ "50-00-0"),
/**
* The Carbohydrate-Active Enzyme (CAZy) database: http://www.cazy.org/.
@@ -65,7 +84,10 @@ public enum MiriamType {
CAZY("CAZy",
"http://commonchemistry.org",
new String[] { "urn:miriam:cazy" },
- new Class<?>[] {}, "MIR:00000195"),
+ new Class<?>[] {}, "MIR:00000195",
+ new Class<?>[] {},
+ "cazy",
+ "GT10"),
/**
* Consensus CDS: http://identifiers.org/ccds/.
@@ -73,7 +95,10 @@ public enum MiriamType {
CCDS("Consensus CDS",
"http://www.ncbi.nlm.nih.gov/CCDS/",
new String[] { "urn:miriam:ccds" },
- new Class<?>[] {}, "MIR:00000375"),
+ new Class<?>[] {}, "MIR:00000375",
+ new Class<?>[] {},
+ "ccds",
+ "CCDS13573.1"),
/**
* Chebi database:
@@ -84,7 +109,9 @@ public enum MiriamType {
new String[] { "urn:miriam:obo.chebi", "urn:miriam:chebi",
"http://identifiers.org/chebi/", "http://identifiers.org/obo.chebi/" },
new Class<?>[] { Chemical.class, Drug.class, }, "MIR:00000002",
- new Class<?>[] { Chemical.class }),
+ new Class<?>[] { Chemical.class },
+ "",
+ "CHEBI:36927"),
/**
* ChemSpider database:
@@ -93,7 +120,10 @@ public enum MiriamType {
CHEMSPIDER("ChemSpider",
"http://www.chemspider.com//",
new String[] { "urn:miriam:chemspider" },
- new Class<?>[] {}, "MIR:00000138"),
+ new Class<?>[] {}, "MIR:00000138",
+ new Class<?>[] {},
+ "chemspider",
+ "56586"),
/**
* Chembl database: https://www.ebi.ac.uk/chembldb/.
@@ -101,7 +131,10 @@ public enum MiriamType {
CHEMBL_COMPOUND("ChEMBL",
"https://www.ebi.ac.uk/chembldb/",
new String[] { "urn:miriam:chembl.compound" },
- new Class<?>[] { Drug.class }, "MIR:00000084"),
+ new Class<?>[] { Drug.class }, "MIR:00000084",
+ new Class<?>[] {},
+ "chembl.compound",
+ "CHEMBL308052"),
/**
* Target in chembl database: https://www.ebi.ac.uk/chembldb/.
@@ -109,12 +142,18 @@ public enum MiriamType {
CHEMBL_TARGET("ChEMBL target",
"https://www.ebi.ac.uk/chembldb/",
new String[] { "urn:miriam:chembl.target" },
- new Class<?>[] { Protein.class, Complex.class }, "MIR:00000085"),
+ new Class<?>[] { Protein.class, Complex.class }, "MIR:00000085",
+ new Class<?>[] {},
+ "chembl.target",
+ "CHEMBL3467"),
CLINICAL_TRIALS_GOV("ClinicalTrials.gov",
"https://clinicaltrials.gov/",
new String[] { "urn:miriam:clinicaltrials" },
- new Class<?>[] {}, "MIR:00000137"),
+ new Class<?>[] {}, "MIR:00000137",
+ new Class<?>[] {},
+ "clinicaltrials",
+ "NCT00222573"),
/**
* Clusters of Orthologous Groups: https://www.ncbi.nlm.nih.gov/COG/.
@@ -122,7 +161,10 @@ public enum MiriamType {
COG("Clusters of Orthologous Groups",
"https://www.ncbi.nlm.nih.gov/COG/",
new String[] { "urn:miriam:cogs" },
- new Class<?>[] { Reaction.class }, "MIR:00000296"),
+ new Class<?>[] { Reaction.class }, "MIR:00000296",
+ new Class<?>[] {},
+ "cogs",
+ "COG0001"),
/**
* Digital Object Identifier: http://www.doi.org/.
@@ -130,7 +172,10 @@ public enum MiriamType {
DOI("Digital Object Identifier",
"http://www.doi.org/",
new String[] { "urn:miriam:doi", "http://identifiers.org/doi/" },
- new Class<?>[] { Reaction.class }, "MIR:00000019"),
+ new Class<?>[] { Reaction.class }, "MIR:00000019",
+ new Class<?>[] {},
+ "doi",
+ "10.1038/nbt1156"),
/**
* Drugbank database: http://www.drugbank.ca/.
@@ -138,14 +183,21 @@ public enum MiriamType {
DRUGBANK("DrugBank",
"http://www.drugbank.ca/",
new String[] { "urn:miriam:drugbank" },
- new Class<?>[] { Drug.class }, "MIR:00000102"),
+ new Class<?>[] { Drug.class }, "MIR:00000102",
+ new Class<?>[] {},
+ "drugbank",
+ "DB00001"),
+
/**
* Drugbank targets: http://www.drugbank.ca/targets.
*/
DRUGBANK_TARGET_V4("DrugBank Target v4",
"http://www.drugbank.ca/targets",
new String[] { "urn:miriam:drugbankv4.target" },
- new Class<?>[] {}, "MIR:00000528"),
+ new Class<?>[] {}, "MIR:00000528",
+ new Class<?>[] {},
+ "drugbankv4.target",
+ "BE0000048"),
/**
* Enzyme Nomenclature: http://www.enzyme-database.org/.
@@ -153,7 +205,10 @@ public enum MiriamType {
EC("Enzyme Nomenclature",
"http://www.enzyme-database.org/",
new String[] { "urn:miriam:ec-code" },
- new Class<?>[] { Protein.class, Complex.class }, "MIR:00000004"),
+ new Class<?>[] { Protein.class, Complex.class }, "MIR:00000004",
+ new Class<?>[] {},
+ "ec-code",
+ "1.1.1.1"),
/**
* Ensembl: www.ensembl.org.
@@ -161,7 +216,10 @@ public enum MiriamType {
ENSEMBL("Ensembl",
"www.ensembl.org",
new String[] { "urn:miriam:ensembl", "http://identifiers.org/ensembl/" },
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000003"),
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000003",
+ new Class<?>[] {},
+ "ensembl",
+ "ENSG00000139618"),
/**
* Ensembl Plants: http://plants.ensembl.org/.
@@ -169,7 +227,10 @@ public enum MiriamType {
ENSEMBL_PLANTS("Ensembl Plants",
"http://plants.ensembl.org/",
new String[] { "urn:miriam:ensembl.plant" },
- new Class<?>[] {}, "MIR:00000205"),
+ new Class<?>[] {}, "MIR:00000205",
+ new Class<?>[] {},
+ "ensembl.plant",
+ "AT1G73965"),
/**
* Entrez Gene: http://www.ncbi.nlm.nih.gov/gene.
@@ -177,7 +238,10 @@ public enum MiriamType {
ENTREZ("Entrez Gene",
"http://www.ncbi.nlm.nih.gov/gene",
new String[] { "urn:miriam:ncbigene", "urn:miriam:entrez.gene" },
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000069"),
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000069",
+ new Class<?>[] {},
+ "ncbigene",
+ "100010"),
/**
* Gene Ontology: http://amigo.geneontology.org/amigo.
@@ -186,7 +250,10 @@ public enum MiriamType {
"http://amigo.geneontology.org/amigo",
new String[] { "urn:miriam:obo.go", "urn:miriam:go", "http://identifiers.org/go/",
"http://identifiers.org/obo.go/" },
- new Class<?>[] { Phenotype.class, Compartment.class, Complex.class }, "MIR:00000022"),
+ new Class<?>[] { Phenotype.class, Compartment.class, Complex.class }, "MIR:00000022",
+ new Class<?>[] {},
+ "",
+ "GO:0006915"),
/**
* HGNC: http://www.genenames.org.
@@ -195,7 +262,9 @@ public enum MiriamType {
"http://www.genenames.org",
new String[] { "urn:miriam:hgnc" },
new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000080",
- new Class<?>[] { Protein.class, Gene.class, Rna.class }),
+ new Class<?>[] { Protein.class, Gene.class, Rna.class },
+ "hgnc",
+ "2674"),
/**
* HGNC symbol: http://www.genenames.org.
@@ -204,7 +273,9 @@ public enum MiriamType {
"http://www.genenames.org",
new String[] { "urn:miriam:hgnc.symbol" },
new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000362",
- new Class<?>[] { Protein.class, Gene.class, Rna.class }),
+ new Class<?>[] { Protein.class, Gene.class, Rna.class },
+ "hgnc.symbol",
+ "DAPK1"),
/**
* HMDB: http://www.hmdb.ca/.
@@ -212,7 +283,10 @@ public enum MiriamType {
HMDB("HMDB",
"http://www.hmdb.ca/",
"urn:miriam:hmdb",
- new Class<?>[] { Chemical.class, Drug.class, }, "MIR:00000051"),
+ new Class<?>[] { Chemical.class, Drug.class, }, "MIR:00000051",
+ new Class<?>[] {},
+ "hmdb",
+ "HMDB00001"),
/**
* InterPro: http://www.ebi.ac.uk/interpro/.
@@ -220,7 +294,10 @@ public enum MiriamType {
INTERPRO("InterPro",
"http://www.ebi.ac.uk/interpro/",
new String[] { "urn:miriam:interpro", "http://identifiers.org/interpro/" },
- new Class<?>[] { Protein.class, Complex.class }, "MIR:00000011"),
+ new Class<?>[] { Protein.class, Complex.class }, "MIR:00000011",
+ new Class<?>[] {},
+ "interpro",
+ "IPR000100"),
/**
* KEGG Compound: http://www.genome.jp/kegg/ligand.html.
@@ -228,15 +305,21 @@ public enum MiriamType {
KEGG_COMPOUND("Kegg Compound",
"http://www.genome.jp/kegg/ligand.html",
new String[] { "urn:miriam:kegg.compound", "http://identifiers.org/kegg.compound/" },
- new Class<?>[] { Chemical.class }, "MIR:00000013"),
+ new Class<?>[] { Chemical.class }, "MIR:00000013",
+ new Class<?>[] {},
+ "kegg.compound",
+ "C12345"),
/**
* KEGG Genes: http://www.genome.jp/kegg/genes.html.
*/
KEGG_GENES("Kegg Genes",
"http://www.genome.jp/kegg/genes.html",
- new String[] { "urn:miriam:kegg.genes"},
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000070"),
+ new String[] { "urn:miriam:kegg.genes" },
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000070",
+ new Class<?>[] {},
+ "kegg.genes",
+ "syn:ssr3451"),
/**
* KEGG Orthology: http://www.genome.jp/kegg/ko.html.
@@ -244,7 +327,10 @@ public enum MiriamType {
KEGG_ORTHOLOGY("KEGG Orthology",
"http://www.genome.jp/kegg/ko.html",
new String[] { "urn:miriam:kegg.orthology" },
- new Class<?>[] {}, "MIR:00000116"),
+ new Class<?>[] {}, "MIR:00000116",
+ new Class<?>[] {},
+ "kegg.orthology",
+ "K00001"),
/**
* KEGG Pathway: http://www.genome.jp/kegg/pathway.html.
@@ -252,7 +338,10 @@ public enum MiriamType {
KEGG_PATHWAY("Kegg Pathway",
"http://www.genome.jp/kegg/pathway.html",
new String[] { "urn:miriam:kegg.pathway", "http://identifiers.org/kegg.pathway/" },
- new Class<?>[] { Reaction.class }, "MIR:00000012"),
+ new Class<?>[] { Reaction.class }, "MIR:00000012",
+ new Class<?>[] {},
+ "kegg.pathway",
+ "hsa00620"),
/**
* KEGG Reaction: http://www.genome.jp/kegg/reaction/.
@@ -260,7 +349,10 @@ public enum MiriamType {
KEGG_REACTION("Kegg Reaction",
"http://www.genome.jp/kegg/reaction/",
new String[] { "urn:miriam:kegg.reaction", "http://identifiers.org/kegg.reaction/" },
- new Class<?>[] { Reaction.class }, "MIR:00000014"),
+ new Class<?>[] { Reaction.class }, "MIR:00000014",
+ new Class<?>[] {},
+ "kegg.reaction",
+ "R00100"),
/**
* MeSH 2012: http://www.nlm.nih.gov/mesh/.
@@ -268,7 +360,10 @@ public enum MiriamType {
MESH_2012("MeSH",
"http://www.nlm.nih.gov/mesh/",
new String[] { "urn:miriam:mesh" },
- new Class<?>[] { Phenotype.class, Compartment.class, Complex.class }, "MIR:00000270"),
+ new Class<?>[] { Phenotype.class, Compartment.class, Complex.class }, "MIR:00000560",
+ new Class<?>[] {},
+ "mesh",
+ "D010300"),
/**
* miRBase Sequence: http://www.mirbase.org/.
@@ -276,7 +371,10 @@ public enum MiriamType {
MI_R_BASE_SEQUENCE("miRBase Sequence Database",
"http://www.mirbase.org/",
new String[] { "urn:miriam:mirbase" },
- new Class<?>[] {}, "MIR:00000078"),
+ new Class<?>[] {}, "MIR:00000078",
+ new Class<?>[] {},
+ "mirbase",
+ "MI0000001"),
/**
* miRBase Mature Sequence: http://www.mirbase.org/.
@@ -284,7 +382,10 @@ public enum MiriamType {
MI_R_BASE_MATURE_SEQUENCE("miRBase Mature Sequence Database",
"http://www.mirbase.org/",
new String[] { "urn:miriam:mirbase.mature" },
- new Class<?>[] {}, "MIR:00000235"),
+ new Class<?>[] {}, "MIR:00000235",
+ new Class<?>[] {},
+ "mirbase.mature",
+ "MIMAT0000001"),
/**
* miRTaRBase Mature Sequence: http://mirtarbase.mbc.nctu.edu.tw/.
@@ -292,7 +393,10 @@ public enum MiriamType {
MIR_TAR_BASE_MATURE_SEQUENCE("miRTarBase Mature Sequence Database",
"http://mirtarbase.mbc.nctu.edu.tw/",
new String[] { "urn:miriam:mirtarbase" },
- new Class<?>[] {}, "MIR:00100739"),
+ new Class<?>[] {}, "MIR:00000562",
+ new Class<?>[] {},
+ "mirtarbase",
+ "MIRT000002"),
/**
* Mouse Genome Database: http://www.informatics.jax.org/.
@@ -300,12 +404,18 @@ public enum MiriamType {
MGD("Mouse Genome Database",
"http://www.informatics.jax.org/",
new String[] { "urn:miriam:mgd" },
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000037"),
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000037",
+ new Class<?>[] {},
+ "",
+ "MGI:2442292"),
OBI("Ontology for Biomedical Investigations",
"https://www.ebi.ac.uk/ols/ontologies/obi/",
new String[] { "urn:miriam:obi", "http://identifiers.org/obi/" },
- new Class<?>[] {}, "MIR:00000127"),
+ new Class<?>[] {}, "MIR:00000127",
+ new Class<?>[] {},
+ "obi",
+ "OBI:0000070"),
/**
* Online Mendelian Inheritance in Man: http://omim.org/.
@@ -313,7 +423,10 @@ public enum MiriamType {
OMIM("Online Mendelian Inheritance in Man",
"http://omim.org/",
new String[] { "urn:miriam:omim", "http://identifiers.org/mim/" },
- new Class<?>[] { Phenotype.class }, "MIR:00000016"),
+ new Class<?>[] { Phenotype.class }, "MIR:00000016",
+ new Class<?>[] {},
+ "mim",
+ "603903"),
/**
* PANTHER Family: http://www.pantherdb.org/.
@@ -321,7 +434,10 @@ public enum MiriamType {
PANTHER("PANTHER Family",
"http://www.pantherdb.org/",
new String[] { "urn:miriam:panther.family", "urn:miriam:panther" },
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000060"),
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000060",
+ new Class<?>[] {},
+ "panther.family",
+ "PTHR12345"),
/**
* PDB: http://www.pdbe.org/.
@@ -329,7 +445,10 @@ public enum MiriamType {
PDB("Protein Data Bank",
"http://www.pdbe.org/",
"urn:miriam:pdb",
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000020"),
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000020",
+ new Class<?>[] {},
+ "pdb",
+ "2gc4"),
/**
* Protein Family Database: http://pfam.xfam.org/.
@@ -337,7 +456,10 @@ public enum MiriamType {
PFAM("Protein Family Database",
"http://pfam.xfam.org//",
"urn:miriam:pfam",
- new Class<?>[] {}, "MIR:00000028"),
+ new Class<?>[] {}, "MIR:00000028",
+ new Class<?>[] {},
+ "pfam",
+ "PF01234"),
/**
* PharmGKB Pathways: http://www.pharmgkb.org/.
@@ -345,7 +467,10 @@ public enum MiriamType {
PHARM("PharmGKB Pathways",
"http://www.pharmgkb.org/",
"urn:miriam:pharmgkb.pathways",
- new Class<?>[] {}, "MIR:00000089"),
+ new Class<?>[] {}, "MIR:00000089",
+ new Class<?>[] {},
+ "pharmgkb.pathways",
+ "PA146123006"),
/**
* PubChem-compound: http://pubchem.ncbi.nlm.nih.gov/.
@@ -354,7 +479,9 @@ public enum MiriamType {
"http://pubchem.ncbi.nlm.nih.gov/",
new String[] { "urn:miriam:pubchem.compound" },
new Class<?>[] { Chemical.class }, "MIR:00000034",
- new Class<?>[] { Chemical.class }),
+ new Class<?>[] { Chemical.class },
+ "pubchem.compound",
+ "100101"),
/**
* PubChem-substance: http://pubchem.ncbi.nlm.nih.gov/.
@@ -363,7 +490,9 @@ public enum MiriamType {
"http://pubchem.ncbi.nlm.nih.gov/",
new String[] { "urn:miriam:pubchem.substance" },
new Class<?>[] { Chemical.class }, "MIR:00000033",
- new Class<?>[] { Chemical.class }),
+ new Class<?>[] { Chemical.class },
+ "pubchem.substance",
+ "100101"),
/**
* PubMed: http://www.ncbi.nlm.nih.gov/PubMed/.
@@ -372,7 +501,9 @@ public enum MiriamType {
"http://www.ncbi.nlm.nih.gov/PubMed/",
new String[] { "urn:miriam:pubmed", "http://identifiers.org/pubmed/" },
new Class<?>[] { BioEntity.class }, "MIR:00000015",
- new Class<?>[] { Reaction.class }),
+ new Class<?>[] { Reaction.class },
+ "pubmed",
+ "28725475"),
/**
* Reactome: http://www.reactome.org/.
@@ -380,7 +511,10 @@ public enum MiriamType {
REACTOME("Reactome",
"http://www.reactome.org/",
new String[] { "urn:miriam:reactome", "http://identifiers.org/reactome/" },
- new Class<?>[] { Reaction.class }, "MIR:00000018"),
+ new Class<?>[] { Reaction.class }, "MIR:00000018",
+ new Class<?>[] {},
+ "reactome",
+ "R-HSA-201451"),
/**
* RefSeq: http://www.ncbi.nlm.nih.gov/projects/RefSeq/.
@@ -388,7 +522,10 @@ public enum MiriamType {
REFSEQ("RefSeq",
"http://www.ncbi.nlm.nih.gov/projects/RefSeq/",
"urn:miriam:refseq",
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000039"),
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000039",
+ new Class<?>[] {},
+ "refseq",
+ "NP_012345"),
/**
* Rhea: http://www.rhea-db.org/.
@@ -396,7 +533,10 @@ public enum MiriamType {
RHEA("Rhea",
"http://www.rhea-db.org/",
"urn:miriam:rhea",
- new Class<?>[] { Reaction.class }, "MIR:00000082"),
+ new Class<?>[] { Reaction.class }, "MIR:00000082",
+ new Class<?>[] {},
+ "rhea",
+ "12345"),
/**
* SGD: http://www.yeastgenome.org/.
@@ -404,7 +544,10 @@ public enum MiriamType {
SGD("Saccharomyces Genome Database",
"http://www.yeastgenome.org/",
"urn:miriam:sgd",
- new Class<?>[] {}, "MIR:00000023"),
+ new Class<?>[] {}, "MIR:00000023",
+ new Class<?>[] {},
+ "sgd",
+ "S000003909"),
/**
* STITCH: http://stitch.embl.de/.
@@ -412,7 +555,10 @@ public enum MiriamType {
STITCH("STITCH",
"http://stitch.embl.de/",
"urn:miriam:stitch",
- new Class<?>[] {}, "MIR:00100343"),
+ new Class<?>[] {}, "MIR:00000266",
+ new Class<?>[] {},
+ "stitch",
+ "BQJCRHHNABKAKU"),
/**
* STRING: http://string-db.org/.
@@ -420,7 +566,10 @@ public enum MiriamType {
STRING("STRING",
"http://string-db.org/",
"urn:miriam:string",
- new Class<?>[] {}, "MIR:00000265"),
+ new Class<?>[] {}, "MIR:00000265",
+ new Class<?>[] {},
+ "string",
+ "P53350"),
/**
* The Arabidopsis Information Resource (TAIR) maintains a database of genetic
@@ -431,7 +580,10 @@ public enum MiriamType {
TAIR_LOCUS("TAIR Locus",
"http://arabidopsis.org/index.jsp",
"urn:miriam:tair.locus",
- new Class<?>[] {}, "MIR:00000050"),
+ new Class<?>[] {}, "MIR:00000050",
+ new Class<?>[] {},
+ "tair.locus",
+ "2200950"),
/**
* Taxonomy: http://www.ncbi.nlm.nih.gov/taxonomy/.
@@ -439,7 +591,10 @@ public enum MiriamType {
TAXONOMY("Taxonomy",
"http://www.ncbi.nlm.nih.gov/taxonomy/",
new String[] { "urn:miriam:taxonomy", "http://identifiers.org/taxonomy/" },
- new Class<?>[] {}, "MIR:00000006"),
+ new Class<?>[] {}, "MIR:00000006",
+ new Class<?>[] {},
+ "taxonomy",
+ "9606"),
/**
* Toxicogenomic: Chemical: http://ctdbase.org/detail.go.
@@ -448,7 +603,10 @@ public enum MiriamType {
TOXICOGENOMIC_CHEMICAL("Toxicogenomic Chemical",
"http://ctdbase.org/",
"urn:miriam:ctd.chemical",
- new Class<?>[] {}, "MIR:00000098"),
+ new Class<?>[] {}, "MIR:00000098",
+ new Class<?>[] {},
+ "ctd.chemical",
+ "D001151"),
/**
* UniGene: http://www.ncbi.nlm.nih.gov/unigene.
@@ -456,7 +614,10 @@ public enum MiriamType {
UNIGENE("UniGene",
"http://www.ncbi.nlm.nih.gov/unigene",
"urn:miriam:unigene",
- new Class<?>[] {}, "MIR:00000346"),
+ new Class<?>[] {}, "MIR:00000346",
+ new Class<?>[] {},
+ "unigene",
+ "4900"),
/**
* Uniprot: http://www.uniprot.org/.
@@ -464,7 +625,10 @@ public enum MiriamType {
UNIPROT("Uniprot",
"http://www.uniprot.org/",
new String[] { "urn:miriam:uniprot", "http://identifiers.org/uniprot/" },
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000005"),
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000005",
+ new Class<?>[] {},
+ "uniprot",
+ "P0DP23"),
/**
* UniProt Isoform: http://www.uniprot.org/.
@@ -472,7 +636,10 @@ public enum MiriamType {
UNIPROT_ISOFORM("UniProt Isoform",
"http://www.uniprot.org/",
"urn:miriam:uniprot.isoform",
- new Class<?>[] { Protein.class }, "MIR:00000388"),
+ new Class<?>[] { Protein.class }, "MIR:00000388",
+ new Class<?>[] {},
+ "uniprot.isoform",
+ "Q5BJF6-3"),
/**
* Unknown reference type...
@@ -480,7 +647,10 @@ public enum MiriamType {
UNKNOWN("Unknown",
null,
new String[] {},
- new Class<?>[] {}, null),
+ new Class<?>[] {}, null,
+ new Class<?>[] {},
+ null,
+ null),
/**
* VMH metabolite: https://vmh.uni.lu/.
@@ -488,7 +658,10 @@ public enum MiriamType {
VMH_METABOLITE("VMH metabolite",
"https://vmh.uni.lu/",
new String[] { "urn:miriam:vmhmetabolite", "http://identifiers.org/vmhmetabolite/" },
- new Class<?>[] { Chemical.class }, "MIR:00000636"),
+ new Class<?>[] { Chemical.class }, "MIR:00000636",
+ new Class<?>[] {},
+ "vmhmetabolite",
+ "h2o"),
/**
* VMH reaction: https://vmh.uni.lu/.
@@ -496,7 +669,10 @@ public enum MiriamType {
VMH_REACTION("VMH reaction",
"https://vmh.uni.lu/",
new String[] { "urn:miriam:vmhreaction", "http://identifiers.org/vmhreaction/" },
- new Class<?>[] { Reaction.class }, "MIR:00000640"),
+ new Class<?>[] { Reaction.class }, "MIR:00000640",
+ new Class<?>[] {},
+ "vmhreaction",
+ "HEX1"),
/**
* Wikidata: https://www.wikidata.org/.
@@ -504,7 +680,10 @@ public enum MiriamType {
WIKIDATA("Wikidata",
"https://www.wikidata.org/",
new String[] { "urn:miriam:wikidata" },
- new Class<?>[] {}, "MIR:00000549"),
+ new Class<?>[] {}, "MIR:00000549",
+ new Class<?>[] {},
+ "wikidata",
+ "Q2207226"),
/**
* WikiPathways: http://www.wikipathways.org/.
@@ -512,7 +691,10 @@ public enum MiriamType {
WIKIPATHWAYS("WikiPathways",
"http://www.wikipathways.org/",
new String[] { "urn:miriam:wikipathways" },
- new Class<?>[] {}, "MIR:00000076"),
+ new Class<?>[] {}, "MIR:00000076",
+ new Class<?>[] {},
+ "wikipathways",
+ "WP100"),
/**
* Wikipedia: http://en.wikipedia.org/wiki/Main_Page.
@@ -520,7 +702,10 @@ public enum MiriamType {
WIKIPEDIA("Wikipedia (English)",
"http://en.wikipedia.org/wiki/Main_Page", // /
new String[] { "urn:miriam:wikipedia.en" },
- new Class<?>[] {}, "MIR:00000384"),
+ new Class<?>[] {}, "MIR:00000384",
+ new Class<?>[] {},
+ "wikipedia.en",
+ "SM_UB-81"),
/**
* WormBase: http://wormbase.bio2rdf.org/fct.
@@ -528,7 +713,10 @@ public enum MiriamType {
WORM_BASE("WormBase",
"http://wormbase.bio2rdf.org/fct", // /
new String[] { "urn:miriam:wormbase" },
- new Class<?>[] {}, "MIR:00000027");
+ new Class<?>[] {}, "MIR:00000027",
+ new Class<?>[] {},
+ "wb",
+ "WBGene00000001");
/**
* User friendly name.
@@ -561,23 +749,9 @@ public enum MiriamType {
*/
private List<Class<? extends BioEntity>> requiredClass = new ArrayList<>();
- /**
- * Constructor that initialize enum object.
- *
- * @param dbHomePage
- * home page of the resource {@link #dbHomepage}
- * @param commonName
- * {@link #commonName}
- * @param uris
- * {@link #uris}
- * @param classes
- * {@link #validClass}
- * @param registryIdentifier
- * {@link #registryIdentifier}
- */
- MiriamType(String commonName, String dbHomePage, String[] uris, Class<?>[] classes, String registryIdentifier) {
- this(commonName, dbHomePage, uris, classes, registryIdentifier, new Class<?>[] {});
- }
+ private String namespace;
+
+ private String exampleIdentifier;
/**
* Constructor that initialize enum object.
@@ -596,7 +770,7 @@ public enum MiriamType {
* {@link #requiredClasses}
*/
MiriamType(String commonName, String dbHomePage, String[] uris, Class<?>[] classes, String registryIdentifier,
- Class<?>[] requiredClasses) {
+ Class<?>[] requiredClasses, String namespace, String exampleIdentifier) {
this.commonName = commonName;
this.dbHomepage = dbHomePage;
for (String string : uris) {
@@ -609,6 +783,8 @@ public enum MiriamType {
this.requiredClass.add((Class<? extends BioEntity>) clazz);
}
this.registryIdentifier = registryIdentifier;
+ this.namespace = namespace;
+ this.exampleIdentifier = exampleIdentifier;
}
/**
@@ -625,8 +801,8 @@ public enum MiriamType {
* @param classes
* {@link #validClass}
*/
- MiriamType(String commonName, String dbHomePage, String uri, Class<?>[] classes, String registryIdentifier) {
- this(commonName, dbHomePage, new String[] { uri }, classes, registryIdentifier);
+ MiriamType(String commonName, String dbHomePage, String uri, Class<?>[] classes, String registryIdentifier, Class<?>[] requiredClasses, String namespace, String exampleIdentifier) {
+ this(commonName, dbHomePage, new String[] { uri }, classes, registryIdentifier, requiredClasses, namespace, exampleIdentifier);
}
/**
@@ -780,4 +956,13 @@ public enum MiriamType {
}
throw new InvalidArgumentException("Invalid miriam uri: " + miriamUri);
}
+
+ public String getNamespace() {
+ return namespace;
+ }
+
+ public String getExampleIdentifier() {
+ return exampleIdentifier;
+ }
+
}
diff --git a/persist/src/main/resources/db/migration/14.0.0~alpha.0/V14.0.0.20190514__old_miriam_queries.sql b/persist/src/main/resources/db/migration/14.0.0~alpha.0/V14.0.0.20190514__old_miriam_queries.sql
new file mode 100644
index 0000000000..6861d29699
--- /dev/null
+++ b/persist/src/main/resources/db/migration/14.0.0~alpha.0/V14.0.0.20190514__old_miriam_queries.sql
@@ -0,0 +1 @@
+delete from cache_query_table where query like 'Validity:%';
\ No newline at end of file
--
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