From a4fe92c12fc19018f7d2899f250d7ab42ceea665 Mon Sep 17 00:00:00 2001
From: David Hoksza <david.hoksza@uni.lu>
Date: Wed, 17 Jan 2018 16:18:29 +0100
Subject: [PATCH] Added associated annotator class to miriam data including
hibernate mapping + createMiriamData in element annotator. without unit tests
---
.../services/annotators/ElementAnnotator.java | 30 +
.../services/annotators/TairAnnotator.java | 4 +-
.../annotators/ElementAnnotatorTest.java | 33 +
.../lcsb/mapviewer/model/map/MiriamData.java | 61 +-
.../lcsb/mapviewer/model/map/MiriamType.java | 1288 ++++++++---------
persist/src/db/12.0.0/fix_db_20180117.sql | 2 +
6 files changed, 764 insertions(+), 654 deletions(-)
create mode 100644 persist/src/db/12.0.0/fix_db_20180117.sql
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
index 84761857a5..e71c85ce6a 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
@@ -12,6 +12,7 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerChemical;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Chemical;
@@ -473,5 +474,34 @@ public abstract class ElementAnnotator extends CachableInterface {
logger.warn(prefix + "MCS in db different: \"" + element.getMechanicalConfidenceScore() + "\", \"" + value + "\"");
}
}
+
+ private void setAnnotator(MiriamData md){
+ md.setAnnotator(this.getClass());
+ }
+
+ protected MiriamData createMiriamData(){
+ MiriamData md = new MiriamData();
+ setAnnotator(md);
+ return md;
+ }
+
+ protected MiriamData createMiriamData(MiriamData _md){
+ MiriamData md = new MiriamData(_md);
+ setAnnotator(md);
+ return md;
+ }
+
+ protected MiriamData createMiriamData(MiriamType mt, String resource){
+ MiriamData md = new MiriamData(mt, resource);
+ setAnnotator(md);
+ return md;
+ }
+
+ protected MiriamData createMiriamData(MiriamRelationType relationType, MiriamType mt, String resource){
+ MiriamData md = new MiriamData(relationType, mt, resource);
+ setAnnotator(md);
+ return md;
+ }
+
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java
index 0388293b12..9dcac43bcd 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java
@@ -58,7 +58,7 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
this.setCache(null);
try {
- MiriamData md = tairToUniprot(new MiriamData(MiriamType.TAIR_LOCUS, "AT1G01030"));
+ MiriamData md = tairToUniprot(createMiriamData(MiriamType.TAIR_LOCUS, "AT1G01030"));
status.setStatus(ExternalServiceStatusType.OK);
if (md == null || !md.getResource().equalsIgnoreCase("Q9MAN1")) {
@@ -122,7 +122,7 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
Collection<MiriamData> result = new HashSet<MiriamData>();
Matcher m = tairToUniprot.matcher(pageContent);
if (m.find()) {
- result.add(new MiriamData(MiriamType.UNIPROT, m.group(1)));
+ result.add(createMiriamData(MiriamType.UNIPROT, m.group(1)));
}
return result;
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotatorTest.java
index 1dac8112d6..f4c613ca90 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotatorTest.java
@@ -2,6 +2,7 @@ package lcsb.mapviewer.annotation.services.annotators;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.assertNull;
import org.junit.After;
import org.junit.AfterClass;
@@ -12,6 +13,9 @@ import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.cache.CachableInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Ion;
@@ -193,5 +197,34 @@ public class ElementAnnotatorTest extends AnnotationTestFunctions {
assertEquals(1, getWarnings().size());
}
+
+ @Test
+ public void createMiriamData1() {
+ MiriamData md = annotator.createMiriamData();
+ assertEquals(md.getAnnotator(), annotator.getClass());
+ }
+
+ @Test
+ public void createMiriamData2() {
+ MiriamData md = annotator.createMiriamData(MiriamType.UNIPROT, "XXX");
+ assertEquals(md.getAnnotator(), annotator.getClass());
+ }
+
+ @Test
+ public void createMiriamData3() {
+ MiriamData md = annotator.createMiriamData(MiriamRelationType.BQ_BIOL_ENCODES, MiriamType.UNIPROT, "XXX");
+ assertEquals(md.getAnnotator(), annotator.getClass());
+ }
+
+ @Test
+ public void createMiriamData4() {
+ MiriamData md1 = new MiriamData(MiriamType.UNIPROT, "XXX");
+ assertNull(md1.getAnnotator());
+
+ MiriamData md2 = annotator.createMiriamData(md1);
+ assertEquals(md2.getAnnotator(), annotator.getClass());
+ }
+
+
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/MiriamData.java b/model/src/main/java/lcsb/mapviewer/model/map/MiriamData.java
index 5e5dffd5a5..491d0f840a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamData.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamData.java
@@ -64,6 +64,13 @@ public class MiriamData implements Comparable<MiriamData>, Serializable {
*/
@Column(name = "resource")
private String resource = "";
+
+ /**
+ * The annotator which created the miriam data or which
+ * should be associated with it.
+ */
+ @Column(name = "annotator")
+ private Class<?> annotator = null;
/**
* Default constructor.
@@ -82,8 +89,9 @@ public class MiriamData implements Comparable<MiriamData>, Serializable {
setRelationType(md.relationType);
setDataType(md.dataType);
setResource(md.resource);
+ setAnnotator(md.annotator);
}
-
+
/**
* Constructor that initialize the data by information from params.
*
@@ -93,8 +101,11 @@ public class MiriamData implements Comparable<MiriamData>, Serializable {
* type of the miriam data (see: {@link MiriamType})
* @param resource
* {@link #resource}
+ * @param annotator
+ * {@link #annotator}
+ *
*/
- public MiriamData(MiriamRelationType relationType, MiriamType mt, String resource) {
+ public MiriamData(MiriamRelationType relationType, MiriamType mt, String resource, Class<?> annotator) {
if (mt == null) {
throw new InvalidArgumentException("MiriamType cannot be null");
}
@@ -104,8 +115,36 @@ public class MiriamData implements Comparable<MiriamData>, Serializable {
setRelationType(relationType);
setDataType(mt);
setResource(resource);
+ setAnnotator(annotator);
+ }
+
+ /**
+ * Constructor that initialize the data by information from params.
+ *
+ * @param relationType
+ * {@link #relationType}
+ * @param mt
+ * type of the miriam data (see: {@link MiriamType})
+ * @param resource
+ * {@link #resource}
+ */
+ public MiriamData(MiriamRelationType relationType, MiriamType mt, String resource) {
+ this(relationType, mt, resource, null);
+ }
+
+ /**
+ * Constructor that initialize the data by information from params.
+ *
+ * @param mt
+ * type of the miriam data (see: {@link MiriamType})
+ * @param resource
+ * {@link #resource}
+ */
+ public MiriamData(MiriamType mt, String resource, Class<?> annotator) {
+ this(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, mt, resource, annotator);
}
+
/**
* Constructor that initialize the data by information from params.
*
@@ -115,7 +154,7 @@ public class MiriamData implements Comparable<MiriamData>, Serializable {
* {@link #resource}
*/
public MiriamData(MiriamType mt, String resource) {
- this(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, mt, resource);
+ this(mt, resource, null);
}
/**
@@ -250,4 +289,20 @@ public class MiriamData implements Comparable<MiriamData>, Serializable {
}
}
+
+ /**
+ *
+ * @return {@link #annotator}
+ */
+ public Class<?> getAnnotator() {
+ return annotator;
+ }
+
+ /**
+ *
+ * @param {@link #annotator}
+ */
+ public void setAnnotator(Class<?> annotator) {
+ this.annotator = annotator;
+ }
}
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 f633cde675..338903c600 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
@@ -39,7 +39,6 @@ public enum MiriamType {
new Class<?>[] {}, "MIR:00000237"), //
/**
-
* The Carbohydrate-Active Enzyme (CAZy) database: http://www.cazy.org/.
*/
CAZY("CAZy", //
@@ -47,326 +46,318 @@ public enum MiriamType {
new String[] { "urn:miriam:cazy" }, //
new Class<?>[] {}, "MIR:00000195"), //
- /**
- * Consensus CDS: http://identifiers.org/ccds/.
- */
- CCDS("Consensus CDS", //
- "http://www.ncbi.nlm.nih.gov/CCDS/", //
- new String[] { "urn:miriam:ccds" }, //
- new Class<?>[] {}, "MIR:00000375"), //
-
- /**
- * Chebi database:
- * <a href = "http://www.ebi.ac.uk/chebi/">http://www.ebi.ac.uk/chebi/</a>.
- */
- CHEBI("Chebi", //
- "http://www.ebi.ac.uk/chebi/", //
- new String[] { "urn:miriam:obo.chebi", "urn:miriam:chebi" }, //
- new Class<?>[] { Chemical.class, Drug.class, }, "MIR:00000002", //
- new Class<?>[] { Chemical.class }), //
-
- /**
- * ChemSpider database:
- * <a href = "http://www.chemspider.com/">http://www.chemspider.com/</a>.
- */
- CHEMSPIDER("ChemSpider", //
- "http://www.chemspider.com//", //
- new String[] { "urn:miriam:chemspider" }, //
- new Class<?>[] {}, "MIR:00000138"), //
-
- /**
- * Chembl database: https://www.ebi.ac.uk/chembldb/.
- */
- CHEMBL_COMPOUND("ChEMBL", //
- "https://www.ebi.ac.uk/chembldb/", //
- new String[] { "urn:miriam:chembl.compound" }, //
- new Class<?>[] { Drug.class }, "MIR:00000084"), //
-
- /**
- * Target in chembl database: https://www.ebi.ac.uk/chembldb/.
- */
- CHEMBL_TARGET("ChEMBL target", //
- "https://www.ebi.ac.uk/chembldb/", //
- new String[] { "urn:miriam:chembl.target" }, //
- new Class<?>[] { Protein.class, Complex.class }, "MIR:00000085"), //
-
- /**
- * Clusters of Orthologous Groups: https://www.ncbi.nlm.nih.gov/COG/.
- */
- COG("Clusters of Orthologous Groups", //
- "https://www.ncbi.nlm.nih.gov/COG/", //
- new String[] { "urn:miriam:cogs" }, //
- new Class<?>[] { Reaction.class }, "MIR:00000296"), //
-
- /**
- * Digital Object Identifier: http://www.doi.org/.
- */
- DOI("Digital Object Identifier", //
- "http://www.doi.org/", //
- new String[] { "urn:miriam:doi" }, //
- new Class<?>[] { Reaction.class }, "MIR:00000019"), //
-
- /**
- * Drugbank database: http://www.drugbank.ca/.
- */
- DRUGBANK("DrugBank", //
- "http://www.drugbank.ca/", //
- new String[] { "urn:miriam:drugbank" }, //
- new Class<?>[] { Drug.class }, "MIR:00000102"), //
- /**
- * 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"), //
-
- /**
- * Enzyme Nomenclature: http://www.enzyme-database.org/.
- */
- EC("Enzyme Nomenclature", //
- "http://www.enzyme-database.org/", //
- new String[] { "urn:miriam:ec-code" }, //
- new Class<?>[] { Protein.class, Complex.class }, "MIR:00000004"), //
-
- /**
- * Ensembl: www.ensembl.org.
- */
- ENSEMBL("Ensembl", //
- "www.ensembl.org", //
- new String[] { "urn:miriam:ensembl" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000003"), //
-
- /**
- * Ensembl Plants: http://plants.ensembl.org/.
- */
- ENSEMBL_PLANTS("Ensembl Plants", //
- "http://plants.ensembl.org/", //
- new String[] { "urn:miriam:ensembl.plant" }, //
- new Class<?>[] {}, "MIR:00000205"), //
-
- /**
- * Entrez Gene: http://www.ncbi.nlm.nih.gov/gene.
- */
- 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"), //
-
- /**
- * Gene Ontology: http://amigo.geneontology.org/amigo.
- */
- GO("Gene Ontology", //
- "http://amigo.geneontology.org/amigo", //
- new String[] { "urn:miriam:obo.go", "urn:miriam:go" }, //
- new Class<?>[] { Phenotype.class, Compartment.class, Complex.class }, "MIR:00000022"), //
-
- /**
- * HGNC: http://www.genenames.org.
- */
- HGNC("HGNC", //
- "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 }), //
-
- /**
- * HGNC symbol: http://www.genenames.org.
- */
- HGNC_SYMBOL("HGNC Symbol", //
- "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 }), //
-
- /**
- * HMDB: http://www.hmdb.ca/.
- */
- HMDB("HMDB", //
- "http://www.hmdb.ca/", //
- "urn:miriam:hmdb", //
- new Class<?>[] { Chemical.class, Drug.class, }, "MIR:00000051"), //
-
- /**
- * InterPro: http://www.ebi.ac.uk/interpro/.
- */
- INTERPRO("InterPro", //
- "http://www.ebi.ac.uk/interpro/", //
- new String[] { "urn:miriam:interpro" }, //
- new Class<?>[] { Protein.class, Complex.class }, "MIR:00000011"), //
-
- /**
- * KEGG Compound: http://www.genome.jp/kegg/ligand.html.
- */
- KEGG_COMPOUND("Kegg Compound", //
- "http://www.genome.jp/kegg/ligand.html", //
- "urn:miriam:kegg.compound", //
- new Class<?>[] { Chemical.class }, "MIR:00000013"), //
-
- /**
- * 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", "urn:miriam:kegg.genes:hsa" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000070"), //
-
- /**
- * KEGG Orthology: http://www.genome.jp/kegg/ko.html.
- */
- KEGG_ORTHOLOGY("KEGG Orthology", //
- "http://www.genome.jp/kegg/ko.html", //
- new String[] { "urn:miriam:kegg.orthology" }, //
- new Class<?>[] {}, "MIR:00000116"), //
-
- /**
- * KEGG Pathway: http://www.genome.jp/kegg/pathway.html.
- */
- KEGG_PATHWAY("Kegg Pathway", //
- "http://www.genome.jp/kegg/pathway.html", //
- "urn:miriam:kegg.pathway", //
- new Class<?>[] { Reaction.class }, "MIR:00000012"), //
-
- /**
- * KEGG Reaction: http://www.genome.jp/kegg/reaction/.
- */
- KEGG_REACTION("Kegg Reaction", //
- "http://www.genome.jp/kegg/reaction/", //
- "urn:miriam:kegg.reaction", //
- new Class<?>[] { Reaction.class }, "MIR:00000014"), //
-
- /**
- * MeSH 2012: http://www.nlm.nih.gov/mesh/.
- */
- MESH_2012("MeSH 2012", //
- "http://www.nlm.nih.gov/mesh/", //
- new String[] { "urn:miriam:mesh.2012", "urn:miriam:mesh" }, //
- new Class<?>[] { Phenotype.class, Compartment.class, Complex.class }, "MIR:00000270"), //
-
- /**
- * miRBase Sequence: http://www.mirbase.org/.
- */
- MI_R_BASE_SEQUENCE("miRBase Sequence Database", //
- "http://www.mirbase.org/", //
- new String[] { "urn:miriam:mirbase" }, //
- new Class<?>[] {}, "MIR:00000078"), //
-
- /**
- * miRBase Mature Sequence: http://www.mirbase.org/.
- */
- MI_R_BASE_MATURE_SEQUENCE("miRBase Mature Sequence Database", //
- "http://www.mirbase.org/", //
- new String[] { "urn:miriam:mirbase.mature" }, //
- new Class<?>[] {}, "MIR:00000235"), //
-
- /**
- * miRTaRBase Mature Sequence: http://mirtarbase.mbc.nctu.edu.tw/.
- */
- MIR_TAR_BASE_MATURE_SEQUENCE("miRTarBase Mature Sequence Database", //
- "http://mirtarbase.mbc.nctu.edu.tw/", //
- new String[] { "urn:miriam:mirtarbase" }, //
- new Class<?>[] {}, "MIR:00100739"), //
-
- /**
- * Mouse Genome Database: http://www.informatics.jax.org/.
- */
- MGD("Mouse Genome Database", //
- "http://www.informatics.jax.org/", //
- new String[] { "urn:miriam:mgd" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000037"), //
-
- /**
- * Online Mendelian Inheritance in Man: http://omim.org/.
- */
- OMIM("Online Mendelian Inheritance in Man", //
- "http://omim.org/", //
- new String[] { "urn:miriam:omim" }, //
- new Class<?>[] { Phenotype.class }, "MIR:00000016"), //
-
- /**
- * PANTHER Family: http://www.pantherdb.org/.
- */
- 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"), //
-
- /**
- * PDB: http://www.pdbe.org/.
- */
- PDB("Protein Data Bank", //
- "http://www.pdbe.org/", //
- "urn:miriam:pdb", //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000020"),
-
- /**
- * Protein Family Database: http://pfam.xfam.org/.
- */
- PFAM("Protein Family Database", //
- "http://pfam.xfam.org//", //
- "urn:miriam:pfam", //
- new Class<?>[] {}, "MIR:00000028"), //
-
- /**
- * PharmGKB Pathways: http://www.pharmgkb.org/.
- */
- PHARM("PharmGKB Pathways", //
- "http://www.pharmgkb.org/", //
- "urn:miriam:pharmgkb.pathways", //
- new Class<?>[] {}, "MIR:00000089"), //
-
- /**
- * PubChem-compound: http://pubchem.ncbi.nlm.nih.gov/.
- */
- PUBCHEM("PubChem-compound", //
- "http://pubchem.ncbi.nlm.nih.gov/", //
- new String[] { "urn:miriam:pubchem.compound" }, //
- new Class<?>[] { Chemical.class }, "MIR:00000034", //
- new Class<?>[] { Chemical.class }), //
-
- /**
- * PubChem-substance: http://pubchem.ncbi.nlm.nih.gov/.
- */
- PUBCHEM_SUBSTANCE("PubChem-substance", //
- "http://pubchem.ncbi.nlm.nih.gov/", //
- new String[] { "urn:miriam:pubchem.substance" }, //
- new Class<?>[] { Chemical.class }, "MIR:00000033", //
- new Class<?>[] { Chemical.class }), //
-
- /**
- * PubMed: http://www.ncbi.nlm.nih.gov/PubMed/.
- */
- PUBMED("PubMed", //
- "http://www.ncbi.nlm.nih.gov/PubMed/", //
- new String[] { "urn:miriam:pubmed" }, //
- new Class<?>[] { BioEntity.class }, "MIR:00000015", //
- new Class<?>[] { Reaction.class }), //
-
- /**
- * Reactome: http://www.reactome.org/.
- */
- REACTOME("Reactome", //
- "http://www.reactome.org/", //
- "urn:miriam:reactome", //
- new Class<?>[] { Reaction.class }, "MIR:00000018"), //
-
- /**
- * RefSeq: http://www.ncbi.nlm.nih.gov/projects/RefSeq/.
- */
- REFSEQ("RefSeq", //
- "http://www.ncbi.nlm.nih.gov/projects/RefSeq/", //
- "urn:miriam:refseq", //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000039"),
-
- /**
- * SGD: http://www.yeastgenome.org/.
- */
- SGD("Saccharomyces Genome Database", //
- "http://www.yeastgenome.org/", //
- "urn:miriam:sgd", //
- new Class<?>[] {}, "MIR:00000023"),
-
- /**
+ /**
+ * Consensus CDS: http://identifiers.org/ccds/.
+ */
+ CCDS("Consensus CDS", //
+ "http://www.ncbi.nlm.nih.gov/CCDS/", //
+ new String[] { "urn:miriam:ccds" }, //
+ new Class<?>[] {}, "MIR:00000375"), //
+
+ /**
+ * Chebi database:
+ * <a href = "http://www.ebi.ac.uk/chebi/">http://www.ebi.ac.uk/chebi/</a>.
+ */
+ CHEBI("Chebi", //
+ "http://www.ebi.ac.uk/chebi/", //
+ new String[] { "urn:miriam:obo.chebi", "urn:miriam:chebi" }, //
+ new Class<?>[] { Chemical.class, Drug.class, }, "MIR:00000002", //
+ new Class<?>[] { Chemical.class }), //
+
+ /**
+ * ChemSpider database:
+ * <a href = "http://www.chemspider.com/">http://www.chemspider.com/</a>.
+ */
+ CHEMSPIDER("ChemSpider", //
+ "http://www.chemspider.com//", //
+ new String[] { "urn:miriam:chemspider" }, //
+ new Class<?>[] {}, "MIR:00000138"), //
+
+ /**
+ * Chembl database: https://www.ebi.ac.uk/chembldb/.
+ */
+ CHEMBL_COMPOUND("ChEMBL", //
+ "https://www.ebi.ac.uk/chembldb/", //
+ new String[] { "urn:miriam:chembl.compound" }, //
+ new Class<?>[] { Drug.class }, "MIR:00000084"), //
+
+ /**
+ * Target in chembl database: https://www.ebi.ac.uk/chembldb/.
+ */
+ CHEMBL_TARGET("ChEMBL target", //
+ "https://www.ebi.ac.uk/chembldb/", //
+ new String[] { "urn:miriam:chembl.target" }, //
+ new Class<?>[] { Protein.class, Complex.class }, "MIR:00000085"), //
+
+ /**
+ * Clusters of Orthologous Groups: https://www.ncbi.nlm.nih.gov/COG/.
+ */
+ COG("Clusters of Orthologous Groups", //
+ "https://www.ncbi.nlm.nih.gov/COG/", //
+ new String[] { "urn:miriam:cogs" }, //
+ new Class<?>[] { Reaction.class }, "MIR:00000296"), //
+
+ /**
+ * Drugbank database: http://www.drugbank.ca/.
+ */
+ DRUGBANK("DrugBank", //
+ "http://www.drugbank.ca/", //
+ new String[] { "urn:miriam:drugbank" }, //
+ new Class<?>[] { Drug.class }, "MIR:00000102"), //
+ /**
+ * Drugbank tagrets: 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"), //
+
+ /**
+ * Enzyme Nomenclature: http://www.enzyme-database.org/.
+ */
+ EC("Enzyme Nomenclature", //
+ "http://www.enzyme-database.org/", //
+ new String[] { "urn:miriam:ec-code" }, //
+ new Class<?>[] { Protein.class, Complex.class }, "MIR:00000004"), //
+
+ /**
+ * Ensembl: www.ensembl.org.
+ */
+ ENSEMBL("Ensembl", //
+ "www.ensembl.org", //
+ new String[] { "urn:miriam:ensembl" }, //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000003"), //
+
+ /**
+ * Ensembl Plants: http://plants.ensembl.org/.
+ */
+ ENSEMBL_PLANTS("Ensembl Plants", //
+ "http://plants.ensembl.org/", //
+ new String[] { "urn:miriam:ensembl.plant" }, //
+ new Class<?>[] {}, "MIR:00000205"), //
+
+ /**
+ * Entrez Gene: http://www.ncbi.nlm.nih.gov/gene.
+ */
+ 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"), //
+
+ /**
+ * Gene Ontology: http://amigo.geneontology.org/amigo.
+ */
+ GO("Gene Ontology", //
+ "http://amigo.geneontology.org/amigo", //
+ new String[] { "urn:miriam:obo.go", "urn:miriam:go" }, //
+ new Class<?>[] { Phenotype.class, Compartment.class, Complex.class }, "MIR:00000022"), //
+
+ /**
+ * HGNC: http://www.genenames.org.
+ */
+ HGNC("HGNC", //
+ "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 }), //
+
+ /**
+ * HGNC symbol: http://www.genenames.org.
+ */
+ HGNC_SYMBOL("HGNC Symbol", //
+ "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 }), //
+
+ /**
+ * HMDB: http://www.hmdb.ca/.
+ */
+ HMDB("HMDB", //
+ "http://www.hmdb.ca/", //
+ "urn:miriam:hmdb", //
+ new Class<?>[] { Chemical.class, Drug.class, }, "MIR:00000051"), //
+
+ /**
+ * InterPro: http://www.ebi.ac.uk/interpro/.
+ */
+ INTERPRO("InterPro", //
+ "http://www.ebi.ac.uk/interpro/", //
+ new String[] { "urn:miriam:interpro" }, //
+ new Class<?>[] { Protein.class, Complex.class }, "MIR:00000011"), //
+
+ /**
+ * KEGG Compound: http://www.genome.jp/kegg/ligand.html.
+ */
+ KEGG_COMPOUND("Kegg Compound", //
+ "http://www.genome.jp/kegg/ligand.html", //
+ "urn:miriam:kegg.compound", //
+ new Class<?>[] { Chemical.class }, "MIR:00000013"), //
+
+ /**
+ * 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", "urn:miriam:kegg.genes:hsa" }, //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000070"), //
+
+ /**
+ * KEGG Orthology: http://www.genome.jp/kegg/ko.html.
+ */
+ KEGG_ORTHOLOGY("KEGG Orthology", //
+ "http://www.genome.jp/kegg/ko.html", //
+ new String[] { "urn:miriam:kegg.orthology" }, //
+ new Class<?>[] {}, "MIR:00000116"), //
+
+ /**
+ * KEGG Pathway: http://www.genome.jp/kegg/pathway.html.
+ */
+ KEGG_PATHWAY("Kegg Pathway", //
+ "http://www.genome.jp/kegg/pathway.html", //
+ "urn:miriam:kegg.pathway", //
+ new Class<?>[] { Reaction.class }, "MIR:00000012"), //
+
+ /**
+ * KEGG Reaction: http://www.genome.jp/kegg/reaction/.
+ */
+ KEGG_REACTION("Kegg Reaction", //
+ "http://www.genome.jp/kegg/reaction/", //
+ "urn:miriam:kegg.reaction", //
+ new Class<?>[] { Reaction.class }, "MIR:00000014"), //
+
+ /**
+ * MeSH 2012: http://www.nlm.nih.gov/mesh/.
+ */
+ MESH_2012("MeSH 2012", //
+ "http://www.nlm.nih.gov/mesh/", //
+ new String[] { "urn:miriam:mesh.2012", "urn:miriam:mesh" }, //
+ new Class<?>[] { Phenotype.class, Compartment.class, Complex.class }, "MIR:00000270"), //
+
+ /**
+ * miRBase Sequence: http://www.mirbase.org/.
+ */
+ MI_R_BASE_SEQUENCE("miRBase Sequence Database", //
+ "http://www.mirbase.org/", //
+ new String[] { "urn:miriam:mirbase" }, //
+ new Class<?>[] {}, "MIR:00000078"), //
+
+ /**
+ * miRBase Mature Sequence: http://www.mirbase.org/.
+ */
+ MI_R_BASE_MATURE_SEQUENCE("miRBase Mature Sequence Database", //
+ "http://www.mirbase.org/", //
+ new String[] { "urn:miriam:mirbase.mature" }, //
+ new Class<?>[] {}, "MIR:00000235"), //
+
+ /**
+ * miRTaRBase Mature Sequence: http://mirtarbase.mbc.nctu.edu.tw/.
+ */
+ MIR_TAR_BASE_MATURE_SEQUENCE("miRTarBase Mature Sequence Database", //
+ "http://mirtarbase.mbc.nctu.edu.tw/", //
+ new String[] { "urn:miriam:mirtarbase" }, //
+ new Class<?>[] {}, "MIR:00100739"), //
+
+ /**
+ * Mouse Genome Database: http://www.informatics.jax.org/.
+ */
+ MGD("Mouse Genome Database", //
+ "http://www.informatics.jax.org/", //
+ new String[] { "urn:miriam:mgd" }, //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000037"), //
+
+ /**
+ * Online Mendelian Inheritance in Man: http://omim.org/.
+ */
+ OMIM("Online Mendelian Inheritance in Man", //
+ "http://omim.org/", //
+ new String[] { "urn:miriam:omim" }, //
+ new Class<?>[] { Phenotype.class }, "MIR:00000016"), //
+
+ /**
+ * PANTHER Family: http://www.pantherdb.org/.
+ */
+ 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"), //
+
+ /**
+ * PDB: http://www.pdbe.org/.
+ */
+ PDB("Protein Data Bank", //
+ "http://www.pdbe.org/", //
+ "urn:miriam:pdb", //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000020"),
+
+ /**
+ * Protein Family Database: http://pfam.xfam.org/.
+ */
+ PFAM("Protein Family Database", //
+ "http://pfam.xfam.org//", //
+ "urn:miriam:pfam", //
+ new Class<?>[] {}, "MIR:00000028"), //
+
+ /**
+ * PharmGKB Pathways: http://www.pharmgkb.org/.
+ */
+ PHARM("PharmGKB Pathways", //
+ "http://www.pharmgkb.org/", //
+ "urn:miriam:pharmgkb.pathways", //
+ new Class<?>[] {}, "MIR:00000089"), //
+
+ /**
+ * PubChem-compound: http://pubchem.ncbi.nlm.nih.gov/.
+ */
+ PUBCHEM("PubChem-compound", //
+ "http://pubchem.ncbi.nlm.nih.gov/", //
+ new String[] { "urn:miriam:pubchem.compound" }, //
+ new Class<?>[] { Chemical.class }, "MIR:00000034", //
+ new Class<?>[] { Chemical.class }), //
+
+ /**
+ * PubChem-substance: http://pubchem.ncbi.nlm.nih.gov/.
+ */
+ PUBCHEM_SUBSTANCE("PubChem-substance", //
+ "http://pubchem.ncbi.nlm.nih.gov/", //
+ new String[] { "urn:miriam:pubchem.substance" }, //
+ new Class<?>[] { Chemical.class }, "MIR:00000033", //
+ new Class<?>[] { Chemical.class }), //
+
+ /**
+ * PubMed: http://www.ncbi.nlm.nih.gov/PubMed/.
+ */
+ PUBMED("PubMed", //
+ "http://www.ncbi.nlm.nih.gov/PubMed/", //
+ new String[] { "urn:miriam:pubmed" }, //
+ new Class<?>[] { BioEntity.class }, "MIR:00000015", //
+ new Class<?>[] { Reaction.class }), //
+
+ /**
+ * Reactome: http://www.reactome.org/.
+ */
+ REACTOME("Reactome", //
+ "http://www.reactome.org/", //
+ "urn:miriam:reactome", //
+ new Class<?>[] { Reaction.class }, "MIR:00000018"), //
+
+ /**
+ * RefSeq: http://www.ncbi.nlm.nih.gov/projects/RefSeq/.
+ */
+ REFSEQ("RefSeq", //
+ "http://www.ncbi.nlm.nih.gov/projects/RefSeq/", //
+ "urn:miriam:refseq", //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000039"),
+
+ /**
+ * SGD: http://www.yeastgenome.org/.
+ */
+ SGD("Saccharomyces Genome Database", //
+ "http://www.yeastgenome.org/", //
+ "urn:miriam:sgd", //
+ new Class<?>[] {}, "MIR:00000023"),
+
+ /**
* STITCH: http://stitch.embl.de/.
*/
STITCH("STITCH", //
@@ -382,333 +373,332 @@ public enum MiriamType {
"urn:miriam:string", //
new Class<?>[] {}, "MIR:00000265"),
- /**
- * The Arabidopsis Information Resource (TAIR) maintains a database of genetic
- * and molecular biology data for the model higher plant Arabidopsis thaliana.
- * The name of a Locus is unique and used by TAIR, TIGR, and MIPS:
- * http://arabidopsis.org/index.jsp.
- */
- TAIR_LOCUS("TAIR Locus", //
- "http://arabidopsis.org/index.jsp", //
- "urn:miriam:tair.locus", //
- new Class<?>[] {}, "MIR:00000050"),
-
- /**
- * Taxonomy: http://www.ncbi.nlm.nih.gov/taxonomy/.
- */
- TAXONOMY("Taxonomy", //
- "http://www.ncbi.nlm.nih.gov/taxonomy/", //
- "urn:miriam:taxonomy", //
- new Class<?>[] {}, "MIR:00000006"),
- /**
- * Toxicogenomic: Chemical: http://ctdbase.org/detail.go.
- * http://ctdbase.org/detail.go
- */
- TOXICOGENOMIC_CHEMICAL("Toxicogenomic Chemical", //
- "http://ctdbase.org/", //
- "urn:miriam:ctd.chemical", //
- new Class<?>[] {}, "MIR:00000098"), //
-
- /**
- * UniGene: http://www.ncbi.nlm.nih.gov/unigene.
- */
- UNIGENE("UniGene", //
- "http://www.ncbi.nlm.nih.gov/unigene", //
- "urn:miriam:unigene", //
- new Class<?>[] {}, "MIR:00000346"),
-
- /**
- * Uniprot: http://www.uniprot.org/.
- */
- UNIPROT("Uniprot", //
- "http://www.uniprot.org/", //
- "urn:miriam:uniprot", //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000005"),
-
- /**
- * UniProt Isoform: http://www.uniprot.org/.
- */
- UNIPROT_ISOFORM("UniProt Isoform", //
- "http://www.uniprot.org/", //
- "urn:miriam:uniprot.isoform", //
- new Class<?>[] { Protein.class }, "MIR:00000388"),
-
- /**
- * Unknown reference type...
- */
- UNKNOWN("Unknown", //
- null, //
- new String[] {}, //
- new Class<?>[] {}, null),
-
- /**
- * Wikidata: https://www.wikidata.org/.
- */
- WIKIDATA("Wikidata", //
- "https://www.wikidata.org/", //
- new String[] { "urn:miriam:wikidata" }, //
- new Class<?>[] {}, "MIR:00000549"), //
-
- /**
- * WikiPathways: http://www.wikipathways.org/.
- */
- WIKIPATHWAYS("WikiPathways", //
- "http://www.wikipathways.org/", //
- new String[] { "urn:miriam:wikipathways" }, //
- new Class<?>[] {}, "MIR:00000076"), //
-
- /**
- * Wikipedia: http://en.wikipedia.org/wiki/Main_Page.
- */
- WIKIPEDIA("Wikipedia (English)", //
- "http://en.wikipedia.org/wiki/Main_Page", // /
- new String[] { "urn:miriam:wikipedia.en" }, //
- new Class<?>[] {}, "MIR:00000384"),
-
- /**
- * WormBase: http://wormbase.bio2rdf.org/fct.
- */
- WORM_BASE("WormBase", //
- "http://wormbase.bio2rdf.org/fct", // /
- new String[] { "urn:miriam:wormbase" }, //
- new Class<?>[] {}, "MIR:00000027");
-
- /**
- * User friendly name.
- */
- private String commonName;
-
- /**
- * url to homepage of given resource type.
- */
- private String dbHomepage;
-
- /**
- * Identifier of the database in miriam registry.
- */
- private String registryIdentifier;
-
- /**
- * Valid uris to this resource.
- */
- private List<String> uris = new ArrayList<String>();
-
- /**
- * Classes that can be annotated by this resource.
- */
- private List<Class<? extends BioEntity>> validClass = new ArrayList<>();
-
- /**
- * When class from this list is marked as "require at least one annotation" then
- * annotation of this type is valid.
- */
- private List<Class<? extends BioEntity>> requiredClass = new ArrayList<>();
-
- /**
- * Constructor that initialize enum object.
- *
- * @param dbHomePage
- * homepage 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<?>[] {});
- }
-
- /**
- * Constructor that initialize enum object.
- *
- * @param dbHomePage
- * homepage of the resource {@link #dbHomepage}
- * @param commonName
- * {@link #commonName}
- * @param uris
- * {@link #uris}
- * @param classes
- * {@link #validClass}
- * @param registryIdentifier
- * {@link #registryIdentifier}
- * @param requiredClasses
- * {@link #requiredClasses}
- */
- MiriamType(String commonName, String dbHomePage, String[] uris, Class<?>[] classes, String registryIdentifier,
- Class<?>[] requiredClasses) {
- this.commonName = commonName;
- this.dbHomepage = dbHomePage;
- for (String string : uris) {
- this.uris.add(string);
- }
- for (Class<?> clazz : classes) {
- this.validClass.add((Class<? extends BioEntity>) clazz);
- }
- for (Class<?> clazz : requiredClasses) {
- this.requiredClass.add((Class<? extends BioEntity>) clazz);
- }
- this.registryIdentifier = registryIdentifier;
- }
-
- /**
- * Constructor that initialize enum object.
- *
- * @param dbHomePage
- * homepage of the resource {@link #dbHomepage}
- * @param commonName
- * {@link #commonName}
- * @param uri
- * one of {@link #uris}
- * @param registryIdentifier
- * {@link #registryIdentifier}
- * @param classes
- * {@link #validClass}
- */
- MiriamType(String commonName, String dbHomePage, String uri, Class<?>[] classes, String registryIdentifier) {
- this(commonName, dbHomePage, new String[] { uri }, classes, registryIdentifier);
- }
-
- /**
- *
- * @return {@link #commonName}
- */
- public String getCommonName() {
- return commonName;
- }
-
- /**
- *
- * @return {@link #uris}
- */
- public List<String> getUris() {
- return uris;
- }
-
- /**
- *
- * @return {@link #validClass}
- */
- public List<Class<? extends BioEntity>> getValidClass() {
- return validClass;
- }
-
- /**
- * Returns {@link MiriamType} associated with parameter uri address.
- *
- * @param uri
- * uri to check
- * @return {@link MiriamType} for given uri
- */
- public static MiriamType getTypeByUri(String uri) {
- for (MiriamType mt : MiriamType.values()) {
- for (String string : mt.getUris()) {
- if (string.equalsIgnoreCase(uri)) {
- return mt;
- }
- }
- }
- return null;
- }
-
- /**
- * @return the dbHomepage
- * @see #dbHomepage
- */
- public String getDbHomepage() {
- return dbHomepage;
- }
-
- /**
- * @return the registryIdentifier
- * @see #registryIdentifier
- */
- public String getRegistryIdentifier() {
- return registryIdentifier;
- }
-
- /**
- * @return the requiredClass
- * @see #requiredClass
- */
- public List<Class<? extends BioEntity>> getRequiredClass() {
- return requiredClass;
- }
-
- /**
- * Returns {@link MiriamType} associated with {@link #commonName}.
- *
- * @param string
- * {@link #commonName}
- * @return {@link MiriamType} for given name
- */
- public static MiriamType getTypeByCommonName(String string) {
- for (MiriamType mt : MiriamType.values()) {
- if (string.equalsIgnoreCase(mt.getCommonName())) {
- return mt;
- }
- }
- return null;
- }
-
- /**
- * Transforms identifier into {@link MiriamData}.
- *
- * @param generalIdentifier
- * identifier in the format NAME:IDENTIFIER. Where NAME is the name
- * from {@link MiriamType#commonName} and IDENTIFIER is reasource
- * identifier.
- * @return {@link MiriamData} representing generalIdentifier, when identifier is
- * invalid InvalidArgumentException is thrown
- */
- public static MiriamData getMiriamDataFromIdentifier(String generalIdentifier) {
- int index = generalIdentifier.indexOf(":");
- if (index < 0) {
- throw new InvalidArgumentException("Identifier doesn't contain type");
- }
- String type = generalIdentifier.substring(0, index);
- String id = generalIdentifier.substring(index + 1);
- for (MiriamType mt : MiriamType.values()) {
- if (mt.getCommonName().equalsIgnoreCase(type)) {
- return new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, mt, id);
- }
- }
- throw new InvalidArgumentException("Unknown miriam type: " + type + " (id: " + id + ")");
- }
-
- /**
- * Creates {@link MiriamData} from miriam uri.
- *
- * @param miriamUri
- * miriam uri defining {@link MiriamData}
- * @return {@link MiriamData} from miriam uri
- */
- public static MiriamData getMiriamByUri(String miriamUri) {
- // this hack is due to CellDesigner issue (CellDesigner incorectly handle
- // with identifiers that have ":" inside resource ":" inside resource with
- // "%3A" and also the last ":"
- miriamUri = miriamUri.replace("%3A", ":");
-
- String foundUri = "";
- MiriamType foundType = null;
-
- for (MiriamType type : MiriamType.values()) {
- for (String uri : type.getUris()) {
- if (miriamUri.startsWith(uri + ":")) {
- if (uri.length() > foundUri.length()) {
- foundType = type;
- foundUri = uri;
- }
- }
- }
- }
- if (foundType != null) {
- return new MiriamData(foundType, miriamUri.substring(foundUri.length() + 1));
- }
- throw new InvalidArgumentException("Invalid miriam uri: " + miriamUri);
- }
+ /**
+ * The Arabidopsis Information Resource (TAIR) maintains a database of genetic
+ * and molecular biology data for the model higher plant Arabidopsis thaliana.
+ * The name of a Locus is unique and used by TAIR, TIGR, and MIPS:
+ * http://arabidopsis.org/index.jsp.
+ */
+ TAIR_LOCUS("TAIR Locus", //
+ "http://arabidopsis.org/index.jsp", //
+ "urn:miriam:tair.locus", //
+ new Class<?>[] {}, "MIR:00000050"),
+
+ /**
+ * Taxonomy: http://www.ncbi.nlm.nih.gov/taxonomy/.
+ */
+ TAXONOMY("Taxonomy", //
+ "http://www.ncbi.nlm.nih.gov/taxonomy/", //
+ "urn:miriam:taxonomy", //
+ new Class<?>[] {}, "MIR:00000006"),
+ /**
+ * Toxicogenomic: Chemical: http://ctdbase.org/detail.go.
+ * http://ctdbase.org/detail.go
+ */
+ TOXICOGENOMIC_CHEMICAL("Toxicogenomic Chemical", //
+ "http://ctdbase.org/", //
+ "urn:miriam:ctd.chemical", //
+ new Class<?>[] {}, "MIR:00000098"), //
+
+ /**
+ * UniGene: http://www.ncbi.nlm.nih.gov/unigene.
+ */
+ UNIGENE("UniGene", //
+ "http://www.ncbi.nlm.nih.gov/unigene", //
+ "urn:miriam:unigene", //
+ new Class<?>[] {}, "MIR:00000346"),
+
+ /**
+ * Uniprot: http://www.uniprot.org/.
+ */
+ UNIPROT("Uniprot", //
+ "http://www.uniprot.org/", //
+ "urn:miriam:uniprot", //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000005"),
+
+ /**
+ * UniProt Isoform: http://www.uniprot.org/.
+ */
+ UNIPROT_ISOFORM("UniProt Isoform", //
+ "http://www.uniprot.org/", //
+ "urn:miriam:uniprot.isoform", //
+ new Class<?>[] { Protein.class }, "MIR:00000388"),
+
+ /**
+ * Unknown reference type...
+ */
+ UNKNOWN("Unknown", //
+ null, //
+ new String[] {}, //
+ new Class<?>[] {}, null),
+
+ /**
+ * Wikidata: https://www.wikidata.org/.
+ */
+ WIKIDATA("Wikidata", //
+ "https://www.wikidata.org/", //
+ new String[] { "urn:miriam:wikidata" }, //
+ new Class<?>[] {}, "MIR:00000549"), //
+
+ /**
+ * WikiPathways: http://www.wikipathways.org/.
+ */
+ WIKIPATHWAYS("WikiPathways", //
+ "http://www.wikipathways.org/", //
+ new String[] { "urn:miriam:wikipathways" }, //
+ new Class<?>[] {}, "MIR:00000076"), //
+
+ /**
+ * Wikipedia: http://en.wikipedia.org/wiki/Main_Page.
+ */
+ WIKIPEDIA("Wikipedia (English)", //
+ "http://en.wikipedia.org/wiki/Main_Page", // /
+ new String[] { "urn:miriam:wikipedia.en" }, //
+ new Class<?>[] {}, "MIR:00000384"),
+
+ /**
+ * WormBase: http://wormbase.bio2rdf.org/fct.
+ */
+ WORM_BASE("WormBase", //
+ "http://wormbase.bio2rdf.org/fct", // /
+ new String[] { "urn:miriam:wormbase" }, //
+ new Class<?>[] {}, "MIR:00000027");
+
+ /**
+ * User friendly name.
+ */
+ private String commonName;
+
+ /**
+ * url to homepage of given resource type.
+ */
+ private String dbHomepage;
+ /**
+ * Identifier of the database in miriam registry.
+ */
+ private String registryIdentifier;
+
+ /**
+ * Valid uris to this resource.
+ */
+ private List<String> uris = new ArrayList<String>();
+
+ /**
+ * Classes that can be annotated by this resource.
+ */
+ private List<Class<? extends BioEntity>> validClass = new ArrayList<>();
+
+ /**
+ * When class from this list is marked as "require at least one annotation"
+ * then annotation of this type is valid.
+ */
+ private List<Class<? extends BioEntity>> requiredClass = new ArrayList<>();
+
+
+ /**
+ * Constructor that initialize enum object.
+ *
+ * @param dbHomePage
+ * homepage 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<?>[] {});
+ }
+
+ /**
+ * Constructor that initialize enum object.
+ *
+ * @param dbHomePage
+ * homepage of the resource {@link #dbHomepage}
+ * @param commonName
+ * {@link #commonName}
+ * @param uris
+ * {@link #uris}
+ * @param classes
+ * {@link #validClass}
+ * @param registryIdentifier
+ * {@link #registryIdentifier}
+ * @param requiredClasses
+ * {@link #requiredClasses}
+ */
+ MiriamType(String commonName, String dbHomePage, String[] uris, Class<?>[] classes, String registryIdentifier, Class<?>[] requiredClasses) {
+ this.commonName = commonName;
+ this.dbHomepage = dbHomePage;
+ for (String string : uris) {
+ this.uris.add(string);
+ }
+ for (Class<?> clazz : classes) {
+ this.validClass.add((Class<? extends BioEntity>) clazz);
+ }
+ for (Class<?> clazz : requiredClasses) {
+ this.requiredClass.add((Class<? extends BioEntity>) clazz);
+ }
+ this.registryIdentifier = registryIdentifier;
+ }
+
+ /**
+ * Constructor that initialize enum object.
+ *
+ * @param dbHomePage
+ * homepage of the resource {@link #dbHomepage}
+ * @param commonName
+ * {@link #commonName}
+ * @param uri
+ * one of {@link #uris}
+ * @param registryIdentifier
+ * {@link #registryIdentifier}
+ * @param classes
+ * {@link #validClass}
+ */
+ MiriamType(String commonName, String dbHomePage, String uri, Class<?>[] classes, String registryIdentifier) {
+ this(commonName, dbHomePage, new String[] { uri }, classes, registryIdentifier);
+ }
+
+ /**
+ *
+ * @return {@link #commonName}
+ */
+ public String getCommonName() {
+ return commonName;
+ }
+
+ /**
+ *
+ * @return {@link #uris}
+ */
+ public List<String> getUris() {
+ return uris;
+ }
+
+ /**
+ *
+ * @return {@link #validClass}
+ */
+ public List<Class<? extends BioEntity>> getValidClass() {
+ return validClass;
+ }
+
+ /**
+ * Returns {@link MiriamType} associated with parameter uri address.
+ *
+ * @param uri
+ * uri to check
+ * @return {@link MiriamType} for given uri
+ */
+ public static MiriamType getTypeByUri(String uri) {
+ for (MiriamType mt : MiriamType.values()) {
+ for (String string : mt.getUris()) {
+ if (string.equalsIgnoreCase(uri)) {
+ return mt;
+ }
+ }
+ }
+ return null;
+ }
+
+ /**
+ * @return the dbHomepage
+ * @see #dbHomepage
+ */
+ public String getDbHomepage() {
+ return dbHomepage;
+ }
+
+ /**
+ * @return the registryIdentifier
+ * @see #registryIdentifier
+ */
+ public String getRegistryIdentifier() {
+ return registryIdentifier;
+ }
+
+ /**
+ * @return the requiredClass
+ * @see #requiredClass
+ */
+ public List<Class<? extends BioEntity>> getRequiredClass() {
+ return requiredClass;
+ }
+
+ /**
+ * Returns {@link MiriamType} associated with {@link #commonName}.
+ *
+ * @param string
+ * {@link #commonName}
+ * @return {@link MiriamType} for given name
+ */
+ public static MiriamType getTypeByCommonName(String string) {
+ for (MiriamType mt : MiriamType.values()) {
+ if (string.equalsIgnoreCase(mt.getCommonName())) {
+ return mt;
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Transforms identifier into {@link MiriamData}.
+ *
+ * @param generalIdentifier
+ * identifier in the format NAME:IDENTIFIER. Where NAME is the name
+ * from {@link MiriamType#commonName} and IDENTIFIER is reasource
+ * identifier.
+ * @return {@link MiriamData} representing generalIdentifier, when identifier
+ * is invalid InvalidArgumentException is thrown
+ */
+ public static MiriamData getMiriamDataFromIdentifier(String generalIdentifier) {
+ int index = generalIdentifier.indexOf(":");
+ if (index < 0) {
+ throw new InvalidArgumentException("Identifier doesn't contain type");
+ }
+ String type = generalIdentifier.substring(0, index);
+ String id = generalIdentifier.substring(index + 1);
+ for (MiriamType mt : MiriamType.values()) {
+ if (mt.getCommonName().equalsIgnoreCase(type)) {
+ return new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, mt, id);
+ }
+ }
+ throw new InvalidArgumentException("Unknown miriam type: " + type + " (id: " + id + ")");
+ }
+
+ /**
+ * Creates {@link MiriamData} from miriam uri.
+ *
+ * @param miriamUri
+ * miriam uri defining {@link MiriamData}
+ * @return {@link MiriamData} from miriam uri
+ */
+ public static MiriamData getMiriamByUri(String miriamUri) {
+ // this hack is due to CellDesigner issue (CellDesigner incorectly handle
+ // with identifiers that have ":" inside resource ":" inside resource with
+ // "%3A" and also the last ":"
+ miriamUri = miriamUri.replace("%3A", ":");
+
+ String foundUri = "";
+ MiriamType foundType = null;
+
+ for (MiriamType type : MiriamType.values()) {
+ for (String uri : type.getUris()) {
+ if (miriamUri.startsWith(uri + ":")) {
+ if (uri.length() > foundUri.length()) {
+ foundType = type;
+ foundUri = uri;
+ }
+ }
+ }
+ }
+ if (foundType != null) {
+ return new MiriamData(foundType, miriamUri.substring(foundUri.length() + 1));
+ }
+ throw new InvalidArgumentException("Invalid miriam uri: " + miriamUri);
+ }
}
diff --git a/persist/src/db/12.0.0/fix_db_20180117.sql b/persist/src/db/12.0.0/fix_db_20180117.sql
new file mode 100644
index 0000000000..af37bf7888
--- /dev/null
+++ b/persist/src/db/12.0.0/fix_db_20180117.sql
@@ -0,0 +1,2 @@
+-- column to store which annotator is responsible for given miriam data
+alter table miriam_data_table add column annotator varchar(256) default null;
--
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