Skip to content
Snippets Groups Projects
Commit 6595bf07 authored by Piotr Gawron's avatar Piotr Gawron
Browse files

doi miriam type introduced

parent 9b2f3fd2
No related branches found
No related tags found
1 merge request!165Resolve "add doi in miriam types"
Hide whitespace changes
Inline Side-by-side
annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java
+ 15
− 0
View file @ 6595bf07
......@@ -208,6 +208,21 @@ public class MiriamConnectorTest extends AnnotationTestFunctions {
}
}
@Test
public void testGetUrlForDoi() throws Exception {
try {
// exclude first cached value
MiriamData md = new MiriamData(MiriamType.DOI, "10.1038/npjsba.2016.20");
String url = miriamConnector.getUrlString(md);
assertNotNull(url);
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testMiriamDataToUri() throws Exception {
try {
......
model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
+ 655
− 646
View file @ 6595bf07
......@@ -22,651 +22,660 @@ import lcsb.mapviewer.model.map.species.Rna;
*/
@SuppressWarnings("unchecked")
public enum MiriamType {
/**
* Chemical Abstracts Service database: http://commonchemistry.org.
*/
CAS("Chemical Abstracts Service", //
"http://commonchemistry.org", //
new String[] { "urn:miriam:cas" }, //
new Class<?>[] {}, "MIR:00000237"), //
/**
* 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"),
/**
* 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);
}
/**
* Chemical Abstracts Service database: http://commonchemistry.org.
*/
CAS("Chemical Abstracts Service", //
"http://commonchemistry.org", //
new String[] { "urn:miriam:cas" }, //
new Class<?>[] {}, "MIR:00000237"), //
/**
* 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"),
/**
* 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);
}
}
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment