Commit fff5c5ab authored by Piotr Gawron's avatar Piotr Gawron
Browse files

Merge branch '1359-identifiers-org-url-not-processed' into 'master'

Resolve "identifiers.org url not processed"

Closes #1359

See merge request !1239
parents b1473e5f c9e19853
Pipeline #31328 passed with stage
in 21 minutes and 3 seconds
minerva (15.1.0~beta.1) unstable; urgency=medium
* Small improvement: "Human Disease Ontology", "IUPHAR ligand" and "Protein
Modification Ontology" annotation types are handled (#1359)
* Bug fix: SBML import - label aligned to top of species was inproperly drawn
(#1354)
* Bug fix: SBML text labels that were referencing layout aliases using
layout:graphicalObject attribute were not handled properly (#1356)
* Bug fix: miriam urls in new format
(like: https://identifiers.org/kegg.compound:197020) are parsed properly for
all know identifier types (#1359)
-- Piotr Gawron <piotr.gawron@uni.lu> Mon, 17 Aug 2020 16:00:00 +0200
......
......@@ -26,7 +26,9 @@ public enum MiriamType {
"http://www.3dmet.dna.affrc.go.jp/",
new String[] { "urn:miriam:3dmet",
"http://identifiers.org/3dmet/",
"https://identifiers.org/3dmet/"
"http://identifiers.org/3dmet",
"https://identifiers.org/3dmet/",
"https://identifiers.org/3dmet",
},
new Class<?>[] {},
" MIR:00000066",
......@@ -38,7 +40,9 @@ public enum MiriamType {
"http://bigg.ucsd.edu/compartments/",
new String[] { "urn:miriam:bigg.compartment",
"http://identifiers.org/bigg.compartment/",
"https://identifiers.org/bigg.compartment/"
"http://identifiers.org/bigg.compartment",
"https://identifiers.org/bigg.compartment/",
"https://identifiers.org/bigg.compartment",
},
new Class<?>[] {},
"MIR:00000555",
......@@ -50,7 +54,9 @@ public enum MiriamType {
"http://bigg.ucsd.edu/universal/metabolites",
new String[] { "urn:miriam:bigg.metabolite",
"http://identifiers.org/bigg.metabolite/",
"https://identifiers.org/bigg.metabolite/"
"http://identifiers.org/bigg.metabolite",
"https://identifiers.org/bigg.metabolite/",
"https://identifiers.org/bigg.metabolite",
},
new Class<?>[] {}, "MIR:00000556",
new Class<?>[] {},
......@@ -61,7 +67,9 @@ public enum MiriamType {
"http://bigg.ucsd.edu/universal/reactions",
new String[] { "urn:miriam:bigg.reaction",
"http://identifiers.org/bigg.reaction/",
"https://identifiers.org/bigg.reaction/"
"http://identifiers.org/bigg.reaction",
"https://identifiers.org/bigg.reaction/",
"https://identifiers.org/bigg.reaction",
},
new Class<?>[] {}, "MIR:00000557",
new Class<?>[] {},
......@@ -72,7 +80,9 @@ public enum MiriamType {
"https://www.ebi.ac.uk/biomodels/",
new String[] { "urn:miriam:biomodels.db",
"http://identifiers.org/biomodels.db/",
"https://identifiers.org/biomodels.db/"
"http://identifiers.org/biomodels.db",
"https://identifiers.org/biomodels.db/",
"https://identifiers.org/biomodels.db",
},
new Class<?>[] {}, "MIR:00000007",
new Class<?>[] {},
......@@ -86,7 +96,9 @@ public enum MiriamType {
"http://www.brenda-enzymes.org",
new String[] { "urn:miriam:brenda",
"http://identifiers.org/brenda/",
"https://identifiers.org/brenda/"
"http://identifiers.org/brenda",
"https://identifiers.org/brenda/",
"https://identifiers.org/brenda",
},
new Class<?>[] {}, "MIR:00000071",
new Class<?>[] {},
......@@ -100,7 +112,9 @@ public enum MiriamType {
"http://commonchemistry.org",
new String[] { "urn:miriam:cas",
"http://identifiers.org/cas/",
"https://identifiers.org/cas/"
"http://identifiers.org/cas",
"https://identifiers.org/cas/",
"https://identifiers.org/cas",
},
new Class<?>[] {}, "MIR:00000237",
new Class<?>[] {},
......@@ -114,7 +128,9 @@ public enum MiriamType {
"http://commonchemistry.org",
new String[] { "urn:miriam:cazy",
"http://identifiers.org/cazy/",
"https://identifiers.org/cazy/"
"http://identifiers.org/cazy",
"https://identifiers.org/cazy/",
"https://identifiers.org/cazy",
},
new Class<?>[] {}, "MIR:00000195",
new Class<?>[] {},
......@@ -128,7 +144,9 @@ public enum MiriamType {
"http://www.ncbi.nlm.nih.gov/CCDS/",
new String[] { "urn:miriam:ccds",
"http://identifiers.org/ccds/",
"https://identifiers.org/ccds/"
"http://identifiers.org/ccds",
"https://identifiers.org/ccds/",
"https://identifiers.org/ccds",
},
new Class<?>[] {}, "MIR:00000375",
new Class<?>[] {},
......@@ -158,7 +176,9 @@ public enum MiriamType {
"https://chem.nlm.nih.gov/chemidplus/",
new String[] { "urn:miriam:chemidplus",
"http://identifiers.org/chemidplus/",
"https://identifiers.org/chemidplus/"
"http://identifiers.org/chemidplus",
"https://identifiers.org/chemidplus/",
"https://identifiers.org/chemidplus",
},
new Class<?>[] { Chemical.class, Drug.class, }, "MIR:00000096",
new Class<?>[] { Chemical.class },
......@@ -173,7 +193,9 @@ public enum MiriamType {
"http://www.chemspider.com//",
new String[] { "urn:miriam:chemspider",
"http://identifiers.org/chemspider/",
"https://identifiers.org/chemspider/"
"http://identifiers.org/chemspider",
"https://identifiers.org/chemspider/",
"https://identifiers.org/chemspider",
},
new Class<?>[] {}, "MIR:00000138",
new Class<?>[] {},
......@@ -187,7 +209,9 @@ public enum MiriamType {
"https://www.ebi.ac.uk/chembldb/",
new String[] { "urn:miriam:chembl.compound",
"http://identifiers.org/chembl.compound/",
"http://identifiers.org/chembl.compound",
"https://identifiers.org/chembl.compound/",
"https://identifiers.org/chembl.compound",
},
new Class<?>[] { Drug.class }, "MIR:00000084",
new Class<?>[] {},
......@@ -201,7 +225,9 @@ public enum MiriamType {
"https://www.ebi.ac.uk/chembldb/",
new String[] { "urn:miriam:chembl.target",
"http://identifiers.org/chembl.target/",
"https://identifiers.org/chembl.target/"
"http://identifiers.org/chembl.target",
"https://identifiers.org/chembl.target/",
"https://identifiers.org/chembl.target",
},
new Class<?>[] { Protein.class, Complex.class }, "MIR:00000085",
new Class<?>[] {},
......@@ -212,7 +238,9 @@ public enum MiriamType {
"https://clinicaltrials.gov/",
new String[] { "urn:miriam:clinicaltrials",
"http://identifiers.org/clinicaltrials/",
"https://identifiers.org/clinicaltrials/"
"http://identifiers.org/clinicaltrials",
"https://identifiers.org/clinicaltrials/",
"https://identifiers.org/clinicaltrials",
},
new Class<?>[] {}, "MIR:00000137",
new Class<?>[] {},
......@@ -238,7 +266,9 @@ public enum MiriamType {
"http://www.doi.org/",
new String[] { "urn:miriam:doi",
"http://identifiers.org/doi/",
"https://identifiers.org/doi/"
"http://identifiers.org/doi",
"https://identifiers.org/doi/",
"https://identifiers.org/doi",
},
new Class<?>[] { Reaction.class }, "MIR:00000019",
new Class<?>[] {},
......@@ -252,7 +282,9 @@ public enum MiriamType {
"http://www.drugbank.ca/",
new String[] { "urn:miriam:drugbank",
"http://identifiers.org/drugbank/",
"https://identifiers.org/drugbank/"
"http://identifiers.org/drugbank",
"https://identifiers.org/drugbank/",
"https://identifiers.org/drugbank",
},
new Class<?>[] { Drug.class }, "MIR:00000102",
new Class<?>[] {},
......@@ -266,7 +298,9 @@ public enum MiriamType {
"http://www.drugbank.ca/targets",
new String[] { "urn:miriam:drugbankv4.target",
"http://identifiers.org/drugbankv4.target/",
"https://identifiers.org/drugbankv4.target/"
"http://identifiers.org/drugbankv4.target",
"https://identifiers.org/drugbankv4.target/",
"https://identifiers.org/drugbankv4.target",
},
new Class<?>[] {}, "MIR:00000528",
new Class<?>[] {},
......@@ -280,7 +314,9 @@ public enum MiriamType {
"http://www.enzyme-database.org/",
new String[] { "urn:miriam:ec-code",
"http://identifiers.org/ec-code/",
"https://identifiers.org/ec-code/"
"http://identifiers.org/ec-code",
"https://identifiers.org/ec-code/",
"https://identifiers.org/ec-code",
},
new Class<?>[] { Protein.class, Complex.class }, "MIR:00000004",
new Class<?>[] {},
......@@ -291,9 +327,9 @@ public enum MiriamType {
"https://www.ebi.ac.uk/ols/ontologies/eco",
new String[] { "urn:miriam:obo.eco",
"http://identifiers.org/obo.eco/",
"http://identifiers.org/ec-code",
"http://identifiers.org/ECO",
"https://identifiers.org/obo.eco/",
"https://identifiers.org/ec-code",
"https://identifiers.org/ECO",
},
new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000055",
new Class<?>[] {},
......@@ -304,7 +340,9 @@ public enum MiriamType {
"http://ecogene.org/",
new String[] { "urn:miriam:ecogene",
"http://identifiers.org/ecogene/",
"https://identifiers.org/ecogene/"
"http://identifiers.org/ecogene",
"https://identifiers.org/ecogene/",
"https://identifiers.org/ecogene",
},
new Class<?>[] {}, "MIR:00000163",
new Class<?>[] {},
......@@ -318,7 +356,9 @@ public enum MiriamType {
"www.ensembl.org",
new String[] { "urn:miriam:ensembl",
"http://identifiers.org/ensembl/",
"https://identifiers.org/ensembl/"
"http://identifiers.org/ensembl",
"https://identifiers.org/ensembl/",
"https://identifiers.org/ensembl",
},
new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000003",
new Class<?>[] {},
......@@ -332,7 +372,9 @@ public enum MiriamType {
"http://plants.ensembl.org/",
new String[] { "urn:miriam:ensembl.plant",
"http://identifiers.org/ensembl.plant/",
"https://identifiers.org/ensembl.plant/"
"http://identifiers.org/ensembl.plant",
"https://identifiers.org/ensembl.plant/",
"https://identifiers.org/ensembl.plant",
},
new Class<?>[] {}, "MIR:00000205",
new Class<?>[] {},
......@@ -360,7 +402,9 @@ public enum MiriamType {
"https://www.alliancegenome.org",
new String[] { "urn:miriam:fb", "urn:miriam:flybase",
"http://identifiers.org/fb/",
"https://identifiers.org/fb/"
"http://identifiers.org/fb",
"https://identifiers.org/fb/",
"https://identifiers.org/fb",
},
new Class<?>[] {}, "MIR:00000030",
new Class<?>[] {},
......@@ -371,7 +415,9 @@ public enum MiriamType {
"https://www.genedb.org/",
new String[] { "urn:miriam:genedb",
"http://identifiers.org/genedb/",
"https://identifiers.org/genedb/"
"http://identifiers.org/genedb",
"https://identifiers.org/genedb/",
"https://identifiers.org/genedb",
},
new Class<?>[] {}, "MIR:00000106",
new Class<?>[] {},
......@@ -419,7 +465,9 @@ public enum MiriamType {
"http://www.genenames.org",
new String[] { "urn:miriam:hgnc.symbol",
"http://identifiers.org/hgnc.symbol/",
"https://identifiers.org/hgnc.symbol/"
"http://identifiers.org/hgnc.symbol",
"https://identifiers.org/hgnc.symbol/",
"https://identifiers.org/hgnc.symbol",
},
new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000362",
new Class<?>[] { Protein.class, Gene.class, Rna.class },
......@@ -433,18 +481,35 @@ public enum MiriamType {
"http://www.hmdb.ca/",
new String[] { "urn:miriam:hmdb",
"http://identifiers.org/hmdb/",
"https://identifiers.org/hmdb/"
"http://identifiers.org/hmdb",
"https://identifiers.org/hmdb/",
"https://identifiers.org/hmdb",
},
new Class<?>[] { Chemical.class, Drug.class, }, "MIR:00000051",
new Class<?>[] {},
"hmdb",
"HMDB00001"),
HUMAN_DISEASE_ONTOLOGY("Human Disease Ontology",
" https://www.ebi.ac.uk/ols/ontologies/doid",
new String[] { "urn:miriam:obo.do",
"http://identifiers.org/doid/",
"http://identifiers.org/DOID",
"https://identifiers.org/doid/",
"https://identifiers.org/DOID",
},
new Class<?>[] { }, "MIR:00000233",
new Class<?>[] {},
"",
"DOID:11337"),
INTACT("IntAct",
"https://www.ebi.ac.uk/intact/",
new String[] { "urn:miriam:intact",
"http://identifiers.org/intact/",
"https://identifiers.org/intact/"
"http://identifiers.org/intact",
"https://identifiers.org/intact/",
"https://identifiers.org/intact",
},
new Class<?>[] {}, "MIR:00000010",
new Class<?>[] {},
......@@ -467,6 +532,19 @@ public enum MiriamType {
"interpro",
"IPR000100"),
IUPHAR_LIGAND("IUPHAR ligand",
"https://www.guidetopharmacology.org/GRAC/LigandListForward?database=all",
new String[] { "urn:miriam:iuphar.ligand",
"http://identifiers.org/iuphar.ligand/",
"http://identifiers.org/iuphar.ligand",
"https://identifiers.org/iuphar.ligand/",
"https://identifiers.org/iuphar.ligand",
},
new Class<?>[] { }, "MIR:00000457",
new Class<?>[] {},
"iuphar.ligand",
"1755"),
/**
* KEGG Compound: http://www.genome.jp/kegg/ligand.html.
*/
......@@ -474,7 +552,9 @@ public enum MiriamType {
"http://www.genome.jp/kegg/ligand.html",
new String[] { "urn:miriam:kegg.compound",
"http://identifiers.org/kegg.compound/",
"https://identifiers.org/kegg.compound/"
"http://identifiers.org/kegg.compound",
"https://identifiers.org/kegg.compound/",
"https://identifiers.org/kegg.compound",
},
new Class<?>[] { Chemical.class }, "MIR:00000013",
new Class<?>[] {},
......@@ -485,7 +565,9 @@ public enum MiriamType {
"https://www.genome.jp/kegg/drug/",
new String[] { "urn:miriam:kegg.drug",
"http://identifiers.org/kegg.drug/",
"https://identifiers.org/kegg.drug/"
"http://identifiers.org/kegg.drug",
"https://identifiers.org/kegg.drug/",
"https://identifiers.org/kegg.drug",
},
new Class<?>[] {}, "MIR:00000025",
new Class<?>[] {},
......@@ -499,7 +581,9 @@ public enum MiriamType {
"http://www.genome.jp/kegg/genes.html",
new String[] { "urn:miriam:kegg.genes",
"http://identifiers.org/kegg.genes/",
"https://identifiers.org/kegg.genes/"
"http://identifiers.org/kegg.genes",
"https://identifiers.org/kegg.genes/",
"https://identifiers.org/kegg.genes",
},
new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000070",
new Class<?>[] {},
......@@ -510,7 +594,9 @@ public enum MiriamType {
"https://www.genome.jp/kegg/glycan/",
new String[] { "urn:miriam:kegg.glycan",
"http://identifiers.org/kegg.glycan/",
"https://identifiers.org/kegg.glycan/"
"http://identifiers.org/kegg.glycan",
"https://identifiers.org/kegg.glycan/",
"https://identifiers.org/kegg.glycan",
},
new Class<?>[] {}, "MIR:00000026",
new Class<?>[] {},
......@@ -524,7 +610,9 @@ public enum MiriamType {
"http://www.genome.jp/kegg/ko.html",
new String[] { "urn:miriam:kegg.orthology",
"http://identifiers.org/kegg.orthology/",
"https://identifiers.org/kegg.orthology/"
"http://identifiers.org/kegg.orthology",
"https://identifiers.org/kegg.orthology/",
"https://identifiers.org/kegg.orthology",
},
new Class<?>[] {}, "MIR:00000116",
new Class<?>[] {},
......@@ -538,7 +626,9 @@ public enum MiriamType {
"http://www.genome.jp/kegg/pathway.html",
new String[] { "urn:miriam:kegg.pathway",
"http://identifiers.org/kegg.pathway/",
"https://identifiers.org/kegg.pathway/"
"http://identifiers.org/kegg.pathway",
"https://identifiers.org/kegg.pathway/",
"https://identifiers.org/kegg.pathway",
},
new Class<?>[] { Reaction.class }, "MIR:00000012",
new Class<?>[] {},
......@@ -552,7 +642,9 @@ public enum MiriamType {
"http://www.genome.jp/kegg/reaction/",
new String[] { "urn:miriam:kegg.reaction",
"http://identifiers.org/kegg.reaction/",
"https://identifiers.org/kegg.reaction/"
"http://identifiers.org/kegg.reaction",
"https://identifiers.org/kegg.reaction/",
"https://identifiers.org/kegg.reaction",
},
new Class<?>[] { Reaction.class }, "MIR:00000014",
new Class<?>[] {},
......@@ -563,7 +655,9 @@ public enum MiriamType {
"http://kanaya.aist-nara.ac.jp/KNApSAcK/",
new String[] { "urn:miriam:knapsack",
"http://identifiers.org/knapsack/",
"https://identifiers.org/knapsack/"
"http://identifiers.org/knapsack",
"https://identifiers.org/knapsack/",
"https://identifiers.org/knapsack",
},
new Class<?>[] {}, "MIR:00000271",
new Class<?>[] {},
......@@ -574,7 +668,9 @@ public enum MiriamType {
"http://lipidbank.jp/index.html",
new String[] { "urn:miriam:lipidbank",
"http://identifiers.org/lipidbank/",
"https://identifiers.org/lipidbank/"
"http://identifiers.org/lipidbank",
"https://identifiers.org/lipidbank/",
"https://identifiers.org/lipidbank",
},
new Class<?>[] {}, "MIR:00000115",
new Class<?>[] {},
......@@ -585,7 +681,9 @@ public enum MiriamType {
"http://www.lipidmaps.org",
new String[] { "urn:miriam:lipidmaps",
"http://identifiers.org/lipidmaps/",
"https://identifiers.org/lipidmaps/"
"http://identifiers.org/lipidmaps",
"https://identifiers.org/lipidmaps/",
"https://identifiers.org/lipidmaps",
},
new Class<?>[] {}, "MIR:00000052",
new Class<?>[] {},
......@@ -616,7 +714,9 @@ public enum MiriamType {
"http://www.mirbase.org/",
new String[] { "urn:miriam:mirbase",
"http://identifiers.org/mirbase/",
"https://identifiers.org/mirbase/"
"http://identifiers.org/mirbase",
"https://identifiers.org/mirbase/",
"https://identifiers.org/mirbase",
},
new Class<?>[] {}, "MIR:00000078",
new Class<?>[] {},
......@@ -630,7 +730,9 @@ public enum MiriamType {
"http://www.mirbase.org/",
new String[] { "urn:miriam:mirbase.mature",
"http://identifiers.org/mirbase.mature/",
"https://identifiers.org/mirbase.mature/"
"http://identifiers.org/mirbase.mature",
"https://identifiers.org/mirbase.mature/",
"https://identifiers.org/mirbase.mature",
},
new Class<?>[] {}, "MIR:00000235",
new Class<?>[] {},
......@@ -644,7 +746,9 @@ public enum MiriamType {
"http://mirtarbase.mbc.nctu.edu.tw/",
new String[] { "urn:miriam:mirtarbase",
"http://identifiers.org/mirtarbase/",
"https://identifiers.org/mirtarbase/"
"http://identifiers.org/mirtarbase",
"https://identifiers.org/mirtarbase/",
"https://identifiers.org/mirtarbase",
},
new Class<?>[] {}, "MIR:00000562",
new Class<?>[] {},
......@@ -658,18 +762,35 @@ public enum MiriamType {
"http://www.informatics.jax.org/",
new String[] { "urn:miriam:mgd",
"http://identifiers.org/mgi/",
"https://identifiers.org/mgi/"
"http://identifiers.org/MGI",
"https://identifiers.org/mgi/",
"https://identifiers.org/MGI",
},
new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000037",
new Class<?>[] {},
"",
"MGI:2442292"),
MOD("Protein Modification Ontology",
"https://bioportal.bioontology.org/ontologies/PSIMOD",
new String[] { "urn:miriam:obo.psi-mod",
"http://identifiers.org/mod/",
"http://identifiers.org/MOD",
"https://identifiers.org/mod/",
"https://identifiers.org/MOD",
},
new Class<?>[] { }, "MIR:00000056",
new Class<?>[] {},
"",
"MOD:00001"),
NCBI_PROTEIN("NCBI Protein",
"https://www.ncbi.nlm.nih.gov/protein",
new String[] { "urn:miriam:ncbiprotein",
"http://identifiers.org/ncbiprotein/",
"https://identifiers.org/ncbiprotein/"
"http://identifiers.org/ncbiprotein",
"https://identifiers.org/ncbiprotein/",
"https://identifiers.org/ncbiprotein",
},
new Class<?>[] {}, "MIR:00000344",
new Class<?>[] {},
......@@ -680,7 +801,9 @@ public enum MiriamType {
"https://www.ebi.ac.uk/ols/ontologies/obi/",
new String[] { "urn:miriam:obi",
"http://identifiers.org/obi/",
"https://identifiers.org/obi/"
"http://identifiers.org/obi",
"https://identifiers.org/obi/",
"https://identifiers.org/obi",
},
new Class<?>[] {}, "MIR:00000127",
new Class<?>[] {},
......@@ -694,7 +817,9 @@ public enum MiriamType {
"http://omim.org/",
new String[] { "urn:miriam:omim",
"http://identifiers.org/mim/",
"https://identifiers.org/mim/"
"http://identifiers.org/mim",
"https://identifiers.org/mim/",
"https://identifiers.org/mim",
},
new Class<?>[] { Phenotype.class }, "MIR:00000016",
new Class<?>[] {},
......@@ -709,7 +834,9 @@ public enum MiriamType {
new String[] { "urn:miriam:panther.family",
"urn:miriam:panther",
"http://identifiers.org/panther.family/",
"https://identifiers.org/panther.family/"
"http://identifiers.org/panther.family",
"https://identifiers.org/panther.family/",
"https://identifiers.org/panther.family",
},
new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000060",
new Class<?>[] {},
......@@ -721,7 +848,9 @@ public enum MiriamType {
new String[] { "urn:miriam:pato",
"urn:miriam:obo.pato",
"http://identifiers.org/pato/",
"https://identifiers.org/pato/"
"http://identifiers.org/PATO",
"https://identifiers.org/pato/",
"https://identifiers.org/PATO",
},
new Class<?>[] {}, "MIR:00000112",
new Class<?>[] {},
......@@ -735,7 +864,9 @@ public enum MiriamType {
"http://www.pdbe.org/",
new String[] { "urn:miriam:pdb",
"http://identifiers.org/pdb/",
"https://identifiers.org/pdb/"
"http://identifiers.org/pdb",
"https://identifiers.org/pdb/",
"https://identifiers.org/pdb",
},
new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000020",
new Class<?>[] {},
......@@ -746,7 +877,9 @@ public enum MiriamType {
"https://www.ebi.ac.uk/pdbe-srv/pdbechem/",
new String[] { "urn:miriam:pdb-ccd",
"http://identifiers.org/pdb-ccd/",
"https://identifiers.org/pdb-ccd/"
"http://identifiers.org/pdb-ccd",
"https://identifiers.org/pdb-ccd/",
"https://identifiers.org/pdb-ccd",
},
new Class<?>[] {}, "MIR:00000113",
new Class<?>[] {},
......@@ -760,7 +893,9 @@ public enum MiriamType {
"http://pfam.xfam.org//",
new String[] { "urn:miriam:pfam",
"http://identifiers.org/pfam/",
"https://identifiers.org/pfam/"
"http://identifiers.org/pfam",
"https://identifiers.org/pfam/",
"https://identifiers.org/pfam",
},
new Class<?>[] {}, "MIR:00000028",
new Class<?>[] {},
......@@ -774,7 +909,9 @@ public enum MiriamType {
"http://www.pharmgkb.org/",
new String[] { "urn:miriam:pharmgkb.pathways",
"http://identifiers.org/pharmgkb.pathways/",
"https://identifiers.org/pharmgkb.pathways/"
"http://identifiers.org/pharmgkb.pathways",
"https://identifiers.org/pharmgkb.pathways/",
"https://identifiers.org/pharmgkb.pathways",
},
new Class<?>[] {}, "MIR:00000089",
new Class<?>[] {},
......@@ -804,7 +941,9 @@ public enum MiriamType {
"http://pubchem.ncbi.nlm.nih.gov/",
new String[] { "urn:miriam:pubchem.substance",
"http://identifiers.org/pubchem.substance/",
"https://identifiers.org/pubchem.substance/"
"http://identifiers.org/pubchem.substance",
"https://identifiers.org/pubchem.substance/",
"https://identifiers.org/pubchem.substance",
},
new Class<?>[] { Chemical.class }, "MIR:00000033",
new Class<?>[] { Chemical.class },
......@@ -850,7 +989,9 @@ public enum MiriamType {
"http://www.ncbi.nlm.nih.gov/projects/RefSeq/",
new String[] { "urn:miriam:refseq",
"http://identifiers.org/refseq/",
"https://identifiers.org/refseq/"
"http://identifiers.org/refseq",
"https://identifiers.org/refseq/",
"https://identifiers.org/refseq",
},
new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000039",
new Class<?>[] {},
......@@ -861,7 +1002,9 @@ public enum MiriamType {
"http://rgd.mcw.edu/",