Updated Metadata to use for PC v14.

Removed unused script (the command is not added to the generated during build data/export.sh script)
Added @JsonIgnore to skip 'files' field when writing the updated metadata back to the orig. file.

src/main/java/cpath/service/metadata/Datasource.java

@@ -5,6 +5,7 @@
 import java.util.Set;
 import java.util.regex.Pattern;
 
+import com.fasterxml.jackson.annotation.JsonIgnore;
 import lombok.*;
 import org.apache.commons.lang3.StringUtils;
 import org.biopax.paxtools.controller.ModelUtils;
@@ -45,6 +46,7 @@ public boolean isNotPathwayData() {
     }
   }
 
+  //the order of fields here matters as the all-args Constructor will be auto-generated!
   private String identifier;
   private List<String> name; //data provider standard names
   private String description;
@@ -54,7 +56,7 @@ public boolean isNotPathwayData() {
   private METADATA_TYPE type;
   private String cleanerClass;
   private String converterClass;
-  private Set<String> files;
+  @JsonIgnore private Set<String> files;
   private String pubmedId;
   private String availability;
   private int numPathways;

work/application.properties

@@ -32,7 +32,7 @@ Feel free to tell us more about yourself and your project.
 cpath2.species=Homo sapiens (9606)
 #cpath2.sbgn-layout-enabled=false
 # uncomment when building a new data model (using --build option)
-#cpath2.metadata-location=file:metadata.v14.json
+#cpath2.metadata-location=file:metadata.json
 
 ## Spring Boot Application
 #configure a different port and context-path, e.g.,

work/metadata.json

@@ -0,0 +1,317 @@
+{
+  "description" : "Pathway Commons data sources (metadata)",
+  "version" : 14,
+  "datasources" : [ {
+    "identifier" : "chebi",
+    "name" : [ "ChEBI" ],
+    "description" : "ChEBI Ontology v233, 27-Apr-2024",
+    "dataUrl" : "ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo",
+    "homepageUrl" : "https://www.ebi.ac.uk/chebi/",
+    "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/chebi.png",
+    "type" : "WAREHOUSE",
+    "cleanerClass" : null,
+    "converterClass" : "cpath.converter.ChebiOboConverter",
+    "pubmedId" : "23180789",
+    "availability" : "free"
+  }, {
+    "identifier" : "uniprot_human",
+    "name" : [ "UniProt", "SwissProt", "UniProtKB" ],
+    "description" : "UniProtKB/Swiss-Prot (human), release 2024_02",
+    "dataUrl" : "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/uniprot_sprot_human.dat.gz",
+    "homepageUrl" : "https://www.uniprot.org",
+    "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/uniprot.png",
+    "type" : "WAREHOUSE",
+    "cleanerClass" : null,
+    "converterClass" : "cpath.converter.UniprotConverter",
+    "pubmedId" : "24253303",
+    "availability" : "free"
+  }, {
+    "identifier" : "unichem_mapping",
+    "name" : [ "UniChem" ],
+    "description" : "Selected whole-source id-mapping files (to ChEBI) from UniChem, 13-May-2024",
+    "dataUrl" : "ftp://ftp.ebi.ac.uk/pub/databases/chembl/UniChem/data/wholeSourceMapping/",
+    "homepageUrl" : "https://www.ebi.ac.uk/unichem/",
+    "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/UniChem_logo2_255.png",
+    "type" : "MAPPING",
+    "cleanerClass" : null,
+    "converterClass" : null,
+    "pubmedId" : "23317286",
+    "availability" : "free"
+  }, {
+    "identifier" : "reactome",
+    "name" : [ "Reactome" ],
+    "description" : "Reactome v88 (only 'Homo_sapiens.owl') 20-Mar-2024",
+    "dataUrl" : "http://www.reactome.org/download/current/biopax.zip",
+    "homepageUrl" : "https://www.reactome.org",
+    "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/reactome.png",
+    "type" : "BIOPAX",
+    "cleanerClass" : "cpath.cleaner.ReactomeCleaner",
+    "converterClass" : null,
+    "pubmedId" : "29145629",
+    "availability" : "free"
+  }, {
+    "identifier" : "pid",
+    "name" : [ "pid", "NCI Pathway Interaction Database: Pathway" ],
+    "description" : "NCI Curated Human Pathways from PID (final); 27-Jul-2015",
+    "dataUrl" : "https://github.com/NCIP/pathway-interaction-database/blob/master/download/NCI-Nature-Curated-final.bp3.owl.gz",
+    "homepageUrl" : "https://en.wikipedia.org/wiki/NCI-Nature_Pathway_Interaction_Database",
+    "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/nci_nature.png",
+    "type" : "BIOPAX",
+    "cleanerClass" : null,
+    "converterClass" : null,
+    "pubmedId" : "18832364",
+    "availability" : "free"
+  }, {
+    "identifier" : "psp",
+    "name" : [ "PhosphoSite", "PhosphoSitePlus" ],
+    "description" : "PhosphoSite Kinase-substrate information; 16-Apr-2024",
+    "dataUrl" : "http://www.phosphosite.org/downloads/Kinase_substrates.owl.gz",
+    "homepageUrl" : "https://www.phosphosite.org",
+    "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/psp.png",
+    "type" : "BIOPAX",
+    "cleanerClass" : null,
+    "converterClass" : null,
+    "pubmedId" : "22135298",
+    "availability" : "free"
+  }, {
+    "identifier" : "humancyc",
+    "name" : [ "HumanCyc", "HumanCyc", "BioCyc" ],
+    "description" : "HumanCyc 27.5; 2023; under license from SRI International, www.biocyc.org",
+    "dataUrl" : "https://humancyc.org/download.shtml",
+    "homepageUrl" : "https://humancyc.org",
+    "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/humancyc.png",
+    "type" : "BIOPAX",
+    "cleanerClass" : "cpath.cleaner.HumanCycCleaner",
+    "converterClass" : null,
+    "pubmedId" : "15642094",
+    "availability" : "academic"
+  }, {
+    "identifier" : "hprd",
+    "name" : [ "HPRD" ],
+    "description" : "HPRD PSI-MI Release 9; 13-Apr-2010",
+    "dataUrl" : "http://www.hprd.org/download",
+    "homepageUrl" : "http://www.hprd.org",
+    "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/hprd.png",
+    "type" : "PSI_MI",
+    "cleanerClass" : "cpath.cleaner.HPRDCleaner",
+    "converterClass" : "cpath.converter.PsimiConverter",
+    "pubmedId" : "18988627",
+    "availability" : "academic"
+  }, {
+    "identifier" : "panther",
+    "name" : [ "PANTHER", "PANTHER Pathway", "PantherDB" ],
+    "description" : "PANTHER Pathways 3.6.7 on 01-Aug-2023 (auto-converted to human-only model)",
+    "dataUrl" : "http://data.pantherdb.org/ftp/pathway/3.6.7/BioPAX.tar.gz",
+    "homepageUrl" : "https://www.pantherdb.org",
+    "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/panther.png",
+    "type" : "BIOPAX",
+    "cleanerClass" : "cpath.cleaner.PantherCleaner",
+    "converterClass" : null,
+    "pubmedId" : "27899595",
+    "availability" : "free"
+  }, {
+    "identifier" : "dip",
+    "name" : [ "DIP", "Database of Interacting Proteins" ],
+    "description" : "DIP (human - converted Hsapi20170205.mif25.gz to BioPAX), 05-Feb-2017",
+    "dataUrl" : "https://dip.doe-mbi.ucla.edu/dip/Download.cgi",
+    "homepageUrl" : "https://dip.doe-mbi.ucla.edu",
+    "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/dip_logo.png",
+    "type" : "PSI_MI",
+    "cleanerClass" : null,
+    "converterClass" : "cpath.converter.PsimiConverter",
+    "pubmedId" : "14681454",
+    "availability" : "free"
+  }, {
+    "identifier" : "biogrid",
+    "name" : [ "BioGRID" ],
+    "description" : "BioGRID Release 4.4.227 (only BIOGRID-ORGANISM-Homo_sapiens-4.4.227.psi25.xml), 25-Oct-2023",
+    "dataUrl" : "https://downloads.thebiogrid.org/File/BioGRID/Release-Archive/BIOGRID-4.4.227/BIOGRID-ORGANISM-4.4.227.psi25.zip",
+    "homepageUrl" : "https://thebiogrid.org/",
+    "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/favicon_bigger.png",
+    "type" : "PSI_MI",
+    "cleanerClass" : null,
+    "converterClass" : "cpath.converter.PsimiConverter",
+    "pubmedId" : "16381927",
+    "availability" : "free"
+  }, {
+    "identifier" : "intact",
+    "name" : [ "IntAct" ],
+    "description" : "IntAct (human), except 'negative', 06-Oct-2023",
+    "dataUrl" : "https://ftp.ebi.ac.uk/pub/databases/intact/2023-10-06/psi25/species/human.zip",
+    "homepageUrl" : "https://www.ebi.ac.uk/intact/",
+    "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/logo_intact_small.gif",
+    "type" : "PSI_MI",
+    "cleanerClass" : null,
+    "converterClass" : "cpath.converter.PsimiConverter",
+    "pubmedId" : "24234451",
+    "availability" : "free"
+  }, {
+    "identifier" : "intact_complex",
+    "name" : [ "IntAct" ],
+    "description" : "IntAct Complex (human), 06-Oct-2023",
+    "dataUrl" : "https://ftp.ebi.ac.uk/pub/databases/intact/complex/2023-10-06/psi25/Homo_sapiens.zip",
+    "homepageUrl" : "https://www.ebi.ac.uk/intact/",
+    "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/logo_intact_small.gif",
+    "type" : "PSI_MI",
+    "cleanerClass" : null,
+    "converterClass" : "cpath.converter.PsimiToComplexesConverter",
+    "pubmedId" : "24234451",
+    "availability" : "free"
+  }, {
+    "identifier" : "bind",
+    "name" : [ "BIND", "BIND", "Biomolecular Interaction Network Database" ],
+    "description" : "BIND (human), 15-Dec-2010",
+    "dataUrl" : "http://download.baderlab.org/BINDTranslation/release1_0/PSIMI25_XML/taxid9606_PSIMI25.xml",
+    "homepageUrl" : "https://en.wikipedia.org/wiki/Biomolecular_Object_Network_Databank#Biomolecular_Interaction_Network_Database_(BIND)",
+    "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/bindinside_logo.jpg",
+    "type" : "PSI_MI",
+    "cleanerClass" : null,
+    "converterClass" : "cpath.converter.PsimiConverter",
+    "pubmedId" : "12519993",
+    "availability" : "free"
+  }, {
+    "identifier" : "corum",
+    "name" : [ "CORUM" ],
+    "description" : "CORUM 3.0 (human complexes), 03-Sep-2018",
+    "dataUrl" : "https://mips.helmholtz-muenchen.de/corum/download/allComplexes.xml.zip",
+    "homepageUrl" : "https://mips.helmholtz-muenchen.de/genre/proj/corum/",
+    "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/topright.jpg",
+    "type" : "PSI_MI",
+    "cleanerClass" : null,
+    "converterClass" : "cpath.converter.PsimiToComplexesConverter",
+    "pubmedId" : "30357367",
+    "availability" : "academic"
+  }, {
+    "identifier" : "msigdb",
+    "name" : [ "MSigDB", "MSigDB", "Molecular Signatures Database" ],
+    "description" : "MSigDB v5.2 (XML), human C3 TFT motif gene sets, 09-2016; converted with http://github.com/PathwayCommons/msigdb-to-biopax",
+    "dataUrl" : "http://software.broadinstitute.org/gsea/msigdb/download_file.jsp?filePath=/resources/msigdb/5.2/msigdb_v5.2.xml",
+    "homepageUrl" : "http://software.broadinstitute.org/gsea/msigdb/",
+    "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/msigdb.gif",
+    "type" : "BIOPAX",
+    "cleanerClass" : null,
+    "converterClass" : null,
+    "pubmedId" : "16199517",
+    "availability" : "academic"
+  }, {
+    "identifier" : "mirtarbase",
+    "name" : [ "miRTarBase" ],
+    "description" : "Human miRNA-target gene relationships from MiRTarBase; v7.0, 15-SEP-2017, converted in Apr-2018 with http://github.com/PathwayCommons/mirtarbase-to-biopax",
+    "dataUrl" : "http://mirtarbase.mbc.nctu.edu.tw/cache/download/7.0/hsa_MTI.xlsx",
+    "homepageUrl" : "http://mirtarbase.mbc.nctu.edu.tw/",
+    "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/mirtarbaselogo.png",
+    "type" : "BIOPAX",
+    "cleanerClass" : null,
+    "converterClass" : null,
+    "pubmedId" : "29126174",
+    "availability" : "academic"
+  }, {
+    "identifier" : "drugbank",
+    "name" : [ "DrugBank" ],
+    "description" : "DrugBank v5.1.11, 03-Jan-2024, converted to BioPAX with our http://github.com/PathwayCommons/drugbank-to-biopax",
+    "dataUrl" : "https://www.drugbank.ca/releases/5-1-4/downloads/all-full-database",
+    "homepageUrl" : "http://www.drugbank.ca/",
+    "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/drugbanklogo.png",
+    "type" : "BIOPAX",
+    "cleanerClass" : "cpath.cleaner.DrugbankCleaner",
+    "converterClass" : null,
+    "pubmedId" : "29126136",
+    "availability" : "academic"
+  }, {
+    "identifier" : "reconx",
+    "name" : [ "Recon X" ],
+    "description" : "Recon X: Reconstruction of the Human Genome; SBML model from BioModels, Recon 2 v2.02 (2013), converted to BioPAX by us using http://github.com/PathwayCommons/reconx-to-biopax library.",
+    "dataUrl" : "http://www.ebi.ac.uk/biomodels-main/MODEL1109130000",
+    "homepageUrl" : "http://humanmetabolism.org/",
+    "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/reconxlogo.png",
+    "type" : "BIOPAX",
+    "cleanerClass" : null,
+    "converterClass" : null,
+    "pubmedId" : "23455439",
+    "availability" : "free"
+  }, {
+    "identifier" : "ctd",
+    "name" : [ "CTD", "Comparative Toxicogenomics Database", "ctdbase" ],
+    "description" : "Curated chemical-gene interactions from Comparative Toxicogenomics Database, MDI Biological Laboratory, and NC State University; 28-Feb-2024; converted with http://github.com/PathwayCommons/ctd-to-biopax",
+    "dataUrl" : "http://ctdbase.org/downloads/",
+    "homepageUrl" : "http://ctdbase.org/",
+    "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/ctdlogo.png",
+    "type" : "BIOPAX",
+    "cleanerClass" : null,
+    "converterClass" : null,
+    "pubmedId" : "27651457",
+    "availability" : "academic"
+  }, {
+    "identifier" : "kegg",
+    "name" : [ "KEGG", "KEGG Pathway" ],
+    "description" : "KEGG 07/2011 (only human, hsa* files), converted to BioPAX by BioModels (http://www.ebi.ac.uk/biomodels-main/) team",
+    "dataUrl" : "http://www.cogsys.cs.uni-tuebingen.de/mitarb/draeger/BioPAX.zip",
+    "homepageUrl" : "https://www.genome.jp/kegg/",
+    "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/kegg128.gif",
+    "type" : "BIOPAX",
+    "cleanerClass" : "cpath.cleaner.KeggHsaCleaner",
+    "converterClass" : null,
+    "pubmedId" : "23433509",
+    "availability" : "academic"
+  }, {
+    "identifier" : "inoh",
+    "name" : [ "INOH", "Integrating Network Objects with Hierarchies" ],
+    "description" : "INOH 4.0 (signal transduction and metabolic data), 22-MAR-2011, archive",
+    "dataUrl" : "http://inoh.hgc.jp/download.html#PathwayData",
+    "homepageUrl" : "http://inoh.hgc.jp",
+    "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/inoh_logo.png",
+    "type" : "BIOPAX",
+    "cleanerClass" : "cpath.cleaner.InohCleaner",
+    "converterClass" : null,
+    "pubmedId" : "22120663",
+    "availability" : "free"
+  }, {
+    "identifier" : "netpath",
+    "name" : [ "NetPath" ],
+    "description" : "NetPath 12/2011",
+    "dataUrl" : "http://www.netpath.org/download/zipped/BioPAX.zip",
+    "homepageUrl" : "http://www.netpath.org",
+    "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/netpath_logo.png",
+    "type" : "BIOPAX",
+    "cleanerClass" : "cpath.cleaner.NetPathCleaner",
+    "converterClass" : null,
+    "pubmedId" : "20067622",
+    "availability" : "free"
+  }, {
+    "identifier" : "pathbank",
+    "name" : [ "Pathbank" ],
+    "description" : "Pathbank 2.0 BioPAX data (primary pathways, human data only), 16-Aug-2019",
+    "dataUrl" : "http://pathbank.org/downloads/pathbank_primary_biopax.zip",
+    "homepageUrl" : "http://pathbank.org",
+    "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/pathbank.png",
+    "type" : "BIOPAX",
+    "cleanerClass" : "cpath.cleaner.PathbankCleaner",
+    "converterClass" : null,
+    "pubmedId" : "31602464",
+    "availability" : "free"
+  }, {
+    "identifier" : "innatedb",
+    "name" : [ "InnateDB" ],
+    "description" : "InnateDB Curated Interactions (human) 2017-06-18 (downloaded 2023-02-10)",
+    "dataUrl" : "https://www.innatedb.ca/download/interactions/innatedb_all.mitab.gz",
+    "homepageUrl" : "https://www.innatedb.ca",
+    "iconUrl" : "https://www.innatedb.com/images/Innatedb-2010-large.png",
+    "type" : "PSI_MITAB",
+    "cleanerClass" : null,
+    "converterClass" : "cpath.converter.PsimiTabConverter",
+    "pubmedId" : "23180781",
+    "availability" : "free"
+  }, {
+    "identifier" : "biofactoid",
+    "name" : [ "Biofactoid" ],
+    "description" : "Biofactoid BioPAX data, 2024-05-13",
+    "dataUrl" : "https://biofactoid.org/api/document/zip/biopax?idMapping=true",
+    "homepageUrl" : "https://biofactoid.org",
+    "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/biofactoid.png",
+    "type" : "BIOPAX",
+    "cleanerClass" : null,
+    "converterClass" : null,
+    "pubmedId" : "34860157",
+    "availability" : "free"
+  } ]
+}