Changeset 549 for trunk

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Timestamp:
11/23/11 17:22:40 (6 months ago)
Author:
martijn
Message:

Deprecated pubchem, created pubchem compound and pubchem substance

Location:
trunk/org.bridgedb.bio
Files:
2 modified

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  • trunk/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.txt

    r543 r549  
    145145PubChem Cp      http://pubchem.ncbi.nlm.nih.gov/        http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?db=pccompound&term=$id      100101  metabolite              1       urn:miriam:pubchem.compound     ^\d+$   PubChem-compound 
    146146PubChem-bioassay                http://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay     http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=$id 1018    metabolite              1       urn:miriam:pubchem.bioassay     ^\d+$   PubChem-bioassay 
    147 PubChem-substance               http://pubchem.ncbi.nlm.nih.gov/        http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=pcsubstance&term=$id     100101  metabolite              1       urn:miriam:pubchem.substance    ^\d+$   PubChem-substance 
     147PubChem-substance       Cps     http://pubchem.ncbi.nlm.nih.gov/        http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=pcsubstance&term=$id     100101  metabolite              1       urn:miriam:pubchem.substance    ^\d+$   PubChem-substance 
     148PubChem-compound        Cpc     http://pubchem.ncbi.nlm.nih.gov/        http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=pccompound&term=$id      100101  metabolite              1       urn:miriam:pubchem.compound     ^\d+$   PubChem-compound 
    148149PubMed          http://www.ncbi.nlm.nih.gov/PubMed/     http://www.ncbi.nlm.nih.gov/pubmed/$id  16333295        publication             1       urn:miriam:pubmed       ^\d+$   PubMed 
    149150Reactome        Re      http://www.reactome.org/        http://www.reactome.org/cgi-bin/eventbrowser_st_id?FROM_REACTOME=1&ST_ID=$id    REACT_1590      pathway         1       urn:miriam:reactome     ^REACT_\d+(\.\d+)?$     Reactome 

  • trunk/org.bridgedb.bio/src/org/bridgedb/bio/BioDataSource.java

    r509 r549  
    6161        public static final DataSource KEGG_COMPOUND = DataSource.register ( 
    6262                "Ck", "Kegg Compound").asDataSource(); 
     63        /** @deprecated use one of the organism-specific system codes instead */  
    6364        public static final DataSource PUBCHEM = DataSource.register ( 
    6465                "Cp", "PubChem").asDataSource(); 
     66        public static final DataSource PUBCHEM_SUBSTANCE = DataSource.register ( 
     67                "Cps", "PubChem substance").asDataSource(); 
     68        public static final DataSource PUBCHEM_COMPOUND = DataSource.register ( 
     69                "Cpc", "PubChem compound").asDataSource(); 
    6570        public static final DataSource CHEMSPIDER = DataSource.register ( 
    6671                "Cs", "Chemspider").asDataSource();