* Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
*/
public static final String UNIPROTKB = "UniProtKB/TrEMBL".toUpperCase();
-
+
public static final String EMBLCDSProduct = "EMBLCDSProtein"
.toUpperCase();
public static String PDB = "PDB";
/**
+ * mmCIF Entry Code
+ */
+ public static String MMCIF = "mmCIF";
+
+ /**
* EMBL ID
*/
public static String EMBL = "EMBL";
public static final String GENEDB = "GeneDB".toUpperCase();
/**
- * List of databases whose sequences might have coding regions annotated
+ * Ensembl
*/
- public static final String[] DNACODINGDBS =
- { EMBL, EMBLCDS, GENEDB };
-
- public static final String[] CODINGDBS =
- { EMBLCDS, GENEDB };
-
- public static final String[] PROTEINDBS =
- { UNIPROT, PDB, UNIPROTKB, EMBLCDSProduct };
-
- public static final String[] PROTEINSEQ =
- { UNIPROT, UNIPROTKB, EMBLCDSProduct };
+ public static final String ENSEMBL = "ENSEMBL";
- public static final String[] PROTEINSTR =
- { PDB };
-
- public static final String[] DOMAINDBS =
- { PFAM, RFAM };
-
- /**
- * set of unique DBRefSource property constants. These could be used to
- * reconstruct the above groupings
- */
- public static final Object SEQDB = "SQ";
-
- /**
- * database of nucleic acid sequences
- */
- public static final Object DNASEQDB = "NASQ";
+ public static final String ENSEMBLGENOMES = "ENSEMBLGENOMES";
/**
- * database of amino acid sequences
- */
- public static final Object PROTSEQDB = "PROTSQ";
-
- /**
- * database of cDNA sequences
- */
- public static final Object CODINGSEQDB = "CODING";
-
- /**
- * database of na sequences with exon annotation
- */
- public static final Object DNACODINGSEQDB = "XONCODING";
-
- /**
- * DB returns several sequences associated with a protein/nucleotide domain
+ * List of databases whose sequences might have coding regions annotated
*/
- public static final Object DOMAINDB = "DOMAIN";
+ public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB,
+ ENSEMBL };
- /**
- * DB query can take multiple accession codes concatenated by a separator.
- * Value of property indicates maximum number of accession codes to send at a
- * time.
- */
- public static final Object MULTIACC = "MULTIACC";
+ public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
- /**
- * DB query returns an alignment for each accession provided.
- */
- public static final Object ALIGNMENTDB = "ALIGNMENTS";
+ public static final String[] PROTEINDBS = { UNIPROT, PDB, UNIPROTKB,
+ EMBLCDSProduct, ENSEMBL }; // Ensembl ENSP* entries are protein
}