Additional Configuration

For XrefRule, XrefSynonymDbRule rules

Special groups of synonyms (or typos) for known databases can be configured via a Spring XML file, and later - auto-completed by standard names from MIRIAM resource and PSI-MI ("database citation").

  1. group:
    1. PDB
    2. RCSB PDB

  2. group:
    1. ENTREZ GENE
    2. ENTREZ_GENE
    3. LOCUS_LINK
    4. LOCUSLINK
    5. LOCUS-LINK
    6. ENTREZGENE
    7. ENTREZ GENE/LOCUSLINK

  3. group:
    1. NCBI GI
    2. ENTREZ GI
    3. GI

  4. group:
    1. PUBCHEM-SUBSTANCE
    2. NCBI PUBCHEM
    3. PUBCHEM SUBSTANCE
    4. PUBCHEM

  5. group:
    1. PUBMED
    2. PMID
    3. MEDLINE

  6. group:
    1. UNIPROT
    2. SWISS-PROT
    3. SWISSPROT
    4. SWISSTREMBL
    5. SWP
    6. SWISS-PROT/TREMBL
    7. UNIPROTKB
    8. REACTOME PROTEIN
    9. UNIPROT KNOWLEDGE BASE
    10. PIR
    11. PIR-SSD

  7. group:
    1. GO
    2. GENE ONTOLOGY
    3. GENE_ONTOLOGY

  8. group:
    1. UM-BBD
    2. UMBBD

  9. group:
    1. PSI-MI
    2. PSI MI
    3. PSIMI
    4. MI

  10. group:
    1. REFSEQ PROTEIN
    2. REFSEQ
    3. REF_SEQ
    4. REF-SEQ
    5. REF_SEQ PROTEIN

  11. group:
    1. GENE SYMBOL
    2. GENE_SYMBOL

  12. group:
    1. TAXONOMY
    2. NCBI TAXONOMY
    3. NCBI_TAXONOMY
    4. NCBI-TAXONOMY
    5. TAXON

  13. group:
    1. NUCLEOTIDE SEQUENCE DATABASE
    2. NCBI GENBANK
    3. GENBANK
    4. DDBJ
    5. EMBL-BANK
    6. EMBL

  14. group:
    1. PROTEIN GENBANK IDENTIFIER
    2. GENPEPT

  15. group:
    1. KEGG
    2. COMPOUND
    3. KEGG COMPOUND

  16. group:
    1. KEGG GENOMES
    2. KEGG GENOME

  17. group:
    1. KEGG LIGAND
    2. LIGAND

  18. group:
    1. AFFYMETRIX

  19. group:
    1. KEGG Glycan
    2. GLYCAN

  20. group:
    1. IOB

  21. group:
    1. SGD

  22. group:
    1. ENCODE

  23. group:
    1. AMAZE

  24. group:
    1. HUGE

  25. group:
    1. HPRD

  26. group:
    1. UNIPARC

  27. group:
    1. SWISS-MODEL

  28. group:
    1. CAS

  29. group:
    1. UNIGENE

  30. group:
    1. EVIDENCE CODE ONTOLOGY
    2. ECO
    3. EVIDENCE CODE

  31. group:
    1. REACTOME
    2. REACTOME STABLE ID

  32. group:
    1. BIOCYC
    2. HUMANCYC
    3. MOUSECYC

  33. group:
    1. CL
    2. CELL TYPE ONTOLOGY
    3. CELL ONTOLOGY