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class DBXRef:
def __init__(self, dbname, dbid, reftype = None, negate = 0):
self.dbname = dbname
self.dbid = dbid
self.reftype = reftype
self.negate = negate
def __str__(self):
if self.reftype is None:
reftype = ""
else:
reftype = self.reftype + "="
s = "%s/%s%s" % (self.dbname, reftype, self.dbid)
if self.negate:
s = "not(%s)" % s
return s
__repr__ = __str__
class BioformatDBName:
def __getitem__(self, name):
return name
class UnknownDBName:
def __getitem__(self, name):
return "x-unknown-" + name.lower()
dbname_conversions = {
"bioformat": BioformatDBName(),
"unknown": UnknownDBName(),
"sp": {"AARHUS/GHENT-2DPAGE": "x-aarhus-ghent-2dpage",
"CARBBANK": "x-carbbank",
"DICTYDB": "x-dictydb",
"ECO2DBASE": "x-eco2dbase",
"ECOGENE": "x-ecogene",
"EMBL": "embl", # EMBL (in GO)
"FLYBASE": "fb", # Flybase (in GO)
"GCRDB": "x-gcrdb",
"HIV": "x-hiv",
"HSC-2DPAGE": "x-hsc",
"HSSP": "x-hssp",
"MAIZE-2DPAGE": "x-maize",
"MAIZEDB": "x-maizedb",
"MENDEL": "x-mendel",
"MGD": "mgd", # (in GO)
"MIM": "x-mim",
"PDB": "x-pdb", # Protein Data Bank
"PFAM": "x-pfam",
"PIR": "pir", # GO
"PROSITE": "x-prosite",
"REBASE": "x-rebase",
"SGD": "sgd", # GO
"STYGENE": "x-stygene",
"SUBTILIST": "x-subtilist",
"SWISS-2DPAGE": "x-swiss",
"TIGR": "tigr", # GO
"TRANSFAC": "x-transfac",
"WORMPEP": "x-wormpep",
"YEPD": "x-yepd",
"ZFIN": "x-zfin",
},
"go": {"CGEN": "cgen", # Compugen, Inc.
"DDB": "ddb", # DictyBase (Dictyostelium discoideum)
"DDBJ": "ddbj", # DNA Database of Japan
"EC": "ec", # Enzyme Commission
"EMBL": "embl", # EMBL Nucleotide Sequence Data Library
"ENSEMBL": "ensembl", # ENSEMBL
"ENZYME": "enzyme", # ENZYME
"FB": "fb", # FlyBase
"GB": "gb", # GenBank
"GO": "go", # Gene Ontology
"GXD": "gxd", # Gene Expression Database (mouse)
"IPR": "ipr", # InterPro
"ISBN": "isbn", # International Standard Book Number
"IUBMB": "iubmb", # International Union of Biochemistry
# and Molecular Biology
"IUPAC": "iupac", # International Union of Pure and Applied
# Chemistry
"MEDLINE": "medline", # MEDLINE
"MGD": "mgd", # Mouse Genome Database
"MGI": "mgi", # Mouse Genome Informatics
"NC-IUBMB": "NC-IUBMB",
# Nomenclature Committee of the International
# Union of Biochemistry and Molecular Biology
"PIR": "pir", # PIR
"PMID": "pmid", # PubMed
"Pombase": "pombase", # Schizosaccharomyces pombe
"Pompep": "pompep", # Schizosaccharomyces pombe Protein
# Sequence Database
"RESID": "resid", # RESID (protein post-translational modifications)
"SGD": "sgd", # Saccharomyces Genome Database
"SP": "sp", # SWISS-PROT
"SWALL": "swall", # SWISS-PROT + TrEMBL + TrEMBLnew
"TAIR": "tair", # The Arabidopsis Information Resource
"taxonID": "taxonid", # Taxonomy ID
"TC": "tc", # Transport Commission
"TIGR": "tigr", # The Institute of Genome Research
"TR": "tr", # TrEMBL
"WB": "wb", # WormBase (Caenorhabditis elegans)
},
# http://www.ncbi.nlm.nih.gov/collab/db_xref.html
"genbank": {
"ATCC": "x-atcc", # American Type Culture Collection database
# /db_xref="ATCC:123456"
"ATCC(in host)": "x-atcc-host", # See above
"ATCC(dna)": "x-atcc-dna", # See above
"BDGP_EST": "x-bdgp-est", # Berkeley Drosophila Genome Project
# EST database
# /db_xref="BDGP_EST:123456"
"BDGP_INS": "x-bdgp-ins", # Berkeley Drosophila Genome Project
# database -- Insertion
# /db_xref="BDGP_INS:123456"
"dbEST": "x-dbest", # EST database maintained at the NCBI.
# /db_xref="dbEST:123456"
"dbSNP": "x-dbsnp", # Variation database maintained at the NCBI.
# /db_xref="dbSNP:4647"
"dbSTS": "x-dbsts", # STS database maintained at the NCBI.
# /db_xref="dbSTS:456789"
"ENSEMBL": "ensembl", # Database of automatically annotated genomic data
# /db_xref="ENSEMBL:HUMAN-Clone-AC005612"
# /db_xref="ENSEMBL:HUMAN-Gene-ENSG00000007102"
"ESTLIB": "x-estlib", # EBI's EST library identifier #'
# /db_xref="ESTLIB:1200"
"FANTOM_DB": "x-fantom-db", # Database of Functional Annotation of Mouse
# /db_xref="FANTOM_DB:0610005A07"
"FLYBASE": "fb", # Database of Genetic and molecular data of Drosophila.
# /db_xref="FLYBASE:FBgn0000024"
"GDB": "x-gdb", # Human Genome Database accession numbers.
# /db_xref="GDB:G00-128-600"
"GI": "x-gi", # GenInfo identifier, used as a unique sequence
# identifier for nucleotide and proteins.
# /db_xref="GI:1234567890"
"GO": "go", # Gene Ontology Database identifier
# /db_xref="GO:123"
"IMGT/LIGM": "x-imgt-ligm", # Immunogenetics database, immunoglobulins
# and T-cell receptors
# /db_xref="IMGT/LIGM:U03895"
"IMGT/HLA": "x-imgt-hla", # Immunogenetics database, human MHC
# /db_xref="IMGT/HLA:HLA00031"
"LocusID": "x-locus-id", # NCBI LocusLink ID.
# /db_xref="LocusID:51199"
"MaizeDB": "x-maizedb", # Maize Genome Database unique identifiers.
# /db_xref="MaizeDB:Probe/79847"
"MGD": "mgd", # Mouse Genome Database accession numbers.
# /db_xref="MGD:123456"
"MGI": "mgi", # Medicago Genome Initiative
# /db_xref="MGI:S:20819"
"MIM": "x-mim", # Mendelian Inheritance in Man numbers.
# /db_xref="MIM:123456"
"niaEST": "x-niaEST", # NIA Mouse cDNA Project
# /db_xref="niaEST:L0304H12-3"
"PIR": "pir", # Protein Information Resource accession numbers.
# /db_xref="PIR:S12345"
"PSEUDO": "x-pseudo-embl", # EMBL pseudo protein identifier
# /db_xref="PSEUDO:CAC44644.1"
"RATMAP": "x-ratmap", # Rat Genome Database
# /db_xref="RATMAP:5"
"RiceGenes": "x-ricegenes", # Rice database accession numbers.
# /db_xref="RiceGenes:AA231856"
"REMTREMBL": "x-remtrembl",
# Computer-annotated protein sequence database containing
# the translations of those codings sequences (CDS) present
# in the EMBL Nucleotide Sequence Database that won't be '
# included in SWISS-PROT. These include: immunoglobulins and
# T-cell receptors, synthetic sequences, patent application
# sequences, small fragments, CDS not coding for real
# proteins and truncated proteins.
# example: /db_xref="REMTREMBL:CAC01666"
"RZPD": "x-rzpd", # Resource Centre Primary Database Clone Identifiers
# /db_xref="RZPD:IMAGp998I142450Q6"
"SGD": "sgd", # Saccharomyces Genome Database accession numbers.
# /db_xref="SGD:L0000470"
"SoyBase": "x-soybase", # Glycine max Genome Database
# /db_xref="SoyBase:Satt005"
"SPTREMBL": "x-sptrembl", # is this the same as "swall" ?
# Computer-annotated protein sequence database
# supplementing SWISS-PROT and containing the
# translations of all coding sequences (CDS)
# present in the EMBL Nucleotide Sequence
# Database not yet integrated in SWISS-PROT.
# /db_xref="SPTREMBL:Q00177"
"SWISS-PROT": "sp", # Swiss-Prot protein database accession numbers.
# /db_xref="SWISS-PROT:P12345"
"taxon": "taxonid", # NCBI taxonomic identifier.
# /db_xref="taxon:4932"
},
}
def from_parser(dbname_style, dbname, idtype, dbid, negate):
try:
dbname = dbname_conversions[dbname_style][dbname]
except KeyError:
dbname = "x-unknown2-%s--%s" % (dbname_style, dbname)
return DBXRef(dbname, dbid, idtype, negate)
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