bio-0.3.3.2: A bioinformatics librarySource codeContentsIndex
Bio.Sequence.GOA
Description

GOA - parse and index Gene Onthology Annotations In particular, the file 'gene_association.goa_uniprot' that contains links between GO terms and UniProt accessions.

(Where to find the hierarchical relationship between GO terms?) http://www.geneontology.org/ontology/gene_ontology.obo contains isA relationships http://www.geneontology.org/GO.format.obo-1_2.shtml describes the format

Synopsis
readGOA :: FilePath -> IO [Annotation]
readGO :: FilePath -> IO [GoDef]
decomment :: ByteString -> [ByteString]
newtype GoTerm = GO Int
type UniProtAcc = ByteString
data GoClass
= Func
| Proc
| Comp
data Annotation = Ann !UniProtAcc !GoTerm !EvidenceCode
mkAnn :: ByteString -> Annotation
data GoDef = GoDef !GoTerm !ByteString !GoClass
mkGoDef :: ByteString -> GoDef
data EvidenceCode
= IC
| IDA
| IEA
| IEP
| IGC
| IGI
| IMP
| IPI
| ISS
| NAS
| ND
| RCA
| TAS
| NR
isCurated :: EvidenceCode -> Bool
Documentation
readGOA :: FilePath -> IO [Annotation]Source
Read the goa_uniprot file (warning: this one is huge!)
readGO :: FilePath -> IO [GoDef]Source
Read GO term definitions
decomment :: ByteString -> [ByteString]Source
newtype GoTerm Source
Constructors
GO Int
show/hide Instances
type UniProtAcc = ByteStringSource
data GoClass Source
Constructors
Func
Proc
Comp
show/hide Instances
data Annotation Source
GOA Annotation - or multiple annotations?
Constructors
Ann !UniProtAcc !GoTerm !EvidenceCode
show/hide Instances
mkAnn :: ByteString -> AnnotationSource
data GoDef Source
GO maps GO terms (GO:xxxx for some number xxxx) to biologically meaningful terms. Defined in http://www.geneontology.org/doc/GO.terms_and_ids The format is GO:0000000 [tab] text string [tab] F|P|C
Constructors
GoDef !GoTerm !ByteString !GoClass
show/hide Instances
mkGoDef :: ByteString -> GoDefSource
data EvidenceCode Source
Evidence codes describe the type of support for an annotation http://www.geneontology.org/GO.evidence.shtml
Constructors
IC
IDA
IEA
IEP
IGC
IGI
IMP
IPI
ISS
NAS
ND
RCA
TAS
NR
show/hide Instances
isCurated :: EvidenceCode -> BoolSource
The vast majority of GOA data is IEA, while the most reliable information is manually curated. Filtering on this is useful to keep data set sizes manageable, too.
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