| bio-0.4.6: A bioinformatics library | Source code | Contents | Index
Bio.Sequence.GeneOntology
Contents
Basic data types Reading the OBO format Reading 'terms and ids' Reading UniProt associations Utility stuff
Description
GeneOntology - parse and index Gene Ontology Annotations In particular, the file 'gene_association.goa_uniprot' that contains links between GO terms and UniProt accessions. http://www.geneontology.org/ontology/gene_ontology.obo -- Contains the hierarchy including isA relationships. http://www.geneontology.org/GO.format.obo-1_2.shtml -- Describes the OBO format. ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/ -- Contains the GOA-UniProt mapping (and a README file). http://www.geneontology.org/ontology/GO.defs -- Contains GO definitions (not supported here yet). http://www.geneontology.org/doc/GO.terms_and_ids -- GO definitions, simpler and more schematically.
Synopsis
newtype GoTerm = GO Int
data GoDef = GoDef !GoTerm !ByteString !GoClass
type GoHierarchy = [(GoDef, [GoTerm])]
readObo :: FilePath -> IO GoHierarchy
readTerms :: FilePath -> IO [GoDef]
data Annotation = Ann !UniProtAcc !GoTerm !EvidenceCode
type UniProtAcc = ByteString
data GoClass
= Func
| Proc
| Comp
data EvidenceCode
= IC
| IDA
| IEA
| IEP
| IGC
| IGI
| IMP
| IPI
| ISS
| NAS
| ND
| RCA
| TAS
| NR
readGOA :: FilePath -> IO [Annotation]
isCurated :: EvidenceCode -> Bool
decomment :: ByteString -> [ByteString]
Basic data types
newtype GoTerm | Source
A GO term is a positive integer
Constructors
GO Int |
Instances
Eq GoTerm
Ord GoTerm
Read GoTerm
Show GoTerm
data GoDef | Source
A GoDef maps a GoTerm to a description and a GoClass.
Constructors
GoDef !GoTerm !ByteString !GoClass |
Instances
Show GoDef
Reading the OBO format
type GoHierarchy = [(GoDef, [GoTerm])] | Source
A list of Go definitions, with pointers to parent nodes. Read from the .obo file. The user may construct the explicit hierachy by storing these in a Map or similar
readObo :: FilePath -> IO GoHierarchy | Source
Read the GO hierarchy from the obo file. Note that this is not quite a tree structure.
Reading 'terms and ids'
readTerms :: FilePath -> IO [GoDef] | Source
Read GO term definitions, from the GO.terms_and_ids file
Reading UniProt associations
data Annotation | Source
A GOA annotation, containing a UniProt identifier, a GoTerm and an evidence code.
Constructors
Ann !UniProtAcc !GoTerm !EvidenceCode |
Instances
Show Annotation
type UniProtAcc = ByteString | Source
A UniProt identifier (short string of capitals and numbers).
data GoClass | Source
Constructors
Func |
Proc |
Comp |
Instances
Read GoClass
Show GoClass
data EvidenceCode | Source
Evidence codes describe the type of support for an annotation http://www.geneontology.org/GO.evidence.shtml
Constructors
IC | Inferred by Curator
IDA | Inferred from Direct Assay
IEA | Inferred from Electronic Annotation
IEP | Inferred from Expression Pattern
IGC | Inferred from Genomic Context
IGI | Inferred from Genetic Interaction
IMP | Inferred from Mutant Phenotype
IPI | Inferred from Physical Interaction
ISS | Inferred from Sequence or Structural Similarity
NAS | Non-traceable Author Statement
ND | No biological Data available
RCA | Inferred from Reviewed Computational Analysis
TAS | Traceable Author Statement
NR | Not Recorded
Instances
Eq EvidenceCode
Read EvidenceCode
Show EvidenceCode
readGOA :: FilePath -> IO [Annotation] | Source
Read the goa_uniprot file (warning: this one is huge!)
isCurated :: EvidenceCode -> Bool | Source
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.
Utility stuff
decomment :: ByteString -> [ByteString] | Source
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