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

data GoDef

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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