Gene Ontology Annotation (GOA) Server Functions

This module defines functions for interfacing with the EBI’s Gene Ontology Annotation (GOA) database for analysing gene/protein functions through the Gene Ontology (GO).

This module is based on the tutorial notebook at https://nbviewer.jupyter.org/urls/dessimozlab.github.io/go-handbook/GO%20Tutorial%20in%20Python%20-%20Solutions.ipynb

class prody.database.goa.GOADictList(parsingList, title='unnamed', **kwargs)

A class for handling the list of GOA Dictionaries returned by queryGOA

__iter__()

Yield go_term instances.

pop(index)

Pop dataBlock with the given index from the list of dataBlocks in GOADictList

prody.database.goa.calcDeepFunctionOverlaps(*goa_data, **kwargs)

Calculate function overlaps between the deep (most detailed) molecular functions in particular from two sets of GO terms.

Parameters:

• goa1 (tuple, list, ndarray) – the first set of GO terms

• goa2 (tuple, list, ndarray) – the second set of GO terms

prody.database.goa.calcEnsembleFunctionOverlaps(ens, **kwargs)

Calculate function overlaps for an ensemble as the mean of the value from calcDeepFunctionOverlaps().

Parameters:

ens (Ensemble) – an ensemble with labels

prody.database.goa.calcGoOverlap(*go_terms, **kwargs)

Calculate overlap between GO terms based on their distance in the graph. GO terms in different namespaces (molecular function, cellular component, and biological process) have undefined distances.

Parameters:

• go_terms (list, tuple, ~numpy.ndarray) – a list of GO terms or GO IDs

• pairwise (bool) – whether to calculate to a matrix of pairwise overlaps default is False

• distance (bool) – whether to return distances rather than calculating overlaps default is False

• go (~goatools.obo_parser.GODag) – GO graph. Default behaviour is to parse it with parseOBO().

prody.database.goa.calcMinBranchLength(go_id1, go_id2, go)

Find the minimum branch length between two terms in the GO DAG.

Parameters:

• go_id1 (str) – the first GO ID

• go_id2 – the second GO ID

:type go_id2:str

Parameters:

go (~goatools.obo_parser.GODag) – object containing a gene ontology (GO) directed acyclic graph (DAG)

prody.database.goa.findCommonParentGoIds(terms, go)

This function finds the common ancestors in the GO tree of the list of terms in the input.

Parameters:

• terms (tuple, list, ndarray) – a list of GO terms

• go (~goatools.obo_parser.GODag) – object containing a gene ontology (GO) directed acyclic graph (DAG)

prody.database.goa.findDeepestCommonAncestor(terms, go)

Find the nearest common ancestor. Only returns single most specific - assumes unique exists.

Parameters:

• terms (tuple, list, ndarray) – a list of GO terms

• go (~goatools.obo_parser.GODag) – object containing a gene ontology (GO) directed acyclic graph (DAG)

prody.database.goa.findDeepestFunctions(go_terms, **kwargs)

Find the deepest (most detailed) molecular functions in a list of GO terms.

Parameters:

go_terms (GOADictList) – a list of GO terms

prody.database.goa.parseGAF(database='PDB', **kwargs)

Parse a GO Association File (GAF) corresponding to a particular database collection into a dictionary for ease of querying.

See GAF for more information on the file format

Parameters:

• database (str) – name of the database of interest default is PDB. Others include UNIPROT and common names of many organisms.

• filename (str) – filename for the gaf of interest default is goa_ and the database name in lower case and .gaf.gz

prody.database.goa.parseOBO(**kwargs)

Parse a GO OBO file containing the GO itself. See OBO for more information on the file format.

prody.database.goa.queryGOA(*ids, **kwargs)

Query a GOA database by identifier.

Parameters:

• ids (str, tuple, list, ndarray) – an identifier or a list-like of identifiers

• database (str) – name of the database of interest default is PDB. Others include UNIPROT and common names of many organisms.

prody.database.goa.showGoLineage(go_term, **kwargs)

Use pygraphviz and IPython notebook to show the lineage of a GO term

Parameters:

go (~goatools.obo_parser.GODag) – object containing a gene ontology (GO) directed acyclic graph (DAG) default is to parse with parseOBO()

arg out_format: format for output.

Currently only output to file. This file will be displayed in Jupyter Notebook.

type out_format: str

arg filename: filename for output

default behaviour is to use the GO term ID and append ‘_lineage.png’

type filename: str