org.biopax.paxtools.io.gsea

Class GSEAConverter

java.lang.Object

org.biopax.paxtools.io.gsea.GSEAConverter

public class GSEAConverter
extends Object

Converts a BioPAX model to the GMT format (used by GSEA software). It creates GSEA entries from the protein reference (PR) xrefs in the BioPAX model as follows:

• Each entry (row) consists of three columns (tab separated): name (e.g., "taxonomyID: pathway_name"), description (e.g. "datasource: pid;reactome; organism: 9606 id type: uniprot"), and the list of identifiers (of the same type). For all PRs not associated with any pathway, "Not pathway" is used instead of the pathway name.
• The "id type" is what specified by Constructor parameter 'database'.
• The list may have one or more IDs of the same type per PR, e.g., UniProt IDs or HGNC Symbols; PRs not having an xref of given db/id type are ignored. If there are less than three protein referencesper entry, it will not be printed.

Note, to effectively enforce cross-species violation, 'organism' property of PRs and pathways must be set to a BioSource object that has a valid unification xref: db="Taxonomy" and some taxonomy id. Note, this code assumes that the model has successfully been validated and perhaps normalized (using the BioPAX Validator, Paxtools Normalizer). A BioPAX L1 or L2 model is first converted to the L3 (lossless conversion if there are no BioPAX errors).

Constructor Summary

Constructors

Constructor and Description
GSEAConverter() Constructor.
GSEAConverter(String database, boolean crossSpeciesCheckEnabled) Constructor.
GSEAConverter(String database, boolean crossSpeciesCheckEnabled, boolean skipSubPathways) Constructor.
GSEAConverter(String database, boolean crossSpeciesCheckEnabled, Set<Provenance> skipSubPathwaysOf) Constructor.

Method Summary

Modifier and Type	Method and Description
Collection<org.biopax.paxtools.io.gsea.GSEAEntry>	convert(Model model) Creates GSEA entries from the pathways contained in the model.
Set<String>	getAllowedOrganisms()
int	getMinNumOfGenesPerEntry() If this value is greater than 0, and the number of proteins/genes in a gene set is less than that value, then this gene set is to skip (no GSEA entry is written).
boolean	isSkipOutsidePathways() If true, then only GSEA entries that (genes) correspond to a Pathway are printed to the output.
void	setAllowedOrganisms(Set<String> allowedOrganisms)
void	setMinNumOfGenesPerEntry(int minNumOfGenesPerEntry)
void	setSkipOutsidePathways(boolean skipOutsidePathways)
void	writeToGSEA(Model model, OutputStream out) Converts model to GSEA (GMT) and writes to out.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GSEAConverter

public GSEAConverter()

Constructor.

GSEAConverter

public GSEAConverter(String database,
                     boolean crossSpeciesCheckEnabled)

Constructor. See class declaration for more information.

Parameters:

database - - identifier type, name of the resource, either the string value of the most of EntityReference's xref.db properties in the BioPAX data, e.g., "HGNC Symbol", "NCBI Gene", "RefSeq", "UniProt" or "UniProt knowledgebase", or the <namespace> part in normalized EntityReference URIs http://identifiers.org/<namespace>/<ID> (it depends on the actual data; so double-check before using in this constructor).

crossSpeciesCheckEnabled - - if true, enforces no cross species participants in output

GSEAConverter

public GSEAConverter(String database,
                     boolean crossSpeciesCheckEnabled,
                     boolean skipSubPathways)

Constructor. See class declaration for more information.

Parameters:

database - - identifier type, name of the resource, either the string value of the most of EntityReference's xref.db properties in the BioPAX data, e.g., "HGNC Symbol", "NCBI Gene", "RefSeq", "UniProt" or "UniProt knowledgebase", or the <namespace> part in normalized EntityReference URIs http://identifiers.org/<namespace>/<ID> (it depends on the actual data; so double-check before using in this constructor).

crossSpeciesCheckEnabled - - if true, enforces no cross species participants in output

skipSubPathways - - if true, do not traverse into any sub-pathways to collect entity references (useful when a model, such as converted to BioPAX KEGG data, has lots of sub-pathways, loops.)

GSEAConverter

public GSEAConverter(String database,
                     boolean crossSpeciesCheckEnabled,
                     Set<Provenance> skipSubPathwaysOf)

Constructor. See class declaration for more information.

Parameters:

database - - identifier type, name of the resource, either the string value of the most of EntityReference's xref.db properties in the BioPAX data, e.g., "HGNC Symbol", "NCBI Gene", "RefSeq", "UniProt" or "UniProt knowledgebase", or the <namespace> part in normalized EntityReference URIs http://identifiers.org/<namespace>/<ID>, such as 'hgnc.symbol', 'uniprot' (it depends on the actual data; so double-check before using in this constructor).

crossSpeciesCheckEnabled - - if true, enforces no cross species participants in output

skipSubPathwaysOf - - do not look inside sub-pathways of pathways of given data sources to collect entity references (useful when a model, such as converted to BioPAX KEGG data, has lots of sub-pathways, loops.)

Method Detail

isSkipOutsidePathways

public boolean isSkipOutsidePathways()

If true, then only GSEA entries that (genes) correspond to a Pathway are printed to the output.

Returns:

true/false

setSkipOutsidePathways

public void setSkipOutsidePathways(boolean skipOutsidePathways)

getAllowedOrganisms

public Set<String> getAllowedOrganisms()

setAllowedOrganisms

public void setAllowedOrganisms(Set<String> allowedOrganisms)

getMinNumOfGenesPerEntry

public int getMinNumOfGenesPerEntry()

If this value is greater than 0, and the number of proteins/genes in a gene set is less than that value, then this gene set is to skip (no GSEA entry is written).

Returns:

the min. value

setMinNumOfGenesPerEntry

public void setMinNumOfGenesPerEntry(int minNumOfGenesPerEntry)

writeToGSEA

public void writeToGSEA(Model model,
                        OutputStream out)
                 throws IOException

Converts model to GSEA (GMT) and writes to out. See class declaration for more information.

Parameters:

model - Model

out - output stream to write the result to

Throws:

IOException - when there's an output stream error

convert

public Collection<org.biopax.paxtools.io.gsea.GSEAEntry> convert(Model model)

Creates GSEA entries from the pathways contained in the model.

Parameters:

model - Model

Returns:

a set of GSEA entries