obo2graphNEL {gwascat} | R Documentation

## convert a typical OBO text file to a graphNEL instance (using Term elements)

### Description

convert a typical OBO text file to a graphNEL instance (using Term elements)

### Usage

    obo2graphNEL(obo, kill = "\\[Typedef\\]", killTrailSp=TRUE)
    node2uri(nn)
    uri2node(us)

### Arguments

`obo` | string naming a file in OBO format
`nn` | node name for converted graph, generally of form EFO:nnnnnnn
`us` | URI string from GWAS catalog annotation MAPPED\_TRAIT\_URI
`kill` | entity types to be excluded from processing – probably this should be in a 'keep' form, but for now this works.
`killTrailSp` | In the textual version of EFO ca. Aug 2015, there is a trailing blank in the tag field defining EFO:0000001, which is not present in references to this term. Set this to TRUE to eliminate this, or graphNEL construction will fail to validate.

### Details

Very rudimentary list and grep operations are used to retain sufficient information to map the DAG to a graphNEL, using formal term identifiers as node names and 'is-a' relationships as edges, and term names and other metadata are assigned to nodeData components.

### Value

a graphNEL instance

### Note

The OBO for Human Disease ontology is serialized as text with this package.

### Author(s)

VJ Carey <stvjc@channing.harvard.edu>

### References

For use with human disease ontology, http://www.obofoundry.org/cgi-bin/detail.cgi?id=disease_ontology

### Examples

    data(efo.obo.g)
    hn = nodes(efo.obo.g)[1:5]
    hn
    nodeData(efo.obo.g, hn[5])

[Package gwascat version 2.12.0 Index]