Loading GAFs Into Solr

loading gene association files into Solr

Introduction

Loading a single gaf:

owltools http://purl.obolibrary.org/obo/go.owl --load-gaf-solr http://localhost:8080/solr/ gene_association.mgi.gz

Loading multiple gafs:

owltools http://purl.obolibrary.org/obo/go.owl --load-gafs-solr http://localhost:8080/solr/ gene_association.*.gz

Notes

Ontologies

You can use a file or url in either obo or owl for loading the ontology. Standard URLs are recommended (in future OWLTools will have support for XML catalogs, allowing you to use local copies of external URLs)

It's recommended you also include the slimmed version of ncbitaxonomy, as well as any external ontologies used in c16 for that gaf. You can list multiple ontologies or use an ontology that has owl:imports (the latter will be recommended in future)

E.g.

owltools http://purl.obolibrary.org/obo/go.owl http://purl.obolibrary.org/obo/cl.owl http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl --load-gafs-solr http://localhost:8080/solr/ gene_association.mgi.gz

GAFs

You can specify URLs or files, gzipped or ucompressed.

TODO - instructions for the giant uniprot file..