automate build

[balhoff]

Need to add a Makefile to automate build tasks, e.g.:

• Download ontologies
• Load ontologies into SciGraph
• Download PubMed XML
• Run Scala app to generate triples
• Load Blazegraph

[balhoff]

Download PubMed data (annual baseline): https://www.nlm.nih.gov/databases/download/pubmed_medline.html

[balhoff]

TODO

• [x] Jim send instructions for building and loading SciGraph to Erik
  • see if Scigraph can load ontologies using catalog file
• [x] Erik try to load ontologies into SciGraph
• [x] Erik start on Makefile, first to just curl PubMed files from FTP
  • example: https://github.com/NCI-Thesaurus/thesaurus-obo-edition/blob/master/src/ontology/Makefile
• [ ] Add instructions/make target for running in parallel on compute cluster
• [ ] Add command for loading Blazegraph