turbomam

from project.Makefile in nmdc-schema repo: make squeaky-clean all test

one output: project/owl/nmdc.owl.ttl

@prefix nmdc: <https://w3id.org/nmdc/> .

nmdc:nmdc a owl:Ontology ;
    rdfs:label "NMDC" ;
    dcterms:license "https://creativecommons.org/publicdomain/zero/1.0/" ;

turbomam

person_set:
  - id: example:ck1
    name: Clark Kent
    primary_email: [email protected]
    age_in_years: 33
  - id: example:superman1
    name: Superman
    primary_email: [email protected]
    age_in_years: 33
  - id: example:kalel1

turbomam

name: has-qualified-identifers-schema
see_also:
- https://turbomam.github.io/reactions-for-owl
- https://gist.githubusercontent.com/turbomam/56956b2d7761fc669d2e8ab15e5cb1f0/raw/64f40292b81d3e04f873e076ae66756059651654/has_qualified_identifers_schema.yaml
id: http://example.com/has_qualified_identifers_schema

prefixes:
  has_qualified_identifers: http://example.com/has_qualified_identifers_schema/
  linkml: https://w3id.org/linkml/
  example: https://example.org/

turbomam

library(devtools)

# requires a properly formatted "graph_db_common.yaml" in the home directory of the user who started this script
# see https://gist.github.com/turbomam/b11adbbff02d5abddaf76d30ba3249a8 for template
devtools::source_gist(id = "https://gist.github.com/turbomam/f620e9e9f042b643e47de730328e3e83",
                      sha1 = "85b1ac5c19571687aed9268e001051547c7998ed",
                      filename = "graph_db_common.R")

turbomam

default:
    # enter local values and save in user's home directory as graph_db_common.yaml 
    # GraphDB standard port = 7200
    # should probably split into server address and port variables
    my.graphdb.base: 'http://graphdbserver:graphdbport'
    my.selected.repo: ''
    my.graphdb.username: ''
    my.graphdb.pw: ''
    # Solr standard port = 8983
    med.map.kb.solr.host: ''

turbomam

options(java.parameters = "-Xmx6g")

# see also https://jangorecki.gitlab.io/data.cube/library/data.table/html/dcast.data.table.html
library(config)
# library(dplyr)
# library(ggplot2)
library(httr)
# library(igraph)
library(jsonlite)
# library(randomForest)

turbomam

default:
    # replace <SECRET>s with settings appropriate for your environment 
    # and save as ~/turbo_R_setup.yaml
    # 
    # still need to make file paths relative
    #
    pds.host: <SECRET>
    pds.port: <SECRET>
    pds.database: <SECRET>
    pds.user: <SECRET>

turbomam

options(java.parameters = "-Xmx6g")

# see also https://jangorecki.gitlab.io/data.cube/library/data.table/html/dcast.data.table.html
library(config)
library(dplyr)
library(ggplot2)
library(httr)
library(igraph)
library(jsonlite)
library(randomForest)