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turbomam / nmdc-graphdb-build-2024-04-11.md
Last active April 25, 2024 18:47

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
turbomam / person_and_qualified_identifier_sets_data.yaml
Last active February 7, 2024 19:58
person_set:
- id: example:ck1
name: Clark Kent
primary_email: clark.kent@example.com
age_in_years: 33
- id: example:superman1
name: Superman
primary_email: superman@example.com
age_in_years: 33
- id: example:kalel1
@turbomam
turbomam / has_qualified_identifers_schema.yaml
Last active February 7, 2024 19:29
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
turbomam / graph_db_use_common.R
Created July 7, 2020 19:02
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
turbomam / graph_db_common_template.yaml
Created July 7, 2020 16:15
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
turbomam / graph_db_common.R
Last active July 7, 2020 16:12
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
turbomam / turbo_R_setup.template.yaml
Last active June 16, 2020 17:50
global configuration for TURBO R scripts
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
turbomam / turbo_R_setup.R
Last active July 7, 2020 21:14
global turbo setup
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)