Skip to content

Instantly share code, notes, and snippets.

View inutano's full-sized avatar

Tazro Inutano Ohta inutano

122 followers · 129 following
View GitHub Profile
@inutano
inutano / SAMD00000345.ttl
Last active February 22, 2019 05:49
@base <http://schema.org/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
<http://identifiers.org/biosample/SAMD00000345> a <DataRecord>,
<BioChemEntity>,
<http://purl.obolibrary.org/obo/OBI_0000747>;
<additionalProperty> [
a <PropertyValue>;
<name> "broad-scale environmental context";
<value> "n.a."
@inutano
inutano / SAMD00000345.jsonld
Last active February 22, 2019 05:49
{"@context":{"@base":"http://schema.org/","@vocab":"http://schema.org/","url":{"@type":"http://www.w3.org/2001/XMLSchema#string"},"dateCreated":{"@type":"http://www.w3.org/2001/XMLSchema#dateTime"},"dateModified":{"@type":"http://www.w3.org/2001/XMLSchema#dateTime"},"Sample":{"@id":"http://purl.obolibrary.org/obo/OBI_0000747"},"name":{"@type":"http://www.w3.org/2001/XMLSchema#string"},"value":{"@type":"http://www.w3.org/2001/XMLSchema#string"}},"@type":["DataRecord","BioChemEntity","Sample"],"identifier":"SAMD00000345","dateCreated":"2014-07-30T00:00:00Z","dateModified":"2019-02-18T00:01:52.977Z","isPartOf":{"@type":"Dataset","@id":"https://www.ebi.ac.uk/biosamples/samples"},"datasetPartOf":{"@type":"Dataset","@id":"https://www.ebi.ac.uk/biosamples/samples"},"@id":"http://identifiers.org/biosample/SAMD00000345","name":"SAMD00000345","description":"type strain of Lactobacillus oryzae","url":"https://www.ebi.ac.uk/biosamples/sample/SAMD00000345","additionalProperty":[{"@type":"PropertyValue","name":"INSDC cente
@inutano
inutano / SAMEA1652233.jsonld
Created November 13, 2018 14:02
{
"@context": "http://schema.org",
"@type": "DataRecord",
"identifier": "biosamples:SAMEA1652233",
"dateCreated": "2012-12-31T00:00:00Z",
"dateModified": "2018-01-20T06:06:51.993Z",
"mainEntity": {
"@context": [
"http://schema.org",
{
@inutano
inutano / SAMEA1652233.jsonld
Last active November 13, 2018 14:02
{
"@context": "http://schema.org",
"@type": "DataRecord",
"identifier": "biosamples:SAMEA1652233",
"dateCreated": "2012-12-31T00:00:00Z",
"dateModified": "2018-01-20T06:06:51.993Z",
"mainEntity": {
"@context": [
"http://schema.org",
{
@inutano
inutano / PRJDB4503.ttl
Created October 29, 2018 05:34
@prefix bao: <http://www.bioassayontology.org/bao#> .
@prefix biocow: <http://bio.cow/> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix ddbj-tax: <http://ddbj.nig.ac.jp/ontologies/taxonomy/> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix pav: <http://purl.org/pav/> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix sio: <http://semanticscience.org/resource/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@inutano
inutano / PRJDB4503.json
Created October 29, 2018 05:32
{
"@context": "https://me.com/jsonld_bioproject_context.json",
"URI": "http://identifiers.org/bioproject/PRJDB4503",
"entry": "biocow:BioProject",
"Submission": {
"date_submitted": "2016-01-13",
"date_last_update": "2016-01-16",
"access": "public",
"organization": {
"organization_name": "Center for Ecological Research, Kyoto University",
@inutano
inutano / basesPerSite.sh
Created July 17, 2018 07:02
#!/bin/sh
# Get ID-total sequences from Quanto data set and calculate total
RDF_PORTAL_EP="http://integbio.jp/rdf/sparql"
QUERY=$(
CAT <<'EOF'
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX sos: <http://purl.jp/bio/01/quanto/ontology/sos#>
@inutano
inutano / iterate_wf.sh
Created June 30, 2018 20:18
#!/bin/sh
find ${HOME}/.pitagora-cwl/workflows -name 'README.md' | \
xargs -I{} grep curl {} | \
awk '{ print $NF }' | \
tr -d '"' | \
while read wf; do
for i in $(seq 10); do
rm -fr ${HOME}/work/*${wf}*
bash ${HOME}/.pitagora-cwl/test/bin/run-cwl ${wf}
rm -fr /tmp/tmp*
@inutano
inutano / half_violin_with_raw_data.R
Created February 22, 2018 02:37 — forked from jbburant/half_violin_with_raw_data.R
## GOAL:
## re-create a figure similar to Fig. 2 in Wilson et al. (2018),
## Nature 554: 183-188. Available from:
## https://www.nature.com/articles/nature25479#s1
##
## combines a boxplot (or violin) with the raw data, by splitting each
## category location in two (box on left, raw data on right)
# initial set-up ----------------------------------------------------------
@inutano
inutano / makelist.sh
Created November 27, 2017 07:11
#!/bin/bash
#
# ./makelist.sh
#
set -eu
#
# Input tables
#