This document is not yet done. Please contact inutano@gmail.com for more details.
This is a guideline for biologists to translate the experimental protocols written in natural language to the Experimental Protocol Language (EPL) format.
added: <file:///data/rnaseq-readcount/rnaseq-readcount.cwl> <https://w3id.org/cwl/cwl#Workflow/steps> <file:///data/rnaseq-readcount/rnaseq-readcount.cwl#pfastq_dump> . | |
added: <file:///data/rnaseq-readcount/rnaseq-readcount.cwl> <https://w3id.org/cwl/cwl#outputs> <file:///data/rnaseq-readcount/rnaseq-readcount.cwl#STAR_logfiles> . | |
added: <file:///data/rnaseq-readcount/rnaseq-readcount.cwl> <https://w3id.org/cwl/cwl#outputs> <file:///data/rnaseq-readcount/rnaseq-readcount.cwl#STAR_readsPerGene> . | |
added: <file:///data/rnaseq-readcount/rnaseq-readcount.cwl> <https://w3id.org/cwl/cwl#outputs> <file:///data/rnaseq-readcount/rnaseq-readcount.cwl#rsem_genes_result> . | |
added: <file:///data/rnaseq-readcount/rnaseq-readcount.cwl> <https://w3id.org/cwl/cwl#outputs> <file:///data/rnaseq-readcount/rnaseq-readcount.cwl#rsem_isoforms_result> . | |
added: <file:///data/rnaseq-readcount/pfastq_dump.cwl> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <https://w3id.org/cwl/cwl#CommandLineTool> . | |
added: <file:///data/rnaseq-readco |
# Calculate average throughput for long read sequencing data | |
PREFIX sos: <http://purl.jp/bio/01/quanto/ontology/sos#> | |
PREFIX quanto: <http://purl.jp/bio/01/quanto/resource/> | |
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | |
PREFIX dct: <http://purl.org/dc/terms/> | |
PREFIX pav: <http://purl.org/pav/> | |
SELECT (AVG(?total_sequences AS ?average_throughput)) | |
FROM <http://quanto.dbcls.jp> |
# Retrieve top 50 high-throughput sequencing runs with filtering by base call quality and read length | |
PREFIX sos: <http://purl.jp/bio/01/quanto/ontology/sos#> | |
PREFIX quanto: <http://purl.jp/bio/01/quanto/resource/> | |
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | |
PREFIX dct: <http://purl.org/dc/terms/> | |
PREFIX pav: <http://purl.org/pav/> | |
SELECT ?id ?insdcId ?median_bc_quality ?total_sequences ?median_seq_length | |
FROM <http://quanto.dbcls.jp> | |
WHERE { |
#!/bin/bash | |
set -eu | |
USER_DIR="/home/galaxy" | |
if [[ -z `sudo ls / 2>/dev/null` ]]; then | |
echo "Permission denied: you have to be granted sudo privileges. Quit" | |
exit 1 | |
fi |
Application Name: ZOOMA (Automatic Ontology Mapper) | |
Version: 2.0 | |
Run at: 01:23.20, 16.12.16 | |
Run from: http://www.ebi.ac.uk/fgpt/zooma | |
PROPERTY TYPE PROPERTY VALUE ONTOLOGY TERM LABEL(S) ONTOLOGY TERM SYNONYM(S) CONFIDENCE ONTOLOGY TERM(S) ONTOLOGY(S) SOURCE(S) STUDY | |
[NO TYPE] 0-12h embryos N/A N/A Did not map N/A N/A N/A [UNKNOWN EXPERIMENTS] | |
[NO TYPE] 0-16h embryos N/A N/A Did not map N/A N/A N/A [UNKNOWN EXPERIMENTS] | |
[NO TYPE] 0-24h embryos N/A N/A Did not map N/A N/A N/A [UNKNOWN EXPERIMENTS] |
require 'set' | |
class Table | |
def initialize(table_path, tax_name, tax_rank) | |
@table = load_table(table_path, "\t") | |
@names = load_table(tax_name, "\t|\t").to_set | |
@ranks = load_table(tax_rank, "\t|\t").to_set | |
end | |
def load_table(path, chr) |
@prefix dcterms: <http://purl.org/dc/terms/> . | |
@prefix foaf: <http://xmlns.com/foaf/0.1/> . | |
@prefix pav: <http://purl.org/pav/> . | |
@prefix quanto: <http://purl.jp/bio/01/quanto/resource/> . | |
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . | |
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . | |
@prefix sos: <http://purl.jp/bio/01/quanto/ontology/sos#> . | |
@prefix uo: <http://purl.obolibrary.org/obo/> . | |
quanto:DRR000001_1_fastqc a sos:SequenceStatisticsReport; |
FROM ubuntu:trusty | |
RUN apt-get -y update && \ | |
apt-get install -y \ | |
wget \ | |
make \ | |
libncurses5-dev \ | |
libncursesw5-dev \ | |
libboost-all-dev \ | |
g++ && \ |
This document is not yet done. Please contact inutano@gmail.com for more details.
This is a guideline for biologists to translate the experimental protocols written in natural language to the Experimental Protocol Language (EPL) format.