marco-brandizi

#!/usr/bin/env python
from __future__ import print_function, absolute_import, division

import logging
import os

from errno import EACCES
from os.path import realpath
from threading import Lock

marco-brandizi

from threading import Thread
from time import sleep

# Support for background execution
alive_flag = True
def alive_msg_task ():
    while alive_flag:
        sleep ( 30 )
        print ( "Still working, please wait...", end = " ", flush = True )
    print ( "\nDownload completed" )

marco-brandizi

PREFIX bk: <http://knetminer.org/data/rdf/terms/biokno/>	PREFIX bkr: <http://knetminer.org/data/rdf/resources/>
PREFIX bka: <http://knetminer.org/data/rdf/terms/biokno/attributes/>	PREFIX bkg: <http://knetminer.org/data/rdf/resources/graphs/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>	PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>	PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX dcterms: <http://purl.org/dc/terms/>	PREFIX agri: <http://agrischemas.org/>
PREFIX bioschema: <http://bioschemas.org/>	PREFIX schema: <http://schema.org/>

SELECT ?pubTitle ?geneName ?scoreStr ?condLabel ?condTerm
{
  ?pub a agri:ScholarlyPublication;

marco-brandizi

Go here: https://knetminer.com/Triticum_aestivum/

Search keywords:
“slow growth” OR “dwarf stature” OR “SUMO Activating Enzyme Complex” OR “after 281 spraying mutant plants” OR “coleoptile length” OR “growth” OR “cell division” OR “cell 282 proliferation” OR “inflorescence” OR “carbohydrate metabolism” OR “photosynthesis” 283 OR “grain number” OR “grain weight” OR “grain hardness” OR “spikelets” OR “tillers” 284 OR “photoperiod” OR “vernalization” OR “vernalisation”

Gene List:
TraesCS3B02G319000
TraesCS3D02G284900
TraesCS7A02G356100
TraesCS7A02G356200

marco-brandizi

#!/usr/bin/env bash

# Downloads multiple files available from an HTML URL, typically the web listing of a directory, 
# as it is rendered by many web servers. 
# ==> Requires lftp
#
set -e

# Example: 
#   ./files-from-url.sh https://knetminer.com/downloads/agri-schemas/gxa/v202110/ gxa

marco-brandizi

package info.marcobrandizi.test.jdk11;

/*
 * These deps are needed:
 *	org.apache.commons:commons-lang3:3.9
 *	com.machinezoo.noexception:noexception:1.3.2
*/

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;

marco-brandizi

Counts the data sources used in the wheat dataset. Try it [here][10].

PREFIX bk: <http://knetminer.org/data/rdf/terms/biokno/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX bkg: <http://knetminer.org/data/rdf/resources/graphs/>

SELECT DISTINCT ?dataSource (COUNT (DISTINCT ?e) AS ?resources)
FROM bkg:wheat
{

marco-brandizi

var o = new Foo ("one");
map.put ( o, o )
...
var o1 = new Foo ( "one" )
...
var o2 = map.get ( o1 ) // fetches o if .equals()/.hashCode() tells that they're equal

marco-brandizi

// Notice the static imports, these makes the syntax below so compact
// (and the IDE will auto-define this section)
import ondex.fluent.EntityFilter.FluentGraphWrapper
import static ondex.fluent.EntityFilter.byType;
import static ondex.fluent.EntityFilter.byDoubleAttribute;
import static ondex.fluent.ConceptFilter.byAccession;
import static ondex.fluent.Filter.byRegEx;
import static ondex.fluent.EntityComparator;
import static ondex.fluent.ConceptMapper.fromRelations;
import static ondex.fluent.RelationMapper.toConcepts;

marco-brandizi

MATCH (pway:Path{prefName:"chlorophyll a biosynthesis I"}) - [po:part_of] - (comp)
RETURN *
LIMIT 20