andrawaag’s gists

andrawaag / apacheredirectforRDF

Created January 24, 2013 12:49

	<VirtualHost *:80>
	ServerName rdf.wikipathways.org


	RewriteEngine on
	RewriteRule ^(.*)$ http://sparql.wikipathways.org/?default-graph-uri=&query=DESCRIBE+<http\:\/\/%{HTTP_HOST}$1> [P]
	ProxyPassReverse / http://sparql.wikipathwys.org/

	# Possible values include: debug, info, notice, warn, error, crit,
	# alert, emerg.

andrawaag / gist:4642824

Created January 26, 2013 15:03

SPARQL query to find streaming media providers through dbpedia

	SELECT DISTINCT * WHERE {
	?resource <http://dbpedia.org/ontology/type> <http://dbpedia.org/resource/Streaming_media> .
	?resource <http://xmlns.com/foaf/0.1/isPrimaryTopicOf> ?wikipediaPage .
	?resource <http://dbpedia.org/property/url> ?website .
	}

andrawaag / GPML representation of a Directed Interaction

Created February 4, 2013 17:13

GPML file of a directed Interaction in WikiPathways

	<?xml version="1.0" encoding="UTF-8"?>
	<Pathway xmlns="http://genmapp.org/GPML/2010a" Name="untitled" Data-Source="COPIED">
	<Graphics BoardWidth="582.0" BoardHeight="369.0" />
	<DataNode TextLabel="GeneProduct" GraphId="eee89" Type="GeneProduct">
	<Graphics CenterX="512.0" CenterY="329.0" Width="80.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" />
	<Xref Database="" ID="" />
	</DataNode>
	<DataNode TextLabel="GeneProduct" GraphId="da3fe" Type="GeneProduct">
	<Graphics CenterX="352.0" CenterY="329.0" Width="80.0" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" />
	<Xref Database="" ID="" />

andrawaag / GPMLsniplet

Created February 5, 2013 16:57

GPML sniplet from WP TCA cycle pathway

	<?xml version="1.0" encoding="UTF-8"?>
	<Pathway xmlns="http://genmapp.org/GPML/2010a" Name="untitled" Data-Source="COPIED">
	<Graphics BoardWidth="177.2833366394043" BoardHeight="500.1666564941406" />
	<DataNode TextLabel="MDH1" GraphId="bceb9" Type="GeneProduct">
	<Attribute Key="org.pathvisio.model.BackpageHead" Value="MDH1" />
	<Graphics CenterX="113.46667098999023" CenterY="415.6666564941406" Width="67.63333129882812" Height="20.0" ZOrder="32768" FontSize="10" Valign="Middle" />
	<Xref Database="Entrez Gene" ID="459271" />
	</DataNode>
	<DataNode TextLabel="Malate" GraphId="b6f7a" Type="Metabolite">
	<Attribute Key="org.pathvisio.model.BackpageHead" Value="Malate" />

andrawaag / gist:4716000

Last active December 12, 2015 04:39

RDF with the WP vocabulary included

	@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
	@prefix ns1: <http://rdf.wikipathways.org/Pathway/WP881_r41576/DataNode/> .
	@prefix wp: <http://vocabularies.wikipathways.org/wp#> .
	@prefix dc: <http://purl.org/dc/elements/1.1/> .
	@prefix dcterms: <http://purl.org/dc/terms/> .
	@prefix wprdf: <http://rdf.wikipathways.org/Pathway/> .
	@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
	@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
	<http://rdf.wikipathways.org/Pathway/WP881_r41576/DataNode/bceb9> rdf:type wp:GeneProduct;
	dc:identifier <http://identifiers.org/ncbigene/459271> .

andrawaag / gist:4716028

Created February 5, 2013 17:22

RDF with only GPML vocabulary

	@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
	@prefix ns1: <http://rdf.wikipathways.org/Pathway/WP881_r41576/DataNode/> .
	@prefix wp: <http://vocabularies.wikipathways.org/wp#> .
	@prefix dc: <http://purl.org/dc/elements/1.1/> .
	@prefix dcterms: <http://purl.org/dc/terms/> .
	@prefix wprdf: <http://rdf.wikipathways.org/Pathway/> .
	@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
	@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
	<http://rdf.wikipathways.org/Pathway/WP881_r41576/DataNode/bceb9> dc:identifier <http://identifiers.org/ncbigene/459271> ;
	dcterms:isPartOf wprdf:WP881_r41576 ;

andrawaag / downloadOPSWpPw.sh

Created March 14, 2013 14:05

Shell script for the RDF serializer for the WikiPathways Pathways with the Analysis tag

	rm -rf /tmp/GPML
	mkdir /tmp/GPML
	rm -rf /tmp/OPSWPRDF
	mkdir /tmp/OPSWPRDF
	rm -rf /tmp/OPSWIKIDUMP
	mkdir /tmp/OPSWIKIDUMP
	wget -O /tmp/OPSWIKIDUMP/Anopheles%20gambiae.zip "http://www.wikipathways.org//wpi/batchDownload.php?species=Anopheles%20gambiae&fileType=gpml&tag=Curation:AnalysisCollection"
	wget -O /tmp/OPSWIKIDUMP/Arabidopsis%20thaliana.zip "http://www.wikipathways.org//wpi/batchDownload.php?species=Arabidopsis%20thaliana&fileType=gpml&tag=Curation:AnalysisCollection"
	wget -O /tmp/OPSWIKIDUMP/Bos%20taurus.zip "http://www.wikipathways.org//wpi/batchDownload.php?species=Bos%20taurus&fileType=gpml&tag=Curation:AnalysisCollection"
	wget -O /tmp/OPSWIKIDUMP/Bacillus%20subtilis.zip "http://www.wikipathways.org//wpi/batchDownload.php?species=Bacillus%20subtilis&fileType=gpml&tag=Curation:AnalysisCollection"

andrawaag / WP2CWSerializer.construct

Last active December 14, 2015 23:08

	CONSTRUCT {?concept a skos:Concept .
	?concept skos:prefLabel ?label .
	?concept skos:notation ?identifier .
	}
	WHERE {
	?concept a skos:Concept .
	OPTIONAL { ?resource2 a gpml:requiresCurationAttention . FILTER(?resource2 = ?concept) }
	FILTER(!bound(?resource2))
	?concept rdfs:label ?label .
	?concept dc:identifier ?identifier.

andrawaag / linksetGenerationWp.construct

Created March 15, 2013 16:15

	construct {?identifier skos:relatedMatch ?relatedId .
	}
	where {
	?uniprotconcept dc:identifier ?identifier .
	?uniprotconcept wp:bdbEnsembl ?relatedId .
	}

andrawaag / test

Created March 20, 2013 12:55

	CONSTRUCT {?concept a skos:Concept .
	?concept skos:prefLabel ?label .
	?concept skos:notation ?identifier .
	}
	WHERE {
	?concept a skos:Concept .
	OPTIONAL { ?resource2 a gpml:requiresCurationAttention . FILTER(?resource2 = ?concept) }
	FILTER(!bound(?resource2))
	?concept rdfs:label ?label .
	?concept dc:identifier ?identifier.