SPARQL BioPortal - Revision history

JenniferVendetti at 01:16, 5 January 2024

2024-01-05T01:16:32Z

JenniferVendetti: Add a deprecation and shut down notification for the open SPARQL endpoint

2024-01-05T01:13:25Z

Add a deprecation and shut down notification for the open SPARQL endpoint

Manuel Salvadores: /* Federated SPARQL queries */

2013-01-25T20:00:55Z

Federated SPARQL queries

Manuel Salvadores: /* Federated SPARQL queries */

2013-01-25T18:32:23Z

Federated SPARQL queries

Manuel Salvadores: /* Federated SPARQL queries */

2013-01-25T18:29:49Z

Federated SPARQL queries

Manuel Salvadores: /* Federated SPARQL queries */

2013-01-25T18:21:42Z

Federated SPARQL queries

Manuel Salvadores: /* Mappings */

2013-01-25T18:09:31Z

Mappings

Manuel Salvadores: /* Slides */

2013-01-23T04:07:00Z

Slides

Manuel Salvadores: /* Mappings */

2013-01-23T03:27:41Z

Mappings

Manuel Salvadores: /* Mappings */

2013-01-23T03:02:00Z

Mappings

@@ Line 3: / Line 3: @@
 The BioPortal open SPARQL endpoint is deprecated and shut down. This decision was made due to lack of resources to maintain the service. We understand the impact this may have on your workflows and apologize for any inconvenience caused.
-To continue accessing data in the BioPortal ontology repository, please use our actively maintained [https://data.bioontology.org/documentation REST API].<br /><br />
+To continue accessing data in the BioPortal ontology repository, please use our actively maintained [https://data.bioontology.org/documentation REST API].
 <hr /><br />

← Older revision		Revision as of 01:13, 5 January 2024
Line 1:		Line 1:
		+	<span style="color:red; font-weight:bold">PLEASE NOTE:</span>
		+
		+	The BioPortal open SPARQL endpoint is deprecated and shut down. This decision was made due to lack of resources to maintain the service. We understand the impact this may have on your workflows and apologize for any inconvenience caused.
		+
		+	To continue accessing data in the BioPortal ontology repository, please use our actively maintained [https://data.bioontology.org/documentation REST API].<br /><br />
		+	<hr /><br />
		+
	NCBO is releasing a free and open SPARQL endpoint to query ontologies hosted in the BioPortal ontology repository. This SPARQL service, that is in BETA status, is stable for testing by our community of users. If you encounter any errors or unexpected behavior please report it to us [mailto:support@bioontology.org support@bioontology.org].		NCBO is releasing a free and open SPARQL endpoint to query ontologies hosted in the BioPortal ontology repository. This SPARQL service, that is in BETA status, is stable for testing by our community of users. If you encounter any errors or unexpected behavior please report it to us [mailto:support@bioontology.org support@bioontology.org].

@@ Line 173: / Line 173: @@
 SPARQL Federation can be used with the Jena ARQ library. The Jena ARQ library handles the SERVICE SPARQL construct and directs sets of triple patterns to different endpoint and handles the joins.
-BioPortal offers two different SPARQL endpoints one for ontologies (metadata and terms) and a second one for mappings. There are use cases that require SPARQL queries containing joins from both endpoints. This can be achieved by using SPARQL federation and the SERVICE construct. The following example looks at the CSP term 'Neck' and retrieves the sources for all the mappings for that term (from the mapping endpoint). For each of those targets then gets the parents (from the ontologies endpoints). Notice the change in the SERVICE endpoint from 'mappings' in the first block to 'ontologies' in the second one.
+BioPortal offers two different SPARQL endpoints one for ontologies (metadata and terms) and a second one for mappings. There are use cases that require queries with joins from both endpoints. This can be achieved by using SPARQL federation and the SERVICE feature (SPARQL 1.1). The following example looks at the CSP term 'Neck' and retrieves the sources for all the mappings for that term (from the mapping endpoint). For each of those sources then gets the parents (from the ontologies endpoint). Notice the change in the SERVICE endpoints from 'mappings' in the first block to 'ontologies' in the second one.
 <pre>

← Older revision		Revision as of 18:32, 25 January 2013
Line 190:		Line 190:
	</pre>		</pre>

		+	Full example: https://github.com/ncbo/sparql-code-examples/blob/master/java/src/org/ncbo/stanford/sparql/examples/JenaARQFederationExample.java

	<div style="margin-top: 10px; background: #F6F9ED; padding: 6px; border: 1px solid #aaaaaa; margin-bottom: 20px;">		<div style="margin-top: 10px; background: #F6F9ED; padding: 6px; border: 1px solid #aaaaaa; margin-bottom: 20px;">

@@ Line 173: / Line 173: @@
 SPARQL Federation can be used with the Jena ARQ library. The Jena ARQ library handles the SERVICE SPARQL construct and directs sets of triple patterns to different endpoint and handles the joins.
-<div style="margin-top: 10px; background: #F6F9ED; padding: 6px; border: 1px solid #aaaaaa; margin-bottom: 20px;">
+BioPortal offers two different SPARQL endpoints one for ontologies (metadata and terms) and a second one for mappings. There are use cases that require SPARQL queries containing joins from both endpoints. This can be achieved by using SPARQL federation and the SERVICE construct. The following example looks at the CSP term 'Neck' and retrieves the sources for all the mappings for that term (from the mapping endpoint). For each of those targets then gets the parents (from the ontologies endpoints). Notice the change in the SERVICE endpoint from 'mappings' in the first block to 'ontologies' in the second one.
 <pre>
@@ Line 183: / Line 180: @@
 PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
 SELECT DISTINCT ?mappedParent WHERE {
-     SERVICE <http://stagesparql.bioontology.org/mappings/sparql/?apikey=YOUR API KEY HERE> {
+     SERVICE <http://sparql.bioontology.org/mappings/sparql/?apikey=YOUR API KEY HERE> {
          ?mapping map:target <http://purl.bioontology.org/ontology/CSP/0468-5952> .
          ?mapping map:source ?source .
+     }
-     SERVICE <http://stagesparql.bioontology.org/ontologies/sparql/?apikey=YOUR API KEY HERE> {
+     SERVICE <http://sparql.bioontology.org/ontologies/sparql/?apikey=YOUR API KEY HERE> {
          ?source rdfs:subClassOf ?mappedParent .
+     }
+}
 </pre>
 === Partial or Incomplete Results ===

← Older revision		Revision as of 18:21, 25 January 2013
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	=== Federated SPARQL queries ===		=== Federated SPARQL queries ===
		+
		+	SPARQL Federation can be used with the Jena ARQ library. The Jena ARQ library handles the SERVICE SPARQL construct and directs sets of triple patterns to different endpoint and handles the joins.
		+
		+	<div style="margin-top: 10px; background: #F6F9ED; padding: 6px; border: 1px solid #aaaaaa; margin-bottom: 20px;">
		+	<b>Note</b> SPARQL Federation can be used grammatically only. Our web front-end at http://sparql.bioontology.org/ does not support mediation for the SERVICE clause.
		+	</div>
		+
		+
		+	<pre>
		+	PREFIX map: <http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#>
		+	PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
		+	PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
		+	SELECT DISTINCT ?mappedParent WHERE {
		+	SERVICE <http://stagesparql.bioontology.org/mappings/sparql/?apikey=YOUR API KEY HERE> {
		+	?mapping map:target <http://purl.bioontology.org/ontology/CSP/0468-5952> .
		+	?mapping map:source ?source .
		+	}
		+	SERVICE <http://stagesparql.bioontology.org/ontologies/sparql/?apikey=YOUR API KEY HERE> {
		+	?source rdfs:subClassOf ?mappedParent .
		+	}
		+	}
		+	</pre>

	=== Partial or Incomplete Results ===		=== Partial or Incomplete Results ===

@@ Line 168: / Line 168: @@
 In this case this query returns a count of 4393 solutions.
 It is important to notice that for mappings we use version based ontology URIs and not the ones that are based on acronyms.
 === Partial or Incomplete Results ===

@@ Line 176: / Line 176: @@
 === Slides ===
+* '''''BioPortal SPARQL presentation at ISWC 2012''''' http://www.slideshare.net/manuelso/using-sparql-to-query-bioportal-ontologies-and-metadata
 * '''''BioPortal SPARQL tutorial from SWAT4LS 2011''''' http://www.bioontology.org/wiki/index.php/File:Whetzel_SPARQL.pdf
 * '''''NCBO Hackathon slides for the SPARQL tutorial''''' http://www.stanford.edu/~manuelso/ncbohack/index.html

← Older revision		Revision as of 03:27, 23 January 2013
Line 99:		Line 99:

	=== Mappings ===		=== Mappings ===
		+
		+	<div style="margin-top: 10px; background: #F6F9ED; padding: 6px; border: 1px solid #aaaaaa; margin-bottom: 20px;">
		+	Notice that as of January 30th (2013) we are hosting the mappings in a separate endpoint. This eases our regular mapping updates. Programmatic queries that target mapping data need to use the following endpoint: http://sparql.bioontology.org/mappings/sparql
		+	</div>

	The mapping data in the triple store is stored in the following graphs:		The mapping data in the triple store is stored in the following graphs:

@@ Line 147: / Line 147: @@
 PREFIX map: <http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#>
 SELECT DISTINCT ?target WHERE {
-   ?s maps:source <http://purl.obolibrary.org/obo/DOID_8545>;
+   ?s map:source <http://purl.obolibrary.org/obo/DOID_8545>;
-      maps:target ?target .
+      map:target ?target .
+}
 </pre>
@@ Line 157: / Line 157: @@
 PREFIX map: <http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#>
 SELECT (count(?m) as ?c) WHERE {
-   ?m maps:source_ontology <http://bioportal.bioontology.org/ontologies/1032> ;
+   ?m map:source_ontology <http://bioportal.bioontology.org/ontologies/1032> ;
-       maps:target_ontology  <http://bioportal.bioontology.org/ontologies/1000> .
+       map:target_ontology  <http://bioportal.bioontology.org/ontologies/1000> .
+}
 </pre>