Ontology Recommender Web service - Revision history

Fergerson at 20:28, 12 September 2011

2011-09-12T20:28:16Z

2011-09-12T20:27:41Z

2011-09-10T23:45:36Z

Service Signature

2011-09-10T23:45:02Z

Service Signature

2011-09-10T01:19:40Z

Service Signature

2011-09-09T21:14:46Z

2011-09-07T23:17:10Z

References

2011-09-07T21:16:52Z

Background

2011-09-07T21:16:01Z

Presentation & Demonstration

2011-09-07T21:14:50Z

Documentation & References

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 * August 2011 - Production release of ontology recommender. http://bioportal.bioontology.org/recommender
 * Prototypes (These will be taken down by the end of 2011.)
 ** November 2009 - Second prototype (v1.1) for the recommender: http://obs.bioontology.org/recommender/Recommender1.1.html
 ** March 2009 - First prototype of UI for the recommender: http://keg.cs.uvic.ca/ncbo/obs/OBARecommender.html
 ** February 2009 - The first prototype (v0) has been released for testing and evaluation. Please check it out: http://obs.bioontology.org/recommender/Recommender.html

@@ Line 39: / Line 39: @@
 === Versions (prototypes & releases) ===
-* November 2009 - Second prototype (v1.1) UI in stage BioPortal http://bioportal.bioontology.org/recommender
+* August 2011 - Production release of ontology recommender. http://bioportal.bioontology.org/recommender
-* November 2009 - Second prototype (v1.1) for the recommender: http://obs.bioontology.org/recommender/Recommender1.1.html
+* Prototypes (These will be taken down by the end of 2011.)
-* March 2009 - First prototype of UI for the recommender: http://keg.cs.uvic.ca/ncbo/obs/OBARecommender.html
+** March 2009 - First prototype of UI for the recommender: http://keg.cs.uvic.ca/ncbo/obs/OBARecommender.html
-* February 2009 - The first prototype (v0) has been released for testing and evaluation. Please check it out: http://obs.bioontology.org/recommender/Recommender.html
+** February 2009 - The first prototype (v0) has been released for testing and evaluation. Please check it out: http://obs.bioontology.org/recommender/Recommender.html
 === Evaluation ===

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 * '''Optional arguments:'''
 ** format=[simpleText/text/xml] – the output format (default: xml)
-** ontologyids=<ontologyid>,<ontologyid>… - limits the recommendations to specific ontologies, using their virtual IDs (default: all ontologies)
+** ontologyids=<ontologyid>,<ontologyid>… - limits the recommendations to specific ontologies, identified by virtual IDs (default: all ontologies)
 === References ===

@@ Line 30: / Line 30: @@
 * '''Optional arguments:'''
 ** format=[simpleText/text/xml] – the output format (default: xml)
-** ontologyids=<ontologyid>,<ontologyid>… - limits the recommendations to specific ontologies (default: all ontologies)
+** ontologyids=<ontologyid>,<ontologyid>… - limits the recommendations to specific ontologies, using their virtual IDs (default: all ontologies)
 === References ===

@@ Line 26: / Line 26: @@
 * '''Example''': http://rest.bioontology.org/recommender
 * '''Required arguments:'''
-** text – the text to be scan for ontology recommendations
+** text – the text to be scanned for ontology recommendations
 * '''Optional arguments:'''

← Older revision		Revision as of 21:14, 9 September 2011
Line 19:		Line 19:

	* See also the [[Annotator Web service]] wiki page.		* See also the [[Annotator Web service]] wiki page.
		+
		+	=== Service Signature ===
		+
		+	* '''Signature''': ./recommender
		+	* '''HTTP Method''': POST
		+	* '''Example''': http://rest.bioontology.org/recommender
		+	* '''Required arguments:'''
		+	** text – the text to be scan for ontology recommendations
		+
		+	* '''Optional arguments:'''
		+	** format=[simpleText/text/xml] – the output format (default: xml)
		+	** ontologyids=<ontologyid>,<ontologyid>… - limits the recommendations to specific ontologies (default: all ontologies)

	=== References ===		=== References ===

@@ Line 23: / Line 23: @@
 * Please refer to:
 ** Jonquet C, Musen MA, Shah NH. Building a biomedical ontology recommender web service. J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S1. PubMed [http://www.ncbi.nlm.nih.gov/pubmed/20626921 PMID: 20626921]; PubMed Central PMCID: PMC2903720.
-** Clement Jonquet, Nigam H. Shah, Mark A. Musen, Prototyping a Biomedical Ontology Recommender Service, Bio-Ontologies: Knowledge in Biology, SIG, ISMBECCB 2009, pp. 65-68, Stockholm, Sweden, July 2009. [http://bio-ontologies.man.ac.uk/2009/programme.html SIG's web site] click on "programme booklet"
+** Clement Jonquet, Nigam H. Shah, Mark A. Musen, Prototyping a Biomedical Ontology Recommender Service, Bio-Ontologies: Knowledge in Biology, SIG, ISMBECCB 2009, pp. 65-68, Stockholm, Sweden, July 2009. [http://bmir.stanford.edu/publications/view.php/prototyping_a_biomedical_ontology_recommender_service Stanford BMIR Publications] [http://bio-ontologies.man.ac.uk/2009/programme.html SIG's web site] click on "programme booklet"
 === Versions (prototypes & releases) ===

@@ Line 6: / Line 6: @@
 [[Image:Recommender_method.png|thumb|NCBO Recommender Web Service workflow]]
-Please try the NCBO Recommender Web Service prototype: http://stage.bioontology.org/recommender
+Please try the Ontology Recommender: http://bioportal.bioontology.org/recommender
 === Contacts ===

@@ Line 1: / Line 1: @@
 ''To automatically recommend an ontology to use for semantic annotations''
-=== Presentation & Demonstration ===
+=== Background ===
 As the use of ontologies for annotation of biomedical datasets rises, a common question researchers face is that of identifying which ontologies are relevant to annotate their datasets. The number and variety of biomedical ontologies is now quite large and it is cumbersome for a scientist to figure out which ontology to (re)use in their annotation tasks. NCBO develops an ontology recommender service, which informs the user of the most appropriate ontologies relevant for their given dataset. The recommender service uses a semantic annotation based approach and scores the ontologies according to those annotations. The recommender service uses the [[Annotator Web service]] . The prototype service can recommend ontologies from UMLS and the NCBO BioPortal.

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 * Technical support: [mailto:support@bioontology.org Support mailing list]
-=== Documentation & References ===
+=== Documentation ===
 * [[Ontology Recommender Client Examples]]
@@ Line 20: / Line 20: @@
 * See also the [[Annotator Web service]] wiki page.
 * Please refer to:
 ** Jonquet C, Musen MA, Shah NH. Building a biomedical ontology recommender web service. J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S1. PubMed [http://www.ncbi.nlm.nih.gov/pubmed/20626921 PMID: 20626921]; PubMed Central PMCID: PMC2903720.