Annotator Web service - Revision history

Graybeal: /* User Documentation */ added link to Annotator Optimizing and Troubleshooting

2017-02-08T02:49:17Z

User Documentation: added link to Annotator Optimizing and Troubleshooting

Whetzel: /* Selected Citations using the Annotator */

2012-08-16T23:12:01Z

Selected Citations using the Annotator

Whetzel: /* Press Releases */

2011-08-17T17:52:59Z

Press Releases

Whetzel at 17:52, 26 May 2011

2011-05-26T17:52:54Z

Whetzel: /* Prototype releases */

2011-05-26T17:45:13Z

Prototype releases

Whetzel: /* Annotator XSD */

2011-05-01T16:30:02Z

Annotator XSD

Whetzel at 16:12, 1 May 2011

2011-05-01T16:12:47Z

Whetzel at 16:11, 1 May 2011

2011-05-01T16:11:34Z

Whetzel: /* Documentation & References */

2011-05-01T16:02:42Z

Documentation & References

Comm: /* Presentation & Demonstration */

2010-08-31T16:22:15Z

Presentation & Demonstration

@@ Line 14: / Line 14: @@
 * Annotator REST Web Service User Guide [[Annotator_User_Guide | Annotator User Guide]]
-*[http://groups.google.com/group/annotator-discuss  Annotator GoogleGroup] for discussions on use cases and experiences, e.g. parameters, ontologies, semantic expansion, with the Annotator.
+* [http://groups.google.com/group/annotator-discuss  Annotator GoogleGroup] for discussions on use cases and experiences, e.g. parameters, ontologies, semantic expansion, with the Annotator.
 === Client Example Code ===

@@ Line 24: / Line 24: @@
 === Selected Citations using the Annotator ===
 * [http://www.ncbi.nlm.nih.gov/pubmed/20157492 Integrating text mining into the MGI biocuration workflow.] Dowell KG, McAndrews-Hill MS, Hill DP, Drabkin HJ, Blake JA. Database (Oxford). 2009;2009:bap019. Epub 2009 Nov 21. PMID: 20157492 [PubMed] Free article
 * Using the NCBO Web Services for Concept Recognition and Ontology Annotation of Expression Datasets Simon Twigger, Joey Geiger, Jennifer Smith. [http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-559/ SWAT4LS-2009].

@@ Line 38: / Line 38: @@
 === Press Releases ===
 * [http://www.genomeweb.com/informatics/stanford-university-and-embl-platforms-aim-give-users-low-pain-handle-ontologies?page=show Stanford University and EMBL Platforms Aim to Give Users a Low-Pain Handle on Ontologies]
 * [http://www.genomeweb.com/informatics/jackson-lab-finds-text-mining-software-can-speed-some-database-curation-tasks?page=showJackson Lab Finds Text-Mining Software Can Speed Some Database Curation Tasks]
-−
 === Collaboration & Acknowledgment ===

@@ Line 2: / Line 2: @@
 ''
-=== Presentation & Demonstration ===
+=== Description ===
 The range of publicly available biomedical data is enormous and continues to rapidly expand. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval. However, this annotation process cannot be easily automated and often requires expert curators. Plus, there is a lack of easy-to-use systems that facilitate the use of ontologies for annotation. The NCBO Annotator (formerly referred to as the Open Biomedical Annotator (OBA)) is an ontology-based Web service that annotates public datasets with biomedical ontology concepts based on their textual metadata. The biomedical community can use the annotator service to tag their data automatically with ontology concepts. These concepts come from the [http://www.nlm.nih.gov/research/umls/ Unified Medical Language System (UMLS) Metathesaurus] and the [http://bioportal.bioontology.org/ National Center for Biomedical Ontology (NCBO) BioPortal] ontologies. Such annotations facilitate translational discoveries by integrating annotated data.
@@ Line 10: / Line 10: @@
 Please try the [http://bioportal.bioontology.org/annotate NCBO Annotator service in BioPortal].
-=== Contacts ===
+=== User Documentation ===
-* For questions or feature requests, contact [mailto:support@bioontology.org?subject=Annotator%20help%20request Support]
+* Annotator REST Web Service User Guide [[Annotator_User_Guide | Annotator User Guide]]
-=== Documentation ===
+*[http://groups.google.com/group/annotator-discuss  Annotator GoogleGroup] for discussions on use cases and experiences, e.g. parameters, ontologies, semantic expansion, with the Annotator.
-* Annotator REST Web Service User Guide [[Annotator_User_Guide | Annotator User Guide]]
+=== Client Example Code ===
-*[http://groups.google.com/group/annotator-discuss  Annotator GoogleGroup] for discussions on use cases and experiences, e.g. parameters, ontologies, semantic expansion, with the Annotator.
+* Annotator REST Web Service client examples [[Annotator_Client_Examples | Annotator Client Examples]]. The sample code includes Java, Perl, Python, Ruby, and R client example code.
 === How to Cite ===
 * Jonquet C, Shah NH, Musen MA. The open biomedical annotator. Summit on Translat Bioinforma. 2009 Mar 1;2009:56-60. [http://www.ncbi.nlm.nih.gov/pubmed/21347171 PubMed PMID: 21347171]; PubMed Central PMCID: PMC3041576.
-=== Client Examples ===
+=== Selected Citations using the Annotator ===
-* Annotator REST Web Service client examples [[Annotator_Client_Examples | Annotator Client Examples]]. The sample code includes Perl, Ruby and Java examples.
+* The NCBO Annotator service uses Mgrep in the concept recognition step. We acknowledge the assistance of Manhong Dai and Fan Meng from the [http://portal.ncibi.org/gateway/ National Center for Integrative Biomedical Informatics] (NCIBI).
-=== Annotator XSD ===
+* The user interface for the Annotator client in BioPortal (http://bioportal.bioontology.org/annotate) is designed & developed by NCBO members from [http://www.thechiselgroup.org/ University of Victoria]
 ----
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 * May 2008 - First prototype (v1.0) - Has been removed from servers.

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 === Annotator XSD ===
 * ''Coming soon''
 === Prototype releases ===

← Older revision		Revision as of 16:12, 1 May 2011
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	* Annotator REST Web Service client examples [[Annotator_Client_Examples \| Annotator Client Examples]]. The sample code includes Perl, Ruby and Java examples.		* Annotator REST Web Service client examples [[Annotator_Client_Examples \| Annotator Client Examples]]. The sample code includes Perl, Ruby and Java examples.
		+
		+	=== Annotator XSD ===
		+

	=== Prototype releases ===		=== Prototype releases ===

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 *[http://groups.google.com/group/annotator-discuss  Annotator GoogleGroup] for discussions on use cases and experiences, e.g. parameters, ontologies, semantic expansion, with the Annotator.
-* Please refer to:
+* Reference:
 ** Clement Jonquet, Nigam H. Shah, Mark A. Musen, '''The Open Biomedical Annotator''', ''AMIA Summit on Translational Bioinformatics'',  p. 56-60, March 2009, San Francisco, CA, USA. [http://summit2009.amia.org/ conference's web site] [http://www.stanford.edu/~jonquet/Publications/Documents/Article-AmiaSTB09_Jonquet_Shah_Musen.pdf pdf - 201Kb]

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 === Presentation & Demonstration ===
-The range of publicly available biomedical data is enormous and continues to rapidly expand. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval. However, this annotation process cannot be easily automated and often requires expert curators. Plus, there is a lack of easy-to-use systems that facilitate the use of ontologies for annotation. The NCBO Annotator (formerly referred to as the Open Biomedical Annotator (OBA)) is an ontology-based Web service that annotates public datasets with biomedical ontology concepts based on their textual metadata. The biomedical community can use the annotator service to tag thier data automatically with ontology concepts. These concepts come from the [http://www.nlm.nih.gov/research/umls/ Unified Medical Language System (UMLS) Metathesaurus] and the [http://bioportal.bioontology.org/ National Center for Biomedical Ontology (NCBO) BioPortal] ontologies. Such annotations facilitate translational discoveries by integrating annotated data.
+The range of publicly available biomedical data is enormous and continues to rapidly expand. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval. However, this annotation process cannot be easily automated and often requires expert curators. Plus, there is a lack of easy-to-use systems that facilitate the use of ontologies for annotation. The NCBO Annotator (formerly referred to as the Open Biomedical Annotator (OBA)) is an ontology-based Web service that annotates public datasets with biomedical ontology concepts based on their textual metadata. The biomedical community can use the annotator service to tag their data automatically with ontology concepts. These concepts come from the [http://www.nlm.nih.gov/research/umls/ Unified Medical Language System (UMLS) Metathesaurus] and the [http://bioportal.bioontology.org/ National Center for Biomedical Ontology (NCBO) BioPortal] ontologies. Such annotations facilitate translational discoveries by integrating annotated data.
 [[Image:OBA_service_workflow.png|thumb|NCBO Annotator Web service workflow]]