Difference between revisions of "Annotator Web service"

Latest revision as of 18:49, 7 February 2017

To automatically process a piece of data text to annotate it with relevant ontology concepts and return the annotations.

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 Unified Medical Language System (UMLS) Metathesaurus and the National Center for Biomedical Ontology (NCBO) BioPortal ontologies. Such annotations facilitate translational discoveries by integrating annotated data.

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NCBO Annotator Web service workflow

Please try the NCBO Annotator service in BioPortal.

User Documentation

Annotator REST Web Service User Guide Annotator User Guide

Annotator GoogleGroup for discussions on use cases and experiences, e.g. parameters, ontologies, semantic expansion, with the Annotator.

Annotator Optimizing and Troublehooting

Client Example Code

Annotator REST Web Service 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. PubMed PMID: 21347171; PubMed Central PMCID: PMC3041576.

Selected Citations using the Annotator

Annotation Analysis for Testing Drug Safety Signals using Unstructured Clinical Notes. Lependu P, Iyer SV, Fairon C, Shah NH. J Biomed Semantics. 2012 Apr 24;3 Suppl 1:S5. PubMed PMID: 22541596; PubMed Central PMCID: PMC3337270.
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. SWAT4LS-2009.

Contacts

For questions or feature requests, contact Support

Community

The NCBO Annotator community a variety of academic groups including UCSF, University of Indiana and the Jackson Laboratory that use the NCBO Annotator Web service in various use case scenarios. Internally, we have used the annotation workflow to index biomedical data resources with ontology concepts (cf. Resource_Index).

Learn more about NCBO Annotator users & use cases: NCBO Annotator community

Press Releases

Collaboration & Acknowledgment

The NCBO Annotator service uses Mgrep in the concept recognition step. We acknowledge the assistance of Manhong Dai and Fan Meng from the National Center for Integrative Biomedical Informatics (NCIBI).

The user interface for the Annotator client in BioPortal (http://bioportal.bioontology.org/annotate) is designed & developed by NCBO members from University of Victoria

Prototype releases

November 2009 - Second prototype including Mmtx: [1]

April 2009 - First production release in BioPortal 2.1

March 2009 - Prototype user interface has been deployed on the BioPortal staging server.

October 2008 - The prototype (v1.1) has bee released for testing and evaluation. The prototype is still available but please don't use it anymore: [2]

May 2008 - First prototype (v1.0) - Has been removed from servers.

@@ Line 1: / Line 1: @@
-''To automatically process a piece of data text to annotate it with relevant ontology concepts and return the annotations
+''To automatically process a piece of data text to annotate it with relevant ontology concepts and return the annotations.
 ''
-=== Presentation & Demonstration ===
+=== Description ===
-The range of publicly available biomedical data is enormous and is expanding fast. 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 (or 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|OBA web service workflow]]
+[[Image:OBA_service_workflow.png|thumb|NCBO Annotator Web service workflow]]
-Please try the [NCBO Annotator service in BioPortal http://bioportal.bioontology.org/annotate].
+Please try the [http://bioportal.bioontology.org/annotate NCBO Annotator service in BioPortal].
-=== Contacts ===
+=== User Documentation ===
-* Community & usage: [[mailto:whetzel@stanford.edu Trish Whetzel]]
+* Annotator REST Web Service User Guide [[Annotator_User_Guide | Annotator User Guide]]
-* Design, utility & applications: [[mailto:nigam@stanford.edu Nigam Shah]] and [[mailto:jonquet@stanford.edu Clement Jonquet]]
-* Technical support: [[mailto:cyoun@stanford.edu Cherie Youn]]
-=== Documentation & References ===
+* [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]]
+* [[Annotator_Optimizing_and_Troublehooting | Annotator Optimizing and Troublehooting]]
-* Annotator Design and underlying Data model: [http://obs.bioontology.org/docs/oba/OBA_v1.1_documentation.htm Documentation here]... to be move to the wiki soon.
+=== Client Example Code ===
-* Please refer to:
+* 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.
-** 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]
-=== Versions (prototypes & releases) ===
+=== 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.
-* April 2009 - First production release in BioPortal 2.1
+=== Selected Citations using the Annotator ===
+* [http://www.ncbi.nlm.nih.gov/pubmed/22541596 Annotation Analysis for Testing Drug Safety Signals using Unstructured Clinical Notes.] Lependu P, Iyer SV, Fairon C, Shah NH. J Biomed Semantics. 2012 Apr 24;3 Suppl 1:S5. PubMed PMID: 22541596; PubMed Central PMCID: PMC3337270.
+* [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].
-* March 2009 - Prototype user interface has been deployed on the BioPortal staging server.
+=== Contacts ===
-* October 2008 - The prototype (v1.1) has bee released for testing and evaluation. The prototype is still available but please don't use it anymore: [http://obs.bioontology.org/oba/OBA_v1.1_rest.html]
-* May 2008 - First prototype (v1.0) - Has been removed from servers.
+* For questions or feature requests, contact [mailto:support@bioontology.org?subject=Annotator%20help%20request Support]
 === Community ===
-After 8 months of existence OBA counts already 8 academic groups (Univ. of California, San Francisco, Univ. of Indiana, Jackson Lab) that use and experiment the service in specific scenarios. Internally, we have used the annotation workflow to index biomedical data resources with ontology concepts (cf. [[Resources index Web services]]).
+The NCBO Annotator community  a variety of academic groups including UCSF, University of Indiana and the Jackson Laboratory that use the NCBO Annotator Web service in various use case scenarios. Internally, we have used the annotation workflow to index biomedical data resources with ontology concepts (cf. [[Resource_Index]]).
 Learn more about NCBO Annotator users & use cases: [[NCBO Annotator community]]
+=== Press Releases ===
+* [http://www.genomeweb.com/informatics/scripps-team-demonstrates-feasibility-unearthing-gene-disease-links-bio-wiki-mas?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed: Scripps Team Demonstrates Feasibility of Unearthing Gene-Disease Links via Bio-Wiki Mashups]
+* [http://www.genomeweb.com/informatics/study-extracts-vioxx-heart-attack-risk-emrs-highlights-shift-ontology-developmen Study Extracts Vioxx Heart-Attack Risk from EMRs, Highlights Shift from Ontology Development to Use]
+* [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 ===
-* The OBA 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).
+* 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).
-* The user interface for the annotator client in BioPortal (http://bioportal.bioontology.org/annotate) is designed & developped by NCBO members from [http://www.thechiselgroup.org/ University of Victoria]
+* 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]
+----
+=== Prototype releases ===
+* November 2009 - Second prototype including Mmtx: [http://obs.bioontology.org/oba/OBA_v1.2_rest.html]
+* April 2009 - First production release in BioPortal 2.1
+* March 2009 - Prototype user interface has been deployed on the BioPortal staging server.
+* October 2008 - The prototype (v1.1) has bee released for testing and evaluation. The prototype is still available but please don't use it anymore: [http://obs.bioontology.org/oba/OBA_v1.1_rest.html]
+* May 2008 - First prototype (v1.0) - Has been removed from servers.