NCBO Wiki - User contributions [en]

Annotator Web service

2010-07-08T10:26:58Z

Rpt:

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

=== 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.

[[Image:OBA_service_workflow.png|thumb|NCBO Annotator Web service workflow]]

Please try the [http://bioportal.bioontology.org/annotate NCBO Annotator service in BioPortal].

=== Contacts ===

* For questions or feature requests, contact [mailto:support@bioontology.org?subject=Annotator%20help%20request Support]

=== Documentation & References ===

* Annotator REST Web Service User Guide [[Annotator_User_Guide | Annotator User Guide]]

* Annotator REST Web Service client examples [[Annotator_Client_Examples | Annotator Client Examples]]. The sample code includes Perl, Ruby and Java examples.

*[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:
** 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) ===

* 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.

=== Community ===

After eight months of existence the NCBO Annotator counts already eight academic groups including UCSF, University of Indiana and the Jackson Laboratory 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. [[Resource_Index]]).

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

=== 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]

=== Papers ===
* [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].

=== 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 [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 & developed by NCBO members from [http://www.thechiselgroup.org/ University of Victoria]

Main Page

2009-12-11T08:17:29Z

Rpt:

Welcome to the '''NCBO Public WIKI'''. This WIKI provides information about collaborative ontology development efforts, dissemination events conducted by the NCBO and publically shared materials from the NCBO.
Please visit our [http://www.bioontology.org Main Site] for more information and materials.

{| class="wikitable"
|-
! style="background:#efefef;" | NCBO Links
! style="background:#efefef;" | Shared Materials
! style="background:#efefef;" | NCBC Links
|-
| [http://www.bioontology.org/ Home page]
| [[Public Requirements Redirect|Public Requirements]]
| [http://www.bisti.nih.gov/ncbc/ Home page of National Centers for Biomedical Computing]
|-
| [http://www.bioontology.org/wiki/index.php/NCBO_FAQ FAQ]
| [[Shared Materials]]
| [http://wiki.na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group NCBC Software and Data Integration Working Group (SDIWG) and Centers Discussion]
|-
| [http://www.bioontology.org/wiki/index.php/News_Events_Publications News, Events and Publications]
| [[Evaluation Activities]]
| [http://wiki.na-mic.org/Wiki/index.php/SDIWG:_NCBC_Scientific_Ontologies NCBC Scientific Ontologies Working Group]
|}

=== Ontology Development Area ===

Below are wikis for some of the current OBO ontologies. Each wiki is housed on the bioontologies.org wiki, in its own partition (wikispace) of the main wiki

*[[PATO:Main_Page]] - An ontology of phenotypic qualities

*[[RO:Main_Page]] - OBO Relations ontology

*[[CARO:Main_Page]] - Reference anatomical ontology

*[[CL:Main_Page]] - OBO Cell ontology

*[[SO:Main_Page]] - Sequence Ontology

*[[Disease:Main_Page]] - Disease Ontology, and other ontologies pertaining to diseases and disorders

*[[OCI:Main_Page]] - Ontology of Clinical Investigation

*[[NPO:Main_Page]] - NanoParticle Ontology

Note that each ontology lives in its own wikispace which corresponds to the [[OBO:IDSpace]] of that ontology. Note for wiki editors: all wiki pages that are to be considered local to a particular ontology should be prefixed with that IDSpace.

=== Software Development Area ===

*[http://bioportal.bioontology.org Bioportal:Main_Page] - Main page for accessing Bioportal
*[[OboInOwl:Main_Page]] - Mapping between OBO and OWL formats
*[[Phenote:Main_Page]] - A Phenotype Annotation Tool using Ontologies
*[[NCBO-OOR Development]] - Documentation on how the Open Ontology Repository community can customize and advance BioPortal capabilities.
*[[RDF Triple Stores]] - Notes, learning and how-tos regarding uploading data to various triple stores
*[[Path to Root]] - Project for consuming the path to root and other OBS rest services
*[[Annotation Summarizer]] - Project utilizing OBS REST services to derive information from datasets referencing ontologies in BioPortal
*[[PURL Server]] - Instructions on how to set-up a PURL server and create Master-Slave architecture for redudancy
*[[Lexicon Builder]] - Project for creating a service that allows building of custom lexicons from bioportal ontologies.

=== Web services ===

* [[BioPortal REST services]] - Documentation on how to use BioPortal functionality as Web services
* [[Annotator Web service]] - Documentation & information about the NCBO Annotator
* [[Ontology Recommender Web service]] - Documentation & information about the NCBO Ontology Recommender
* [[Resource Index]] - Documentation & information about the annotation-based NCBO biomedical Resources Index
* [[UMLS_REST_Services]] - Documentation on how to use our ''prototype'' UMLS services (NetKernel)

Resource Index

2009-10-24T09:29:54Z

Rpt:

''Indexing biomedical resources with ontology concepts ''

=== Presentation & Demonstration ===

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.

Using the annotation workflow of the [[Annotator_Web_service|Annotator Web Service]] NCBO has built an biomedical resources index in which biomedical data is indexed by ontology concepts. The index allows a user to search for biomedical data based on ontology concepts. The NCBO Resource Index is directly queriable in the [http://bioportal.bioontology.org BioPortal] ontology repository: when a user browses a given concept, he has access (link) to the list of resource elements that have been annotated with this concept. A user can also search for resources direclty using the 'All resources' tab.

In the OBR index, we have processed the textual metadata of elements from several biomedical resources such as: [http://www.ebi.ac.uk/arrayexpress/ ArrayExpress], [http://clinicaltrials.gov/ Clinical Trials.gov], [http://goldminer.arrs.org GoldMiner], [http://www.ncbi.nlm.nih.gov/geo/ Gene Expression Omnibus (GEO)] and others. The annotations in the index keeps track of the structures of elements that have been annotated i.e., from which part of the element (e.g., title, description) an annotation has been produced. This information is used to score annotations.

[[Image:NCBO_BRI_workflow.png|thumb|NCBO Biomedical Resources Index workflow]]

[[Image:OBR_index_creation_resources.png|thumb|NCBO Biomedical Resources Index creation]]

Please try the [http://rest.bioontology.org/bioportal/virtual/1104?email=example@example.org|NCBO Biomedical Resource Index in BioPortal].

=== Contacts ===

*For questions or feature requests, contact [mailto:support@bioontology.org?subject=NCBO%20Resources%20Index%20support Support]

=== Documentation ===

* [[Resource Index REST Web Service User Guide]]

* [http://rest.bioontology.org/resource_index/resources/list/ Currently available resource list.]

* Resource index design and underlying data model (see the bottom image on the right) [[Image:OBR_result_model.png|thumb| NCBO Biomedical Resources Index data model]]

* [[Processing_OBR_Resources]] - Notes on resources being processed - Developers only.

* [[Populating_OBS_database]] - Notes on the population of the OBS DB used in the annotation workflow - Developers only.

* [https://bmir-gforge.stanford.edu/gf/project/obs/ Corresponding Gforge project] - Developers only.

=== References ===

* Clement Jonquet, Mark A. Musen and Nigam H. Shah, '''A System for Ontology-Based Annotation of Biomedical Data''', ''In A. Bairoch, S. Cohen-Boulakia and C. Froidevaux (eds): International Workshop on Data Integration in The Life Sciences 2008, DILS'08,'' Vol. 5109, Lecture Notes in BioInformatics, p.144-152, Springer-Verlag, June 2008, Evry, France. [http://dils2008.lri.fr/ conference's web site] [http://www.stanford.edu/~jonquet/Publications/Documents/Article-DILS08_Jonquet_Musen_Shah_published.pdf pdf - 431Kb]

* Nigam H. Shah, Clement Jonquet, Annie P. Chiang, Atul J. Butte, Rong Chen, Mark A. Musen, '''Ontology-driven Indexing of Public Datasets for Translational Bioinformatics''', ''BMC Bioinformatics'', Vol. 10, February 2009. [http://www.biomedcentral.com/bmcbioinformatics/ journal's web site] [http://www.stanford.edu/~jonquet/Publications/Documents/Article-BMCBioInformatics08-Shah-Jonquet-Ontolgy-based_Indexing.pdf pdf - 651 Kb]

=== Versions (prototypes & releases) ===

* February 2009 - New prototype release (v1.2). API: http://obs.bioontology.org/obr/OBR_v1.2_rest.html

* March 2008 - First prototype (v1 and v1.1) API: http://ncbolabs-dev2.stanford.edu:8080/Ontrez_v1_API/ - not maintained anymore, please do not use.

* December 2008 - API specification for the new prototype (v1.2) - not maintained anymore, please do not use.

=== Collaboration & Acknowledgment ===

* The annotation workflow used to create the NCBO Biomedical Resource Index 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 NCBO Biomedical Resource Index client in BioPortal (http://bioportal.bioontology.org/all_resources) is designed & developped by NCBO members from [http://www.thechiselgroup.org/ University of Victoria]

NCBO Developer Documentation

2009-10-24T09:25:45Z

Rpt:

With the explosion of information in the biomedical domain, it has become much harder for scientists to access knowledge and experimental data with rapidity and accuracy. The NCBO is currently developing products and solutions that will advance biology and medicine by enhancing the structured organization of knowledge and improving access to large repositories of biomedical knowledge and data.

=NCBO Source Code Repository=
NCBO source code for all products and solutions can be found on our [https://bmir-gforge.stanford.edu/gf/project/ncbo/|NCBO GForge site].

=NCBO Products=
Below are developer links associated with the various NCBO products and solutions.

==BioPortal==
Focus: Browsing and searching biomedical ontologies.

BioPortal provides access via both Web browsers and Web services to biomedical ontologies. Features include browsing, searching and exploring biomedical ontologies. BioPortal also contains mappings between ontologies and facilitates point-to-point mappings to be added as well as bulk upload of mappings. The Notes feature allows comments to be added to individual ontology terms for discussion with the ontology curators. The Project section of BioPortal contains a list of ontology-based projects. Login and add your ontology-based project to the list!

Additional features include a text annotation tool where the user can select any or all ontologies in BioPortal to use for the annotation. One can also search ontology-indexed resources such as GEO (Gene Expression Omnibus), ClinicalTrials.gov, and Reactome through BioPortal.

===BioPortal REST Web Services ===
All BioPortal REST web service calls '''MUST append a search query parameter''' with the pattern of "email=YourEmail". Note that some clients may need to use a URL encoded email address, for example ''user@example.edu'' would look like ''user%40example.edu''. This is critical to ensure we can maintain the quality of service expected for you as our customer. Later in 2009, we may start challenging REST service calls that do not have this parameter. In the meantime, please start adding this URL parameter to all your web service invocations.

- See [[NCBO_REST_services|BioPortal 2.0 REST web service]] for API documentation and examples.

Previous documentation:

[[Media:BioPortal2.0 User Guide v4.doc|BioPortal 2.0 REST Web Service URL Documentation]]

[[Media:BioPortal2.0_Admin_Guide_v2.doc|BioPortal 2.0 REST Web Service URL Documentation (with Admin role)]]

===BioPortal Widgets===
See [[NCBO_Widgets|BioPortal Widgets]] for information on how to add BioPortal widgets to your web site.

===Local Installation===
Please contact [mailto:support@bioontology.org BioPortal Support] for information on how to request or contribute features.

===Release Notes===
[[BioPortal 2.0.1 (Label 1005) Release Notes]] - 9/19/2008

[[BioPortal 2.0.2 (Label 1006) Release Notes]] - 11/13/2008

[[BioPortal 2.0.3 (Label 1012) Release Notes]] - 11/21/2008

[[BioPortal 2.0.4 (Label 1016) Release Notes]] - 1/13/2009

[[BioPortal 2.1 (Core 1014; UI 1019) Release Notes]] - 5/1/2009

[[BioPortal 2.2 (Core 1017) Release Notes]] - 7/29/2009

==Open Biomedical Resources==
Focus: Using Ontologies to Access Public Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

Ongoing work on the stand-alone OBR User Interface: [[OBR Stand-Alone User Interface]].

==Open Biomedical Annotator==
Focus: Using Ontologies to Annotate Your Data

Technical documentation, prototypes and products will be available here:
http://obs.bioontology.org/

==UMLS Services==
The prototype UMLS Services pertain to a number of internally reusable services and APIs. Our [[UMLS REST Services]] are currently deployed on our local Staging services. We will continue to solidify and merge our recent research advancements. Once the merge has been completed, we will transition the services to Production.

==Developer Documentation Under Development==

===NCBO PURL Server===
Focus: Providing URIs for Biomedical Concepts

The NCBO PURL server is accessible at http://purl.bioontology.org. We will release the final version in partnership with OCLC and Zepheira in early 2009.

===BioPortal Repository Plugin for Protege 4 ===
Focus: Leveraging BioPortal Ontologies in Protege 4

[[BioPortal Repository Plugin for Protege 4]] - Documentation Under Construction

=NCBO Partner Development=
This section presents links to NCBO partners who are deploying and/or contributing to the NCBO software code-base.

==Marine Metadata Interoperability==
The Marine Metadata Interoperability project is deploying the BioPortal 2.0 software as a basis for their "MMI Ontology Registry and Repository" for their marine science community. MMI is an NSF-funded organization made up of primary investigators from the Monterey Bay Aquarium Research Institute, Gulf of Maine Ocean Observing System, Southeastern Universities Research Association, Texas A&M University, Woods Hole Oceanographic Institution, and San Diego Supercomputing Center.

*For more information about MMI, please peruse their web site: http://marinemetadata.org/
*Information about ongoing Ontology Repository architecture, design, and development is accessible from the following page: [[MMI Development]]
*The MMI Ontology Repository is nearing a public release (location: http://mmisw.org/or).

==OOR==
The Ontology Open Repository (OOR) initiative is using the BioPortal 2.x software as a basis for their first "OOR" deployment to begin serving its diverse communities. The OOR promotes global use and sharing of ontologies by:

*Establishing a host registry-repository
*Enabling and facilitating open, federated, collaborative ontology repositories
*Establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.

The "NCBO-OOR" will be executed in two phases:

1) NCBO-OOR Sandbox - Deployment of the BioPortal software for the upcoming February 19, 2009 OOR panel meeting.

2) NCBO-OOR Production - Deployment of the BioPortal software in early March 2009.

For OOR developers who have interest in contributing to the NCBO-OOR development, please start by perusing the [[NCBO-OOR Development]] page. For more information about OOR, please visit the following URL: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR

==National Cancer Institute==
The NCI has leveraged BioPortal 1.0 software as a basis for their Terminology Browser which is accessible from the following URL: http://bioportal.nci.nih.gov/

NCBO Annotator community

2009-10-19T04:25:31Z

Rpt:

== Mouse Genome Informatics (MGI), The Jackson Laboratory ==

Contacts: [[mailto:judith.blake@jax.org Judith A. Blake]] and [[mailto:kgd@informatics.jax.org Karen Dowell]]

=== Use case ===

Researchers at the [http://www.jax.org Jackson Lab] are evaluating the utility of the OBA service in triaging articles for curation based on the ontology terms recognized in their title and abstract.

=== Latest news ===

=== Ontologies used ===

* Mouse gross anatomy and development (EMAP)
* Mouse adult gross anatomy (MA)
* Mouse pathology (MPATH)
* Mammalian phenotype (MP)
* Human disease (DOID)
* Human developmental anatomy – Timed version (EHDA)
* Human developmental anatomy – Abstract version (EHDAA)
* Biological process
* Cellular component
* Molecular function
* Mouse/Human Gene dictionary (JAXMGD)

== Center for Computational Biology and Bioinformatics, Indiana University ==

Contacts: [mailto:sdmooney@iupui.edu Sean Mooney] and [mailto:peter@compbio.iupui.edu Peter H. Baenziger]

=== Use case ===

Researchers at the [http://www.compbio.iupui.edu/mooney/ Mooney Lab] are evaluating the utility of embedding the service in their research management system called [http://laboratree.org Laboratree]; so that any textual annotation created in Laboratree would also have corresponding ontology concept annotations.

=== Latest news ===

=== Ontologies used ===

* SNOMEDCT
* MeSH
* NCI

== Center for Computational Pharmacology (CCP), University of Colorado, Denver ==

Contacts: [mailto:Larry.Hunter@uchsc.edu Larry Hunter] and [mailto:William.Baumgartner@ucdenver.edu Bill Baumgartner]

=== Use case ===

Researchers at the [http://compbio.uchsc.edu/Hunter_lab/CCP_website/index.html Center for Computational Pharmacology] are testing the OBA in their UIAA plafform.

=== Latest news ===

=== Ontologies used ===

* GO (BP, MF, CC)
* BRENDA tissue / enzyme source (BTO)
* Cell Type (CL)
* Chemical entities of biological interest (ChEBI)
* Evidence codes (ECO)
* FMA
* Mammalian phenotype (MP)
* OBO relationship types (OBO_REL)
* Protein Ontology (PRO)
* Protein-protein Interaction (MI)
* Sequence Ontology (SO)

== Center for Computational Pharmacology, University of California, San Francisco (UCSF) ==

Contacts: [mailto:ida.sim@ucsf.edu Ida Sim] and [mailto:michael.bobak@ucsf.edu Michael Bobak]

=== Use case ===

Researchers working on [http://rctbank.ucsf.edu/ Trialbank] create annotations for HIV/AIDS clinical trials in order to provide a Web application for visualizing, and comparing the trials. They are evaluating the use of OBA to process the ‘health condition’, ‘intervention’ and ‘outcomes’ fields for trial records from [[http://clinicaltrials.gov/ clinicaltrials.gov]].

This reasearch was initiated in the context of the NCBO DBP: [http://bioontology.org/dbp_hiv.html Analyzing Evidence in HIV Clinical Trials].

=== Latest news ===

Requirement: recent interaction with Michael has confirmed they would need annotations in OWL in order to open them into an application like Protege and query them.

Requirement: semantic distance service(s) provided (i) within the annotation workflow and (ii) independently within NCBO ontology services.

=== Ontologies used ===

* Human disease
* Infectious disease
* GALEN
* UMLS

== Department of Biomedical Informatics (DBMI), University of Pittsburgh ==

Contacts: [mailto:CrowleyRS@upmc.edu Rebecca Crowley] and [mailto:mitchellkj@upmc.edu Kevin Mitchell]

=== Use case ===

Researcher of Pr. Crowley's group are testing the OBA in the context of developing ODIE, a toolkit for using ontologies to extract information from free-text clinical documents and using free-text clinical documents to enrich existing ontologies.

This research was initiated in the context of the NCBO RO1: [[Ontology Development Information Extraction (ODIE)]].

=== Latest news ===

=== Ontologies used ===

== Human and Molecular Genetics Center (HMGC), Medical College of Wisconsin ==

Contacts: [mailto:simont@hmgc.mcw.edu Simon Twigger] and [mailto:jfgeiger@mcw.edu Joey Geiger]

=== Use case ===

=== Latest news ===

=== Ontologies used ===

== Radiological Sciences Lab (RSL), Stanford University ==

Contacts: [mailto:david.paik@stanford.edu David Paik] and [mailto:baker@biochem.wustl.edu Nathan Baker] and [mailto:srikanth_adiga@persistent.co.in Srikanth Adiga] and [mailto:madhurima_bhattacharjee@persistent.co.in Madhurima Bhattacharjee]

=== Use case ===

=== Latest news ===

=== Ontologies used ===

* NPO
* GO
* ChEBI

== CollabRx ==

Contacts: [mailto:jshrager@stanford.edu Jeff Shrager] and [mailto:mt@alum.mit.edu Mike Travers]

=== Use case ===

Developers at [http://collabrx.com Collabrx] are embedding the service in their Rex platform for processing user generated content; and will evaluate the suitability of using medical dictionaries for processing such content.

=== Latest news ===

=== Ontologies used ===

== Butte Lab, Center for Biomedical Informatics Research, Stanford University ==

Contacts: [mailto:abutte@stanford.edu Atul Butte] and [mailto:shenorr@stanford.edu Shai Shen-Orr]

=== Use case ===

=== Latest news ===

=== Ontologies used ===

* SNOMEDCT
* NCBI Taxonomy

Annotator Web service

2009-10-02T06:20:04Z

Rpt:

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

=== Presentation & Demonstration ===

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.

[[Image:OBA_service_workflow.png|thumb|OBA web service workflow]]

Please try the [http://bioportal.bioontology.org/annotate|NCBO Annotator service in BioPortal].

=== Contacts ===

* For questions or feature requests, contact [mailto:support@bioontology.org?subject=Annotator%20help%20request Support]

=== Documentation & References ===

* Annotator REST Web Service User Guide [[Annotator_User_Guide | Annotator User Guide]]

* Annotator REST Web Service client examples [[Annotator_Client_Examples | Annotator Client Examples]]

* 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.

* Please refer to:
** 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) ===

* 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.

=== 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]]).

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

=== 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 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]