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Using the NCBO Web Services for Concept Recognition and Ontology Annotation of Expression Datasets

Simon N. Twigger, Joey Geiger, Jennifer R. Smith
2009 Workshop on Semantic Web Applications and Tools for Life Sciences  
To provide enhanced access to expression datasets housed in the NCBI's Gene Expression Omnibus database and to enable new opportunities for data mining we are using the NCBO's Open Biomedical Annotator  ...  Based on this first pass annotation we are curating these datasets using a variety of ontologies covering concepts of relevance to rat researchers, these include anatomy, rat strains, phenotypes and disease  ...  The goal of our project is two fold: 1 -to explore the use of ontologies and the National Center for Biomedical Ontology's Web service technologies to annotate large scale repositories such as NCBI's Gene  ... 
dblp:conf/swat4ls/TwiggerGS09 fatcat:b2w6ct2nmjdqvonik3op57kzk4

The open biomedical annotator

Clement Jonquet, Nigam H Shah, Mark A Musen
2009 Summit on translational bioinformatics  
The biomedical community can use the annotator service to tag datasets automatically with ontology terms (from UMLS and NCBO BioPortal ontologies).  ...  This paper presents the Open Biomedical Annotator (OBA), an ontology-based Web service that annotates public datasets with biomedical ontology concepts based on their textual metadata (www.bioontology.org  ...  Acknowledgments This work is supported by NIH grant U54 HG004028 in support of the National Center for Biomedical Ontology, one of the National Centers for Biomedical Computing.  ... 
pmid:21347171 pmcid:PMC3041576 fatcat:x67rj7ysrvd3dfrlagigsez5te

Comparison of concept recognizers for building the Open Biomedical Annotator

Nigam H Shah, Nipun Bhatia, Clement Jonquet, Daniel Rubin, Annie P Chiang, Mark A Musen
2009 BMC Bioinformatics  
The Annotator service is available to the community as a REST Web service for creating ontology-based annotations of their data.  ...  This indexing requires the use of a concept-recognition tool to identify ontology concepts in the resource's textual metadata.  ...  We have used Mgrep to create a Web service for ontology based annotation of biomedical data. Our Annotator service has access to a large dictionary, which is composed of UMLS and NCBO ontologies.  ... 
doi:10.1186/1471-2105-10-s9-s14 pmid:19761568 pmcid:PMC2745685 fatcat:h6pctljc5jc6ffffwb3ijl42ze

NCBO Resource Index: Ontology-based search and mining of biomedical resources

Clement Jonquet, Paea LePendu, Sean Falconer, Adrien Coulet, Natalya F. Noy, Mark A. Musen, Nigam H. Shah
2011 Journal of Web Semantics  
For example, researchers and curators widely use the Gene Ontology to describe the molecular functions, cellular location, and biological processes of gene products.  ...  Under the auspices of the National Center for Biomedical Ontology (NCBO), we have developed the Resource Index-a growing, large-scale ontology-based index of more than twenty heterogeneous biomedical resources  ...  Acknowledgements This work was supported in part by the National Center for Biomedical Ontology, under roadmap-initiative grant U54 HG004028 from the National Institutes of Health.  ... 
doi:10.1016/j.websem.2011.06.005 pmid:21918645 pmcid:PMC3170774 fatcat:4rbicvxpdrf3bgzol2ferrolda

NCBO Resource Index: Ontology-Based Search and Mining of Biomedical Resources

Clement Jonquet, Paea LePendu, Sean Falconer, Adrien Coulet, Natasha F. Noy, Mark A. Musen, Nigam H. Shah
2011 Social Science Research Network  
We use the semantics that the ontologies encode, such as different properties of classes, the class hierarchies, and the mappings between ontologies, in order to improve the search experience for the Resource  ...  Under the auspices of the National Center for Biomedical Ontology (NCBO), we have developed the Resource Index-a growing, large-scale ontology-based index of more than twenty heterogeneous biomedical resources  ...  Acknowledgements This work was supported in part by the National Center for Biomedical Ontology, under roadmap-initiative grant U54 HG004028 from the National Institutes of Health.  ... 
doi:10.2139/ssrn.3199526 fatcat:pjp4jwykt5d23juzfnnnlhxkvu

ICD10 Coding of Death Certificates with the NCBO and SIFR Annotator(s) at CLEF eHealth 2017 Task 1

Andon Tchechmedjiev, Amine Abdaoui, Vincent Emonet, Clément Jonquet
2017 Conference and Labs of the Evaluation Forum  
The portal facilitates the use and fostering of terminologies and ontologies by offering a set of services including semantic annotation.  ...  We then submitted the vocabularies to the NCBO and SIFR BioPortal and ran the annotation services on the task 1 datasets. We obtained, for our best runs on each corpus the following results:  ...  We also thanks the US National Center for Biomedical Ontology for their assistance with the NCBO Annotator and the CLEF eHealth 2017 organizers for their help.  ... 
dblp:conf/clef/TchechmedjievAE17 fatcat:uendh37uxjapldstjglprkaije

Building a biomedical ontology recommender web service

Clement Jonquet, Mark A Musen, Nigam H Shah
2010 Journal of Biomedical Semantics  
The service scores the ontologies as a function of scores of the annotations created using the National Center for Biomedical Ontology (NCBO) Annotator web service.  ...  As the use of ontologies for annotation of biomedical datasets has risen, a common challenge is to identify ontologies that are best suited to annotating specific datasets.  ...  Acknowledgements This work is supported by NIH grant U54 HG004028 in support of the National Center for Biomedical Ontology.  ... 
doi:10.1186/2041-1480-1-s1-s1 pmid:20626921 pmcid:PMC2903720 fatcat:d7mxashoyjhsbphqqlpsi3ugxq

SIFR annotator: ontology-based semantic annotation of French biomedical text and clinical notes

Andon Tchechmedjiev, Amine Abdaoui, Vincent Emonet, Stella Zevio, Clement Jonquet
2018 BMC Bioinformatics  
The portal facilitates use and fostering of ontologies by offering a set of services -search, mappings, metadata, versioning, visualization, recommendation-including for annotation purposes.  ...  Additionally, the SIFR Annotator is the first openly web accessible tool to annotate and contextualize French biomedical text with ontology concepts leveraging a dictionary currently made of 28 terminologies  ...  Acknowledgements We would like to thank the US National Center for Biomedical Ontology at Stanford University, for their assistance with the NCBO Annotator, the CépiDC and CLEF eHealth organizers (Aurélie  ... 
doi:10.1186/s12859-018-2429-2 pmid:30400805 pmcid:PMC6218966 fatcat:dmwmnr4qs5fbfgcz2obqualfpq

National Center for Biomedical Ontology [chapter]

Mark A. Musen
2013 Encyclopedia of Systems Biology  
the cornerstone of software for bridging systems, domains, and resources. 2 Ontologies are the foundation of all semantic technologies in e-science, and are a critical component of multi-disciplinary  ...  In biomedicine, one of the most fruitful approaches has been to use software tools and knowledge resources known as ontologies-machineprocessable descriptions of scientific domains-that can promote the  ...  The NCBO has supported a series of Driving Biological Projects that have provided important use cases for the NCBO Annotator (e.g., in the annotation of rat genome data 19 ) and for the NCBO Resource Index  ... 
doi:10.1007/978-1-4419-9863-7_1515 fatcat:3fb7uzhelvgdzlcbmuaekggtyu

ADEpedia: a scalable and standardized knowledge base of Adverse Drug Events using semantic web technology

Guoqian Jiang, Harold R Solbrig, Christopher G Chute
2011 AMIA Annual Symposium Proceedings  
A prototype is successfully implemented to demonstrate the capability of the system to integrate multiple drug data and ontology resources and open web services for the ADE data standardization.  ...  A preliminary evaluation is performed to demonstrate the usefulness of the system, including the performance of the NCBO annotator.  ...  The study is supported in part by the Mayo Clinic Center for Clinical and Translational Research (CTSA) grant -Common adverse event phenotyping related to pharmacogenomics (RR 24150).  ... 
pmid:22195116 pmcid:PMC3243176 fatcat:s3l2726pdjhtrpqi2leyznqhxi

Semantic Metadata Annotation Services in the Biomedical Domain—A Literature Review

Julia Sasse, Johannes Darms, Juliane Fluck
2022 Applied Sciences  
In NFDI4Health, we identified basic requirements for semantic metadata annotation software in the biomedical field and in the context of the FAIR principles.  ...  To understand the market and find out what techniques and technologies support retrospective semantic annotation/enrichment of metadata, we conducted a literature review.  ...  Schmidt (UM Greifswald) for their contributions during the requirement specification and Carsten Oliver Schmidt for the contribution during review and editing.  ... 
doi:10.3390/app12020796 fatcat:dcycecuvsna4pnx6hr4ez3sxpi

The Lexicon Builder Web service: Building Custom Lexicons from two hundred Biomedical Ontologies

Gautam K Parai, Clement Jonquet, Rong Xu, Mark A Musen, Nigam H Shah
2010 AMIA Annual Symposium Proceedings  
The Lexicon Builder Web service addresses this need and reduces the investment of time and effort involved in lexicon maintenance.  ...  The service has three components: Inclusion - selects one or several ontologies (or its branches) and includes preferred names and synonym terms; Exclusion - filters terms based on the term's Medline frequency  ...  Acknowledgments This work is supported by NIH grant U54 HG004028 in support of the National Center for Biomedical Ontology, one of the National Centers for Biomedical Computing.  ... 
pmid:21347046 pmcid:PMC3041331 fatcat:ssd6h5izpzcc3hplvttaf3vdjy

AgroPortal: A vocabulary and ontology repository for agronomy

Clément Jonquet, Anne Toulet, Elizabeth Arnaud, Sophie Aubin, Esther Dzalé Yeumo, Vincent Emonet, John Graybeal, Marie-Angélique Laporte, Mark A. Musen, Valeria Pesce, Pierre Larmande
2018 Computers and Electronics in Agriculture  
By reusing the National Center for Biomedical Ontologies (NCBO) BioPortal technology, we have designed AgroPortal, an ontology repository for the agronomy domain.  ...  with the semantic web.  ...  We also thank the National Center for Biomedical Ontologies for their help and time spent with us in deploying the AgroPortal.  ... 
doi:10.1016/j.compag.2017.10.012 fatcat:tsvou7l42bg5hn6cw43ogtj2je

Biotea: RDFizing PubMed Central in support for the paper as an interface to the Web of Data

L Garcia Castro, C McLaughlin, A Garcia
2013 Journal of Biomedical Semantics  
Our RDF model and resulting dataset make extensive use of existing ontologies and semantic enrichment services.  ...  We expose our model, services, prototype, and datasets at http://biotea.idiginfo.org/ Conclusions: The semantic processing of biomedical literature presented in this paper embeds documents within the Web  ...  List of Abbreviations Acknowledgements We thank John Gómez, the main developer of the gene-based search and retrieval prototype.  ... 
doi:10.1186/2041-1480-4-s1-s5 pmid:23734622 pmcid:PMC3804025 fatcat:kqdu3vlkenbp7o2s7bj2uspqva

A survey of named-entity recognition methods for food information extraction

Gorjan Popovski, Barbara Korousic Seljak, Tome Eftimov
2020 IEEE Access  
In this paper, we provide an overview and a comparison of named-entity recognition methods in the food domain, which can be used for automated extraction of food information from text.  ...  Four methods are discussed: FoodIE, NCBO (SNOMED CT), NCBO (OntoFood), and NCBO (FoodON).  ...  The National Center for Biomedical Ontology (NCBO) Annotator is an ontology-based web service that is used for annotating unstructured textual data with biomedical ontology entities.  ... 
doi:10.1109/access.2020.2973502 fatcat:k2bg5fbujfdv7acbjtkpnsu6wi
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