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Article: NCBO Technology: Powering semantically aware applications.

Whetzel, Patricia L

2013 Volume 4 Suppl 1, Page(s) S8

Abstract: As new biomedical technologies are developed, the amount of publically available biomedical data continues to increase. To help manage these vast and disparate data sources, researchers have turned to the Semantic Web. Specifically, ontologies are used ... ...

Abstract	As new biomedical technologies are developed, the amount of publically available biomedical data continues to increase. To help manage these vast and disparate data sources, researchers have turned to the Semantic Web. Specifically, ontologies are used in data annotation, natural language processing, information retrieval, clinical decision support, and data integration tasks. The development of software applications to perform these tasks requires the integration of Web services to incorporate the wide variety of ontologies used in the health care and life sciences. The National Center for Biomedical Ontology, a National Center for Biomedical Computing created under the NIH Roadmap, developed BioPortal, which provides access to one of the largest repositories of biomedical ontologies. The NCBO Web services provide programmtic access to these ontologies and can be grouped into four categories; Ontology, Mapping, Annotation, and Data Access. The Ontology Web services provide access to ontologies, their metadata, ontology versions, downloads, navigation of the class hierarchy (parents, children, siblings) and details of each term. The Mapping Web services provide access to the millions of ontology mappings published in BioPortal. The NCBO Annotator Web service "tags" text automatically with terms from ontologies in BioPortal, and the NCBO Resource Index Web services provides access to an ontology-based index of public, online data resources. The NCBO Widgets package the Ontology Web services for use directly in Web sites. The functionality of the NCBO Web services and widgets are incorporated into semantically aware applications for ontology development and visualization, data annotation, and data integration. This overview will describe these classes of applications, discuss a few examples of each type, and which NCBO Web services are used by these applications.
Language	English
Publishing date	2013-04-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2548651-2
ISSN	2041-1480
ISSN	2041-1480
DOI	10.1186/2041-1480-4-S1-S8
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The NIDDK Information Network: A Community Portal for Finding Data, Materials, and Tools for Researchers Studying Diabetes, Digestive, and Kidney Diseases.

Whetzel, Patricia L / Grethe, Jeffrey S / Banks, Davis E / Martone, Maryann E

PloS one

2015 Volume 10, Issue 9, Page(s) e0136206

Abstract: The NIDDK Information Network (dkNET; http://dknet.org) was launched to serve the needs of basic and clinical investigators in metabolic, digestive and kidney disease by facilitating access to research resources that advance the mission of the National ... ...

Abstract	The NIDDK Information Network (dkNET; http://dknet.org) was launched to serve the needs of basic and clinical investigators in metabolic, digestive and kidney disease by facilitating access to research resources that advance the mission of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK). By research resources, we mean the multitude of data, software tools, materials, services, projects and organizations available to researchers in the public domain. Most of these are accessed via web-accessible databases or web portals, each developed, designed and maintained by numerous different projects, organizations and individuals. While many of the large government funded databases, maintained by agencies such as European Bioinformatics Institute and the National Center for Biotechnology Information, are well known to researchers, many more that have been developed by and for the biomedical research community are unknown or underutilized. At least part of the problem is the nature of dynamic databases, which are considered part of the "hidden" web, that is, content that is not easily accessed by search engines. dkNET was created specifically to address the challenge of connecting researchers to research resources via these types of community databases and web portals. dkNET functions as a "search engine for data", searching across millions of database records contained in hundreds of biomedical databases developed and maintained by independent projects around the world. A primary focus of dkNET are centers and projects specifically created to provide high quality data and resources to NIDDK researchers. Through the novel data ingest process used in dkNET, additional data sources can easily be incorporated, allowing it to scale with the growth of digital data and the needs of the dkNET community. Here, we provide an overview of the dkNET portal and its functions. We show how dkNET can be used to address a variety of use cases that involve searching for research resources.
MeSH term(s)	Animals ; Databases, Factual ; Diabetes Mellitus/pathology ; Digestive System Diseases/pathology ; Humans ; Information Services ; Kidney Diseases/pathology ; Models, Animal ; National Institute of Diabetes and Digestive and Kidney Diseases (U.S.) ; Research ; Search Engine ; United States
Language	English
Publishing date	2015
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0136206
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Workshop proceedings: GWAS summary statistics standards and sharing.

MacArthur, Jacqueline A L / Buniello, Annalisa / Harris, Laura W / Hayhurst, James / McMahon, Aoife / Sollis, Elliot / Cerezo, Maria / Hall, Peggy / Lewis, Elizabeth / Whetzel, Patricia L / Bahcall, Orli G / Barroso, Inês / Carroll, Robert J / Inouye, Michael / Manolio, Teri A / Rich, Stephen S / Hindorff, Lucia A / Wiley, Ken / Parkinson, Helen

Cell genomics

2022 Volume 1, Issue 1

Abstract: Genome-wide association studies (GWASs) have enabled robust mapping of complex traits in humans. The open sharing of GWAS summary statistics (SumStats) is essential in facilitating the larger meta-analyses needed for increased power in resolving the ... ...

Abstract	Genome-wide association studies (GWASs) have enabled robust mapping of complex traits in humans. The open sharing of GWAS summary statistics (SumStats) is essential in facilitating the larger meta-analyses needed for increased power in resolving the genetic basis of disease. However, most GWAS SumStats are not readily accessible because of limited sharing and a lack of defined standards. With the aim of increasing the availability, quality, and utility of GWAS SumStats, the National Human Genome Research Institute-European Bioinformatics Institute (NHGRI-EBI) GWAS Catalog organized a community workshop to address the standards, infrastructure, and incentives required to promote and enable sharing. We evaluated the barriers to SumStats sharing, both technological and sociological, and developed an action plan to address those challenges and ensure that SumStats and study metadata are findable, accessible, interoperable, and reusable (FAIR). We encourage early deposition of datasets in the GWAS Catalog as the recognized central repository. We recommend standard requirements for reporting elements and formats for SumStats and accompanying metadata as guidelines for community standards and a basis for submission to the GWAS Catalog. Finally, we provide recommendations to enable, promote, and incentivize broader data sharing, standards and FAIRness in order to advance genomic medicine.
Language	English
Publishing date	2022-09-03
Publishing country	United States
Document type	Journal Article
ISSN	2666-979X
ISSN (online)	2666-979X
DOI	10.1016/j.xgen.2021.100004
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: BioSamples database: an updated sample metadata hub.

Courtot, Mélanie / Cherubin, Luca / Faulconbridge, Adam / Vaughan, Daniel / Green, Matthew / Richardson, David / Harrison, Peter / Whetzel, Patricia L / Parkinson, Helen / Burdett, Tony

Nucleic acids research

2018 Volume 47, Issue D1, Page(s) D1172–D1178

Abstract: The BioSamples database at EMBL-EBI provides a central hub for sample metadata storage and linkage to other EMBL-EBI resources. BioSamples has recently undergone major changes, both in terms of data content and supporting infrastructure. The data content ...

Abstract	The BioSamples database at EMBL-EBI provides a central hub for sample metadata storage and linkage to other EMBL-EBI resources. BioSamples has recently undergone major changes, both in terms of data content and supporting infrastructure. The data content has more than doubled from around 2 million samples in 2014 to just over 5 million samples in 2018. Fast, reciprocal data exchange was fully established between sister Biosample databases and other INSDC partners, enabling a worldwide common representation and centralization of sample metadata. The BioSamples platform has been upgraded to accommodate anticipated increases in the number of submissions via GA4GH driver projects such as the Human Cell Atlas and the EGA, as well as from mirroring of NCBI dbGaP data. The BioSamples database is now the authoritative repository for all INSDC sample metadata, an ELIXIR Deposition Database for Biomolecular Data and the EMBL-EBI sample metadata hub. To support faster turnaround for sample submission, and to increase scalability and resilience, we have upgraded the BioSamples database backend storage, APIs and user interface. Finally, the website has been redesigned to allow search and retrieval of records based on specific filters, such as 'disease' or 'organism'. These changes are targeted at answering current use cases as well as providing functionalities for future emerging and anticipated developments. Availability: The BioSamples database is freely available at http://www.ebi.ac.uk/biosamples. Content is distributed under the EMBL-EBI Terms of Use available at https://www.ebi.ac.uk/about/terms-of-use.
MeSH term(s)	Biological Specimen Banks ; Computational Biology/methods ; Computational Biology/statistics & numerical data ; Databases, Genetic ; Databases, Nucleic Acid ; Genomics/methods ; Genomics/statistics & numerical data ; Humans ; Information Storage and Retrieval/methods ; Internet ; Metadata/statistics & numerical data ; User-Computer Interface
Language	English
Publishing date	2018-11-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gky1061
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: OntoMaton: a bioportal powered ontology widget for Google Spreadsheets.

Maguire, Eamonn / González-Beltrán, Alejandra / Whetzel, Patricia L / Sansone, Susanna-Assunta / Rocca-Serra, Philippe

Bioinformatics (Oxford, England)

2012 Volume 29, Issue 4, Page(s) 525–527

Abstract: Motivation: Data collection in spreadsheets is ubiquitous, but current solutions lack support for collaborative semantic annotation that would promote shared and interdisciplinary annotation practices, supporting geographically distributed players.: ... ...

Abstract	Motivation: Data collection in spreadsheets is ubiquitous, but current solutions lack support for collaborative semantic annotation that would promote shared and interdisciplinary annotation practices, supporting geographically distributed players. Results: OntoMaton is an open source solution that brings ontology lookup and tagging capabilities into a cloud-based collaborative editing environment, harnessing Google Spreadsheets and the NCBO Web services. It is a general purpose, format-agnostic tool that may serve as a component of the ISA software suite. OntoMaton can also be used to assist the ontology development process. Availability: OntoMaton is freely available from Google widgets under the CPAL open source license; documentation and examples at: https://github.com/ISA-tools/OntoMaton.
MeSH term(s)	Internet ; Software ; Vocabulary, Controlled
Language	English
Publishing date	2012-12-24
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/bts718
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Article: Using ontologies to annotate microarray experiments.

Whetzel, Patricia L / Parkinson, Helen / Stoeckert, Christian J

Methods in enzymology

2006 Volume 411, Page(s) 325–339

Abstract: Consistent annotation of studies using microarrays is critical to optimal management and use of microarray data. Ontologies provide defined and structured terminology suited for this purpose. The Gene Ontology (GO) has aided the analysis of expression ... ...

Abstract	Consistent annotation of studies using microarrays is critical to optimal management and use of microarray data. Ontologies provide defined and structured terminology suited for this purpose. The Gene Ontology (GO) has aided the analysis of expression studies greatly by providing consistent functional annotation of array sequence features. The intent of the MGED Ontology (MO) is to provide consistent experimental annotation. The MO has been developed as a community effort in support of the Minimum Information About a Microarray Experiment standard and is tied to the Microarray Gene Expression object model. The MO is freely available and has been incorporated into the annotation systems of several public microarray database systems.
MeSH term(s)	Animals ; Databases, Genetic ; Humans ; Oligonucleotide Array Sequence Analysis/methods ; Software ; Terminology as Topic
Language	English
Publishing date	2006
Publishing country	United States
Document type	Journal Article ; Review
ISSN	0076-6879
ISSN	0076-6879
DOI	10.1016/S0076-6879(06)11017-4
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Article ; Online: The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species.

Putman, Tim E / Schaper, Kevin / Matentzoglu, Nicolas / Rubinetti, Vincent P / Alquaddoomi, Faisal S / Cox, Corey / Caufield, J Harry / Elsarboukh, Glass / Gehrke, Sarah / Hegde, Harshad / Reese, Justin T / Braun, Ian / Bruskiewich, Richard M / Cappelletti, Luca / Carbon, Seth / Caron, Anita R / Chan, Lauren E / Chute, Christopher G / Cortes, Katherina G /

De Souza, Vinícius / Fontana, Tommaso / Harris, Nomi L / Hartley, Emily L / Hurwitz, Eric / Jacobsen, Julius O B / Krishnamurthy, Madan / Laraway, Bryan J / McLaughlin, James A / McMurry, Julie A / Moxon, Sierra A T / Mullen, Kathleen R / O'Neil, Shawn T / Shefchek, Kent A / Stefancsik, Ray / Toro, Sabrina / Vasilevsky, Nicole A / Walls, Ramona L / Whetzel, Patricia L / Osumi-Sutherland, David / Smedley, Damian / Robinson, Peter N / Mungall, Christopher J / Haendel, Melissa A / Munoz-Torres, Monica C

Nucleic acids research

2023 Volume 52, Issue D1, Page(s) D938–D949

Abstract: Bridging the gap between genetic variations, environmental determinants, and phenotypic outcomes is critical for supporting clinical diagnosis and understanding mechanisms of diseases. It requires integrating open data at a global scale. The Monarch ... ...

Abstract	Bridging the gap between genetic variations, environmental determinants, and phenotypic outcomes is critical for supporting clinical diagnosis and understanding mechanisms of diseases. It requires integrating open data at a global scale. The Monarch Initiative advances these goals by developing open ontologies, semantic data models, and knowledge graphs for translational research. The Monarch App is an integrated platform combining data about genes, phenotypes, and diseases across species. Monarch's APIs enable access to carefully curated datasets and advanced analysis tools that support the understanding and diagnosis of disease for diverse applications such as variant prioritization, deep phenotyping, and patient profile-matching. We have migrated our system into a scalable, cloud-based infrastructure; simplified Monarch's data ingestion and knowledge graph integration systems; enhanced data mapping and integration standards; and developed a new user interface with novel search and graph navigation features. Furthermore, we advanced Monarch's analytic tools by developing a customized plugin for OpenAI's ChatGPT to increase the reliability of its responses about phenotypic data, allowing us to interrogate the knowledge in the Monarch graph using state-of-the-art Large Language Models. The resources of the Monarch Initiative can be found at monarchinitiative.org and its corresponding code repository at github.com/monarch-initiative/monarch-app.
MeSH term(s)	Humans ; Phenotype ; Internet ; Databases, Factual/standards ; Software ; Genes/genetics ; Disease/genetics
Language	English
Publishing date	2023-11-22
Publishing country	England
Document type	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkad1082
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications.

Whetzel, Patricia L / Noy, Natalya F / Shah, Nigam H / Alexander, Paul R / Nyulas, Csongor / Tudorache, Tania / Musen, Mark A

Nucleic acids research

2011 Volume 39, Issue Web Server issue, Page(s) W541–5

Abstract: The National Center for Biomedical Ontology (NCBO) is one of the National Centers for Biomedical Computing funded under the NIH Roadmap Initiative. Contributing to the national computing infrastructure, NCBO has developed BioPortal, a web portal that ... ...

Abstract	The National Center for Biomedical Ontology (NCBO) is one of the National Centers for Biomedical Computing funded under the NIH Roadmap Initiative. Contributing to the national computing infrastructure, NCBO has developed BioPortal, a web portal that provides access to a library of biomedical ontologies and terminologies (http://bioportal.bioontology.org) via the NCBO Web services. BioPortal enables community participation in the evaluation and evolution of ontology content by providing features to add mappings between terms, to add comments linked to specific ontology terms and to provide ontology reviews. The NCBO Web services (http://www.bioontology.org/wiki/index.php/NCBO_REST_services) enable this functionality and provide a uniform mechanism to access ontologies from a variety of knowledge representation formats, such as Web Ontology Language (OWL) and Open Biological and Biomedical Ontologies (OBO) format. The Web services provide multi-layered access to the ontology content, from getting all terms in an ontology to retrieving metadata about a term. Users can easily incorporate the NCBO Web services into software applications to generate semantically aware applications and to facilitate structured data collection.
MeSH term(s)	Internet ; Software ; Terminology as Topic ; Vocabulary, Controlled
Language	English
Publishing date	2011-06-14
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkr469
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The National Center for Biomedical Ontology.

Musen, Mark A / Noy, Natalya F / Shah, Nigam H / Whetzel, Patricia L / Chute, Christopher G / Story, Margaret-Anne / Smith, Barry

Journal of the American Medical Informatics Association : JAMIA

2011 Volume 19, Issue 2, Page(s) 190–195

Abstract: The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable ...

Abstract	The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data.
MeSH term(s)	Forecasting ; Goals ; Medical Informatics ; United States ; User-Computer Interface ; Vocabulary, Controlled
Language	English
Publishing date	2011-11-10
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1205156-1
ISSN	1527-974X ; 1067-5027
ISSN (online)	1527-974X
ISSN	1067-5027
DOI	10.1136/amiajnl-2011-000523
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Article: BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications

Whetzel, Patricia L / Noy, Natalya F / Shah, Nigam H / Alexander, Paul R / Nyulas, Csongor / Tudorache, Tania / Musen, Mark A

Nucleic acids research. 2011 July 1, v. 39, no. suppl_2

2011

Abstract	The National Center for Biomedical Ontology (NCBO) is one of the National Centers for Biomedical Computing funded under the NIH Roadmap Initiative. Contributing to the national computing infrastructure, NCBO has developed BioPortal, a web portal that provides access to a library of biomedical ontologies and terminologies (http://bioportal.bioontology.org) via the NCBO Web services. BioPortal enables community participation in the evaluation and evolution of ontology content by providing features to add mappings between terms, to add comments linked to specific ontology terms and to provide ontology reviews. The NCBO Web services (http://www.bioontology.org/wiki/index.php/NCBO_REST_services) enable this functionality and provide a uniform mechanism to access ontologies from a variety of knowledge representation formats, such as Web Ontology Language (OWL) and Open Biological and Biomedical Ontologies (OBO) format. The Web services provide multi-layered access to the ontology content, from getting all terms in an ontology to retrieving metadata about a term. Users can easily incorporate the NCBO Web services into software applications to generate semantically aware applications and to facilitate structured data collection.
Keywords	Internet ; community service ; computer software ; data collection ; evolution ; infrastructure ; nucleic acids
Language	English
Dates of publication	2011-0701
Size	p. W541-W545.
Document type	Article
ZDB-ID	186809-3
ISSN	0301-5610 ; 0305-1048
ISSN	0301-5610 ; 0305-1048
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