OntoMaton: a Bioportal powered ontology widget for Google Spreadsheets

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

doi:10.1093/bioinformatics/bts718

Cited by 48 publications

(37 citation statements)

References 13 publications

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“…For data fields requiring an ontology term, the user can search for these terms from the ISAcreator application using the “Search” Web service. These fatures are also included within OntoMaton [16] available from the Google Script Gallery. Rightfield [17] also constrains data annotation to certain ontologies via an Excel spreadsheet.…”

Section: Classes Of Applications Incorporating Ontologies Via Ncbo Tementioning

confidence: 99%

NCBO Technology: Powering semantically aware applications

Whetzel

Team²

2013

Journal of Biomedical Semantics

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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.

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Section: Classes Of Applications Incorporating Ontologies Via Ncbo Tementioning

confidence: 99%

NCBO Technology: Powering semantically aware applications

Whetzel

Team²

2013

Journal of Biomedical Semantics

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“…Finally, there are many other relevant tools being developed and released for Google Sheets, so Keemei users will have access to other useful functionality within this interface. For example, users can easily obtain graphical summaries of their data using the Explore function that is built into spreadsheets (e.g., a patient age histogram can automatically be generated from their sample metadata mapping files), or tag their metadata with relevant ontology terms using OntoMaton [8] .…”

Section: Resultsmentioning

confidence: 99%

Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets

Rideout

Chase

Bolyen

et al. 2016

Preprint

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“…Columns that accept values from a constrained set offer a pick list of valid choices to choose from and restrict entry to valid terms only. Columns that accept terms from specific ontologies use the OntoMaton (13) plug-in for Google Spreadsheets to restrict valid choices to terms from the current version of the correct ontology at BioPortal (14). The OntoMaton plugin will not be available if the workbook is saved as an Excel file.…”

Section: Data Submission Templatesmentioning

confidence: 99%

A scientist's guide for submitting data to ZFIN

Howe

Bradford

Eagle

et al. 2016

Methods in Cell Biology

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The Zebrafish Model Organism Database (ZFIN; zfin.org) serves as the central repository for genetic and genomic data produced using zebrafish (Danio rerio). Data in ZFIN are either manually curated from peer-reviewed publications or submitted directly to ZFIN from various data repositories. Data types currently supported include mutants, transgenic lines, DNA constructs, gene expression, phenotypes, antibodies, morpholinos, TALENs, CRISPRs, disease models, movies, and images. The rapidly changing methods of genomic science have increased the production of data that cannot readily be represented in standard journal publications. These large data sets require web-based presentation. As the central repository for zebrafish research data, it has become increasingly important for ZFIN to provide the zebrafish research community with support for their data sets and guidance on what is required to submit these data to ZFIN. Regardless of their volume, all data that are submitted for inclusion in ZFIN must include a minimum set of information that describes the data. The aim of this chapter is to identify data types that fit into the current ZFIN database and explain how to provide those data in the optimal format for integration. We identify the required and optional data elements, define jargon, and present tools and templates that can help with the acquisition and organization of data as they are being prepared for submission to ZFIN. This information will also appear in the ZFIN wiki, where it will be updated as our services evolve over time.

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OntoMaton: a Bioportal powered ontology widget for Google Spreadsheets

Cited by 48 publications

References 13 publications

NCBO Technology: Powering semantically aware applications

NCBO Technology: Powering semantically aware applications

Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets

A scientist's guide for submitting data to ZFIN

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