RightField is an open-source tool for adding ontology term selection to Excel spreadsheets. RightField is used by a ‘Template Creator’ to create semantically aware Excel spreadsheet templates. The Excel templates are then reused by Scientists to collect and annotate their data; without any need to understand, or even be aware of, RightField or the ontologies used. For each annotation field, RightField can specify a range of allowed terms from a chosen ontology (subclasses, individuals or combinations). The resulting spreadsheet presents these terms to the users as a simple drop-down list. This reduces the adoption barrier for using community ontologies as the annotation is made by the scientist that generated the data rather than a third party, and the annotation is collected at the time of data collection.
RightField is a standalone Java application which uses Apache-POI for interacting with Microsoft documents. It enables users to import Excel spreadsheets, or generate new ones from scratch. Ontologies can either be imported from their local file systems, or from the BioPortal ontology repository. Individual cells, or whole columns or rows can be marked with the required ranges of ontology terms and an individual spreadsheet can be annotated with terms from multiple ontologies.
Once marked-up and saved, the RightField-enabled spreadsheet contains ‘hidden’ sheets with information concerning the origins and versions of ontologies used in the annotation. This provenance information is important in the event of future ontology changes, which may deprecate values already chosen, or may add more fine-grained options and prompt re-annotation.
For the scientist, the main advantages of RightField are that it enables them to consistently annotate their data without the need to explore and understand the numerous standards and ontologies available to them, and it does not require them to change normal practice. Everything is embedded in the Excel spreadsheet.
To help support future development of RightField, please register your interest in, or current use of, RightField using our short optional Registration Form.
For information on how to use RightField, please read the User Guide.
RightField was developed as part of the SysMO-DB project, which supports a consortium of more than 300 Systems Biologists with data management and exchange. SysMO is a pan-European project to study the Systems Biology of Micro-Organisms, which involves a mixture of high-throughput ‘omics experiments, such as microarray analysis or proteomics, as well as traditional molecular biology and enzyme reaction kinetics.
If you have been using RightField in your research, please cite it using the following paper:
Wolstencroft, K.; Owen, S.; Horridge, M.; Krebs, O.; Mueller, W.; Snoep, J. L.; du Preez, F. & Goble, C. RightField: embedding ontology annotation in spreadsheets Bioinformatics, Oxford Univ Press, 2011, 27, 2021-2022 PUBMED: 21622664
Other publications about RightField
- Goble, C.; De Roure, D. & Bechhofer, S. Accelerating scientists’ knowledge turns Knowledge Discovery, Knowledge Engineering and Knowledge Management, Springer, 2013, 3-25
- Goble C, Wolstencroft K, & Bechhofer S The Semantic Web and Interoperability in Systems Biology iEncyclopedia of Systems Biology, Springer Verlag, to appear
- du Preez, F.B., Snoep, J.L. (2011) JWS Online Encyclopedia of Systems Biology, Springer Verlag, to appear
- Wolstencroft, K.; Owen, S.; Horridge, M.; Jupp, S.; Krebs, O.; Snoep, J.; Preez, F.; Mueller, W.; Stevens, R. & Goble, C. Stealthy annotation of experimental biology by spreadsheets Concurrency and Computation: Practice and Experience, Wiley Online Library,2012, DOI: 10.1002/cpe.2941
- Jupp, S.; Horridge, M.; Iannone, L.; Klein, J.; Owen, S.; Schanstra, J.; Wolstencroft, K. & Stevens, R. Populous: a tool for building OWL ontologies from templates BMC bioinformatics, BioMed Central Ltd, 2012, 13, S5
- Wolstencroft, K.; Owen, S.; du Preez, F.; Krebs, O.; Mueller, W.; Goble, C.; Snoep, J. L. & others The SEEK: a platform for sharing data and models in systems biology. Methods in enzymology, 2011, 500, 629
- Sansone, S.-A.; Rocca-Serra, P.; Field, D.; Maguire, E.; Taylor, C.; Hofmann, O.; Fang, H.; Neumann, S.; Tong, W.; Amaral-Zettler, L. & others Toward interoperable bioscience data Nature genetics, Nature Publishing Group, 2012, 44, 121-126 doi:10.1038/ng.1054
- Bechhofer, S.; Ainsworth, J.; Bhagat, J.; Buchan, I.; Couch, P.; Cruickshank, D.; Roure, D. D.; Delderfield, M.; Dunlop, I.; Gamble, M. & others Why linked data is not enough for scientists e-Science (e-Science), 2010 IEEE Sixth International Conference on, 2010, 300-307, ISSN 0167-739X, 10.1016/j.future.2011.08.004.
- Waltemath, D.; Adams, R.; Bergmann, F. T.; Hucka, M.; Kolpakov, F.; Miller, A. K.; Moraru, I. I.; Nickerson, D.; Sahle, S.; Snoep, J. L. & others, Reproducible computational biology experiments with SED-ML-the simulation experiment description markup language, BMC systems biology, BioMed Central Ltd, 2011, 5, 198
Download the correct distribution of RightField for your machine. Once the download is complete, un-compress the distribution into an appropriate folder, as you will be running RightField from this folder. Java 6 or higher is a pre-requisite for using RightField, please download Java 6 and install it if it is not currently present.
To start using RightField, open the folder it was de-compressed into and double-click on the icon that is just titled rightfield.
A dialogue box will then appear asking if you wish to Open an existing spreadsheet or Start with an empty spreadsheet. If an empty spreadsheet is selected, the following screen will appear which shows an empty spreadsheet in the left window pane and an empty ontology in the right window pane.
If an existing spreadsheet is opened and it has already been marked-up in RightField, a dialogue box will ask you if you wish to open the same ontologies as before. In this case, select ‘no’.
We can now start marking-up individual cells by importing ontologies from your local machine, or from the BioPortal, or from a URL. To open an ontology from the BioPortal, select ‘File’ -> ‘Open from BioPortal’. For this example, find the Microarray and Gene Expression Data (MGED) ontology from the drop-down list, either by typing in the first few characters in the ‘Filter’ field box, or by scrolling down the list, select the entry, and then click ‘OK’.
The chosen ontology will then appear in the right windows pane. In the search box at the top, labelled ‘Ontology Hierarchy’, search for ExperimentDesignType. Explore the subclasses by clicking on the plus box left of the label ‘ExperimentDesignType’ and expanding its tree.
To Mark-up a cell, or a range of cells, select them in the spreadsheet view, then select the ontology term. Next select the ‘Type of allowed values’ under the Ontology Hierarchies window. Once you are happy with your selection, click the Apply button to apply the change made to the cells selected. For example, we will mark-up cell B10 with all the direct subclasses of ExperimentDesignType. Select cell B10, then select ‘ExperimentDesignType’ in the ontology and select ‘Direct subclasses’ form the drop down menu titled ‘Value Type and Property’, which lies just below the Ontology Hierarchy window pane. Clicking ‘Apply’ confirms the change.
When a cell has been marked-up, the cell will change colour to green.
Mark-up other cells, or ranges of cells and save the spreadsheet by selecting ‘File’ -> ‘Save Spreadsheet’.
A property can also be assigned to a marked up cell by clicking on the ‘Include a property’ check box, which will result in the drop down menu below it being enabled, and then selecting a property form this drop down menu. This property is then applied to the predicate in the RDF associated with the spreadsheet.
When you open the spreadsheet normally, i.e. using Excel as opposed to RightField, any marked-up cells will be shown in yellow. Each yellow cell will have a drop-down list of allowed values from your chosen ontologies.
Viewing Hidden Data
RightField encapsulates and stores information about ontology terms used inside the spreadsheets in hidden sheets. This ensures that no provenance information is lost regarding the ontology version used for annotation and it allows the storage of unique identifiers for ontology terms as well as the term labels.
The information in hidden sheets is cruicial for the extraction and storage of the spreadsheet data in other formats and for searching over the data. If you want to view this hidden information, you can use the RightField Inspector. In future versions of RightField, this hidden information will also be accessible from the native, marked-up spreadsheets.