NCBO User Profile: Dr. Susanna-Assunta Sansone, Eamonn Maguire and Dr. Philippe Rocca-Serra, University of Oxford, UK
ISA Software and ISA Commons - Standards-Driven Biocuration in Action
“Our job is to contribute to the realization of the data sharing vision, by empowering scientists to take data management and sharing into their own hands and minimizing the curation effort. The NCBO BioPortal helps us to serve actionable ontologies to our users, shielding them from the underlying complexities.”
Dr. Susanna-Assunta Sansone, Eamonn Maguire and Dr. Philippe Rocca-Serra
Infrastructure and Standards for Data Sharing Team
University of Oxford
Dr. Susanna-Assunta Sansone, Eamonn Maguire and Dr. Philippe Rocca-Serra (as in the photo) are, respectively, the driving mind, the leading hands and the skilled user/technical coordination behind the ISA software suite and the ‘ISA commons’ (isacommons.org).
Based at the University of Oxford in UK, our fast growing team focuses on standards, ontologies and infrastructures for data management and sharing. We work closely with an increasingly diverse set of researchers and biocurators world-wide dealing with experiments from environmental health, environmental genomics, metabolomics, metagenomics, stem cell discovery, system biology and toxicogenomics domains. The ISA commons is a growing ecosystem of data curation and sharing solutions, including the ISA software suite, built on a common, metadata-focused ISA framework, to create and manage large, heterogeneous data sets from different domain of life science in a coherent manner. The NCBO BioPortal’s web services enables the ISA software to serve actionable ontologies to researchers and biocurators, as described below.
Use of NCBO’s Web Services:
1. The first approach: Restricting free text by means of field embedded controlled terminology. This is achieved through the definition of community tailored ISA configurations, sets of xml files defining structure and behavior of spreadsheets edited with ISAcreator. ISAconfigurator relies on an ontology widget which calls BioPortal’s web services for ontology selection and navigation. Biocurators can therefore fine tune the ranges of allowed ontology in the different ISA tables. Each of the ISA components relies on those ISA configuration files to carry out validation tasks.
Figure 2 - Browsing and restricting ontologies in ISAconfigurator
Figure 3 - Searching and browsing ontologies in ISAcreator
Figure 4- Browsing restricted ontologies inside ISAcreator
2. The second approach: Allow users to use free text at the time of data entry and enable term tagging based on restrictions and definitions collected from ISA configuration files. This approach rests on the ability to carry out automated tagging calling the Annotator service from ISAcreator. The ISAcreator Term Tagger widget harvests string tokens from entries found in cells and hands them over to the NCBO Annotator service along side with ontology name and , when application, optional class identifiers as declared in the configuration. String matching on the class labels is displayed in the centre pane and users can vet or reject suggestions prompted by NCBO service.
Figure 5 - The NCBO annotator drives the term tagging functionality present in ISAcreator
The set of web-services and architectures provided by NCBO has allowed ISA developers to provide a unique, built-in set of features, encompassing a range of annotation scenarios with data manager and curators in mind. Our interaction with NCBO team has also enabled refining requirements and contributing use cases to the service.