=Paper=
{{Paper
|id=Vol-1515/poster13
|storemode=property
|title=FAIRDOM approach for semantic interoperability of systems biology data and models
|pdfUrl=https://ceur-ws.org/Vol-1515/poster13.pdf
|volume=Vol-1515
|dblpUrl=https://dblp.org/rec/conf/icbo/KrebsWSMGONSMG15
}}
==FAIRDOM approach for semantic interoperability of systems biology data and models==
https://ceur-ws.org/Vol-1515/poster13.pdf
FAIRDOM approach for semantic interoperability
of systems biology data and models
Olga Krebs1, Katy Wolstencroft3, Natalie Stanford2, Norman Morrison 2,, Martin Golebiewski1,
Stuart Owen2, Quyen Nguyen1, Jacky Snoep2, Wolfgang Mueller1 , and Carole Goble2.
1
Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
2
School of Computer Science, University of Manchester, UK
3
Leiden Institute of Advanced Computer Science, Leiden, NL
ABSTRACT ample, data, models, experiment descriptions, samples, pro-
The ability to collect and interlink heterogeneous data and model tocols, standard operating procedures and publications); and
collections is essential in Systems Biology. Effective data exchange
and comparison requires sufficient data annotation. This is particu- to enable these relationships to be expressed with formal
larly apparent in Systems Biology, where data heterogeneity means semantics. It is based on the idea of the Minimal Infor-
that multiple community metadata standards are required for the mation Models (https://www.biosharing.org), which have been
annotation of a whole investigation, including data, models and pro-
tocols. collected under the umbrella of MIBBI (Minimum Infor-
Here we describe FAIRDOM (http://fair-dom.org/) strategy in the mation for Biological and Biomedical Investigations). The
context of semantic data management in the openSEEK , a web- JERM takes the specification one step further, expressing
based resource for sharing and exchanging Systems Biology data
and models.
the minimum information model as an OWL ontology
(http://bioportal.bioontology.org/ontologies/JERM).
1 INTRODUCTION The majority of laboratory scientists use spreadsheets for
the daily management and manipulation of data, so the
Data integration is an essential part of Systems Biology. RightField semantic spreadsheet application [3] (also devel-
Scientists need to combine different sources of information oped during this work) is used to embed semantic annota-
in order to model biological systems, and relate those mod- tion into the data. RightField-enabled spreadsheets allow the
els to available experimental data for validation. . Currently, collection of semantic information by stealth.
only a small fraction of the data and models produced dur- By embedding the JERM metadata model in a spreadsheet
ing Systems Biology investigations are deposited for reuse format, and enabling the use of JERM (and other) vocabu-
by the community, and only a smaller fraction of that data is lary terms for annotation, the process of standardized se-
standards compliant, semantic content. mantic data collection can become part of the existing data
By embedding semantic technologies into familiar data management activities in the laboratory. JERM spreadsheet
management tools, the SEEK [1] enables semantic annota- templates have been developed for a wide range of experi-
tion of new data and the generation and querying of linked- mental data types.
data compliant datasets, whilst hiding the complexities of
ontologies and metadata from its users. The SEEK is based
REFERENCES
on the ISA infrastructure (Investigations, Studies and As-
says), a standard format for describing how individual ex- 1.Wolstencroft, K., Owen, S., du Preez, F., Krebs, O., Mueller, W., Goble,
periments (assays) are aggregated into wider studies and C. and Snoep, J.L. (2011) The SEEK: a platform for sharing data and
investigations [2]. This poster will present the semantic models in Systems Biology. Methods Enzymol, 500, 629-655.
data integration in SEEK, and how it supports the whole 2. Rocca-Serra, P., Brandizi, M., Maguire, E., Sklyar, N., Taylor, C.,
life cycle of data collection, annotation, sharing and reuse of Begley, K., Field, D., Harris, S., Hide, W., Hofmann, O. et
Systems Biology data and resources. al.(2010) ISA software suite: supporting standards-compliant
experimental annotation and enabling curation at the communi-
2 THE JERM ONTOLOGY AND JERM ty level. Bioinformatics, 26, 2354-2356.
3. Wolstencroft, K., Owen, S., Horridge, M., Krebs, O., Mueller, W.,
TEMPLATES
Snoep, J.L., du Preez, F. and Goble, C. (2011) RightField:
The JERM Ontology is an application ontology designed to embedding ontology annotation in spreadsheets. Bioinformatics,
describe the relationships between items in SEEK (for ex- 27, 2021-2022
* To whom correspondence should be addressed: olga.krebs@h-its.org
Copyright c 2015 for this paper by its authors. Copying permitted for private and academic purposes 1