Biomedical Engineering Reference
In-Depth Information
the PredTox data sets defi ne a landmark for data curation, highlighting
the diffi culties of structuring multi-assays studies according to common
standards.
Raw and processed data, as well as experimental descriptions,
protocols, compounds and sample collection procedures were provided
by GeneData [31], a member of the PredTox consortium, in tab-delimited
free text, with audit information detailing the person by whom data fi les
were produced or sample processing performed, along with the date. As
a fi rst step, the identifi cation schemas devised by the data producers to
model animals, samples and aliquots and to link those to data fi les were
disambiguated. Tabular information was then mapped to ISA-Tab
syntactic elements, and the data imported by ISAcreator using that
mapping, allowing for quick upload.
Sixteen studies were created, one per drug candidate. Experimental
descriptions were harmonized to meet the requirement of relevant
community-standards, and semantic tagging was performed using OBO
foundry ontologies [32] accessed via the ISAcreator ontology widget
(Figure 7.3). The Ontology of Biomedical Investigations (OBI [33]) was
used for many elements of experimental steps; the vocabulary from the
HUPO Proteomics Standards Initiative (PSI) [34] was used to identify
and describe mass spectrometers and analytical columns. The same terms
were also used for metabolite-focused applications of that analytical
technique. Biological annotations relating to organ or tissue were sourced
from the Foundational Model of Anatomy (FMA [35]). The drug
candidates were submitted to the Chemical entities of biological interest
(CHEBI [36]) database and ontology for inclusion. For targeted
metabolomics applications, internal standards were used (lactate and
trimethylsilyl propionate); those were also tagged using CHEBI as well as
all identifi ed metabolites identifi ed and used in the data matrices, whereas
units were expressed using Unit ontology [37].
Completing the semantic tagging, raw and processed data fi les were
linked to the detailed description of the studies. Then ISA-Tab formatted
fi les were run through the ISAvalidator, which checked and ensured
that all annotation followed the community-defi ned minimum
information requirements set for each of the omics components:
MIAME (transcriptomics [38]), MIAPE-MS (proteomics [39]) and
CIMR (metabolomics [40]). The completed PredTox data set was
then uploaded to a public instance of the BioInvestigation Index hosted
at The European Bioinformatics Institute (accession numbers: BII-S-8 to
BII-S-23).
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