Biomedical Engineering Reference
In-Depth Information
Table 17.2
The composition of an assertion
Name
Description
Example values
Semantically
indexed
Type
Describes the nature
of the assertion
Hypothesis or
observation
Y
Role
The type of disease
biology the assertion
concerns
Disease mechanism;
biomarker;
therapeutic intervention;
patient stratifi cation
Y
Known negative†
predicted negative;
known positive;
predicted positive;
unknown
Y
Outcome
The ultimate effect
of the assertion on
disease pathology
(where relevant)
Evidence level The clinical relevance
of the assertion
Established disease
biology; clinical
fi nding; pre-clinical
fi nding
Y
Parent
The parent assertion
Y
Status
Current status of the
curation around this
assertion
Not started; in
progress; under review;
complete
Y
Informative
text
Free text entry of
synopsis, fi gures, and
other pertinent
information
Free text and image
entry
N
Semantic
tags
Tag entry with key
entities of interest
Genes, cells,
diseases etc.
Y
￿ ￿ ￿ ￿ ￿
References
Literature references
Y
† in this context, 'negative' means making the disease or symptoms worse
Although we did not want to force scientists to encode extensive
complex interpretations into a structured form, there was a need to
identify and capture the important components of any assertion. Thus, a
second class of concepts within the workbench were created, known as
'objects'. An object represents a single biomedical entity such as a gene,
protein, target, drug, disease, cellular process and so on. Software
developed on the Targetpedia project allowed us to load sets of known
entities from source databases and vocabularies into the system, in bulk.
 
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