Information Technology Reference
In-Depth Information
5.1.2
Role of Biomedical Literature: The “Bibliome”
The array of data repositories collectively provides an infrastructure for cataloguing
and providing access to artifacts that are generated as part of the scientifi c process.
By themselves, the data may not directly convey their meaning; the transformation
to knowledge is recorded as wisdom that, within the biomedical context, commonly
takes the form of publications. The transformation of individual datum points into
actionable knowledge results in an array of artifacts that can be catalogued and be
deemed “wisdom” that form the foundation for future studies. It is essential to
understand that the transformation of data into wisdom is not necessarily linear in
structure; Data might lead to wisdom that, in turn, may be perceived as data for
another context. In addition to the interpretations of data that impart wisdom for a
particular context, it is essential that the process of transformation is catalogued and
that the data themselves are preserved in a potentially reusable form. Indeed, it is
important to accept that the ultimate purpose of a given set of data may not actually
be known at the time of collection. In biomedical research parlance, this is often
referred to as “secondary use” of data - e.g . , data that may have been collected for
the purposes of monitoring the progress of treatment for a given individual may be
aggregated with a population of patients with similar conditions or treatments and
form the basis of future studies [ 3 - 5 ].
The ultimate utility of archived data is determined not only by the ability to
understand associated interpretations, but also by the ability to leverage the data
in combination with other data. To facilitate the archiving of data for potential
future uses, it is imperative that a defi ned standard be used for the representation of
the data. In biomedicine and health care, there are defi ned standards for how data
should be represented (e.g . , as defi ned by standards organizations such as Health
Level 7 [HL7] and the International Health Terminology Standards Development
Organisation [IHTSDO]) or as archived in catalogues of standardized nomencla-
tures or ontologies (e.g., by the National Library of Medicine as part of the Unifi ed
Medical Language System [UMLS [ 6 ]] or as indexed in the BioPortal maintained
by the National Center for Biomedical Ontology [NCBO [ 7 ]]).
There are a multitude of data repositories that can be categorized by data type.
For example, nucleotide sequence data are commonly archived (often by journal
publisher mandate) in a repository that participates in the International Nucleotide
Sequence Database Consortium (INSDC, which consists of GenBank [maintained
by the National Center for Biotechnology Information at the United States National
Library of Medicine], European Nucleotide Archive [maintained by the European
Bioinformatics Institute in Europe] or the DNA Databank of Japan). Many data
repositories, such as those associated with nucleotide sequence data, are freely
accessible either through direct search interfaces or programmatically. Other data
repositories may be more restrictive due to either privacy or confi dentiality rea-
sons. For example, patient data may be archived in a clinical data warehouse that is
associated with a healthcare organization and their access is restricted to only those
that have approved human subjects research protocols that are in accordance with
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