1. e-mail: david.shotton@zoo.ox.ac.uk
David Shotton
MIBBI Workshop
Jagdschloss Niederwald Hotel
Rüdesheim
1st December 2010
MIIDI – Minimal Information for an
Infectious Disease Investigation
Image Bioinformatics Research Group
Department of Zoology
University of Oxford, UK
"It is a very sad thing
that nowadays there is
so little useless information“
Oscar Wilde

2. The PLoS NTD article Study Summary
 The Study Summary of our chosen PLoS NTD article:
 was specific to that individual paper
 was not in machine-readable form
 What was required was a proper machine-readable metadata standard that
could be used to summarize any infectious disease investigation

3. MIIDI and other MIBBI standards
 So we have started to develop MIIDI, a Minimal Information standard for
reporting an Infectious Disease Investigation
 MIIDI is designed to provides a metadata check list for investigations relevant to
infectious diseases, building on IDO, the Infectious Disease Ontology
 MIIDI extends the scope of previous MIBBI standards (Minimum Information for
Biological and Biomedical Investigations), which are largely focused on metadata
for research datasets of laboratory origin
 MIIDI is designed for use in describing both datasets and publications
 For the latter, it has items not found in any other MIBBI standard

e.g. investigation conclusions
 We had an international MIIDI planning meeting in September 2009, attended by
26 people including Chris Taylor, Susanna Sansone and Dawn Field,
representatives of health protection agencies (HPA, WHO), ontologists and other
information scientists, STM publishers, clinicians, vets and epidemiologies
 I have just received short-term JISC funding to permit this work to go forward,
and I’m now looking for a suitably qualified researcher to work with me on it

4. How will MIIDI help?
 MIIDI has several potential uses:
 It can act as a content checklist for authors, editors and reviewers
 It can underpin machine-readable Structured Digital Abstracts
 It can ensure metadata for a research dataset is adequate
 It can underpin tools for metadata creation
 It can aid resource discovery by providing semantically defined search terms
 MIIDI metadata files in RDF can facilitate automated data integration
 MIIDI Structured Digital Abstracts in RDF can facilitate automated publication
selection

e.g. of clinical trial reports, for systematic reviews
 To do: Refine the MIIDI model – requires community involvement
Define terms using ontologies, so that metadata may be recorded as RDF
Test with real-world data, then use routinely

5. Minimal Information Standards, Ontologies and Tools
Ontologies
Minimal Information Standards
Define essential metadata components
Metadata creation tools
e.g. ISA-Creator
Datasets
Structured digital abstracts
machine-readable
Articles
Metadata-rich datasets Semantically rich papers
Sources of structured
vocabularies of classes,
e.g. ‘protein’ or ‘city’
Sources of disambiguated
defined names of instances,
e.g. ‘trypsin’ or ‘Salvador’
Gazetteers and CVs

6. Minimal Information Standards, Ontologies and Tools
Ontologies
Minimal Information Standards
Define essential metadata components
Metadata creation tools
e.g. ISA-Creator
Datasets
Structured digital abstracts
machine-readable
Articles
Metadata-rich datasets Semantically rich papers
Sources of structured
vocabularies of classes,
e.g. ‘protein’ or ‘city’
Sources of disambiguated
defined names of instances,
e.g. ‘trypsin’ or ‘Salvador’
Gazetteers and CVs