Working Groups/Science/swat4ls hackathon/ORR

Presentations

 * David Shotton at Science Online London 2011 (Presentation)
 * Peter Murray Rust and Jenny Molloy at Open Science Summit 2011 (Slides, Video)

Specific Ideas
Please add any ideas for features or functionality you would like to see below (and your name!)
 * Test the hypothesis that rare diseases have fewer Open Access/data resources. (Gilles Frydman)
 * Create a navigation interface for papers and their citations (geographical or chronological if possible). (Mat Todd/ORR)
 * Create an interface for community annotation of papers. (ORR)
 * Generate a method of 'hopping' to other papers which are relevant but not formally connected by a citation network. (Mat Todd)
 * Create an application where a doctor can insert symptoms and get a list of possible 1) diseases, 2) affected genes and 3) drugs/treatments (Helena Deus)
 * Create a matrix of genes vs diseases and count how many papers cite the association of a gene with a disease (Helena Deus)


 * Perhaps link via UniProt entries or GeneRIF records (UniProt has both and more of this in RDF). (Jerven Bolleman)
 * Apply indications/selections to papers: (Jim Pitman)
 * important papers
 * Determine which papers are important according to other people
 * intellectually accessible papers at various levels
 * open access papers
 * appropriate open ontology
 * preferably some intersection of all 4 aspects.

Tasks

 * List of publications relating to LMS from ACOR [Gilles Frydman]
 * Integrate MIIDI output with open metadata [Mark MacGillivray and Tanya Gray]
 * Plan visualisations/UI for ORRs [Jenny Molloy and Graham Steel]

Datasets/References

 * UK PubMedCentral Bibliographic Data
 * Open Citation Corpus
 * Minimal Information standard for reporting an Infectious Disease Investigation (MIIDI)
 * Most cited disease papers. Target papers for Open Research Reports.
 * Exemplar Open Research Report for Reis et al. (2008) paper on risk factors of contracting leptospirosis in an urban slum: XML version of the MIIDI report ; Turtle version of the MIIDI Report

Tools

 * BibSever
 * MIIDI Metadata web input form (for creating an Open Research Report)
 * MIIDI Metadata Java input form for creating an Open Research Report without stressing the MIIDI server!! - available on a memory stick from Tanya.
 * MIIDI XML schema on GitHub.

Exemplars/Models

 * Epispider health surveillance (facet based browsing with map visualisation) http://www.epispider.net/
 * Semantically enhanced leptosporiosis paper http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000361