Mduke sagecite-jisc-march11

UKOLN is supported by: Monica Duke Project Manager/Researcher 29 th March 2011 Aston Business School SageCite Project http://blogs.ukoln.ac.uk/sagecite/ #sagecite [email_address]

Citation in the domain of disease network modelling

Data Process Publication Research Object Citation Chains Credit and Attribution

Data Process Publication ?

Sage data and processes
The idealised Sage modelling process can be divided into 7 stages
A combination of phenotypic, genetic, and expression data are processed to determine a list of genes associated with diseases
Different people are responsible for different stages of the modelling process. One person oversees the whole process though.

Stage 2: Statistical QC
Actual values in data sets are validated for quality to check for experimental artifacts
The checks made are dependent on the type of data set and involves the use of R scripts and tools like Plink
The output is a normalised data set
Validated & curated data sets Curated data sets Statistical QC

Domain Complexity
Multistage process
Each stage is specialised
Several people involved
Size/specialisation

Unpacking Citation
I cite others
I need to give attribute to others
I make my work citable
Make it easy to cite my work
Others cite me
Get credit when others attribute me

I cite others
Challenges
Tracking what data I have used
Some information may be confidential
Some data may be restricted access
What if I have modified the data?

I make my work citable Discover
Support others to:
Re-use Access

DataCite sagecitedemorepository Citable data Produces Register, submit metadata Generate landing page for data and store DOIs Mint DataCite API Google API Resolve to landing page Taverna workflow The relationships between data via DataCite DOIs with tools are captured by the provenance (OPM) produced by Taverna 1 2 3 4 5 6 Workflow metadata For referring to data reported in the provenance

Additional steps for citing data

I make my work citable
Challenges
Making my work re-usable
Granularity of credit
When to assign a new identifier
What type of identifier
What represents intellectual input – which contributions deserve to be cited?

Others cite me
Recognising contributions other than publications
Granularity of roles and contribution
Will added value be recognised?
What metrics to use
Linking all my contributions together
What constitutes “publication”?

Workflow Provenance Gene URI myExperiment URI Data sets in GEO database Register Submit Open Provenance Model W3C Provenance Incubator RDF Data creator ORCID DOI, Pubmed Id Scientific publication Publication? Sage bionetwork model (Co-expn, Bayesian) DataCite Workflow user ORCID

Identity Workshop prep-meeting, Helsinki, January 27 2011 Publishing a journal article Publishing a dataset G. A. Thorisson, University of Leicester

Different forms of publication
As support for an article
Publish to a repository/archive
Blogs or other social networking sites
Micro-attribution (nano-publication)

Working with ORCID
Contributor ID

Identity Workshop prep-meeting, Helsinki, January 27 2011 Centrally-managed informatics infrastructure: i) for researchers to manage & use profile ii) for tracking author-to-publication attribution links iii) interaction with other systems (e.g. publishers, digital libraries ORCID ID: G-1442-2009 J. Smith, Univ. North Pole ORCID ID: D-2400-2010 J. Smith, Luthor Corporation ORCID ID: B-1242-2010 G. Thorisson, Univ. Leicester G. A. Thorisson, Univ. Leicester G. A. Thorisson, Cold Spring Harbor Lab. G. A. Thorisson, University of Leicester

Special issue
New Models of Semantic Publishing in Science
http://www.semantic-web-journal.net/blog/special-issue-semantic-web-journal-new-models-semantic-publishing-science
Deadline: 1 st May

Acknowledgements
University of Manchester
Carole Goble
Peter Li
British Library
Max Wilkinson
Tom Pollard
Sage Bionetworks
UKOLN
Liz Lyon
Monica Duke
Nature Genetics
Myles Axton
PLoS Comp Bio
Phil Bourne

Mduke sagecite-jisc-march11

by monicaduke on Apr 05, 2011

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