sagecite demonstrator overview

SageCite workflow citation demonstrator

Peter Li

Workflows

• Two workflows have been developed with Brig Mecham from Sage Bionetworks

MetaGEO project

• The 2 workflows have been developed in the context of Brig’s MetaGEO project which normalises gene expression data sets in the GEO database

• The normalised data sets enable meta-analyses, e.g. identification of disease signatures

• Difference between MetaGEO and other similar projects is that all research objects in MetaGEO is open access– Data, results, intermediate results, data analysis and integration

procedures, etc• Enhances the trust of MetaGEO data by researchers• For more information on MetaGEO, see Brig’s slides on

SageCite wiki

Anders Rosengren, Diabetes & Perturbations

Lilyana Margaretha, Stem Cell BiologyPete Nelson, Prostate CancerBin Zhang, AMLJoyoti Dey, MedulloblastomaMette Peters, Alzheimers

metaGEO: Current Users/Contributors

Roel Verhaak, Updated GSE6891

Ji Zhang, AML

Peter Li, Workflows

Brig Mecham, Sage Bionetworks

metaGEO: Automated Workflows

(2) Curation (3) QC (4) Inference

(1) Acquire Data

Brig Mecham, Sage Bionetworks

Workflow 1

• This workflow produces an annotation library that is used to map gene probes on Affymetrix chips to a specific gene for an organism

• The library is used as part of the curation step for gene expression data sets in GEO

Workflow 2

• This workflow performs normalisation and inference analysis on GEO data

• Produces normalised data and statistics of gene expression

Workflow citation demonstrator

• Developed a Taverna plugin for registering workflow results with a DOI using DataCite service

Workflow citation demonstrator

• Plugin provides an operation in Taverna’s service palette that can be incorporated into workflows to register a data set with a DOI via DataCite

Registration of data

• To register data, the plugin provides it with a DOI

• For example:– 10.5520/SAGECITE-1

SageCite demo repository web site• The plugin stores data in a local sqlite database and creates a

web page on the SageCite demo repository web site to display data

Registration of data using DataCite

• The plugin uses the DOI to register the data on DataCite using its Web API

Clicking on the DOI link takes you to the web page for the data on the SageCite demo repository site

Registration of data using DataCite

To do and issues

• Need to register metadata for workflow results using DataCite API

• Large size of data generated from Brig’s pipelines sometimes breaks plugin