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SageCite demonstrator overview
SageCite demonstrator overview
SageCite demonstrator overview
SageCite demonstrator overview
SageCite demonstrator overview
SageCite demonstrator overview
SageCite demonstrator overview
SageCite demonstrator overview
SageCite demonstrator overview
SageCite demonstrator overview
SageCite demonstrator overview
SageCite demonstrator overview
SageCite demonstrator overview
SageCite demonstrator overview
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SageCite demonstrator overview

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A description of the demon

A description of the demon

Published in: Technology, Health & Medicine
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  • 1. SageCite workflow citation demonstrator<br />Peter Li<br />
  • 2. Workflows<br />Two workflows have been developed with Brig Mecham from Sage Bionetworks<br />
  • 3. MetaGEO project<br />The 2 workflows have been developed in the context ofBrig’s MetaGEO project which normalises gene expression data sets in the GEO database<br />The normalised data sets enable meta-analyses, e.g. identification of disease signatures<br />Difference between MetaGEO and other similar projects is that all research objects in MetaGEO is open access<br />Data, results, intermediate results, data analysis and integration procedures, etc<br />Enhances the trust of MetaGEO data by researchers<br />For more information on MetaGEO, see Brig’s slides on SageCite wiki<br />
  • 4. metaGEO: Current Users/Contributors<br />Lilyana Margaretha,Stem Cell Biology<br />Pete Nelson, Prostate Cancer<br />Bin Zhang,AML<br />Joyoti Dey,Medulloblastoma<br />Mette Peters, Alzheimers<br />Peter Li, Workflows<br />Anders Rosengren, Diabetes &amp; Perturbations<br />Ji Zhang, AML<br />Brig Mecham, Sage Bionetworks<br />Roel Verhaak, Updated GSE6891<br />
  • 5. metaGEO: Automated Workflows<br />(1) Acquire Data<br />(2) Curation<br />(4) Inference<br />(3) QC<br />Brig Mecham, Sage Bionetworks<br />
  • 6. Workflow 1<br />This workflow produces an annotation library that is used to map gene probes on Affymetrix chips to a specific gene for an organism<br />The library is used as part of the curation step for gene expression data sets in GEO<br />
  • 7. Workflow 2<br />This workflow performs normalisation and inference analysis on GEO data<br />Produces normalised data and statistics of gene expression<br />
  • 8. Workflow citation demonstrator<br />Developed a Taverna plugin for registering workflow results with a DOI using DataCite service<br />
  • 9. Workflow citation demonstrator<br />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<br />
  • 10. Registration of data<br />To register data, the plugin provides it with a DOI<br />For example:<br />10.5520/SAGECITE-1<br />
  • 11. SageCite demo repository web site<br />The plugin stores data in a local sqlite database and creates a web page on the SageCite demo repository web site to display data<br />
  • 12. Registration of data using DataCite<br />The plugin uses the DOI to register the data on DataCite using its Web API<br />
  • 13. Registration of data using DataCite<br />Clicking on the DOI link takes you to the web page for the data on the SageCite demo repository site<br />
  • 14. To do and issues<br />Need to register metadata for workflow results using DataCite API<br />Large size of data generated from Brig’s pipelines sometimes breaks plugin<br />

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