SageCite workflow citation demonstrator<br />Peter Li<br />
Workflows<br />Two workflows have been developed with Brig Mecham from Sage Bionetworks<br />
MetaGEO project<br />The 2 workflows have been developed in the context ofBrig’s MetaGEO project which normalises gene exp...
metaGEO: Current Users/Contributors<br />Lilyana Margaretha,Stem Cell Biology<br />Pete Nelson, Prostate Cancer<br />Bin Z...
metaGEO: Automated Workflows<br />(1) Acquire Data<br />(2) Curation<br />(4) Inference<br />(3) QC<br />Brig Mecham, Sage...
Workflow 1<br />This workflow produces an annotation library that is used to map gene probes on Affymetrix chips to a spec...
Workflow 2<br />This workflow performs normalisation and inference analysis on GEO data<br />Produces normalised data and ...
Workflow citation demonstrator<br />Developed a Taverna plugin for registering workflow results with a DOI using DataCite ...
Workflow citation demonstrator<br />Plugin provides an operation in Taverna’s service palette that can be incorporated int...
Registration of data<br />To register data, the plugin provides it with a DOI<br />For example:<br />10.5520/SAGECITE-1<br />
SageCite demo repository web site<br />The plugin stores data in a local sqlite database and creates a web page on the Sag...
Registration of data using DataCite<br />The plugin uses the DOI to register the data on DataCite using its Web API<br />
Registration of data using DataCite<br />Clicking on the DOI link takes you to the web page for the data on the SageCite d...
To do and issues<br />Need to register metadata for workflow results using DataCite API<br />Large size of data generated ...
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SageCite demonstrator overview

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SageCite demonstrator overview

  1. 1. SageCite workflow citation demonstrator<br />Peter Li<br />
  2. 2. Workflows<br />Two workflows have been developed with Brig Mecham from Sage Bionetworks<br />
  3. 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. 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 & Perturbations<br />Ji Zhang, AML<br />Brig Mecham, Sage Bionetworks<br />Roel Verhaak, Updated GSE6891<br />
  5. 5. metaGEO: Automated Workflows<br />(1) Acquire Data<br />(2) Curation<br />(4) Inference<br />(3) QC<br />Brig Mecham, Sage Bionetworks<br />
  6. 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. 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. 8. Workflow citation demonstrator<br />Developed a Taverna plugin for registering workflow results with a DOI using DataCite service<br />
  9. 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. 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. 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. 12. Registration of data using DataCite<br />The plugin uses the DOI to register the data on DataCite using its Web API<br />
  13. 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. 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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