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SageCite demonstrator overview


A description of the demon

A description of the demon

Published in Technology , Health & Medicine
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  • 1. SageCite workflow citation demonstrator
    Peter Li
  • 2. Workflows
    Two workflows have been developed with Brig Mecham from Sage Bionetworks
  • 3. MetaGEO project
    The 2 workflows have been developed in the context ofBrig’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
  • 4. metaGEO: Current Users/Contributors
    Lilyana Margaretha,Stem Cell Biology
    Pete Nelson, Prostate Cancer
    Bin Zhang,AML
    Joyoti Dey,Medulloblastoma
    Mette Peters, Alzheimers
    Peter Li, Workflows
    Anders Rosengren, Diabetes & Perturbations
    Ji Zhang, AML
    Brig Mecham, Sage Bionetworks
    Roel Verhaak, Updated GSE6891
  • 5. metaGEO: Automated Workflows
    (1) Acquire Data
    (2) Curation
    (4) Inference
    (3) QC
    Brig Mecham, Sage Bionetworks
  • 6. 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
  • 7. Workflow 2
    This workflow performs normalisation and inference analysis on GEO data
    Produces normalised data and statistics of gene expression
  • 8. Workflow citation demonstrator
    Developed a Taverna plugin for registering workflow results with a DOI using DataCite service
  • 9. 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
  • 10. Registration of data
    To register data, the plugin provides it with a DOI
    For example:
  • 11. 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
  • 12. Registration of data using DataCite
    The plugin uses the DOI to register the data on DataCite using its Web API
  • 13. Registration of data using DataCite
    Clicking on the DOI link takes you to the web page for the data on the SageCite demo repository site
  • 14. 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