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SageCite demonstrator overview

SageCite demonstrator overview



A description of the demon

A description of the demon



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    SageCite demonstrator overview SageCite demonstrator overview Presentation Transcript

    • 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 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
    • 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
    • metaGEO: Automated Workflows
      (1) Acquire Data
      (2) Curation
      (4) Inference
      (3) QC
      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:
    • 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
    • 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
    • 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