MorphoSource oVert Demo

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Hands-on demonstration of issues related to DOIs, iDigBio integration, etc

In preparation for some of the MorphoSource related stuff, it might be useful to bring a couple of ct scan datasets as tiff stacks. Specifically have the following ready:

Data:

  1. CT tiff/dicom/jpeg/bmp stacks
  2. Metadata files for those stacks generated by the scanner
  3. Any surface files derived from those datasets you might want to post in ply, stl or obj format
  4. (optional) gray scale preview images of surfaces with (preferably) white background in tiff or jpeg format


Software:

  1. ImageJ
  2. Meshlab
  3. (optional) more advanced segmentation/rendering software (Avizo, Mimics, VgStudioMax, Dragonfly, etc.)


Agenda

Topics:

DOI assignment

  • How/when do DOI’s get assigned?
  • Why assign DOI’s?
  • What gets a DOI in Morphosource? Why don’t projects or specimens get DOI’s?

Adding new specimens

  • Finding specimens on the iDigBio portal (tips and issues related to API limitations)
  • Procedure for replacing incorrect specimen numbers on media post hoc

Adding Derivative data on existing scans

  • Mechanisms for adding derivative data for project members
  • Mechanisms for adding derivative data for external members
  • Credit amplification

Managing large projects and datasets

  • Zip file best practices
  • Batch uploading and uploading large files (SFTP and batch upload sheet).
  • Batch editing (entity viewer demo)
  • Coordinating and tracking work by multiple project members (entity viewer demo)

How to cite MorphoSource data

  • Purpose of citation (transparency in data identity and source, effort credit/ownership, grant progress)
  • Key citation fields that should always be filled in/reported
  • Work on metadata reporting and format standards
  • IPT development for iDigBio (key fields and vocabularies)
  • Workflows for other kinds of data