HIPC Dashboard pipeline v1.2.0

HIPC Dashboard Pipeline

Changes in version 1.2.0

• Update column headers:
  -- baseline_time to baseline_time_event
  -- exposure_material to exposure_material_id
  -- exposure_material_text to exposure_material
  -- publication_reference to publication_reference_id
  -- submission_date to curation_date
  -- extra_comments to curator_comments
• Remove certain columns from templates:
  -- remove submission_name and template_name, as values are generated in code
  -- remove addntl_time_point_units, group1 and group0 because not in use
• Merge certain columns into cohort and remove from templates
  -- merge subgroup into cohort, remove subgroup and update code
  -- merge age_group into cohort, remove age_group
• New columns added by pipeline now added at end of templates rather than at fixed locations
• Use tab-delimited files rather than Excel for all input and public output files
• Change code to extract pubmed publish date (may be epub for some),
  and remove more complex code to construct pubmed-based print publish date
• Use publication_year column for actual print year.
  Previously retrieved from Pubmed as PubDate option but value not always present.
• No longer reconstruct article abstract from xml.
  It preserved special characters that are not wanted.
  Only used by mSigDB code.
• Add time_point, time_point_units, and baseline_time_event to observation summary statements to disambiguate.
• Add additional_exposure_material to observation summary statements if it has an entry (most do not).
• Template data cleaning:
  -- change all ontology references to type:value format
  -- remove confirmed redundant subgroup entries
• Add changelog.txt and HIPC_Dashboard_curation_template_fields.pdf to project.
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