Commits for vsmalladi

v251_preview2 to v251_base (2011-05-03 to 2011-05-10) v251

• Updated the CTCF meta-data to be associated with the correct antibody name CTCF_(SC-5916)
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra - lines changed 17, context: html, text, full: html, text
• Added validation list for the attic meta-data variable.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
• Truncated longLabel ENCODE/Stanford/Yale/Davis/Harvard -> ENCODE/SYDH
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.ra - lines changed 28, context: html, text, full: html, text
• Registered 2 cell lines Patski and ZhBTc4. As a consequence had to register strain 129/Ola.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 37, context: html, text, full: html, text
• Added experiment Spleen Pol2.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra - lines changed 157, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra - lines changed 18, context: html, text, full: html, text
• Updated Short label abbreviation for Signal from Sig -> Sg.
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.ra - lines changed 27, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra - lines changed 27, context: html, text, full: html, text
• Added validation for tissueSourceType so that it can accept either Individual or Pooled or None when the term is not applicable.
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
• Updated the metaData to include controlId and labExpId to match hg19. Update meta-data in trackDb and mdb.ra for protocol changes. Dropped meta-data and tracks for data that lab requested to revoke.
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra - lines changed 4278, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.new.ra - lines changed 581, context: html, text, full: html, text
• Updated labVersion based on lab recomended information. If lab removed information from field, field was deleted.
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra - lines changed 336, context: html, text, full: html, text
• Merge branch 'HudsonAlpha-hg18'
• Changed antibody=Control to antibody=Input to match hg18 data.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 142, context: html, text, full: html, text
• Removed Version 1 file meta-data so as not to show up on the RR in fileUi, since deprecated files are still present on the RR.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra - lines changed 169, context: html, text, full: html, text
• Added strain information for ES-Bruce4 and updated registered sex for ZhBTc4 from U -> M.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 2, context: html, text, full: html, text
• Added 8 experiments for TFBS and Histone Track. Update long and short labels. Errors in long labels were 'TFBS TFBS' and 'Histone Histone'.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra - lines changed 443, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra - lines changed 755, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.ra - lines changed 39, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra - lines changed 94, context: html, text, full: html, text
• Added tissueSourceType for each experiment as provided by the lab. Added new term Both, that identifies that processed data was made from replicates using pooled and individual sampling of tissues.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra - lines changed 154, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra - lines changed 164, context: html, text, full: html, text
• Merge branch 'Development-Mouse'
• Added attic terms into the cv, so that validation is against cv and not a list. Fulfills redmine issue: #3830.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 31, context: html, text, full: html, text