User:Kawaji/120126 data

Data to be loaded into the resource browser

Note & tips

• how to make page with 'FF:xxxxx' in the main name space (rather than separate name space) ?
  • add colon at the head of page. For example, in order to create "test:test" page, you have to specify the page name as ":test:test" . See http://www.mediawiki.org/wiki/Manual:Title.php

sample ontology

• URL: https://fantom5-collaboration.gsc.riken.jp/files/data/shared/contrib/sample_ontology/
• page name: FF:xxxx , CL:xxxx
• property: in the same manner to resource_wiki

motif activity

• URL: http://www.swissregulon.unibas.ch/data/hg18_2/wms.p1
• URL: http://www.swissregulon.unibas.ch/data/hg18_2/WMs2TF.txt
• http://www.swissregulon.unibas.ch/data/hg18_2/WMs2TF_format.txt (format description)

• page name - (example) swissregulon_wm_hg18_2:SMAD1..7,9.p1
• property name: entrezgene (example) entrezgene:4654

• Contact to Michiel about the actual 'motif activity'

Gene

• URL: https://fantom5-collaboration.gsc.riken.jp/files/data/shared/external/entrez_gene/2012-01-19/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz
• http://www.ncbi.nlm.nih.gov/pubmed/19274049

• page name - (example) entrezgene:123

• property
  • tax_id:xx
  • Symbol:xx
  • Synonyms:xx
  • dbXrefs:xx

• assign "Category:TranscriptionFactor" , when it is listed in the paper above (PMID:19274049)

CAGE peak

• URL: https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/hg19/description120126/tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.tpm.selected.clustername_update.desc.osc.txt.gz
• URL: https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/mm9/description120126/tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.tpm.selected.clustername_update.desc.osc.txt.gz

• page name - (exmaple) hg19::chr1:234..567,+

• property name
  • FREEZE_PHASE1_expression
  • short_description
  • description
  • association_with_transcript
  • entrezgene:xx
  • hgnc:xx
  • uniprot:xx