Here's a URL to the ENCODE registered cell-lines:

https://bison.cacr.caltech.edu/cgi-bin/hgEncodeVocab?ra=/usr/local/apache/cgi-bin/encode/cv.ra&type=Cell+Line

Here's a template:

# Human cell types, template below
# --------------------------
# term (human-readable cell type name)
# tag (machine-readable cell type name, no special characters)
# type (informs pipeline code of stanza type.  Should always be Cell Line)
# organism (used by pipeline in ways I don't fully understand.  Should be human)
# description (human-readable description of cell type, for cell type cellTypes.html)
# tissue (general tissue type, for categorizing cell types)
# vendorName (name of vendor or lab that provides these cells)
# vendorId (the ID of the cell type in the vendor's catalog)
# orderUrl (URL for ordering the cell type. Links with vendorId on cellTypes.html)
# karyotype (optional human-readable karyotype, for .html page)
# lineage (optional human-readable source of cell lines, e.g. 18 year old male)
# termId (ID for best term in the BTO.  Optional but encouraged. Shown in cellTypes.html)
# termUrl (URL for term in the ontology. Links with termId on cellTypes.html)
# color (specifies color code for track data of this cell type, rgb values)
# sex (M, F, B, or U.  If "F", then the track data shouldn't contain chrY)
# tier (1,2, or 3.  Specifies which table the cell type appears in in cellTypes.html.  Not used in mouse)
# protocol (comma-separated list with entries of format: tag_submittingLab_protocol.pdf)
# category: (T for tissue, L for cell line, or P for primary cells.  Not used in human)

Here's an example:

term GM12878
tag GM12878
type Cell Line
organism Human
description lymphoblastoid
tissue Blood
vendorName Coriell
vendorId GM12878
orderUrl http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878&PgId=166
karyotype relatively normal
lineage International HapMap Project - CEPH/Utah - European Caucasion; Epstein-Barr Virus
termId BTO:0002026 (non-specific)
termUrl http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BTO&termId=BTO:0002026
color 153,38,0
sex F
tier 1
protocol GM12878_protocol.pdf

EncodeControlledVocabulary (last edited 2011-06-01 21:23:15 by hamrhein)