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Miscellaneous Terms

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This page lists the controlled vocabulary for a variety of terms. Before submitting data to the DCC all references in DAFs and DDFs to controlled vocabulary terms be registered. To register a term, add it to the appropriate table below and inform your data wrangler. The DCC will register your entry, and it will shortly appear in the registered terms section at the bottom of this page.

Antibodies

Antibodies are registered here.

Cell Types

Cell types are registered here.

Controls

Term: control Also known as Input.

Enter new terms into the following table of yet to be registered terms (which includes one already registered term as an example):

Term Description Added By
Control This data represents a control being compared with the other tracks in the set. DCC

Registered Controls

The following special control terms have been registered to the ENCODE validator, and can be used in data submissions: <embedurl>http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=control{scrolling=auto}{height=300}</embedurl>

Fragment Size

Term: fragSize
Updated: 2008-10-07
Enter new terms into the following table of yet to be registered terms (which includes one already registered term as an example):

Fragment Size Description
1k 1kb DNA fragments

Registered fragSize

<embedurl>http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=fragSize{scrolling=auto}{height=170}</embedurl>

Localizations

Term: localization Also known as Subcellular localizations or Cell components.
Updated: 2008-07-23
Enter new terms into the following table of yet to be registered terms (which includes one already registered term as an example):

Localization Description termId Source
nucleus Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA GO:0005634 [1]

Registered localizations

<embedurl>http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=localization{scrolling=auto}{height=300}</embedurl>

Map Algorithms

Term: mapAlgorithm
Updated: 2008-07-23
Enter new terms into the following table of yet to be registered terms (which includes one already registered term as an example):

Algorithm Description
erng3 erange v3.0

Registered Map Algorithms

<embedurl>http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=mapAlgorithm{scrolling=auto}{height=260}</embedurl>

Promoters

Term: promoter
The following promoters are used by Elnitski (NHGRI) Negative Regulatory Elements (NRE) Data type.
Enter new terms into the following table of yet to be registered terms (which includes one already registered term as an example):

Promoter Description Added By
G-gamma promoter for the G-gamma globulin genes Elnitski

Registered Promoters

<embedurl>http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=promoter{scrolling=auto}{height=150}</embedurl>

Protocols

Term: protocol
The following protocols are used by HudsonAlpha. Updated: 2009-12-09
Enter new terms into the following table of yet to be registered terms (which includes one already registered term as an example):

Protocol Description Added By
PCR1x 1-Cycle of PCR Myers

Registered Protocols

<embedurl>http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=protocol{scrolling=auto}{height=150}</embedurl>

RIP Antibodies

Term: ripAntibody
Updated: 2008-11
Enter new terms into the following table of yet to be registered terms (which includes one already registered term as an example):

RIP Antibody Description RIP Target Protein Vendor Name Vendor ID Lot #s (Used Thru) Order URL
Nov_69522 Negative Control Ab (T7 Tag Mouse Monoclonal) T7Tag Novagen 69522 unknown(Nov2008) embiosciences.com

Registered RIP Antibodies

<embedurl>http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=ripAntibody{scrolling=auto}{height=240}</embedurl>

RIP Target Proteins

Term: ripTgtProtein
Updated: 2008-11
Enter new terms into the following table of yet to be registered terms (which includes one already registered term as an example):

RIP Target Protein Alternative Symbols Description
T7Tag Novagen T7 Tag Cat# 69522 Negative Control Ab (T7 Tag Mouse Monoclonal) Novagen

Registered RIP Target Proteins

<embedurl>http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=ripTgtProtein{scrolling=auto}{height=240}</embedurl>


RNA extracts

Term: rnaExtract
Updated: 2008-07-23
Enter new terms into the following table of yet to be registered terms (which includes one already registered term as an example):

RNA extract Description
longPolyA Poly(A)+ RNA longer than 200 nt

Registered RNA extracts

<embedurl>http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=rnaExtract{scrolling=auto}{height=330}</embedurl>

Treatments

Term: treatment
The following treatments were defined by Yale/UCDavis/Harvard, HudsonAlpha and Duke/UNC/UT.
Enter new terms into the following table of yet to be registered terms (which includes one already registered term as an example):

Treatment Description Added By
Betamethasone_100nM 1h,100nM Betamethasone Myers

Registered Treaments

<embedurl>http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=treatment{scrolling=auto}{height=400}</embedurl>