#26 ntr: gel electrophoresis terms



I'd like to request some new terms for gel electrophoresis:

id: ECO:new1
name: gel electrophoresis assay
def: "A direct assay enables the sorting of molecules based on size and charge. Using an electric field, molecules (such as DNA) can be made to move through a gel made of agarose or polyacrylamide." []

(def cribbed approximately from Wikipedia; might cite Sambrook & Russel, ref 2 on the wikipedia page http://en.wikipedia.org/wiki/Gel_electrophoresis\)
is_a: ECO:0000002 ! direct assay result

id: ECO:new2
name: pulsed-field gel electrophoresis assay
def: "An agarose gel electrophoresis assay that employs alternately pulsed, perpendicularly oriented electrical fields, at least one of which is inhomogeneous to separate large DNA molecules." [PMID:6373014]
synonym: "PFGE" EXACT []
is_a: ECO:new1 ! gel electrophoresis assay

id: ECO:new3
name: two-dimensional agarose gel electrophoresis assay
def: "An agarose gel electrophoresis assay in which the first dimension gel is run at low voltage in low percentage agarose to separate DNA molecules in proportion to their mass. The second dimension is run at high voltage in a gel of higher agarose concentration in the presence of Ethidium bromide so that the mobility of a non-linear molecule is drastically influenced by its shape." [PMID: 8594382, http://fangman-brewer.genetics.washington.edu/2Dgel.html\]
is_a: ECO:new1 ! gel electrophoresis assay

The term Antonia requested for SDS-PAGE (https://sourceforge.net/tracker/?func=detail&aid=3497789&group_id=36855&atid=1127740) can also be is_a ECO:new1.



  • Sandra Orchard

    Sandra Orchard - 2012-03-08

    There will be consequences when you import the PSI-MI terms into the Physical interaction branch of ECO as that already contains terms such as 'comigration in gel' with child terms relating to sds gel and non-denaturing gels. These would also be children of ECO:new1 above. We also have a parent term 'electrophoretic mobility-based method' - the definition of which would need tightening up to make it clear we are referring to molecular interactions.

  • Midori Harris

    Midori Harris - 2012-08-10
    • status: open --> closed-out-of-date

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