How to use BV-2 microglial cells as annotation?

[Reagon Karki]

Hello BEL users,

I came across an article that performed an experiment on microglial BV-2 cell line. I want to annotate my BEL statements with this cell line but it doesn't exist in the .belanno CellLine file (http://resource.belframework.org/belframework/20150611/annotation/cell-line.belanno). However, after reading some information in http://bioinformatics.hsanmartino.it/hypercldb/cl7130.html, I found out that microglial BV-2 cell lines could possibly be represented as "ES-C57BL/6 cell", which does exist in the CellLine annotation name file. Now the question is, can I use the annotation as SET CellLine = "ES-C57BL/6 cell" for the microglial BV-2 cell line I came across?

Now let me add one confusion ;)
There's also a CellLine, "MEF (C57BL/6) cell", which is similar to "ES-C57BL/6 cell" (where MEF stands for Mouse embryonic fibroblasts and ES stands for Embryonic Stem(true?)). C57BL/6 is a strain of mouse used in performing lab experiments. MEFs and ESs are just different cell types of C57BL/6, hence I'm skeptic that they do not necessarily represent the microglial cells. Does using anyone of these as annotation correctly refer to BV-2 microglial cells?

I hope to get some explanation and solution to this.

Thanking you in advance,
Reagon

[Natalie Catlett]

Hi Reagon,

I suggest either:

(1) use the term "BV-2" knowing that you will get warnings since it is not in the .belanno file
(2) create a new custom annotations file that contains the "BV-2" (as well as any other terms you may need)

There is already an issue opened in the OpenBEL resource-generator repository (https://github.com/OpenBEL/resource-generator) suggesting adding Cellosaurus (http://web.expasy.org/cellosaurus/) as a source for Cell Line annotations; this enhancement to the current resource pipeline would also solve your issue.

Best,
Natalie