#707 new term request for chromatin immunoprecipitation

[plloyd]

Hi,

We need an OBI term for Chromatin immunoprecipitation (ChIP, not ChIP-chip or ChIP-seq etc). The existing immunoprecipitation OBI term is not suitable and the high throughput assays are outside the scope of the experiments being described and not all the experiments end up as Western blots. The protein interactions type terms are also unsuitable.

I propose adding chromatin immunoprecipitation assay as a child of the existing immunoprecipitation term.

The original reference for chromatin immunoprecipitation is
Gilmour & Lis. Proc Natl Acad Sci U S A. 1984 Jul;81(14):4275-9.
and can be found linked from here: http://www.ncbi.nlm.nih.gov/pubmed/6379641

ps. The link for your documentation on submission guidelines is broken, let me know if you require further information.

[James A. Overton]

Thanks for the term request and for pointing out that broken link. I'll suggest that this issue be added to the agenda for Monday's OBI conference call.

It would be helpful if you could propose a textual definition for the new term, along the lines of the definitions of similar terms in OBI. Do you propose that ChIP-seq and ChIP-chip should be children of the new term? If possible, suggestions for the logical axioms of the proposed term would also be helpful.

[Alan Ruttenberg]

ChIP-seq and ChIP-chip would have part chromatin immunoprecipitation. The
other parts would be the sequencing or hybridization processes.

If you wanted a parent term it would need to be something like: 'Assay
using chromatin immunoprecipitation' and then all three would be children
of that.

-Alan

On Fri, May 30, 2014 at 11:29 AM, James A. Overton jamesaoverton@users.sf.net wrote:

Thanks for the term request and for pointing out that broken link. I'll
suggest that this issue be added to the agenda for Monday's OBI conference
call.

It would be helpful if you could propose a textual definition for the new
term, along the lines of the definitions of similar terms in OBI. Do you
propose that ChIP-seq and ChIP-chip should be children of the new term? If
possible, suggestions for the logical axioms of the proposed term would
also be helpful.

---

• [obi-terms:#707] http://sourceforge.net/p/obi/obi-terms/707/ new term
  request for chromatin immunoprecipitation *

Status: open
Group: general
Created: Wed May 28, 2014 10:53 PM UTC by plloyd
Last Updated: Wed May 28, 2014 10:53 PM UTC
Owner: nobody

Hi,

We need an OBI term for Chromatin immunoprecipitation (ChIP, not ChIP-chip
or ChIP-seq etc). The existing immunoprecipitation OBI term is not suitable
and the high throughput assays are outside the scope of the experiments
being described and not all the experiments end up as Western blots. The
protein interactions type terms are also unsuitable.

I propose adding chromatin immunoprecipitation assay as a child of the
existing immunoprecipitation term.

The original reference for chromatin immunoprecipitation is
Gilmour & Lis. Proc Natl Acad Sci U S A. 1984 Jul;81(14):4275-9.
and can be found linked from here:
http://www.ncbi.nlm.nih.gov/pubmed/6379641

ps. The link for your documentation on submission guidelines is broken,
let me know if you require further information.

---

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[plloyd]

I agree that using it as a parent term 'Assay using chromatin immunoprecipitation' and having ChIP-seq etc as child terms as suggested by Alan fits well.

A term definition based on general ChIP protocols (I can't find anything that sums it already, so this is my attempt based on CHS protocols, wikipedia, life tech, ChIP-seq term definition):

An assay in which protein-DNA complexes are extracted from short regions of chromatin and are reversibly cross linked, immunoprecipitated with antibodies or tags, purified, and amplified for gene- and promoter-specific analysis of known targets

[Alan Ruttenberg]

On Friday, May 30, 2014, plloyd dyollluap@users.sf.net wrote:

I agree that using it as a parent term 'Assay using chromatin
immunoprecipitation' and having ChIP-seq etc as child terms as suggested by
Alan fits well.

A term definition based on general ChIP protocols (I can't find anything
that sums it already, so this is my attempt based on CHS protocols,
wikipedia, life tech, ChIP-seq term definition):

An assay in which protein-DNA complexes are extracted from short regions
of chromatin and are reversibly cross linked, immunoprecipitated with
antibodies or tags,

Maybe stop here (or include the purification)? Imagine there are a slew of
other applications and I don't think there's anything specific to CHP in
the below.

This part from Wikipedia does reasonably well.

"protein and associated chromatin http://en.m.wikipedia.org/wiki/Chromatin in
a living cells or tissues are temporarily bonded, the DNA-protein complexes
(chromatin-protein) are then sheared into ~500 bp DNA fragments by
sonication and DNA fragments associated with the protein(s) of interest are
selectively immunoprecipitated from the cell debris using appropriate
antibody along with cross-linked http://en.m.wikipedia.org/wiki/Cross-linkDNA
fragments, and the associated DNA fragments are purified"

There's a bit that should be edited if you use the above - it's not the
DNA-protein that is sheared , it's the DNA.

purified, and amplified for gene- and promoter-specific analysis of known
targets

---

• [obi-terms:#707] http://sourceforge.net/p/obi/obi-terms/707/ new term
  request for chromatin immunoprecipitation *

Status: open
Group: general
Created: Wed May 28, 2014 10:53 PM UTC by plloyd
Last Updated: Fri May 30, 2014 03:29 PM UTC
Owner: nobody

Hi,

We need an OBI term for Chromatin immunoprecipitation (ChIP, not ChIP-chip
or ChIP-seq etc). The existing immunoprecipitation OBI term is not suitable
and the high throughput assays are outside the scope of the experiments
being described and not all the experiments end up as Western blots. The
protein interactions type terms are also unsuitable.

I propose adding chromatin immunoprecipitation assay as a child of the
existing immunoprecipitation term.

The original reference for chromatin immunoprecipitation is
Gilmour & Lis. Proc Natl Acad Sci U S A. 1984 Jul;81(14):4275-9.
and can be found linked from here:
http://www.ncbi.nlm.nih.gov/pubmed/6379641

ps. The link for your documentation on submission guidelines is broken,
let me know if you require further information.

---

Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/obi/obi-terms/707/

To unsubscribe from further messages, please visit
https://sourceforge.net/auth/subscriptions/

[Philippe Rocca-Serra]

closed with comit revision 3937