From 6b87792bec33eec793c45246f7ea939ae19233f7 Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Tue, 17 Jul 2018 14:04:36 +0200
Subject: [PATCH 1/2] Create BEP-0006.md

---
 docs/drafts/BEP-0006.md | 61 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 61 insertions(+)
 create mode 100644 docs/drafts/BEP-0006.md

diff --git a/docs/drafts/BEP-0006.md b/docs/drafts/BEP-0006.md
new file mode 100644
index 0000000..9fb55d8
--- /dev/null
+++ b/docs/drafts/BEP-0006.md
@@ -0,0 +1,61 @@
+# Add Gene Modification Syntax
+
+## Abstract
+
+This BEP adds gene modification syntax (`geneModification`/`gmod`) that supports encoding modifications
+to genes with similar syntax/semantics as protein modifications.
+
+## Preamble
+
+BEP-Id: BEP-0006
+
+Status: Draft
+
+Version: 1
+
+BEL-Version: 2.0.0+
+
+Authors: Charles Tapley Hoyt (charles.hoyt@scai.fraunhofer.de)
+
+Created-Date: 2018-07-17
+
+Type: Standards Track
+
+## Rationale and Goals
+
+The current BEL specification does not allow for encoding modifications to genes, which may have impact that would be nicely captured in BEL. Among the modifications that are targeted by this BEP are the methylation and acetylation of genes, but other types of modifications might also be appropriate.
+
+While it relied on the non-strict parsing from the BEL Framework and did not provide a specification, some ideas from this BEP can be attributed to: Khanam Irin, A., Kodamullil, A. T., Gündel, M., & Hofmann-Apitius, M. (2015). [Computational Modelling Approaches on Epigenetic Factors in Neurodegenerative and Autoimmune Diseases and Their Mechanistic Analysis](https://doi.org/10.1155/2015/737168). Journal of Immunology Research, 2015, 737168. 
+
+## Use Cases
+
+Adding the `geneModification`/`gmod` would allow capturing the effects on several levels from gene modifications.
+
+```
+SET Citation = {"PubMed", "17948130"}
+SET Evidence = "the methylation of NDUFB6 was found to be negatively correlated with its expression in a study of insulin resistance and Type II diabetes"
+
+SET Disease = "Type II diabetes"
+
+g(HGNC:NDUFB6, gmod(Me)) negativeCorrelation r(HGNC:NDUFB6)
+````
+
+## Discussion
+
+- What other types of gene modifications might be nice to represent? What about histone proteins?
+- Should further syntax for specifying the position be added to mirror `pmod()`? For people interested in generating BEL from resources like ENCODE, this might be useful.
+
+## Specification
+
+The `geneModification`/`gmod` function takes a single namespace argument corresponding to the modification:
+
+`gmod(<nsarg>)`
+
+Reasonable arguments:
+
+- From the BEL standard namespace, `M`, `Me`, and `methylation`all refer to methylation on the given gene.
+- Descendants of the Gene Ontology entry, GO_0006304: "DNA modification", are also appropriate.
+
+## Backwards Compatibility
+
+This proposed feature is for 2.0.0+ and will be added to the language so does not require any efforts to migrate older BEL knowledge.

From 1827326070435863f2f6e69b6326e99e45a14616 Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Tue, 17 Jul 2018 14:09:01 +0200
Subject: [PATCH 2/2] Update BEP-0006.md

Add more explanation on how gmod is used in geneAbundance
---
 docs/drafts/BEP-0006.md | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/docs/drafts/BEP-0006.md b/docs/drafts/BEP-0006.md
index 9fb55d8..8b30eb4 100644
--- a/docs/drafts/BEP-0006.md
+++ b/docs/drafts/BEP-0006.md
@@ -49,13 +49,22 @@ g(HGNC:NDUFB6, gmod(Me)) negativeCorrelation r(HGNC:NDUFB6)
 
 The `geneModification`/`gmod` function takes a single namespace argument corresponding to the modification:
 
-`gmod(<nsarg>)`
+`gmod(ns:v)`
 
 Reasonable arguments:
 
 - From the BEL standard namespace, `M`, `Me`, and `methylation`all refer to methylation on the given gene.
 - Descendants of the Gene Ontology entry, GO_0006304: "DNA modification", are also appropriate.
 
+This will also modify the semantics of the `geneAbundance()`/`g()` function to go from having a specification of:
+
+`geneAbundance(ns:v)` 
+
+to have 0 or more `gmod()` modifications.
+
+`geneAbundance(ns:v [, gmod(ns:v]*)` 
+
+
 ## Backwards Compatibility
 
 This proposed feature is for 2.0.0+ and will be added to the language so does not require any efforts to migrate older BEL knowledge.