From 2bec8993a4fdb9c79fd002ca3269b9000e30892f Mon Sep 17 00:00:00 2001 From: Georgie Hau Sorensen <113031495+GeorgieHauSorensen@users.noreply.github.com> Date: Thu, 26 Feb 2026 13:52:39 +0000 Subject: [PATCH 1/6] Add files via upload --- SEPs/SEP_V026.md | 177 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 177 insertions(+) create mode 100644 SEPs/SEP_V026.md diff --git a/SEPs/SEP_V026.md b/SEPs/SEP_V026.md new file mode 100644 index 0000000..11c8c1e --- /dev/null +++ b/SEPs/SEP_V026.md @@ -0,0 +1,177 @@ +# SEP V026: Introduction of “//” as a Glyph for Generic DNA Breaks in SBOL Visual + + + +| SEP | | + +| --- | --- | + +| **Title** | Introduction of “//” as a Glyph for Generic DNA Breaks in SBOL Visual| + +| **Authors** | Georgie Hau Sorensen (georgiehausorensen@gmail.com), Lukas Buecherl | + +| **Editor** | Felipe Buson (fxbuson@gmail.com)| + +| **Type** | Specification | + +| **SBOL Visual Version** | | + +| **Status** | Draft | + +| **Created** | 26 Feb 2026 | + +| **Last modified** | 26 Feb 2026 | + +| **Issue** | | + + + + + +## Abstract + +This proposal introduces a new SBOL Visual glyph, represented by the character sequence “//”, to denote generic breaks in DNA. These breaks include regions where sequence continuity is intentionally unspecified, undefined, interrupted, or skipped for schematic clarity. The use of “//” aligns with widespread conventions in biological schematics and provides a simple, intuitive, and compact symbol to improve readability. + + + +## Table of Contents + +- [1. Rationale](#rationale) + +- [2. Specification](#specification) + +- [3. Example or Use Case](#example) + +- [4. Backwards Compatibility](#compatibility) + +- [5. Discussion](#discussion) + +- [References](#references) + +- [Copyright](#copyright) + + + +## 1. Rationale + + + +1.1. Widespread Use + +The “//” mark is traditionally used in biological schematics to indicate: + +- “region removed/not drawn” + +- “break in continuity” + +- “shift in sequence” + +This convention is common in textbooks, research illustrations, and even circuit diagrams in other fields. + +The familiarity of this symbol lowers the cognitive load for new users, and it makes diagrams more immediately interpretable. + + + +1.2. Glyph Simplicity + +The “//” glyph: + +- Is visually compact + +- Does not resemble any existing SBOL Visual glyph + +- Can be rendered easily in both digital and hand-drawn form + +- Maintains clarity even at small scale + + + +## 2. Specification + +2.1. Glyph Definition + + + +The “//” glyph consists of two short, parallel, diagonal slashes. + + + +These may be oriented: + +- Forward-slanted (primary, recommended) + +- Backward-slanted (optional alternative for stylistic compatibility with other diagram elements) + + + +2.2. Placement + +The glyph placed in-line on a DNA backbone to indicate that: + +- A region of arbitrary length is not shown + +- Sequence continuity is intentionally omitted + + + +Example: + + + +[ promoter ] —— // —— [ CDS ] + + + +2.3. Semantic Meaning + +The glyph may represent a non-specific sequence gap + + + +## 3. Backwards Compatibility + +This SEP is backward compatible insofar as it doesn't directly introduces conflicts with existing glyphs. There is an argument to be made whether its function can be fully covered using the existing "engineered region" glyph. It is worth noting that any diagrams without this introduced break glyph will remain valid. + + + +## 4. Discussion + + + +## Copyright + + + +

+ + + + CC0 + + + +
+ + To the extent possible under law, + + + + SBOL developers + + has waived all copyright and related or neighboring rights to + + SEP V001. + +This work is published from: + + + + United States. + +

\ No newline at end of file From 640b1e9bdfdaf801facd5a6fb63309e2859f9dc9 Mon Sep 17 00:00:00 2001 From: Felipe Buson <55743903+fxbuson@users.noreply.github.com> Date: Tue, 24 Mar 2026 17:59:24 +0000 Subject: [PATCH 2/6] exclude extra linebreaks --- SEPs/SEP_V026.md | 31 +++---------------------------- 1 file changed, 3 insertions(+), 28 deletions(-) diff --git a/SEPs/SEP_V026.md b/SEPs/SEP_V026.md index 11c8c1e..cd5cb70 100644 --- a/SEPs/SEP_V026.md +++ b/SEPs/SEP_V026.md @@ -3,26 +3,16 @@ | SEP | | - | --- | --- | - -| **Title** | Introduction of “//” as a Glyph for Generic DNA Breaks in SBOL Visual| - +| **Title** | Introduction of “//” as a Glyph for Generic DNA Breaks in SBOL Visual | | **Authors** | Georgie Hau Sorensen (georgiehausorensen@gmail.com), Lukas Buecherl | - | **Editor** | Felipe Buson (fxbuson@gmail.com)| - | **Type** | Specification | - | **SBOL Visual Version** | | - | **Status** | Draft | - | **Created** | 26 Feb 2026 | - | **Last modified** | 26 Feb 2026 | - -| **Issue** | | +| **Issue** | | @@ -37,17 +27,11 @@ This proposal introduces a new SBOL Visual glyph, represented by the character s ## Table of Contents - [1. Rationale](#rationale) - - [2. Specification](#specification) - - [3. Example or Use Case](#example) - - [4. Backwards Compatibility](#compatibility) - - [5. Discussion](#discussion) - - [References](#references) - - [Copyright](#copyright) @@ -61,9 +45,7 @@ This proposal introduces a new SBOL Visual glyph, represented by the character s The “//” mark is traditionally used in biological schematics to indicate: - “region removed/not drawn” - - “break in continuity” - - “shift in sequence” This convention is common in textbooks, research illustrations, and even circuit diagrams in other fields. @@ -77,11 +59,8 @@ The familiarity of this symbol lowers the cognitive load for new users, and it m The “//” glyph: - Is visually compact - - Does not resemble any existing SBOL Visual glyph - - Can be rendered easily in both digital and hand-drawn form - - Maintains clarity even at small scale @@ -99,21 +78,17 @@ The “//” glyph consists of two short, parallel, diagonal slashes. These may be oriented: - Forward-slanted (primary, recommended) - - Backward-slanted (optional alternative for stylistic compatibility with other diagram elements) - 2.2. Placement The glyph placed in-line on a DNA backbone to indicate that: - A region of arbitrary length is not shown - - Sequence continuity is intentionally omitted - Example: @@ -174,4 +149,4 @@ This work is published from: United States. -

\ No newline at end of file +

From 50d759d3f6e4345565f656498ad6f7f0805237b1 Mon Sep 17 00:00:00 2001 From: ERIK-KE <58416565+ERIK-KE@users.noreply.github.com> Date: Tue, 24 Mar 2026 19:05:08 +0100 Subject: [PATCH 3/6] Updated formatting of SEP_V026.md --- SEPs/SEP_V026.md | 29 +++++------------------------ 1 file changed, 5 insertions(+), 24 deletions(-) diff --git a/SEPs/SEP_V026.md b/SEPs/SEP_V026.md index cd5cb70..c707f00 100644 --- a/SEPs/SEP_V026.md +++ b/SEPs/SEP_V026.md @@ -31,7 +31,6 @@ This proposal introduces a new SBOL Visual glyph, represented by the character s - [3. Example or Use Case](#example) - [4. Backwards Compatibility](#compatibility) - [5. Discussion](#discussion) -- [References](#references) - [Copyright](#copyright) @@ -88,28 +87,26 @@ The glyph placed in-line on a DNA backbone to indicate that: - A region of arbitrary length is not shown - Sequence continuity is intentionally omitted +2.3. Semantic Meaning -Example: +The glyph may represent a non-specific sequence gap +## 3. Example or Use case : [ promoter ] —— // —— [ CDS ] -2.3. Semantic Meaning - -The glyph may represent a non-specific sequence gap - -## 3. Backwards Compatibility +## 4. Backwards Compatibility This SEP is backward compatible insofar as it doesn't directly introduces conflicts with existing glyphs. There is an argument to be made whether its function can be fully covered using the existing "engineered region" glyph. It is worth noting that any diagrams without this introduced break glyph will remain valid. -## 4. Discussion +## 5. Discussion @@ -118,35 +115,19 @@ This SEP is backward compatible insofar as it doesn't directly introduces confli

- - CC0 - -
- To the extent possible under law, - - SBOL developers - has waived all copyright and related or neighboring rights to - SEP V001. - This work is published from: - - United States. -

From f9d31bcbaff5adae1a3843f081fcaedf593d5471 Mon Sep 17 00:00:00 2001 From: Felipe Buson <55743903+fxbuson@users.noreply.github.com> Date: Wed, 25 Mar 2026 01:01:47 +0000 Subject: [PATCH 4/6] change SEP version at end --- SEPs/SEP_V026.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/SEPs/SEP_V026.md b/SEPs/SEP_V026.md index c707f00..ce4bb73 100644 --- a/SEPs/SEP_V026.md +++ b/SEPs/SEP_V026.md @@ -125,7 +125,7 @@ This SEP is backward compatible insofar as it doesn't directly introduces confli href="sbolstandard.org"> SBOL developers has waived all copyright and related or neighboring rights to - SEP V001. + SEP V026. This work is published from: From 6803a67265fcaa1584bf68c9cf733184e24cf714 Mon Sep 17 00:00:00 2001 From: Felipe Buson <55743903+fxbuson@users.noreply.github.com> Date: Wed, 25 Mar 2026 02:45:23 +0000 Subject: [PATCH 5/6] added figure for SEP V026 --- SEPs/img/SEP_V026_Fig-1.png | Bin 0 -> 5163 bytes 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 SEPs/img/SEP_V026_Fig-1.png diff --git a/SEPs/img/SEP_V026_Fig-1.png b/SEPs/img/SEP_V026_Fig-1.png new file mode 100644 index 0000000000000000000000000000000000000000..1b52a80f6ce1e53e0c97fdc70acb982905423861 GIT binary patch literal 5163 zcmc&&cQo8xyPfdrW<+PAMejAQgb=+aq9wW*y|>Xt9eoI*L=aI!f`}R=B1R{O=!WPe zh^R9{#CN>+yWhI&{(1ko)*3Tw&iqb!p1q&FpOc`cs{tj4lS3d7sFtRx0R%z-1)uFm ziNSxO$An_wjm%5a6bXUAIxk;WdOgeSz?aOvY9_vho({eN2p@Y$KtO<~vxh6v7U5+t z>gnT{yDJBWKxmt^RF#YZ^M1^S=ozhDknG`opjTu5;?59@51IBq zi2sP_S=i7{eTZyG{>X9|j6HuNZ$p3cI9NU&{IPW^?LxqNpY%H?4o*%^eUlqksj1WW zh2h{!O*#gss;VkCIhq&@(Zr|`Qd3hWV2UEam?~ma5sVf6=dr%K)l(~bOP#lZ4oc<< zug>tSbEE|d!|fVF&;0M^N<(XEYD^kj=yP&&*I)^KZ^cOxx@<=|>IR>QQH;EI$Hq1z zH;UfA)$NIo-=RRJYRVBAH)j|-I}0o?FY6f?aJpUl+l3CsCP(V&>B-E+RZI0*iF1E? zjH7OG(K=5CNjy3_ifK$rqEyw;Seb2bl~h-^W6wsZF4s7{BY1H;pl3wkBI&hZ897$e zvL$+{Gj3(B8Tp?dy>og;v%9-{%WDymC2A??R#9I5DOGv`(ucnLphUVtz?_*`Q8^bRoH8jTmNRTA3B{M1~W@KeKjP4JOmEE_+ z@6J29xzRONS+&8<8{KM5C{-t;Wi+`J7@(Xxvkes0ZMd8{1O)OlJzXOF&*SD!j#_>Y zIX|zbw;|@K>FHbnq)`}*as)Pp^lu%0`>kIrQHdD?p(LaX%MQ zz~%?xaT3`mJM#4cUy~bhg$T?Q=4@&AoQ{4$QBjzHfWYSX>vU5r?{|9# zhk>wKf{68X2RjFc*&{LvYuMLxTbOp78Y)vJaF4?(?3cY$gBbz~=1D9m;l6eI_8=28 zv(9THPI>wHP4r2mWHGR_FabQ^$93aF7&svD}T0!Jab+n^@!8Ykx2!--X)zvjuu5 z7Z(gT{QivNOERp5rDcull<0?}uR8xD+o{jhi#v8^>bzI`s1dm-DO8t{DKF|jdi->?U0U2k{|$5R z6?IhlgP-5pE+;+OnHgKIF)}i;Ug=5J)YVmYcmJV+Zw@<`g)H{6hj*R*Y)|o+Z$V7F zd7vkl>E-9wVArJj)EY*U(Cb`cKN;NEoW`ZWdHXhYnXjU!N4?VgJxo3X*R}C7{M&l} z7Ghv^P^I+SqV{Lys1!kZ^Nzf9me;F8VPwK5mWM znbFkIk(%CJU5(z{bV_2DB94rV+&er}QBffTTOn#NOSbKOQdm%+INe@fPq)9nuX*=w zSBu~Fw57H*3LusZP5eA4IM@c9sJ1?Idr~BcU4e~J%!;njZ)cji;$amgkzQzVZEa#b z3SIbx@Du|;E@ZF-O5`T2QTPEKN9pJw@l z3pj$XWeZ(QOw5O(R#wwyAD)lD4|E{-jnVLp7Xf!?N30}B`XAPmb-=1DTOVfczcqjF zG2M(T<7T|~3ouhgh8YIKw?8Z`EyW1C*qwbH8%xW`;GPM?CCO+uCdxzo*8yxb@7<%f z3O^dvcq;mdmX;PZQ|D+4Km~~yxpPJdVtVs5I&fo{736lYC;8gb?&+*7ise)MPfuK< zTQWfPB`qd+Q7BZ6+l*u}zRvM;N23Hu6+4>vc3lYGV=4MumHExOyJ@Y#$1Y3Je!mXv z?HnDsWMyZ|Z9@73t;6Q3dpYd~NORb12C z+ZAYNX|F(B8sI>>`uh4J+S}V_X6yY~vQioTYqOWgEmPJuLW+1uM=4hsr6>KZ3X zbr?~!HbFtnrr7j>SNC%F)^k0{s~-r`^WMve4#DsCGi9!Mn_%R!Q7OGF^&Z0T9nI~M zLmW=p)f@(c5x-BHZwr~K{GsK%Jy~T^@07MD3rIuDryH$aoF*YSxcn|UNSve_0W%W= zlu<1kBO7@cyd_Zgeq(o6RBp%%XE+y;k-dp zLh7-Ej3~MG6m>kQ|Ex%&m@P4!XZC({eB2I)D_Py#j9*=~Lsei?*cG10AlD0OYV>>h zKBGHn*1K8gMy!xuW^0@{Tu^m&QU(SF;?7^W5!enCiA2DzMegk@=xzjAEiVq>>4_TQ zC|6Tc69*3uQL%b5O=D?EiS-gD2J>j<2T>ePAAH6THcJrmEirrxo=gm=#4jYI0XYL+JcXx08`YK-%Tf_($mwQ0CIZcc1-CQ7?wfd;1>{B zA`(%3$SWyXJA_Ec%VS~YbG!$c4pgV!8kQ3);{?}vd|@_Q4rCiRhJ7G5E9*nKMe9?*bgAm=Qzs@SQZ~j# zM{@`YlCSip^kxVc?j4QY&t)lFRqM1P1wQ$XM zLmRxN(>3uqFZ$xraA|~;VlD=Rs;xm<{*iv}Odg#qQa&EwPeRXd9lgC9k>`Ix-m7YB zlZ%Db(|%S8niwA^?Zg>ZThZsgmwWT(&Ftf9v#MCLs-A#_P!dK)#t(ZK3X}G*woxK( z4)4*_{QM`(QV#W|Y9T;mH@_5;Qc-DK{5g+_Yj#xUl6(m8vAnVZeMpv+lG1x~;j!%@ zpU^iErN#pJjRK|@vVO{eflVD|oK@$CBMMD{`<&$Di9Bc^1suA5J^3x~tuSJ~N9fM}9q z9X@AAwuRtlf8(>$Z>5PijmYrR10&wm)y2Wft3EwBJ|0cMD7rZQ+VBKOu=mci#8Lp# z-Cg8c@U}>?m{X>2ek>R#9ibq@A!1l0!VXi6kWX z+>%jK>SYr3&uXtTGc!S{q39bKiPJ8{0Oi%Uu$Wt4H6F|ok!lgqLdOEY6d^Z;FO3mk zCgq=(R@E8^#C38C3TR_UP|$T@VM+u70lFhaurdhbr*;QTY0tLftd75=J7b}pHMYH# z4nFjTU`02jkYOdmxz+$GMp26h?b0aiQsuC)I|qk{`j(a=Tjw1e9nQ``Q_JW!Q`zKKCOIl0t~3_Aln`3$VoK;Sn4Iw`3OsMyfg;p6S8 z{cgrbq}3|Q%Bg8-k#8+qb4ulP#++_|gk24$nl&?5-U+i)$VO#dIwk&0ZKsA=X}mXp zAmB}mE1@|XaH8+~e73)sGgm#V7#SG&8V;PvDQKd$LqkK4A#8zpw*z!{_4)}I#H@aQ z2@gl!0si@wam9pBxUZH#ruNdI03CU#nOTn3S=zZZ%uL7VUP0&LxCg$cUNBa9mQ?A_{ULn4T`_lsdG{9bgezbWTh$L z;>CSc(0ND&D{x9uC99(@`y(;2pEYOxyK~HzExwV})nb=Iv#~)UCMMR@+}wf1Ui0wq z@CpdfDARqhxU_WT=FOYFpi^O$^}WjQ+>oDc@8BSK`PRKH=gR^wjv%P5t-ULgaE7O6+nW1OvLngyrwKb<1OSmrT@-!q-Xm%xEM$_YYjb<2FfR*)hZz& z0a`3nYin!yIhYkV`EF2)J$JC|0^;I&n~6cV8Al11asJkwT24tdOUoBtBWJmuA7|Eo z7~9~vI0yNKg;jxv1?_G0^|ONmpSpTK&`RFTmopvz$V(3e%m@TCu**!Yt*-uc|Ni~J z;9$)BJnJPx#$VHdDi4}3qDPM&ot&L@E-bJERBg^S2n8Q)BJfh-fHe)TMxDS_N)(tH z2zp^r5dp9OJi{9RE{`~| wHj&?p0ny6kt^e1>(f{$j>Hqt&fr~3ot?{91yc}1-MIS^ Date: Wed, 25 Mar 2026 02:59:14 +0000 Subject: [PATCH 6/6] added example section --- SEPs/SEP_V026.md | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/SEPs/SEP_V026.md b/SEPs/SEP_V026.md index ce4bb73..65f3f9a 100644 --- a/SEPs/SEP_V026.md +++ b/SEPs/SEP_V026.md @@ -94,11 +94,9 @@ The glyph may represent a non-specific sequence gap ## 3. Example or Use case : -[ promoter ] —— // —— [ CDS ] - - - +![Figure1](img/SEP_V026_Fig-1.png) +Here, the diagram represents two genes in distinct loci in the genome, separated by omitted genomic context,represented by the proposed glyph. ## 4. Backwards Compatibility