Many GenBank feature types do not have SBOL Visual Glyphs

[cjmyers]

https://docs.google.com/spreadsheets/d/1X870i3NhO7xEhqhLXK4eravNd72x-O-xbrpmlT835nY/edit?usp=sharing

[jakebeal]

Note that these are not so much official as a community-sources list of things that people often find in GenBank. Coping in from the spreadsheet:

GenBank	SO Term	SBOL Visual
allele	SO:0001023
attenuator	SO:0000140
C_region	SO:0001834
CAAT_signal	SO:0000172
CDS	SO:0000316	cds
D-loop	SO:0000297	origin-of-replication
D_segment	SO:0000458
enhancer	SO:0000165
exon	SO:0000147		can be shown as CDS minus intron
gene	SO:0000704
GC_signal	SO:0000173
iDNA	SO:0000723
intron	SO:0000188	intron
J_region	SO:0000470
LTR	SO:0000286
mat_peptide	SO:0000419
misc_binding	SO:0000409	operator
misc_difference	SO:0000413
misc_feature	SO:0000001
misc_marker	SO:0001645
misc_recomb	SO:0000298
misc_RNA	SO:0000233
misc_signal	SO:0001411
misc_structure	SO:0000002
modified_base	SO:0000305
mRNA	SO:0000234
N_region	SO:0001835
polyA_signal	SO:0000551
polyA_site	SO:0000553	poly-a
precursor_RNA	SO:0000185
prim_transcript	SO:0000185
primer	SO:0000112
primer_bind	SO:0005850	primer-binding-site
promoter	SO:0000167	promoter
protein_bind	SO:0000410	operator
RBS	SO:0000139	rbs
rep_origin	SO:0000296	origin-of-replication
repeat_region	SO:0000657
repeat_unit	SO:0000726
rRNA	SO:0000252
S_region	SO:0001836
satellite	SO:0000005
scRNA	SO:0000013
sig_peptide	SO:0000418
snRNA	SO:0000274
source	SO:0000149
stem_loop	SO:0000313
STS	SO:0000331
TATA_signal	SO:0000174
terminator	SO:0000141	terminator
transit_peptide	SO:0000725
transposon	SO:0001054
tRNA	SO:0000253
V_region	SO:0001833
variation	SO:0001060
-10_signal	SO:0000175
-35_signal	SO:0000176
3'clip	SO:0000557
3'UTR	SO:0000205
5'clip	SO:0000555
5'UTR	SO:0000204
regulatory	SO:0005836
snoRNA	SO:0000275
none of above	SO:0000110	unspecified
GenBank	SO Term		Synonyms:	SO Term
assembly_gap	NA		gap	SO:0000730
centromere	SO:0000577
gap	SO:0000730
J_segment			J_gene_segment	SO:0000470
mobile_element	NA		mobile_genetic_element	SO:0001037
ncRNA	SO:0000655
old_sequence	NA
operon	SO:0000178
oriT	SO:0000724
propeptide	SO:0001062
telomere	SO:0000624
tmRNA	SO:0000584
unsure			sequence_uncertainty	SO:0001086
V_segment			V_gene_segment	SO:0000466

(edited to add missing information)

[jakebeal]

Looking at these, I'm not sure how many we actually really need to fill in, until such time as somebody wants them. How often does a synbio system actually work with rRNA, for example? A better solution might be to have an alternative to the "no glyph assigned" bracket that looks nicer on diagrams.

[shyambhakta]

I think several of these are represented at some level, for which the question is whether or not to make a specialty glyph for it or formalize repurposing an existing one for the SO terms.

attenuator - terminator (conditionally repressed based on translation rate of upstream leader peptide; not ever used in syn bio) oriT - origin of transfer glyph. polyA_signal - no different than polyA site? transit peptide / signal peptide - protein location? This superimposition of protein stem glyphs with CDS/domain glyphs raises an old, unresolved question from issue 78. J_segment and V_segment are exons specific to the V(D)J recombination locus, and we have exon glyphs.

These are special kinds of protein-binding sites, the latter 4 inside promoters which I think can just be labeled inside the protein-binding site glyph, especially the last three.

• centromere
• enhancer
• TATA_signal
• -10_signal
• -35_signal

These RNA terms can use an ncRNA gene or squiggly RNA backbone, depending on whether the DNA gene or RNA itself is being referred to. We don't have different CDS glyphs for different types of proteins. No need to have different ncRNA glyphs for different ncRNAs, like rRNAs or tRNAs, I think.

• misc_RNA
• ncRNA
• rRNA
• scRNA
• tRNA
• snoRNA
• tmRNA (though it technically has a tiny CDS inside encoding the degradation peptide tag, as it's a hybrid transfer-messenger RNA)

And these terms bring up unresolved issue #113 :

• gene
• operon
• mobile_element

[cjmyers]

Good point. We likely should have more alternative SO terms for some of our glyphs based upon this.