the-sequence-ontology/so-ontologies

Collect of SO Ontologies

so-ontologies's Issues

gamma turn synonyms [sf#28]

Reported by batchelorc on 2007-08-20 10:38 UTC
Hello,

"classic gamma turn" EXACT for gamma_turn_classic (SO:0001139)

"inverse gamma turn" EXACT for gamma_turn_inverse (SO:0001140)

The beta turns are complicated and I'll send more about them later today.

best wishes,
Colin.

fragment: for parts of interrupted elements [sf#13]

Reported by h-gundlach on 2007-05-16 09:07 UTC
I need a SO-term as gff3 type, for describing fragments of interrupted (e.g. by insertions of other transposons) transposons/genetic elements, that belong to one (transposon) element. The situation is analogous to exons belonging to a gene (gff Parent relationship). It is probably best to create a general term, not restricted to transposons.

new sequence variant terms. [sf#7]

Reported by eilbeck on 2007-02-09 20:54 UTC
Submitting discussion from Gudmundur.

Hi Gudmundur,
Thanks for the suggestions.

I think MNP is either a child of or a synonym of "complex_substitution"

heterozygous, variable but undefined at nucleotide level is quite a mouthful. This term cannot be a sequence feature since it is undefined at the sequence level. How would you use this term if it existed in SO?

Named insertion, insertion/deletion polymorphism of named repetitive element. Does this mean you have a polymorphism in a repeat or the repeat is the polymorphism?

Incidentally, we use a tracker to submit term requests to SO. That way we can keep track of all the requests, and get the stats all from one place. It also stops requests from getting lost. I will submit this request for you.

There is a paragraph detailing how to use the term tracker here:
http://www.sequenceontology.org/so\_how\_to.shtml
or you can go directly to the tracker page here:
http://sourceforge.net/tracker/?atid=810408&group\_id=72703&func=browse

Thanks,
Karen

On Feb 9, 2007, at 6:33 AM, Guðmundur Árni Þórisson wrote:

Hi. I'd like to propose that the 'sequence_variant' collection be
expanded a little bit. I just noticed that there's a number of
variation classes not represented in the current SO:

A) MNP, multiple nucleotide polymorphism with alleles of common
length > 1. Example AAA/TTT ( http://www.ncbi.nlm.nih.gov/SNP/
snp_ref.cgi?rs=rs2067431)

B) Heterozygous, variable, but undefined at nucleotide level

C) Named insertion, insertion/deletion polymorphism of named
repetitive element.

Here's a list of classes currently in use in dbSNP, the classes above
are all from that list:
http://www.ncbi.nlm.nih.gov/SNP/snp\_legend.cgi?legend=snpClass

PS I'm also looking into structural variation (e.g. copy number
variation), but will have more to say about that later.

Mummi, Leicester

add disjoint_from tags [sf#43]

Reported by cmungall on 2007-10-04 03:25 UTC
Can the next SO release include explicit disjointness tags

eg mutually between all root nodes (SF, chromosome_variation, ..)

region, junction, sequence_alteration

ntr: internal_guide_sequence [sf#10]

Reported by batchelorc on 2007-03-06 15:23 UTC
Hello,

Currently annotating a paper (DOI: 10.1039/b617574k) about RNA self-splicing in Tetrahymena.

Could we have internal_guide_sequence?

name: internal_guide_sequence
synonym: "IGS" EXACT []
def: "A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity." [SO:cb] --- can't find a decent definition easily, and Stryer (p. 805, 5th edn) simply calls it a "purine-rich guide sequence".

Not sure what it should be a child of. ribozyme (SO:0000374) ?

PMID: 8784205 is a paper from 1996 which explores mutations in the IGS of Tetrahymena.

Best wishes,
Colin.

promoter motif 8 [sf#36]

Reported by nlw on 2007-09-11 19:13 UTC
Name: Motif 8

Def:
A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with motif 7. Tends to not occur with DPE motif (SO:0000015) or motif 10.

DBxref: PMID:12537576

Comment:
This consensus sequence was identified computationally using the MEME algorithm within core promoter sequences from -60 to +40, with an E value of 5.1e-29.

ntr: wobble_base_pair [sf#9]

Reported by batchelorc on 2007-02-23 16:05 UTC
child of SO:0000028 ("base_pair")

definition "A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C."

exact synonym: "wobble pair"
dbxref - PMID: 11256617

Best wishes,
Colin.

strand attribute - forward, reverse? [sf#19]

Reported by whetzel on 2007-07-02 03:38 UTC
Would the terms 'forward' and 'reverse' fit as kinds of strand attributes? Looking to map the above MO terms to terms in SO.

Trish

DNA constraints [sf#6]

Reported by eilbeck on 2007-02-07 16:44 UTC
Submitting another request from Colin, so it does not get lost.

It's all to do with annotating a paper: "Control of macromolecular
structure and function using covalently attached double-stranded DNA
constraints", PMID 17216052.

* Currently I've annotated the paper with SO:0000442 (dsDNA oligos) but
I was wondering whether "DNA constraint" ought to be a new term,

• child of "reagent" (SO:0000695)
• tentative definition "A double-stranded DNA used to control
  macromolecular structure and function."

* Also, what about chemically substituted DNAs and RNAs? The paper
mentions "5'-tethered-aldehyde DNA" and "2'-amino-RNA". Would they fall
within the scope of SO?

* "P4-P6 domain". This is a 160 nucleotide RNA domain in the
Tetrahymena group I intron. It gets 60 hits on PubMed. It looks like a
model domain for people studying folding. Is it within scope?

* "tetraloop". Currently annotated as SO:0000313 "stem_loop". Should
tetraloop be a child of stem_loop?

I think that's it for that paper.

synonyms for rRNAs, polypeptides etc. [sf#30]

Reported by batchelorc on 2007-08-23 15:23 UTC
Hello,

(1) Could we have the RELATED synonyms for SO:0001000 (rRNA_16S), SO:0001001 (rRNA_23S) and SO:0001002 (rRNA_25S) upgraded to EXACT?

(2) Could we have "virus sequence" and "viral sequence" as EXACT for SO:0001041 (virus) and "phage sequence" as EXACT for SO:0001042 (phage)? ("nucletide" in def. for SO:0001041 should read "nucleotide")

(3) Could "repeat" as an EXACT synonym for SO:0001068 (polypeptide_repeat) be downgraded to RELATED? (Not a problem if not; I shall stoplist it, but surely people describing other sorts of sequence say "repeat" too.)

(4) Could we have "3(10) helix" and "310 helix" as EXACT synonyms for SO:0001119 (three_ten_helix)?

(5) "nest motif" as EXACT for SO:0001120 (nest).

(6) "peptide turn" as EXACT for SO:0001128 (turn).

Many thanks,
Colin.

error in XP def consensus_mRNA [sf#15]

Reported by nlw on 2007-06-29 02:24 UTC
[Term]
id: SO:0000995
name: consensus_mRNA
comment: DO not obsolete without considering MGED mapping.
is_a: SO:0000234 ! mRNA
intersection_of: SO:0000993 ! consensus
intersection_of: has_quality SO:0000993 ! consensus

did you mean to have intersection_of consensus twice?

piRNA [sf#21]

Reported by eilbeck on 2007-07-24 16:30 UTC
New term suggestion

Genes Dev. 2007 Jul 15;21(14):1707-13.

piRNAs--the ancient hunters of genome invaders.

Hartig JV, Tomari Y, Förstemann K.

Abstract:
In addition to miRNAs and siRNAs, a third small RNA silencing system has been uncovered that prevents the spreading of selfish genetic elements. Production of the Piwi-associated RNAs (piRNAs), which mediate the silencing activity in this pathway, is initiated at a few master control regions within the genome. The nature of the primary piRNA-generating transcript is still unknown, but RNA interference (RNAi)-like cleavage events are likely defining the 5'-ends of mature piRNAs. We summarize the recent literature on piRNA biogenesis and function with an emphasis on work in Drosophila, where genetics and biochemistry have met very successfully.

transfer RNA definitions [sf#31]

Reported by batchelorc on 2007-09-06 16:25 UTC
Hello,

I think these are the correct definitions for SO:0000254, SO:0000256 to SO:0000273, SO:0000766, SO:0001036 and SO:0005857 (the existing ones contain typoes or all mention a 3' alanine binding region).

Hopefully they won't get too mangled by the web form.

alanyl_tRNA A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region. SO:0000254
asparaginyl_tRNA A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region. SO:0000256
aspartyl_tRNA A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region. SO:0000257
cysteinyl_tRNA A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region. SO:0000258
glutaminyl_tRNA A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region. SO:0000259
glutamyl_tRNA A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region. SO:0000260
glycyl_tRNA A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region. SO:0000261
histidyl_tRNA A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region. SO:0000262
isoleucyl_tRNA A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region. SO:0000263
leucyl_tRNA A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region. SO:0000264
lysyl_tRNA A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region. SO:0000265
methionyl_tRNA A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region. SO:0000266
phenylalanyl_tRNA A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region. SO:0000267
prolyl_tRNA A tRNA sequence that has a proline anticodon, and a 3' proline binding region. SO:0000268
seryl_tRNA A tRNA sequence that has a serine anticodon, and a 3' serine binding region. SO:0000269
threonyl_tRNA A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region. SO:0000270
tryptophanyl_tRNA A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region. SO:0000271
tyrosyl_tRNA A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region. SO:0000272
valyl_tRNA A tRNA sequence that has a valine anticodon, and a 3' valine binding region. SO:0000273
pyrrolysyl_tRNA A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region. SO:0000766
arginyl_tRNA A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region. SO:0001036
selenocysteinyl_tRNA A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region. SO:0005857

Best wishes,
Colin.

term request : genome [sf#1]

Reported by jcmatese on 2006-02-14 19:57 UTC
Suggestion: How about a term "genome" ?

It itself is used within other term names, their definitions, and even a
relationship (genome_of). Primarily, I was simply hoping to reason that a
chromosome was part_of a genome, but presumably this term would be
wide-reaching (many possible "parts")...

Possible defs:
http://www.google.com/search?oi=defmore&defl=en&q=define:Genome

-John

Request for new term - epitope [sf#12]

Reported by whetzel on 2007-04-01 14:45 UTC
Can epitope be added?

Proposed parent: protein_binding_domain, probably others based on SO structure.

Definition: part of a macromolecule that is recognized by the immune system

Definition Source: Wikipedia, http://en.wikipedia.org/wiki/Epitope

Trish

CG_rich_region...don't like def [sf#40]

Reported by nlw on 2007-09-11 22:02 UTC
For the term CG_rich_region (SO:0000173), the definition and name don't seem quite right and/or doesn't have the right parentage. Since a CG rich region could occur anywhere within a sequence, and not just in a promotor, then i don't think CG_rich_region should be a child of RNA_II_promoter_region.... if you want to keep the definition the same, perhaps the name of the term should change to CG_rich_promoter_region?

new term request: mitron [sf#20]

Reported by ma11 on 2007-07-12 07:58 UTC
Karen

Ruby et al. Nature 448:83 desribe a new class of miRNAs that are derived from debranched introns. They name the class, intronic mRNA. It will be is_a miRNA but derived from an intron. The class of introns from which these are derived are called : mitron.

mitron
def: An intron from whose debranched product an miRNA is derived.

intronic miRNA
def: A miRNA derived by DROSHA-independent processing from a mitron.

Michael

New term: rRNA_21S [sf#48]

Reported by batchelorc on 2007-10-16 09:13 UTC
name: rRNA_21S
definition: "A component of the large ribosomal subunit in mitochondrial rRNA."

(I can find plenty of recent papers on it, but not the key paper that identifies it first.)

Some EXACT synonyms:
"21S rRNA"
"21S ribosomal RNA"

Best wishes,
Colin.

PNA, and motifs [sf#5]

Reported by eilbeck on 2007-02-07 16:41 UTC
Submitting this on behalf of Colin, so it gets in the system.
--K

Hello,

A colleague draws my attention to a paper titled "PNA forms an i-motif",
abstract:
"A C-rich PNA hexanucleotide, p(C5T), has been shown to form an i-motif
by nanoelectrospray ionization mass spectrometry coupled with H/D
exchange, to have thermal stability comparable with its DNA analogue,
but to exist over a much narrower pH range."

It looks as if i-motifs are definitely within scope, sample first
sentence of paper "At moderately acidic pH, cytosine-rich DNA and RNA
strands can associate both inter- and intramolecularly to form an
i-motif." And i-motif turns out to be short for "intercalated cytosine
motif", paper giving the structure at
http://nar.oxfordjournals.org/cgi/content/abstract/26/20/4696

What about PNAs, though? People seem to be using them in sequency ways.
I can give more details.

Best wishes,
Colin.

--
Dr Colin Batchelor MChem MRSC,
Production Systems Analyst
Royal Society of Chemistry, Thomas Graham House, Cambridge UK CB4 0WF
[email protected] t: [phone]

synonym for G_quartet (SO:0000003) [sf#23]

Reported by batchelorc on 2007-08-15 13:00 UTC
Hello,

Could we have the following as EXACT synonyms for G_quartet:

G_quadruplex
G-quadruplex

?

Best wishes,
Colin.

error in XP def predicted_gene [sf#16]

Reported by nlw on 2007-06-29 02:25 UTC
[Term]
id: SO:0000996
name: predicted_gene
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
intersection_of: SO:0000704 ! gene
intersection_of: has_quality SO:0000704 ! gene

did you mean to list intersection_of gene twice?

rename "virus" (SO:0001041)? [sf#45]

Reported by batchelorc on 2007-10-11 08:45 UTC
Hello,

I think I'd prefer "virus_nucleotide_sequence", given that the definition for "virus" begins "The region of nucle[o]tide sequence of a virus", which looks circular to me. And a virus consists of at least a nucleotide sequence and a protein coating anyway, so there's the capsid sequence to worry about as well.

Similarly "phage" and its EXACT synonym "bacteriophage".

Best wishes,
Colin.

Request to include CDS_predicted in SOFA [sf#22]

Reported by pcanaran on 2007-07-25 17:47 UTC
Hi,

We are looking for a feature for describing predicted CDS features in GFF3 files. The SO term "CDS_predicted", seems to be well suited for this. Can this term be included in SOFA as well?

Thank you.

Payan Canaran

update to mapping for MO term mtDNA? [sf#18]

Reported by whetzel on 2007-07-01 11:47 UTC
Similar to the post re:ctDNA.

The MO term mtDNA is mapped to the SO term mitochondrial_location. Would it be possible to create a new SO term mitochondrial_DNA that is the intersection of mitochondrial_location and DNA?

Trish

New term of miRNA target sites [sf#3]

Reported by cdsmith_lbl on 2006-11-01 18:22 UTC
microRNA (miRNA) sequences are biologically important molecules that
play a variety of roles in regulation. While SO has 3 terms to describe
miRNA, miRNA_gene, and miRNA_primary_transcript there is no term to
denote where the functional, processed miRNA sequence binds to.
Typically miRNAs have been found clustered in 3' UTRs, but recent studies
show miRNA binding sites in TEs and intergenic regions.

In my opinions a new term of 'miRNA_target_site' should be added to
denote a region where miRNAs bind and this terms should be able to be
applied top any stretch of sequence.

new terms: anticodon, tRNA region, etc. [sf#50]

Reported by batchelorc on 2007-10-17 10:17 UTC
Hello,

I noticed "anticodon" was missing, so I've been investigating.

Firstly, I think we need

name: tRNA_region
def: "A region of a tRNA." [RSC:cb]
is_a: SO:0000834 ! processed_transcript_region
relationship: part_of SO:0000253 ! tRNA

(not sure about the is_a there: do we need ncRNA_region as well?)

then:

name: anticodon_loop
def: "A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3'." [ISBN:0716719207]
is_a: ! tRNA_region
synonym: "anti-codon loop" EXACT []

name: anticodon
def: "A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA"
relationship: part_of ! anticodon_loop
is_a: ! tRNA_region
synonym: "anti-codon" EXACT []

(not sure about the is_a, again)

name: CCA_tail
def: "Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid." [ISBN:0716719207]
is_a: ! tRNA_region
synonym: "CCA sequence" EXACT []

name: DHU_loop
def: "Non-base-paired sequence of nucleotide bases in tRNA. Contains several dihydrouracil residues." [ISBN:0716719207]
is_a: ! tRNA_region
synonym: "D loop" RELATED []

name: T_loop
def: "Non-base-paired sequence of three nucleotide bases in tRNA. Has sequence T-Psi-C." [ISBN:0716719207]
is_a: ! tRNA_region
synonym: "TpsiC loop" EXACT []

The loops are themselves parts of arms, but I think I want to find out what the best thing to do with the anticodon being part of the anticodon loop and how to ensure is_a completeness there before asking for any more.

Best wishes,
Colni.

ntr: deoxyribozyme [sf#8]

Reported by batchelorc on 2007-02-12 17:01 UTC
(Already discussed, just posted so it doesn't get lost.)

Could we have "deoxyribozyme", exact synonyms "DNAzyme", "DNA enzyme", maybe "catalytic DNA", definition "An artificial DNA with catalytic activity", child of "reagent"?

Colin.

promoter motif 6 [sf#34]

Reported by nlw on 2007-09-11 19:09 UTC
Name: Motif 6

Def:
A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with motif 1. Tends to not occur with DPE motif (SO:0000015) or motif 10.

DBxref: PMID:12537576

Comment:
This consensus sequence was identified computationally using the MEME algorithm within core promoter sequences from -60 to +40, with an E value of 1.9e-62.

poor use of "region" in defintion of "sequence_variant" [sf#25]

Reported by ddeluca on 2007-08-17 14:37 UTC
Region has become a very powerful concept in the SO, and I think we need to be more careful now about using it in the definitions of other terms.

the def. of sequence_variant is:
"A region of sequence where variation has been observed."

This implies that sequence_variant is_a region, which would not be useful at all.

I think that the strongest definition of sequence_variant should allow for the use of the variant_of relation. However if we say that sequence_variant is variant_of region, then we force sequence_variant to be continuous, which conflicts with genotype.

In fact, I think the best definition for sequence_variant is the definition we already have for genotype:
"is a variant [of] genome, complete or incomplete."

This is good because it allows for variants of continuous or discontinuous sequences.

The questions then arise:

1. Should we replace sequence_variant with genotype, or make it a synonym, using the definition of genotype?

2. Should genotype be a subclass of sequence_variant, perhaps with the definition: is_a sequence_variant of whole genes?

3. Because most of the subclasses of sequence_variant are all variant_of region, should we create a subclass of sequence_variant called region_variant having the variant_of region relation, and then pack allele, insertion, etc into "region_variant"? This middle class would only serve to clarify that its children are variants of continuous sequences ...

food for thought!

David DeLuca

beta turn synonyms, definitions and terms [sf#29]

Reported by batchelorc on 2007-08-21 08:59 UTC
Hello,

Couldn't send this yesterday as connection to sourceforge was dicky. It might be one for Gabby to sort out as it's quite complicated.

I've been mapping the SO terms for beta turns to the Richardson classification, which is (a) what they seem to be based on and (b) how they seem to be referred to in plain text. (Fantastically, the phrases Type I turn only seem to refer to beta turns---there is no polysemy). It looks like this:

SO:0001136
name: beta_turn_right_handed_type_one
synonym: "Type I beta turn" EXACT
synonym: "Type I turn" EXACT

SO:0001134
name: beta_turn_left_handed_type_one
synonym: "Type I' beta turn" EXACT
synonym: "Type I' turn" EXACT

SO:0001137
name: beta_turn_right_handed_type_two
synonym: "Type II beta turn" EXACT
synonym: "Type II turn" EXACT

SO:0001135
name: beta_turn_left_handed_type_two
synonym: "Type II' beta turn" EXACT
synonym: "Type II' turn" EXACT

I think there's a problem with the definitions of the left-handed turns: all of the signs on the angles (and the directions of the greater-than/less-than signs) should be reversed, because they're currently the same as the definitions of the right-handed turns!

Finally, in the Richardson classification, and in the literature, there are further sorts of beta turn, which all ought to be children of beta_turn:

beta_turn_type_six

• beta_turn_type_six_a
  ++ beta_turn_type_six_a_one
  ++ beta_turn_type_six_a_two
• beta_turn_type_six_b
  beta_turn-type_eight

with synonyms as above (that is, "type VIa2 turn" and "type VIa2 beta turn") EXCEPT no left-handed or right-handed variants.

There is, nastily, a Type IV as well, which means "animal not included in this classification". I don't like this, but maybe it ought to go in?

Best wishes,
Colin.

pseudogenic defs [sf#44]

Reported by cmungall on 2007-10-07 00:38 UTC
the following terms lack defs:

SO:0000507 pseudogenic_exon
SO:0000516 pseudogenic_transcript
SO:0000777 pseudogenic_rRNA
SO:0000778 pseudogenic_tRNA

I suggest a genus-differentia def based on the "pseudogenic region" is_a parent:

"A non-functional descendant of a X"

It should be made clear in the definition gloss or comments whether pseudogenic transcripts are ever transcribed.

"Non-functional" should also be clarified.

Sequence_feature recursive definition [sf#24]

Reported by ddeluca on 2007-08-17 14:11 UTC
I would like to offer a suggestion to clear up a problem with sequence_feature:

sequence feature is defined as a "feature that can be attributed to a region"

but region is defined as is_a sequence_feature.

Possible Solution: change definition of sequence feature to "a feature that can be attributed to a genome, or part of a genome."

Best Regards,

David

promoter motif 10 [sf#37]

Reported by nlw on 2007-09-11 19:17 UTC
Name: Motif 10

Def:
A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or motif 6.

DBxref: PMID:12537576

Comment:
This consensus sequence was identified computationally using the MEME algorithm within core promoter sequences from -60 to +40, with an E value of 8.3e-9.

promoter motif 7 [sf#35]

Reported by nlw on 2007-09-11 19:11 UTC
Name: Motif 7

Def:
A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with motif 8. Tends to not occur with DPE motif (SO:0000015) or motif 10.

DBxref: PMID:12537576

Comment:
This consensus sequence was identified computationally using the MEME algorithm within core promoter sequences from -60 to +40, with an E value of 1.9e-63.

Schellmann loop synonyms [sf#27]

Reported by batchelorc on 2007-08-20 10:10 UTC
Hello,

Could we have

"six-residue Schellmann loop" as an EXACT synonym for schellmann_loop_six (SO:0001125)

"seven-residue Schellmann loop" as an EXACT synonym for
schellmann_loop_seven (SO:0001124)

I've seen "paperclip" and "paperclip loop" used to mean Schellmann loops (SO:0001123), but I think they should only be RELATED, because paperclip looks nastily polysemous, even within the scope of SO.

best wishes,
Colin.

promoter motif DRE [sf#39]

Reported by nlw on 2007-09-11 19:29 UTC
Name: DRE_motif

Def:
A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW. Tends to co-occur with Motif 7. Tends to
not occur with DPE motif (SO:0000015) or motif 10.

DBxref: PMID:12537576

Comment:
This consensus sequence was identified computationally using the MEME algorithm within core promoter sequences from -60 to +40, with an E value of 1.7e-183.

more rRNA synonyms, and definition suggestions [sf#47]

Reported by batchelorc on 2007-10-16 09:03 UTC
Hello,

I've been looking at the ribosomal RNA subunit terms.

"rRNA_primary_transcript" (SO:0000209)

"ribosomal RNA primary transcript" should be EXACT.

"rRNA" (SO:0000252)

Remove leading space from " ribosomal ribonucleic acid"
"ribsomal RNA" should read "ribosomal RNA"

"rRNA_5.8S" (SO:0000375)

Replace "5. 8S" with "5.8S" throughout. (Has this been introduced by OBOEdit?)

"rRNA_18S" (SO:0000407)

Add to def something like " in eukaryotes". Is it worth mentioning that the small ribosomal subunit ONLY contains rRNA_18S?

"18S rRNA" should be EXACT.
New EXACT synonym: "18S ribosomal RNA"

"rRNA_16S" (SO:0001000)

Add to def something like " in Bacteria and Archaea". Is it worth mentioning that the small ribosomal subunit ONLY contains rRNA_16S?

"16S rRNA" should be EXACT.
New EXACT synonym: "16S ribosomal RNA"

"rRNA_23S" (SO:0001001)

For consistency, do we want the definition to read

"A large polynucleotide which functions as a part of the large subunit of the ribosome."? Add " in Bacteria and Archaea"?

"23S rRNA" should be EXACT.
New EXACT synonym: "23S ribosomal RNA"

"rRNA_25S" (SO:0001002)

Definition needed: I suggest "A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes."

New EXACT synonym: "25S ribosomal RNA"

Best wishes,
Colin.

transcript_region part of genome or mRNA? [sf#26]

Reported by ddeluca on 2007-08-17 15:08 UTC
The definition of transcript_region is "region of a transcript", which for me means region of an mRNA. Is this is what is implied?

If so, then there is a problem with exon, because exon is_a transcript_region, but is defined as a "region of the genome"

A possible solution would be to define "transcript_region" as a region of the genome which is transcribed into RNA.

The other solution would be to make exon ambiguous by removing the term "genome" from its definition. Then exon could be part of a DNA or an mRNA ...

Cheers,

David

transcription_end_site: junction or region? [sf#42]

Reported by cmungall on 2007-10-02 22:59 UTC
presumably nothing can be both a junction and a region?

I explicitly added mutual disjoint_from links to the ontology and got the following reasoner check result from oboedit:

2 fatal errors:

transcription_end_site (SO:0000616) generated 1 error.
transcription_end_site (SO:0000616) has disjoint superclasses region and junction
transcription_start_site (SO:0000315) generated 1 error.
transcription_start_site (SO:0000315) has disjoint superclasses region and junction

double-stranded_RNA? [sf#41]

Reported by agussman on 2007-09-20 19:51 UTC
Could there be a term for just 'double-stranded_RNA'? I don't feel like any of the existing terms under RNA_chromosome would be appropriate for the sequence content of, for instance, this refseq record <a href="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&val=120407016"> NC_008732</a>.

update to DPE motif [sf#38]

Reported by nlw on 2007-09-11 19:20 UTC
would like to add the

dbxref:PMID:12537576

is it really ALWAYS found ith INR motif? According to this paper, it is computationally found to co-locate only 14.9% of the time.

fragment: for parts of interrupted elements [sf#13]

Reported by h-gundlach on 2007-05-16 15:49 UTC
I need a SO-term as gff3 type, for describing fragments of interrupted (e.g. by insertions of other transposons) transposons/genetic elements, that belong to one (transposon) element. The situation is analogous to exons belonging to a gene (gff Parent relationship). It is probably best to create a general term, not restricted to transposons.

l_s_f.obo broken [sf#46]

Reported by batchelorc on 2007-10-11 09:39 UTC
Hello,

Tracker item "[ 1807279 ] add disjoint_from tags" has caused l_s_f.obo to contain pretty much all of SO. Not sure how easy that will be to fix. I should have spotted this bit:

"Changes since 1.42: +2449 -10 lines"

on the CVS, really.

Best wishes,
Colin.

update to mapping for MO term ctDNA? [sf#17]

Reported by whetzel on 2007-07-01 11:41 UTC
Currently the MO term ctDNA is mapped to the SO term chloroplast_location.

Would it be possible to create a new SO term called chloroplast_DNA that is the intersection of chloroplast_location and DNA?

Trish

promoter motif 1 [sf#32]

Reported by nlw on 2007-09-11 18:54 UTC
Here's the first of a set of new promoter element motifs. These are similar in their category to DRE elements, and should be at the same depth of the graph I think. Anyway, here's the details:

Name: Motif 1

Def:
A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR.

DBxref: PMID:12537576

Comment:
This consensus sequence was identified computationally using the MEME algorithm, with an E value of 5.1e-415. Tends to coincide with Motif 6.

promoter motif 5 [sf#33]

Reported by nlw on 2007-09-11 19:05 UTC
Name: Motif 5

Def:
A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with motif 8. Tends to not occur with DPE motif (SO:0000015).

DBxref: PMID:12537576

Comment:
This consensus sequence was identified computationally using the MEME algorithm within core promoter sequences from -60 to +40, with an E value of 2.9e-93.

add chromosome_band to SOFA [sf#11]

Reported by sheldon_mckay on 2007-03-30 16:15 UTC
Would it be possible to add chromosome_band (SO:0000341) to SOFA? It is a locatable sequence feature, at least as I understand it.

Thanks
Sheldon McKay
<[email protected]>

prophage terms [sf#4]

Reported by jl242 on 2007-01-25 16:16 UTC
Hi Karen - are prophage terms within the scope of SO? The two terms in question are:

prophage
A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated "island".

cryptic_prophage
A remnant of an integrated prophage in the host genome or an "island" in the host genome that includes phage like-genes.

They're from a phage ontology being developed by Ariane Toussaint at the University of Brussels.

thanks,

Jane

ntr: Class I and Class II RNAs [sf#2]

Reported by kpilcher on 2006-10-10 14:59 UTC
Hello,

I'd like to request two new terms from PMID: 15333696.

ncRNA ; SO:0000655
--Class I RNA ; SO:new
--Class II RNA ; SO:new

Class I RNA def:
Small non-coding RNA (55-65 nt long) containing highly
conserved 5' and 3' ends (16 and 8 nt, respectively)
that are predicted to come together to form a stem
structure. Identified in the social amoeba
Dictyostelium discoideum and localized in the cytoplasm.

Class II RNA def:
Small non-coding RNA (59-60 nt long) containing 5' and
3' ends that are predicted to come together to form a
stem structure. Identified in the social amoeba
Dictyostelium discoideum and localized in the cytoplasm.

Feel free to edit my definitions to fit the style of
existing SO defs.

Thanks so much,

Karen

definition of ncRNA (SO:0000655) [sf#49]

Reported by batchelorc on 2007-10-17 09:42 UTC
Hello,

I'm confused. The definition reads "An mRNA sequence that does not encode for a protein rather the RNA molecule is the gene product" which by Aristotle would say that ncRNA is_a mRNA, although ncRNA is a sibling of mRNA.

Should it read something like "A processed transcript that does not encode a protein; rather, the RNA molecule itself is the gene product."?

Best wishes,
Colin.