Closed obi-bot closed 6 years ago
obi-bot
commented
16 years ago Logged In: YES user_id=138355 Originator: NO
probably want some length restrictions here, as well as the ability to use SO to associate sequence features with the DNA, e.g. some gene or promoter that has been inserted in to it. Also, protocol applications that create plasmids for experimental use.
Similar, cosmid
Original comment by: alanruttenberg
obi-bot
commented
16 years ago Original comment by: mcourtot
obi-bot
commented
16 years ago Logged In: YES user_id=1473024 Originator: NO
Hi Melanie,
We can't use the PATO terms "linear" and "circular" because that's not what they mean when they refer to plasmids!
SO lacks definitions for these---I will fix them.
Colin.
Original comment by: batchelorc
obi-bot
commented
16 years ago Logged In: YES user_id=1473024 Originator: NO
Hello,
Sorry for delay.
We've added defs. to "circular" (SO:0000988) and "linear" (SO:0000987) in SO, now, so you could use those.
Best wishes, Colin.
Original comment by: batchelorc
obi-bot
commented
15 years ago DNA plasmid has been added to OBI (OBI_0000430). Should probably be renamed DNA plasmid (restriction says double stranded DNA) and its sibling RNA plasmid should be added. Same with linear and circular. We should end up with: - plasmid ----DNA plasmid --------circular DNA plasmid --------linear DNA plasmid ----RNA plasmid --------circular RNA plasmid --------linear RNA plasmid
Original comment by: mcourtot
obi-bot
commented
9 years ago Consider obsoleting OBI term in favor of SO term. Problem remains that SO doesn't distinguish clearly between molecules and sequences. http://www.ontobee.org/browser/rdf.php?o=SO&iri=http://purl.obolibrary.org/obo/SO_0000155 http://www.ontobee.org/browser/rdf.php?o=OBI&iri=http://purl.obolibrary.org/obo/OBI_0000430
Original comment by: bpeters42
obi-bot
commented
9 years ago This is a related recent discussion on the RO tracker: https://github.com/oborel/obo-relations/issues/76
Original comment by: jamesaoverton
turbomam
commented
6 years ago Closed because dependent term request #26 (has_function replicon_function) were closed.
@mcourtot feel free to reopen if relevant
dna_plasmid: dna and has_function replicon_function
see http://sourceforge.net/tracker/index.php?func=detail&aid=1894635&group\_id=177891&atid=886178 for replicon_function
circular_dna_plasmid: dna_plasmid and has_quality circular (PATO)
on the same model, circular_rna_plasmid, linear_dna_plasmid, linear_rna_plasmid
Reported by: mcourtot
Original Ticket: "obi/obi-terms/27":https://sourceforge.net/p/obi/obi-terms/27