#27 plasmids (DNA and RNA)

[Melanie Courtot]

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

[Alan Ruttenberg]

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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

[Colin Batchelor]

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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.

[Colin Batchelor]

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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.

[Melanie Courtot]

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

[bjoernpeters]

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

[James A. Overton]

This is a related recent discussion on the RO tracker: https://github.com/oborel/obo-relations/issues/76