fragments, fingerprint_contig, maps, has_part [sf#83]

[srynobio]

Reported by batchelorc on 2008-02-08 12:04 UTC On the developers list, Suzanna Lewis writes:

[types of map in addition to fingerprint_map as children of physical_map] > STS map certainly (sequence tag sites). RFLP map (restriction fragment length > polymorphism), RH map (radiation hybrid) > > Perhaps put in another generation directly beneath region (now has assembly > and assembly_component both of which are only defined in terms of sequence > assembly, so this would need to be broadened) and then these two children of > assembly: sequence_assembly and physical_map (or fragment_assembly), and so > on. (hmm, is there a reason that there is no fragment part_of vector? > missing synonyms?) > > I see that RFLP_fragment is already there as a child of restriction_fragment > and this would need to be a part of a RFLP_map.
> Other kinds of fragments needed too (sonicate_fragment?) to serve as components

So, actions:

1. redefine assembly (SO:0000353) and assembly_component (SO:0000143)
2. ntrs: sequence_assembly and fragment_assembly (EXACT synonym physical_map)
3. ntrs: as children of fragment_assembly? - STS_map, fingerprint_map, RFLP_map, RH_map
4. ntr: sonication_fragment. Does it make sense for this and restriction_fragment to be children of reagent (SO:0000695)?
5. relationships: RFLP_map has_part RFLP_fragment, STS_map has_part STS (SO:0000331). fingerprint_map has_part restriction_fragment (SO:0000412)?

What's missing from the above?

Best wishes, Colin.

[srynobio]

Commented by eilbeck on 2008-03-14 17:16 UTC Logged In: YES user_id=742851 Originator: NO

I am going to attempt to define these new terms. Sorry for the delay in getting to these terms/restructure.

Fragment_assembly (physical_map) A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths. Synonym: physical_map

fingerprint_map A fingerprint_map is a physical map composed of restriction fragments. Has_part restriction_fragment Synonyms BACmap, FPCmap, FPC, restriction map

STS_map An STS map is a physical map organized by the unique STS landmarks. Has_part STS

*RFLP_map An RFLP map is a kind of genetic map. Distance between markers is measured in recombination units. Has_part RFLP_fragment

RH_map A radiation hybrid map is a physical map (I am finding this hard to define without launching into the details of the method) Has_part STS Synonym radiation hybrid

Sonicate_fragment A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments.

Sequence_assembly A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences.

Assembly Old def: A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences.

New def: A region of the genome of known length that is composed by ordering and aligning two or more different regions.

Assembly component Old def: A region of sequence which may be used to manufacture a longer assembled, sequence.

New def: A region of known length which may be used to manufacture a longer region.

Assembly Sequence_assembly … fragment_assembly Fingerprint_map STS_map *RFLP_map RH_map

Assembly_component Sonicate_fragment Restriction_fragment RFLP

* Help. Genetics maps! Do we want to include this?

Comments on the definitions and structure please. Thanks K

[srynobio]

Commented by eilbeck on 2008-03-26 21:08 UTC Logged In: YES user_id=742851 Originator: NO

I have added the terms, apart from RFLP_map. I moved restriction_fragment to be a kind of assembly component.

[srynobio]

Updated by eilbeck on 2008-03-26 21:08 UTC

• status: open --> closed-accepted