#86 describing reagents


As we saw with the plasmid debate, there are biological entities that are used as tools.
We have gone some way to clarify the situation for plasmids - they are replicons - but need to address reagents in some way.
WWe have an attribute 'engineered', and a features 'reagent' and 'vector'.

We need to answer these questions proposed by Colin in the tracker about plasmids, and straighten out the ontology.

engineered_plasmid (SO:0000637)---are there any plasmids used as reagents
which haven't been engineered? (I know Michelle mentioned this last week.)
Should it have the quality of being a vector rather than a reagent?

integrated_plasmid (SO:0001040)---not currently a child of plasmid.

plasmid_vector (SO:0000755)---not currently defined. How does it differ
from an engineered_plasmid?


  • Karen Eilbeck

    Karen Eilbeck - 2008-03-27
    • status: open --> closed-accepted
  • Karen Eilbeck

    Karen Eilbeck - 2008-03-27

    Logged In: YES
    Originator: YES

    This lists the changes made to the reagent terms in SO.

    EST is_a tag
    BAC_end is_a read

    New term:
    Synthetic_oligo (needs definition)

    GNA_oligo, PNA_oligo, LNA_oligo, NA_oligo and morpholine_oligo are now kinds
    of synthetic_oligo

    RNAi_reagent is_a ds_oligo

    Probe_is_a oligo

    Mini_gene is_a ORF *need to remember to add reagent as a quality when I get
    that far in the rearrangements.

    Renamed vector to be vector_replicon as a child of replicon. A replicon that has been modified to act as a vector for foreign sequence.

    Moved BAC, cosmid, fosmid, lambda_vector, PAC phagemid, YAC and plasmid_vector to be is_a vector_replicon.

    clone is composed of a clone_insert and a replicon_vector
    A clone insert may be composed of many cloned_regions

    A plasmid_vector derives from a plasmid

    DNAzyme moved to be an oligo has_quality enzymic.

    enzymic moved to be a feature_attribute

    An integrated_plasmid derives_from a plasmid

    Vector should not be a quality. It refers to a single kind of feature.

    There is still the possibility to have 'reagent' be a quality, but currently it seems like most of the problems have been resolved.
    I'm still waiting on merging engineered_plasmid and plasmid_vector.

    databank_entry is a problematic term. A possible candidate for obsoletion.


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