WS241 Models.wrm

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Models Proposals Summary Pre sign off.

?Person class

ORCID is becoming more widely used so it would be good to store peoples ID in their WBPerson record

?Person PostgreSQL_id UNIQUE Text     // for linking to internal RDB // Text instead of Int so it says WBperson####
        DB_info Database ?Database ?Database_field ?Text     //used for storing ORCID IDs etc.

?Interaction and ?Feature models

Accommodate Sequence Feature objects as interactors (e.g. for protein-DNA physical interactions or cis-regulatory control regions in regulatory interactions). Thus, we would like to propose the following model changes:

?Interaction model:

1) Add a "Feature_interactor" tag in the model like this:


       Feature_interactor ?Feature XREF Associated_with_Interaction
  1. Interactor_info

2) Delete the "Interaction_associated_feature" tag

?Feature model:

1) Change:


       Associated_with_Interaction ?Interaction XREF




       Associated_with_Interaction ?Interaction XREF Feature_interactor

Gary (Williams), one concern I have is whether or not it will be an issue to make the appropriate changes to the existing annotations that you and others have been generating over the last few months. More specifically, I think we will need to either:

1) Make all features that are currently in the "Interaction_associated_feature" tag of an Interaction object a "Feature_interactor"


2) Branch off several new interactions for each individual interaction involving a Feature object. For example, WBInteraction000501384 has 6 associated feature objects. It's not clear from the object how they are associated, but I'm presuming they all have evidence for direct (physical) or indirect (regulatory) interactions and thus could each be a "Feature_interactor" in their own respective interactions.

?Movie linking

What has changed: - Text in DB_INFO tag not indexed as it is just a reference to an external accession. - Microarray and Tiling_array now linking to ?Microarray_experiment and ?Analysis


Reference ?Paper XREF Movie
DB_INFO ?Database ?Database_field Text

DB_INFO ?Database ?Database_field Text # PaulD Can go at the very bottom
Type    Reporter_gene ?Text
                        In_situ Text
                        Antibody ?Text
                        Northern Text // Wen [krb 030425]
                        Western Text  // Wen
                        RT_PCR Text   // Wen
                        Localizome ?Text //added by Wen
                        Microarray ?Microarray_experiment 
                        Tiling_array ?Analysis 

Detail: 1) Expr_pattern

Add: DB_INFO ?Database ?Database_field Text # PaulD Can go at the very bottom of the model

Add Tiling_array and Microarray under Type

               Type    Reporter_gene ?Text
                       In_situ Text
                       Antibody ?Text
                       Northern Text // Wen [krb 030425]
                       Western Text  // Wen
                       RT_PCR Text   // Wen
                       Localizome ?Text //added by Wen
                       Microarray Text
                       Tiling_array Text

Both changes are required to allow linking to Miller's Tiling array graphs.

The DB_INFO tag will contain the links and the tags for the type will serve to distinguish Microarrays and Tiling Arrays for separate display in the Expression widget -see enclosed screenshot.

2) Movie


DB_INFO ?Database ?Database_field Text Reference ?Paper XREF Movie

The DB_INFO tag will allow us to link out to the database. Since we did not hear back from Kris Gunsalus for downloading and storing the movies we are going to store the urls and link from there. The Reference tag is needed to have a more structured organization of the files that will allow easier addition.


Karen would like to use this underused class for phylogenetic gene clusters

This class was designed for clustering genes such as the rRNAs and act-123, but can definitely be used for other functions. Currently this is not displayed on the site

Example publication Tabach et al concerning a C. elegans phylogenetic profile based gene clustering that would be included in the Biological Topics pages.

Nature (2012) doi:10.1038/nature11779

?Construct Class A new class for storing Construct reagents used for generating Variation data




    Driven_by_gene ?Gene

    Altered_promoter ?Gene

Reporter_product    Gene XREF ?Gene


            Altered_gene ?Gene

3’UTR Gene XREF ?Gene

    Altered_gene ?Gene

5’UTR Gene XREF ?Gene

    Altered_gene ?Gene


fluorescent proteins (GFP, RFP, mCherry, etc)

Purification_tag (FLAG, HA, Myc, TAP, etc).  

Reporter_type      Transcriptional_fusion





Included_marker         //for unc-119(+), lin-15(+)

Construction_summary     //Backbone vector, mol bio



    Transgene XREF ?Transgene

    Allele XREF  ?Variation Engineered_allele