WS241 Models.wrm

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Models Proposals Summary Pre sign off.


?Person class

DONE

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

DONE


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:

?Interaction

   Interactor
             Feature_interactor ?Feature XREF Associated_with_Interaction #Interactor_info

2) Delete the "Interaction_associated_feature" tag


?Feature model:

1) Change:

?Feature

   Associations 
               Associated_with_Interaction ?Interaction XREF Interaction_associated_feature

To:

?Feature

   Associations
               Associated_with_Interaction ?Interaction XREF Feature_interactor

?Movie and Expression_pattern changes

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

Summary:

?Movie
Reference ?Paper XREF Movie
DB_INFO ?Database ?Database_field Text

?Expr_pattern
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:

Expr_pattern

DONE

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.

Movie

DONE

Add

DB_INFO ?Database ?Database_field Text Reference ?Paper XREF Movie

The DB_INFO tag will allow us to link out to the rnai.org 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.


?Protein Class

DONE

Remove the UNIQUE from the DB_info Database Database_field UNIQUE TEXT

This prevents the addition of multiple DB connections for a protein.

Extras from the deadline call

?Expression_cluster and ?Analysis class - Wen

ADDED

Remove the line of "Analysis ?Analysis", and replace it with these two tags:


?Expression_cluster Description  ?Text // refers to Biological meaning of this cluster group

                               ....
                               Attribute_of Microarray_experiment ?Microarray_experiment  XREF Expression_cluster //Wen
                                                 RNAseq ?Analysis XREF Expression_cluster_RNAseq
                                                 Tiling_array ?Analysis XREF Expression_cluster_tiling_array


Also in ?Analysis class, we will need to update the tag:

?Analysis ...

              Expression_cluster_RNAseq ?Expression_cluster XREF RNAseq
              Expression_cluster_tiling_array ?Expression_cluster XREF Tiling_array

?DO_term - Ranjana

ADDED

Worm_disease_model ?Text ?Species #Evidence

For capturing a human readable description of the worm model.

Format: free-text description.

Rational: Indexed ?Text and attached to DO_term, so if someone searched on a disease they would find the worm model. Currently I have no way of curating such disease models, because I don't have an object to attach it to.

Postponed to WS242 Models

?Gene_cluster

POSTPONE for WS242

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 http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11779.html

?Construct Class

Bumped to WS242

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

https://docs.google.com/a/wormbase.org/document/d/16QadWhwTuER8K4pbGlC1_UVfJ9Ia7JuQfQW6cknmE8w/edit?usp=sharing

?Construct 
Summary   ?Text
Feature_object ?Feature XREF Construct
Gene ?Gene
Gene_site_targeted ?SO_term    
Fusion_reporter ?Text //fluorescent proteins GFP, RFP, mCherry, etc. (these can be put in model if people wish)
Purification_tag ?Text //FLAG, HA, Myc, TAP, etc. (these can be put in model if people wish)
Other_reporter ?Text //(if fusion reporter and purification tags are included in model, this tag is needed to other reporters) 
Type_of_construct
    Chimera
    Domain_swap
    Engineered mutation
    Fusion
    Complex // complex changes (e.g. GFP fusion plus point mutations)  
    Transcriptional_fusion
    Translational_fusion 
    N-terminal_translational_fusion
    C-terminal_translational_fusion
    Internal_coding_fusion
    Selection_marker     ?Text    //for unc-119(+), lin-15(+), drug selection
    Construction_summary  ?Text    //Backbone vector, mol bio 
Used_for
    Transgene_construction ?Transgene XREF Construct
    Variation ?Variation XREF Engineered_allele    
Reference ?Paper XREF Construct  
Person ?Person XREF Construct
Laboratory ?Laboratory #Lab_Location 
Remark ?Text #Evidence