Models Proposals Summary Pre sign off.
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:
1) Add a "Feature_interactor" tag in the model like this:
Interactor Feature_interactor ?Feature XREF Associated_with_Interaction
2) Delete the "Interaction_associated_feature" tag
Associations Associated_with_Interaction ?Interaction XREF
Associations 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.
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
?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: 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.
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 additions.