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
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 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 http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11779.html
A new class for storing Construct reagents used for generating Variation data
?Construct Summary Text Promoter Driven_by_gene ?Gene Altered_promoter ?Gene Reporter_product Gene XREF ?Gene Other_gene Altered_gene ?Gene 3_prime_UTR Gene XREF ?Gene Altered_gene ?Gene 5_prime_UTR Gene XREF ?Gene Altered_gene ?Gene Fusion_reporter fluorescent proteins (GFP, RFP, mCherry, etc) Purification_tag (FLAG, HA, Myc, TAP, etc). Reporter_type Transcriptional_fusion Translational_fusion N-terminal_fusion C-terminal_fusion Internal_coding_fusion Included_marker //for unc-119(+), lin-15(+) Construction_summary //Backbone vector, mol bio Sequence Used_for Transgene XREF ?Transgene Allele XREF ?Variation Engineered_allele