Models Proposals Summary Pre sign off.
- 1 ?Person class
- 2 ?Interaction and ?Feature models
- 3 ?Movie and Expression_pattern changes
- 4 ?Gene_cluster
- 5 ?Construct Class
- 6 ?Protein Class
- 7 Extras from the deadline call
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
?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
?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
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.
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
Bumped to WS242
A new class for storing Construct reagents used for generating Variation data
?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
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
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:
Expression_cluster_RNAseq ?Expression_cluster XREF RNAseq Expression_cluster_tiling_array ?Expression_cluster XREF Tiling_array
?DO_term - Ranjana
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.