Difference between revisions of "WS237 Models.wrm"
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These were seen to be the only remaining primary attribute classes and acedb does have kernal code expecting some of these tags to be present in the models.wrm file. | These were seen to be the only remaining primary attribute classes and acedb does have kernal code expecting some of these tags to be present in the models.wrm file. | ||
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+ | Standardised tag structure/order. | ||
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<b> | <b> | ||
== Curator Models proposals == | == Curator Models proposals == |
Revision as of 14:44, 19 February 2013
Contents
General housekeeping
?Accession class retirement phase 2
- Remove simple and XREF examples of:
Database ?Database ?Database_field ?Accession (XREF ?Class Tag)
from the models file in favor of:
?Database_field ?Text
This will significantly reduce the numbers of empty objects in the ?Accession class
?Text was implemented in favor of Text to avoid duplication in objects that are touched more than once.
The Accession Class now only contains links to:
- Clone
- Sequence
- Motif
These were seen to be the only remaining primary attribute classes and acedb does have kernal code expecting some of these tags to be present in the models.wrm file.
Standardised tag structure/order.
Curator Models proposals
homol_data - Kevin
?Homol_data Oligo_set_homol ?Oligo_set XREF Homol_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
- Oligo_set mapping as we do for other classes.
Transgene - Karen
?Transgene Construction_summary Text
Transcript - Paul
- Add biotype lincRNA.
?Transcript Properties Transcript UNIQUE asRNA UNIQUE Text lincRNA UNIQUE Text // lincRNAs
Oligo_set & Microarray_result - wen/kev
- Addition of ?Species
?Oligo_set Species UNIQUE ?Species ?Microarray_results Species UNIQUE ?Species
?YH & ?Gene_regulation retirement - Chris
- Complicated change as needs interaction adding in lots of classes.
------- Classes to delete ------- ?YH ?Gene_regulation #Boolean ------- Tags to delete ------- ?Gene Gene_regulation Trans_regulator ?Gene_regulation XREF Trans_regulator_gene Trans_target ?Gene_regulation XREF Trans_regulated_gene YH_bait ?YH XREF Bait_overlapping_gene ?Text YH_target ?YH XREF Target_overlapping_gene ?Text <?Gene model note: move "Regulate_expr_cluster" tag out from under "Gene_regulation" tag (now deleted) and put directly under "Experimental_info" tag> #Evidence Gene_regulation_evidence ?Gene_regulation ?Sequence Gene_regulation Cis_regulator ?Gene_regulation XREF Cis_regulator_seq YH_bait ?YH XREF Sequence_bait ?Text YH_target ?YH XREF Sequence_target ?Text ?CDS Gene_regulation Trans_regulator ?Gene_regulation XREF Trans_regulator_seq Trans_target ?Gene_regulation XREF Trans_regulated_seq Cis_target ?Gene_regulation XREF Cis_regulated_seq YH_bait ?YH XREF Bait_overlapping_CDS ?Text YH_target ?YH XREF Target_overlapping_CDS ?Text ?Feature Associated_with_gene_regulation ?Gene_regulation XREF Associated_feature #Evidence ?Antibody Gene_regulation ?Gene_regulation XREF Antibody_info ?Transgene Gene_regulation ?Gene_regulation XREF Transgene ?RNAi Gene_regulation ?Gene_regulation XREF RNAi ?Paper Gene_regulation ?Gene_regulation XREF Reference YH ?YH XREF Reference ?Molecule Gene_regulation Gene_regulator ?Gene_regulation XREF Molecule_regulator <?Molecule model note: move "Regulate_expr_cluster" tag out from under "Gene_regulation" tag (now deleted) and make it a main tag> ?PCR_product YH_bait ?YH XREF PCR_bait ?Text YH_target ?YH XREF PCR_target ?Text ------- Tags to add ------- ?Sequence Interaction ?Interaction ?CDS Interaction ?Interaction ?PCR_product Interaction ?Interaction ------- XREFs to add ------- ?Interaction Interactor PCR_interactor ?PCR_product XREF Interaction #Interactor_info Sequence_interactor ?Sequence XREF Interaction #Interactor_info Interactor_overlapping_CDS ?CDS XREF Interaction #Interactor_info