WS237 Models.wrm

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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

        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

        Construction_summary Text

Transcript - Paul

  • Add biotype lincRNA.
   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 deleted -------


------- Tags deleted -------

  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

  Delete Gene_regulation rooted tag and move branches under Experimental_info.

  Gene_regulation_evidence ?Gene_regulation

  Gene_regulation	Cis_regulator    ?Gene_regulation	XREF	Cis_regulator_seq
  YH_bait	?YH	XREF	Sequence_bait		?Text
  YH_target	?YH	XREF	Sequence_target		?Text

  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

  Associated_with_gene_regulation ?Gene_regulation XREF Associated_feature #Evidence

  Gene_regulation ?Gene_regulation XREF Antibody_info

  Gene_regulation ?Gene_regulation XREF Transgene

  Gene_regulation ?Gene_regulation XREF RNAi

  Gene_regulation ?Gene_regulation XREF Reference
  YH	?YH	XREF	Reference	

  Gene_regulation Gene_regulator ?Gene_regulation XREF Molecule_regulator

Delete Gene_regulation rooted tag and move branches up

  YH_bait	?YH	XREF	PCR_bait	?Text
  YH_target	?YH	XREF	PCR_target	?Text

------- Tags added -------

  Interaction  ?Interaction

  Interaction  ?Interaction

  Interaction  ?Interaction

------- XREFs added -------

	Interactor	PCR_interactor			?PCR_product	XREF	Interaction	#Interactor_info
			Sequence_interactor		?Sequence	XREF	Interaction	#Interactor_info
			Interactor_overlapping_CDS	?CDS		XREF	Interaction	#Interactor_info