WS237 Models.wrm

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 deleted -------

?YH
?Gene_regulation
#Boolean



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

?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

  Delete Gene_regulation rooted tag and move branches under Experimental_info.


#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

Delete Gene_regulation rooted tag and move branches up


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



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

?Sequence
  Interaction  ?Interaction


?CDS
  Interaction  ?Interaction


?PCR_product
  Interaction  ?Interaction



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

?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