Difference between revisions of "LEGO Curation"

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(25,26) as compared to Atp7a-/- MEFs transfected with an empty vector (Supplemental Fig. S3A). Over-accumulated Cu in Atp7a-/- MEFs was  
 
(25,26) as compared to Atp7a-/- MEFs transfected with an empty vector (Supplemental Fig. S3A). Over-accumulated Cu in Atp7a-/- MEFs was  
 
rescued by ectopic expression of CUA-1.1::GFP (Supplemental Fig.S3B), further indicating that CUA-1.1 can export Cu. Moreover, these  results  demonstrate  that  a  C-terminal  GFP tag  does  not  significantly  interfere  with  CUA-1 function.
 
rescued by ectopic expression of CUA-1.1::GFP (Supplemental Fig.S3B), further indicating that CUA-1.1 can export Cu. Moreover, these  results  demonstrate  that  a  C-terminal  GFP tag  does  not  significantly  interfere  with  CUA-1 function.
 
  
 
   is_a GO:0005375 copper ion transmembrane transporter activity
 
   is_a GO:0005375 copper ion transmembrane transporter activity

Revision as of 16:33, 23 January 2017

Agenda

Logins

  • Everyone set up okay?

LEGO Principles

  • Pieces of biological information are connected using a controlled vocabulary of relations
  • Assertions made using these relations are supported with evidence statements, i.e. ECO codes, references
  • LEGO models are 'models of instances' meaning that these are models of specific individuals and events

LEGO at its Most Basic

  • Molecular functions are enabled_by genes/gene products
  • Molecular functions may be part_of larger biological processes
  • Molecular functions occur_in some location
    • Subcellular locations are part_of some larger anatomical structure

LEGO Beyond Basics

  • Some biological processes and molecular functions regulate other biological processes
    • The regulation may be positive or negative and may be 'direct' or 'indirect'
  • Some biological processes and molecular functions are causally upstream of other biological processes
  • Sometimes you don't know how two things are related - 'causally upstream of or within'

Paper for Curation

  • The Intestinal Copper Exporter CUA-1 Is Required for Systemic Copper Homeostasis in Caenorhabditis elegans. PMID:27881675
  • The entities:
    • cua-1 (WBGene00000834)
      • WP:CE26305 CUA-1, isoform a, 1238 aa
      • WP:CE19271 CUA-1, isoform b, 1116 aa
    • cuc-1 (WBGene00000835)
    • pgp-2 (WBGene00003996)

CUA-1 Molecular Function

  • Is the molecular function demonstrated in this paper?

pg. 4 To further confirm whether the CUA-1.1::GFP translational fusion protein can transport Cu, we exploited previously established assays in Atp7a+/+ and Atp7a-/- mouse embryonic fibroblasts (MEFs) (24). Atp7a-/- MEFs transiently transfected with CUA-1.1::GFP showed increased expression of Cu chaperone for superoxide dismutase (CCS), indicating decreased levels of cellular Cu (25,26) as compared to Atp7a-/- MEFs transfected with an empty vector (Supplemental Fig. S3A). Over-accumulated Cu in Atp7a-/- MEFs was rescued by ectopic expression of CUA-1.1::GFP (Supplemental Fig.S3B), further indicating that CUA-1.1 can export Cu. Moreover, these results demonstrate that a C-terminal GFP tag does not significantly interfere with CUA-1 function.

 is_a GO:0005375 copper ion transmembrane transporter activity
   part_of GO:0060003 copper ion export
   is_a GO:0043682 copper-transporting ATPase activity
     GO:0004008 copper-exporting ATPase activity