LEGO Curation

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Agenda

Logins

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
    • Evidence from more than one paper may be used within a single model
    • Evidence from more than one paper may be used to support a single assertion
  • 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)
  • 2 uM is optimal Cu for C. elegans growth
  • Summary figures at the end of papers, e.g. Figure 7B in this paper, or in reviews can be very helpful for LEGO models, but assertions need to be supported by as much evidence as possible
  • What is the role of CUA-1 when Cu levels are optimal? When Cu levels are toxic? When Cu levels are limiting or zero?
  • Link to collaborative model

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
  • What is the correct evidence code?

What are the Biological Processes?

Copper-Related Terms

  • GO:006003 copper ion export
    • Contextual information to indicate start location and end location?
  • GO:0055070 copper ion homeostasis
  • GO:0006878 cellular copper ion homeostasis
    • GO:0097580 intracellular sequestering of copper ion
      • part_of cellular copper ion homeostasis
      • No annotations - any organism
      • Note that this is a child of localization but not transport
  • GO:1990169 stress response to copper ion

Development-Related Terms

  • GO:0002119 nematode larval development
  • GO:0009792 embryo development ending in birth or egg hatching
  • GO:0048609 multicellular organismal reproductive process
    • GO:0090728 negative regulation of brood size
  • GO:0040010 positive regulation of growth rate

Other Processes

  • transcription from RNA polymerase II promoter
  • gut granule assembly

Where do the Molecular Functions Occur?

Expression Patterns

  • Subcellular locations
    • Basolateral plasma membrane
    • Plasma membrane
    • Golgi membrane
    • Gut granule
  • Tissue locations
    • Intestine
    • Hypodermis
    • Neurons
    • Pharynx

Site-of-Action Studies

  • Tissue-specific RNAi
    • Intestine
    • Muscle
    • Hypodermis
  • Tissue-specific expression
    • Intestine

CUA-1.1 Expression

Tissue Sub-tissue Subcellular Localization Low copper changes High copper changes Life stage Tissue-specific RNAi Knockdown (Embryonic Lethal Phenotype) Tissue-specific Rescue (Embryonic Lethal Phenotype) Tissue-specific RNAi Knockdown (Reproduction) Tissue-specific Rescue (Reproduction) Tissue-specific RNAi Knockdown (Growth) Tissue-specific Rescue (Growth)
Intestine (endogenous promoter) Anterior intestine, mainly concentrated (endogenous promoter) Basolateral plasma membranes, intracellular compartments identified as Golgi by co-localization with MANS (vha-6 promoter) None (endogenous promoter) Moves from Golgi to overlap with gut granules (endogenous and vha-6 promoter) Post-embryonic Intestine Intestine (under control of vha-6 promoter) Knockdown of cua-1 in the intestine resulted in reduced fecundity similar to that of whole-body RNAi (Fig. 3F), indicating that intestinal CUA-1 is crucial for the survival of worms. Transgenic animals expressing CUA-1.1::GFP under control of the vha-6 promoter exhibited a reduced growth phenotype when exposed to high copper and enhanced growth under copper restriction in a dose-dependent manner (Fig. 4, C and D).
Hypodermis (endogenous promoter) Seam cells, hyp7 ? (See Figure S5B) Plasma membrane (dpy-7 promoter; not affected by changing copper) Stronger (endogenous promoter) Post-embryonic ...depletion of cua-1 in the hypodermis caused a severe reduction in brood size under low dietary copper conditions (Fig. 3F).
Neurons (endogenous promoter) None (endogenous promoter) Post-embryonic
Pharynx (endogenous promoter) Post-embryonic
  • No expression reported in muscle, but the authors did perform muscle-specific knockdown and there was no apparent effect

What are the other players and how do we define their roles?

  • cuc-1 (WBGene00000835)
  • pgp-2 (WBGene00003996)
  • copper - see ChEBI entries

GPAD Output Files

  • These files represent the translation of annotations made in LEGO to conventional GO annotations
  • They are generated via SPARQL queries of a graphstore of LEGO annotations
  • Found here, according to model id: GPAD outputs from SPARQL Queries
  • Not real-time; updates to the GPAD files are supposed to be triggered by changes to the Noctua models github repository

Comments and Questions

WikiPathways comparative pathway: copper_homeostasis
Within LEGO how do we represent:

  • stimulus based activity
    • CUA-1.2 relocalizes to intestinal membrane upon Cu binding
    • increased copper induces copper sequestered by gut granules via CUA-1.1
    • depleted Cu redirects CUA-1.1 activity to golgi

Use of evidence codes is a bit opaque

  • RNAi evidence is captured as mutant analysis
  • expression evidence is captured by direct assay rather than fluorescence marker analysis