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Table 3 Common knowledge representations desired the transition

From: Supporting cognition in systems biology analysis: findings on users' processes and design implications

Analytical Function Knowledge representations/interactions needed for the transition to causal modeling Available? Easy to view/anticipate using?
Contextualizing Expression values from one's own experimental data as cues about regulatory processes and paths Yes, but not found
  Indirect relationships and paths between proteins in networks of interactions Required time-consuming filtering
  Functional pathways related to sets of interactions SAGA, but not inter-active; or side by side
  Homology or pathway comparisons between species to see if molecules or interactions are conserved Yes
  Ability to filter by multiple variables at once or to filter to only the shared interactors between specified genes No No; strings in a field
  Test statistics No No
Detail Types of interactions: Physical binding, activation/inhibition, family member interactions, transcription/expression, translocation/secretion, phosphorylation Partly Buried in NLP free text; incomplete knowledge
  Types of molecules: Distinctions between genes, proteins, chemical effectors DNA, mRNA, protein complexes, mRNA, enzyme Partly Incomplete knowledge
  Experiment type Strings in a field
  Ability to color code by attributes Time consuming