Cheatsheet 2.1.0 (current)

Functions

Go to: Relations

abundance(), a()

abundance(NSArg, loc()?)

  1. Namespace argument of following type(s): Abundance

  2. Zero or one of each function(s): location

activity(), act()

activity(g|r|m|p|complex(), ma()?)

  1. One of following function(s): geneAbundance, rnaAbundance, microRNAAbundance, proteinAbundance, complexAbundance

  2. Zero or one of each function(s): molecularActivity

biologicalProcess(), bp()

biologicalProcess(NSArg)
  1. Namespace argument of following type(s): BiologicalProcess

cellSecretion(), sec()

cellSecretion(p|complex|a())
  1. One of following function(s): proteinAbundance, complexAbundance, abundance

cellSurfaceExpression(), surf()

cellSurfaceExpression(p|complex|a())
  1. One of following function(s): proteinAbundance, complexAbundance, abundance

complexAbundance(), complex()

complexAbundance(a|p|g|m|r|pop(), NSArg, loc()?)

  1. Zero or more of each function(s): abundance, proteinAbundance, geneAbundance, microRNAAbundance, rnaAbundance, populationAbundance

  2. Zero or more namespace arguments of following type(s): Complex

  3. Zero or one of each function(s): location

compositeAbundance(), composite()

compositeAbundance(a|act|p|g|m|r|complex|pop(), NSArg)

  1. Zero or more of each function(s): abundance, activity, proteinAbundance, geneAbundance, microRNAAbundance, rnaAbundance, complexAbundance, populationAbundance

  2. Zero or more namespace arguments of following type(s): Complex

degradation(), deg()

degradation(p|complex|m|r())
  1. One of following function(s): proteinAbundance, complexAbundance, microRNAAbundance, rnaAbundance

fragment(), frag()

fragment(StrArg, StrArg)

  1. String argument of following type(s): /[\d_\?*]+/

  2. String argument of following type(s): /.*?/

fusion(), fus()

fusion(NSArg, StrArg, NSArg, StrArg)

  1. Namespace argument of following type(s): Gene, RNA, Micro_RNA, Protein

  2. String argument of following type(s): /\S+/

  3. Namespace argument of following type(s): Gene, RNA, Micro_RNA, Protein

  4. String argument of following type(s): /\S+/

geneAbundance(), g()

geneAbundance(NSArg, loc()?, var()*)

  1. Namespace argument of following type(s): Gene

  2. Zero or one of each function(s): location

  3. Zero or more of each function(s): variant

geneAbundance(fus(), loc()?, var()*)

  1. One of following function(s): fusion

  2. Zero or one of each function(s): location

  3. Zero or more of each function(s): variant

location(), loc()

location(NSArg)
  1. Namespace argument of following type(s): Location

microRNAAbundance(), m()

microRNAAbundance(NSArg, loc()?, var()*)

  1. Namespace argument of following type(s): Micro_RNA

  2. Zero or one of each function(s): location

  3. Zero or more of each function(s): variant

microRNAAbundance(fus(), loc()?, var()*)

  1. One of following function(s): fusion

  2. Zero or one of each function(s): location

  3. Zero or more of each function(s): variant

molecularActivity(), ma()

molecularActivity(StrArgNSArg)
  1. Namespace argument or default namespace argument (without prefix) of following type(s): Activity

pathology(), path()

pathology(NSArg)
  1. Namespace argument of following type(s): Pathology

populationAbundance(), pop()

populationAbundance(NSArg, loc()?)

  1. Namespace argument of following type(s): Species, Cell

  2. Zero or one of each function(s): location

proteinAbundance(), p()

proteinAbundance(NSArg, loc|frag()?, var|pmod()*)

  1. Namespace argument of following type(s): Protein

  2. Zero or one of each function(s): location, fragment

  3. Zero or more of each function(s): variant, proteinModification

proteinAbundance(fus(), loc()?, var()*)

  1. One of following function(s): fusion

  2. Zero or one of each function(s): location

  3. Zero or more of each function(s): variant

proteinModification(), pmod()

proteinModification(StrArgNSArg, StrArgNSArg?, StrArg?)

  1. Namespace argument or default namespace argument (without prefix) of following type(s): ProteinModification

  2. Zero or one amespace argument or default namespace argument (without prefix) of following type(s): AminoAcid

  3. Zero or one string argument of following type(s): /\d+/

reaction(), rxn()

reaction(reactants(), products())

  1. One of following function(s): reactants

  2. One of following function(s): products

rnaAbundance(), r()

rnaAbundance(NSArg, loc()?, var()*)

  1. Namespace argument of following type(s): RNA

  2. Zero or one of each function(s): location

  3. Zero or more of each function(s): variant

rnaAbundance(fus(), loc()?, var()*)

  1. One of following function(s): fusion

  2. Zero or one of each function(s): location

  3. Zero or more of each function(s): variant

translocation(), tloc()

translocation(g|p|r|m|complex|pop|a(), fromLoc(), toLoc())

  1. One of following function(s): geneAbundance, proteinAbundance, rnaAbundance, microRNAAbundance, complexAbundance, populationAbundance, abundance

  2. One of following function(s): fromLoc

  3. One of following function(s): toLoc

variant(), var()

variant(StrArg)
  1. String argument of following type(s): /\S+/

Relations

Go to: Functions

analogous

Deprecated – A is analogous to B

association, –

A is associated with B - least informative relationship

biomarkerFor

Deprecated – A is a biomarker for B

causesNoChange, cnc

A causes no change in B

decreases, -|

A indirectly decreases B

directlyDecreases, =|

A directly decreases B

directlyIncreases, =>

A directly increases B

hasActivity

A has activity B, e.g. kinase activity

hasComponent

A has component B (for complexes)

hasComponents

A has components list(B, C, D, …)

hasMember

A has a member B

hasMembers

A has members list(B, C, D, …)

increases, ->

A indirectly increases B

isA

A is a subset of B

negativeCorrelation, neg

A is negatively correlated with B

orthologous

A is orthologous to B

positiveCorrelation, pos

A is positively correlated with B

prognosticBiomarkerFor

Deprecated – A is a prognostic biomarker for B

rateLimitingStepOf

A is a rate limiting step of B

regulates, reg

A regulates (effects) B somehow

subProcessOf

A is a subprocess of B

transcribedTo, :>

gene is transcribed to RNA

translatedTo, >>

RNA is translated to protein

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