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• List of topics:   Abbreviations   amino-acid   AMR Annotation Dictionary   domain   downregulation/upregulation   effector   enzyme   phosphorylation   protein   upregulation   when       ‎(10 topics + 1 sub-topics)

• -/-   Both copies of a gene have a mutation that renders the expressed protein inoperable.
• 3'-end   ("three prime end") trailing end of DNA or RNA   (more in Wikipedia)
• 5'-end   ("five prime end") leading end of DNA or RNA
• CR   complete response (to treatment)
• DNA   (n / nucleic-acid :wiki "DNA" :name (n2 / name :op1 "DNA"))
• EMT   (e / event :wiki "Epithelial−mesenchymal_transition" :name (n / name :op1 "epithelial-mesenchymal" :op2 "transition"))
• IR   ionizing radiation
• KD
  • knockdown   [more in Wikipedia]
  • dissociation constant K_d   [more in Wikipedia]
  • kinase-deficient, kinase-inactivated
• MI
  • molecular interaction (code)
  • Example: MI:0118 = "mutation"
  • Example: MI:0326 = "protein"
  • Example: MI:0328 = "small molecule"
  • Example: MI:0573 = "mutation disrupting interaction"
  • Example: MI:1133 = "mutation decreasing interaction strength"
• p < 0.05   p-value when determining the statistical significance of a hypothesis   (more in Wikipedia)
• PD   progressive disease
• PR   partial response (to treatment)
• RNA   (n / nucleic-acid :wiki "RNA" :name (n2 / name :op1 "RNA"))
• s.d.   stable disease
• UTR   untranslated region
• WT   wild-type

• definition
  • An amino-acid is an organic molecule.
  • Amino acids can be chained together and folded to form proteins. Proteins contain 23 types of amino acids, such as serine.   Table .
  • Technically, when they two amino acids are chained together, they lose an -H and an -OH respectively (combined to water), leaving two amino acid residues.
• example
  • ERK phosphorylates B-Raf on the S151 site.     (phosphorylate-01 :ARG1 (amino-acid :mod 151 "serine" :part-of (enzyme "B-Raf")) :ARG2 (enzyme "ERK"))    Example
    
    

    Example: ERK phosphorylates B-Raf on the S151 site. [isi_0011.1] (p / phosphorylate-01      :ARG1 (a / amino-acid           :mod 151           :wiki "Serine"           :name (n2 / name                :op1 "serine")           :part-of (e2 / enzyme                :wiki "BRAF_(gene)"                :name (n3 / name                     :op1 "B-Raf")))      :ARG2 (e / enzyme           :wiki "Extracellular_signal-regulated_kinases"           :name (n / name                :op1 "ERK")))

• related topic protein

AMR Annotation Dictionary

• primary AMR Annotation Dictionary

domain

• definition
  • a larger protein-segment
  • :part-of a protein
  • often with specific function(s)
  • often relatively independent of other parts of the protein
• examples
  • G-domain
• related topic protein

downregulation/upregulation

• definition
  • Downregulation (or downmodulation) is a process where some instances of a protein (or other molecule) are deactivated or dismantled. If the downregulated molecule is an enzyme, the activity ("signaling") from that type of enzyme is reduced.
  • Conversely, upregulation (or upmodulation) is a process where some instances of a protein (or other molecule) are activated or built up. If the upregulated molecule is an enzyme, the activity ("signaling") from that type of enzyme is increased.
• frame downregulate/upregulate
  • Both the agent and the target of downregulation/upregulation can be enzymes.

enzyme

• definition
  • large organic molecule (typically a protein) or macro-molecular-complex (containing a protein)
  • acts as an :instrument of biochemical processes, more specifically as a catalyst
  • often has activated and deactivated forms (e.g. activated by phosphorylation)
• entity type
  • Annotate an enzyme as an enzyme even if the text describes it as a "protein" (which is more general). But if the text uses something more specific than an enzyme, such as kinase, use that more specific type.
• examples
  • ERK phosphorylates B-Raf on the S151 site.     (phosphorylate-01 :ARG1 (amino-acid :mod 151 "serine" :part-of (enzyme "B-Raf")) :ARG2 (enzyme "ERK"))    Example
    
    

    Example: ERK phosphorylates B-Raf on the S151 site. [isi_0011.1] (p / phosphorylate-01      :ARG1 (a / amino-acid           :mod 151           :wiki "Serine"           :name (n2 / name                :op1 "serine")           :part-of (e2 / enzyme                :wiki "BRAF_(gene)"                :name (n3 / name                     :op1 "B-Raf")))      :ARG2 (e / enzyme           :wiki "Extracellular_signal-regulated_kinases"           :name (n / name                :op1 "ERK")))

  • Raf proteins     (enzyme :name (name :op1 "Raf"))    Example
    
    

    Example: Strikingly, the Raf proteins themselves are also substrates of activated ERK. [bio.mskcc_0001.6] (c / catalyze-01      :ARG0 (e / enzyme           :name (n / name                :op1 "ERK")           :ARG1-of (a / activate-01))      :ARG1 (p / protein-family           :name (n2 / name                :op1 "Raf"))      :ARG1-of (s / strike-04))

phosphorylation

• definition
  • process that modifies an organic molecule by adding a phosphate
  • often applied to a protein, more specifically to certain amino acids that are part of a protein
  • often activates or deactivates enzymes and other proteins
    Example: If amino acid Serine-473 ("S473") in the protein AKT is phosphorylated, AKT is, in general, functionally active as a kinase. If not, it is an inactive kinase.
  • Reverse process: dephosphorylation
  • hyperphosphorylation: protein with multiple phosphorylation sites is fully saturated
  • Common source of phosphate added in phosphorylation: ATP (= adenosine triphosphate) which donates one of its phosphates and becomes ADP (= adenosine diphosphate)
  • Typical agent: enzyme
• frame for phosphorylate-01
  • :ARG0 agent of phosphorylation (e.g. person, process)
  • :ARG1 thing phosphorylated; typically a protein or other organic molecule
  • :ARG2 instrument (typically an enzyme)
  • :ARG3 product of phosphorylation; typically a protein or other organic molecule
• examples
  • ERK phosphorylates B-Raf on the S151 site.     (phosphorylate-01 :ARG1 S151 :ARG2 ERK)    Example
    
    

    Example: ERK phosphorylates B-Raf on the S151 site. [isi_0011.1] (p / phosphorylate-01      :ARG1 (a / amino-acid           :mod 151           :wiki "Serine"           :name (n2 / name                :op1 "serine")           :part-of (e2 / enzyme                :wiki "BRAF_(gene)"                :name (n3 / name                     :op1 "B-Raf")))      :ARG2 (e / enzyme           :wiki "Extracellular_signal-regulated_kinases"           :name (n / name                :op1 "ERK")))

  • phosphorylated ATM   [Use :ARG3 for product of phosphorylation.]     (ATM :ARG3-of phosphorylate-01)    Example
    
    

    Example: phosphorylated ATM [isi_0011.2] (e / enzyme      :wiki "Ataxia_telangiectasia_mutated"      :name (n / name           :op1 "ATM")      :ARG3-of (p / phosphorylate-01))

protein

• definition
  • large organic molecule
  • major building block of living things
  • can be agents of biochemical processes (enzymes)
  • Proteins are encoded by genes. The physical expression of genes into proteins consists of two steps: (1) enzymes transcribe genes into messenger RNAs (mRNAs) and then (2) ribosomes translate these messenger RNAs into proteins.
• components of a protein
  • A protein is a chain of many amino acid residues (An amino acid residue is an amino acid minus a -OH and a -H group, which are discarded as water when two amino acids are bound together as links in a protein chain in a process called polymerization).
  • A term such as "S151" refers to a specific amino acid ("S" = serine; table ) at a specific position ("151") in the chain of amino acid residues that make up a protein. A prefix "p" (as in "pS151") indicates that the amino acid is phosphorylated.
  • A protein-segment is a sub-chain of one or more amino acids.
  • Some protein-segments are referred to as a domain or motif or (binding) site.
• types of proteins
  • enzyme   [We annotate proteins that are also enzymes as an enzyme.]

• :time
  • When she arrived, he was still asleep.     (sleep-01 :ARG0 he :mod still :time (arrive-01 :ARG1 she))    Example
    
    

    Example: When she arrived, he was still asleep. [isi_0002.612] (s / sleep-01      :ARG0 (h / he)      :mod (s2 / still)      :time (a / arrive-01           :ARG1 (s3 / she)))

• :condition
  • When all else fails, I use superglue.     (use-01 :ARG0 i :ARG1 superglue :condition (fail-01 :ARG1 (all :mod else)))    Example
    
    

    Example: When all else fails, I use superglue. [isi_0002.613] (u / use-01      :ARG0 (i / i)      :ARG1 (s / superglue)      :condition (f / fail-01           :ARG1 (a / all                :mod (e / else))))

  • When PP2A was inhibited, certain B-Raf mutants accumulated.     (accumulate :ARG1 enzyme :condition (inhibit-01 :ARG1 PP2A))    Example
    
    

    Example: As indicated in Fig. 7A, when PP2A was inhibited with okadaic acid treatment, slower-migrating forms of the V600E, G466A, and D594G B-Raf proteins were found to accumulate. [bio.mskcc_0001.44] (f / find-01      :ARG1 (a / accumulate-01           :ARG1 (a2 / and                :op1 (e2 / enzyme                     :name (n / name                          :op1 "B-Raf")                     :ARG2-of (m / mutate-01                          :value "V600E"))                :op2 (e3 / enzyme                     :name (n4 / name                          :op1 "B-Raf")                     :ARG2-of (m4 / mutate-01                          :value "G466A"))                :op3 (e4 / enzyme                     :name (n5 / name                          :op1 "B-Raf")                     :ARG2-of (m5 / mutate-01                          :value "D594G"))                :ARG0-of (m2 / migrate-01                     :ARG1-of (s / slow-05                          :degree (m3 / more))))           :condition (i / inhibit-01                :ARG1 (e / enzyme                     :name (n3 / name                          :op1 "PP2A"))                :instrument (t / treat-04                     :ARG2 (s2 / small-molecule                          :name (n2 / name                               :op1 "okadaic"                               :op2 "acid")))))      :ARG1-of (i2 / indicate-01           :ARG0 (f2 / figure                :mod "7A")))

• see general AMR Dict for more examples

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The dictionary above shows additions and modifications from days ago = Aug 24, 2016   to days ago = Sep 23, 2016.
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