Pathway / BioPAX 정리

BioPAX - Biological Pathways Exchange Language Level2

□ 출처: BioPAX

□ 분야: Pathway

□ 키워드: BioPAX, Pathway Exchange Form

□ 연관 내용:

biopax-level2-documentation.pdf

biopax-level2-diagram-utility.pdf

biopax-level2-diagram-main.pdf

□ 내용 요약:

BioPAX
- Enables the integration of diverse pathway resources by defining an open file format specification for the exchange of biological pathway data.


BioPAX Ontology Class Structure

- Top level entity classes
  - 4 basic concepts in the ontology: entity, interaction, physicalEntity, pathway
  #Entity
    - A discrete biological unit used when describing pathways
  #Interaction
    - A single biological relationship between two or more entities.
    - PPI, biochemical reaction, enzyme catalysis
  #Pathway
    - A set or series of interactions, often forming a network, which biologists have found useful to group together for organizational, historic, biophysical or other reasons.
    - Glycoysis, valine biosynthesis
  #Physical Entity
    - An entity with a physical structure. A pool of entities, not a specific molecular instance of an entity in a cell.
    - Protein, small molecule, RNA

- Interaction subclasses
  #Physical Interaction
    - An interaction in which at least one participant is a physical entity.
  #Control
    - An interaction in which one entity regulates, modifies, or otherwise infuluences another.
    - activation and inhibition
  #Conversion
    - An interaction in which one or more entities is physically transformed into one or more other entities.
    - A biochemical reaction converts substrates to products.

- Control subclasses
  #Catalysis
    - A control interaction in which a physical entity increases the rate of a conversion interaction by lowering its activation energy.
  #Modulation
    - A control interaction in which a physical entity modulates a catalysis interaction.
    - Allosteric activation and competitive inhibition of an enzyme's ability to catalyze a specific reaction.
 

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