Informatics/Genome Informatics
Pathway / BioPAX 정리
Yonglae Cho
2010. 2. 24. 16:07
BioPAX - Biological Pathways Exchange Language Level2
□ 출처: BioPAX
□ 분야: Pathway
□ 키워드: BioPAX, Pathway Exchange Form
□ 연관 내용:
biopax-level2-documentation.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.
□ 내용 평가:
#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.
□ 내용 평가: