CRN entities shouldn't use SBO #16

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FreakyBytes opened this Issue Jan 30, 2017 · 0 comments

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FreakyBytes commented Jan 30, 2017

Trac Ticket #16

component: code
owner: martin
reporter: martin
created: 2014-02-06 15:44:56
milestone:
type: proposal
version:
keywords:

currently, CRN entities just evaluate SBO terms which is quite senseless. (just because we started with SBML...)

better option:

  1. map SBO (and other annotations) to central statements (maybe SBGN?)
  2. build graph based on that
  3. provide mappers from central description to respective graph language

see:

  • source:src/main/java/de/unirostock/sems/bives/ds/graph/CRN.java
  • source:src/main/java/de/unirostock/sems/bives/ds/graph/CRNCompartment.java
  • source:src/main/java/de/unirostock/sems/bives/ds/graph/CRNReaction.java
  • source:src/main/java/de/unirostock/sems/bives/ds/graph/CRNSubstance.java
  • all classes that create a CRN, e.g. source:src/main/java/de/unirostock/sems/bives/algorithm/GraphProducer.java and its extensions
  • all classes that use/evaluate a CRN, e.g. source:src/main/java/de/unirostock/sems/bives/ds/graph/GraphTranslator.java and its extensions

comment 1

time: 2014-02-06 16:04:36
author: martin

see also:

  • /src/main/java/de/unirostock/sems/bives/ds/graph/CRNSubstanceRef

comment 2

time: 2014-05-11 19:31:31
author: martin

now it is chemical reaction network, see bives-core:#40

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