CRN entities shouldn't use SBO

[FreakyBytes]

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