Noctua meeting 140929
AE in Noctua call 29th September 2014
The ultimate aim of this call + work in Barcelona is to test the use of LEGO/notcuta in clarifying and simplifying complex annotations that are currently achieved through some mix of TermGenie requests for long compound terms + annotation extensions.
We currently have two test models to play with:
1. An example from Ruth and Becky where a rather complicated compound biological process term (negative regulation of adrenergic signalling pathway involved in positive regulation of the force of heart contraction) was requested in order to provide context for a straightforward MF annotation (nitric-oxide synthase inhibitor activity). Please see the attached slide for details.
2. Kimberly has kindly provided a lovely detailed example on RNAi mediation of behavioral adaption to odor (see DropBox link . This paper describes a whole pathway, and the annotations make extensive and quite advanced use of annotation extensions.
1. To link MF, BP and CC is it necessary to enter the GP twice: once for MF and once for BP?
Answer: No. Can make a box without a GP for BP and link this to MF/GP box using part_of
2. Should Noctua modelling bring in work from multiple papers (see example from Ruth and Becky)
Not discussed. Note that Kimberley's model includes experimental info from multiple papers.
- inhibiting_NOS_In_force_of_heart_contraction - this neatly models the requested long term: 'negative regulation of the adrengergic signaling involved in positive regulation of the force of heart contraction'.
- RNAi mediates behavioral adaptation to odor (PMID:23993094) - incomplete model.
- AI: we will remove 'enabled by' from BP
- AI: check it is possible to paste in an ID (for relations(?))
- AI: check why PMCA4 is not listed as syn for ATP2B4
- Where was this? It seems to work for me? -Seth
- AI: ontology group to check property chains to ensure LEGO diagram is consistent with proposed GAF annotation to folded term
- One example to check in inhibiting_NOS_In_force_of_heart_contraction - can we get inference of positive regulation based on chaining of directly inhibits with positively regulates.
- AI: add export GAF option to Noctua (clearly document it is lossy)
- AI: add worm anatomy ontology
- Make relations AC lists.