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.
For discussion:
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.
Models built
- 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.
AIs
- 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.