Ontology meeting 2015-05-14

Attendees:David H, Harold, Paola, Chris, Heiko, James O, Tanya, David OS, Paul T

Minutes:David H

Release still failing

See email '[go-ontology] release-go - Build # 1043 - Still Failing!':

ERROR: multiply-labeled-edge: GO:0098772 [molecular function regulator] GO:0003674 [molecular_function] --> regulates is_a

Should we have a rule that drops relations when a multiply labeled edge appears with is_a taking precedence? Perhaps we should just do it the proper way. How would we fix the regulates isa issue? Chris will capture some of this on the ROBOT tracker. For a quick fix, David OS will create a ranking and go that route.

Using ROBOT in our pipeline

James Overton will join us as we talk about our plan to use ROBOT in our Jenkins pipelines. ROBOT does similar things to owltools/oort, but the idea is to break things down into small granular well-documented steps that members of the ontology group understand the purpose of.

The issue tracker for ROBOT is here: https://github.com/ontodev/robot/issues

Idea is to tidy up owltools/oort and get around some of the patches that we have made over time. There are install instructions. Need jar file and shell script. If the paths don't make sense, bug Chris. Easiest would be to use maven if you already have it installed. There is an example file illustrating all of the commands that you can perform: diff, filter, merge, convert, etc. Can also chain commands together and run your ontology through a user-defined pipeline. Using JSON-LD. Idea be able to use the tool throughout the OBO community. Chris-for a while the pipeline will be heterogeneous but we will begin to replace things with ROBOT. Editors should start to use ROBOT to interconvert OBO-OWL files. robot convert --input annotated.owl --output results/annotated.obo

New TG templates

Are we ready to advertise these?

Tanya's definition changes are already implemented. Heiko will update that it can be chemical or complex. Do we want to do the export terms as well? David OS will make the templates. Then we will advertise them.

cellular component binding

cellular component organization

import_across_membrane

import_across_plasma_membrane

import_into_cell

Feedback from annotation call

There has been some discussion on the representation of ion channels since the call yesterday. It seems we need to find a way to represent which ions a non-selective channel is capable of transporting and to distinguish that or combine it with the specific channels. There are a couple of ways we could do this. One would be to leave the ontology as is with all of the x ion channel activity terms representing selective ion channels and to retain the new non-selective ion channel terms. We could use an annotation extension for the latter terms to represent ions that have been tested for example, has_participant calcium ion. Alternatively, we could revert all of the current terms back to their previous definitions that state that a channel is simply capable of passing a specific type of ion and we could create new terms for selective channels.

Idea now is to change the definitions back to being non-selective and then to create selective children. This would mean that all of the annotations would currently be correct, but we would want to re-annotate the selective ones to the new terms. We should have a standard way of representing specificity.

= obo to owl conversion and relation shorthand

For historical reasons, we have 2 types of ID for relations: one human readable, one a regular ID. The former is gradually being deprecated and is stored under AP:shorthand in OWL. The annotation extensions are still very much stuck in a world that revolved around these old identifiers. This makes it very hard to change names. It turns out we can't even add new labels to these as the OWL to OBO conversion is unreliable - sometimes creating a new 'readable ID' from the label, rather than using the shorthand. Need to discuss what behavior should be and fix ASAP.

Chris answered the ticket. We need to be able to change everything across the board. s

GO-SO issues (not discussed)

Copying from last week:

There are various problems with our use of SO, some of which requires co-ordination with SO dev:

1. We need a bridge from SO transcript terms -> ChEBI:RNA. In the absence of this, lots of inference is missing. Will the long planned SO molecular save us, or do we need our own bridge axoims?
2. We need a differentium for recording which RNA metabolic processes are processing (involve maturation). We may be able to do this using terms from SO (see next item), or we could use a similar strategy to the one we use for developmental progression via a 'results in maturation of' relation. (We may, in fact, need a combination of these).
3. We use the SO terms nRNA, ncRNA and its children as if they refer to both mature and immature states of transcripts. In fact, according to SO they refer to the mature state. To align with SO properly we would need to review usage and use alternative SO terms where available. SO has an additional set of terms for primary transcripts, but no terms for immature. Primary transcript refers only to before splicing so no terms for intermediate state after splcing and before other modifications involved in maturation such as capping and polyadenylation for mRNA. Need to discuss possibilities of adding these with SO.

DOS organising meeting with Karen Elibeck. Who wants to be involved?

part_of vs has_part in export from nucleus (not discussed)

dph-All of the named RNAs that are exported from the nucleus are exported as part of RNP complexes. In the ontology we had asserted that the RNA export has_part RNP export. This seemed backwards to me since the RNA is part of the RNP. I reversed these relations to make the RNA transport part_of the RNP transport.

Intersections vs. relationships in children of 'protein complex' (not discussed)

(Paola and David OS to elaborate) To avoid mis-classification of protein complexes that may be involved in the same processes, we need to retrospectively check all children of 'protein complex' that have intersections (not relationships!) with capable_of_part_of process links. David OS is preparing a list.

list of protein complexes with EC def + axiom linking to MF/BP