@matentzn The Xenopus Phenotype Ontology (tentatively XPO) is now in very rough draft form as a precomposed ontology. I won't go into exhaustive detail here, but it was seeded with many classes cloned from the MP that Xenbase curators identified as relevant to Xenopus, based on what phenotype data they had collected. As a result it contains a good number of morphology and physiology phenotypes as a start, though we'll want to add more development phenotypes. The curators also required that the XPO include an "abnormality of xx" class for each anatomy class that exists in the XAO, which I've autogenerated. So, the XPO currently comprises two big trees, the MP-derived part and the "abnormality of" classes, which are not yet integrated. There is still much, much work to be done on it, but it is at least in a state where we can concentrate on ensuring that it is aligned with established ontologies and follows the design patterns that are agreed on.
Do you have a link to github?
Hey Erik! That is great! It sounds like you have been doing quite a bit of "copy-paste”. Your case will be a very interesting to discuss at the Workshop, to see whether we can’t find a more sustainable solution! As Chris said, it would be good if we could take a look at the current artefact (XP.owl), no matter how preliminary it is. :)
We have already plenty of suggestions for the discussion session in the afternoon (Session 4). However, I wanted to give you (or at least the ones in this room) a chance to add 1 (or maximum 2) issues they want to raise to the group. However, it is possible we do not get to discuss some of them in the end; It think its better to have a few solid discussions rather than two many issues that do not get the space they deserve. Anyhow: Fill in your name a conversation topic if you have something you want discussed, and we will try to fiddle it in.
https://docs.google.com/document/d/1e4oZ3CDkBbkZNVkwCSuJN6ra-7pBxmmw1ZjbRhnihUY/edit?usp=sharing
@cmungall Did my own autogenerate code. At the moment the draft resides in a subdirectory in the XAO repository: https://github.com/xenopus-anatomy/xao/tree/xpo/xpo_draft/xpo.owl - it will get its own repository at some point, and I'll also need to formally request the XPO (or XP?) prefix.
@matentzn Yes, I can do a lightning talk.
you need to formally request. XP is more consistent with HP, MP, ZP… but this causes difficulties as people refer to them as HPO, MPO, and I hate inconsistency… causes additional confusion when in the OBO library we have both VT (vertebrate traits) and VTO (vertebtrate taxonomy ontology) arrgghh
here w david thinking about slides
Thanks for letting us know
I got myself a ride with Sue Bello at 12.45
Or 1pm
and maybe also to download https://github.com/INCATools/ontology-development-kit/releases/tag/v1.1.2
and try it (better to download images from dockerhub in advance)
There is now an interactive mode, as described in the README, so folks can just run ./seed-via-docker.sh (not tested on windows)
I think Nicole has the master list of participants?
Here is the participant list: https://docs.google.com/spreadsheets/d/1RkovLGZk3Ag1f-UsvWOF5Np94PDbivSuvW7FLXm-dTg/edit#gid=0
Hey @/all- I added the room locations to the website, on our workshop page: http://icbo2018.cgrb.oregonstate.edu/W01
Should I put the schedule for today on that page as well?
@mellybelly - I put together some closing remarks slides for you: https://docs.google.com/presentation/d/1uTRN1Wc8NNJxsgSeeNnA_V34eHQqGvs8uuH4OAmIa9k/edit#slide=id.p
@matentzn asked that I include some of the results from the survey
(survey results are here: https://docs.google.com/forms/d/1TrI9eiYmWheglf3XZtYUDSqFs0tQi3E-0QXw0nIBPMA/edit#responses)
We have more people who need rides than we have drivers so far: https://docs.google.com/spreadsheets/d/1rYxNMqhhvFDGk9CQr1ELTn8FI2sumKeukZkEUBXeTa4/edit#gid=0
@mellybelly does Uber go to your house?
maybe a taxi service?
i can take two people but not back :-)
I imagine a taxi would be more
Heh, anyone without a ride will be taken care of but Julie is already staying with us.