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    Nicole Vasilevsky
    @nicolevasilevsky

    Deep Learning in the Life Sciences
    Phenotype Ontologies Traversing All The Organisms (POTATO) at ICBO2018
    http://icbo2018.cgrb.oregonstate.edu/node/29

    Announcing the POTATO workshop at ICBO: Phenotype Ontologies Traversing All The Organisms (POTATO),
    scheduled for August 6 and 7 at OSU.

    This workshop will take place over two days – day 1 (Aug 6) is invite only, but day 2 (Aug 7) is open to all. This workshop aims to address challenges with developing interoperable phenotype ontologies. More specifically, we will address the use of standardized design patterns for logical definitions both within and between phenotype ontologies.

    The public workshop will take place on Tuesday, August 07 from 4-6pm. This will start with an introduction to pattern-based ontology development emphasizing its benefits and importance, illustrated using the dead simple OWL design pattern (DOSDP framework) and examples from phenotype ontologies. Following this we will present and discuss strategies to maintain patterns in a multi-species context. We will run a hands-on practical session on setting up ontology repositories for pattern-based development.

    Logistical details (housing, food) and registration details for ICBO can be found here: http://icbo2018.cgrb.oregonstate.edu/

    Please pass this announcement along, and we hope to see you there!

    Sincerely,
    Workshop Organizers:
    David Osumi-Sutherland
    Nico Matentzoglu
    Nicole Vasilevsky
    Melissa Haendel
    Chris Mungall
    Jim Balhoff

    let me know if you have any edits, I’ll send to him tomorrow
    Jim Balhoff
    @balhoff
    Hi Nicole, I would just change:
    dead simple OWL design pattern (DOSDP framework)
    to
    dead simple OWL design pattern (DOSDP) framework
    Nicole Vasilevsky
    @nicolevasilevsky
    thank! I fixed that on the draft
    Jim Balhoff
    @balhoff
    great
    Nico Matentzoglu
    @matentzn

    In case anyone wants to get a peek at some of the inconsistencies between MP and HP definitions, check https://docs.google.com/document/d/1_56zpH7dYI-_GxRsii1DTnR8-7rCRPnkHuUERzvc0l0/edit?usp=sharing

    Some of those will be discussed as part of the workshop.

    Nico Matentzoglu
    @matentzn
    I want to take a closer look at all phenotype ontologies related to participants of the workshop. Glancing through the participant list, I found some associations with HP, MP, ZP, WBPhenotype, CMPO, DPO and the future XP (XAO). Am I missing any phenotype ontology? Is FYPO represented for example?
    Chris Mungall
    @cmungall
    I don’t think Midori is coming
    Jim Balhoff
    @balhoff
    @matentzn in Phenoscape we create phenotype classes during annotation, but we don’t publish a fixed ontology: https://wiki.phenoscape.org/wiki/Guide_to_Character_Annotation
    our curator @wdahdul is coming
    Jim Balhoff
    @balhoff
    Oh - wrong channel
    Jim Balhoff
    @balhoff
    Planning to meet today?
    aargh, wrong channel again
    Nico Matentzoglu
    @matentzn
    Does anyone know what the state is of Xenopus Phenotype Ontology dev? Will it be something along the lines of WBPHENOTYPE or more towards ZP?
    Melissa Haendel
    @mellybelly
    we have been pushing for precomposed, but ideally we could autogenerate a draft and then go from there
    ok i have asked Pankaj for a talk slot on the Weds for our outcomes, as well as another session on Friday to finalize any hacking
    Nico Matentzoglu
    @matentzn
    You mean along the lines of ZFIN, yes? The workshop does not cover generating ontologies from scratch, but is more about reconciling existing ones and agreeing on patterns that can be used community wide.
    (we do however leave a good amount of space for individuals to voice their own issues and discuss them in the group)
    Melissa Haendel
    @mellybelly
    hi all, i need to set up an evite to our invited participants on Monday for a party at my house. Where is the list of attendees?
    Nico Matentzoglu
    @matentzn
    Send it to you in PM
    Erik Segerdell
    @seger
    @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.
    Chris Mungall
    @cmungall
    great! did you do your own autogenerate code or did you use dosdp templates?
    Do you have a link to github?
    Melissa Haendel
    @mellybelly
    Btw- all, please feel free to bring fav colleagues to my party on Monday. Just use the evite so i have a headcount.
    Nico Matentzoglu
    @matentzn
    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. :)
    Nico Matentzoglu
    @matentzn
    @seger Would you mind to give a 5 minute lightning talk on what you did so far on XP at the workshop? There is a session where we talk briefly about a number of select phenotype ontologies, and I think it would be a great addition.
    Nico Matentzoglu
    @matentzn

    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

    Erik Segerdell
    @seger
    @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.
    Chris Mungall
    @cmungall
    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
    Jim Balhoff
    @balhoff
    Does that ontology acronym show up as 😝 for everyone else? :-)
    Nico Matentzoglu
    @matentzn
    That’s the best argument against X P :smile:
    Erik Segerdell
    @seger
    XP just makes me think of the old Microsoft OS. And since our anatomy ontology is XAO, it seems natural to go with XPO...
    Melissa Haendel
    @mellybelly
    heh
    Chris Mungall
    @cmungall
    I always though experience points (D&D)
    Nico Matentzoglu
    @matentzn
    :smile: seems Erik has a tough choice ahead of him..
    Chris Mungall
    @cmungall
    I get in to Eugene at 5.38pm, I’m staying at the Hilton Garden Inn
    Chris Mungall
    @cmungall
    …and omnishuttle is all booked up - anyone know any other options?
    Chris Mungall
    @cmungall
    got a taxi. Sorry for the spam
    Melissa Haendel
    @mellybelly
    Np!
    here w david thinking about slides
    Nico Matentzoglu
    @matentzn
    Wow
    Thanks for letting us know
    I got myself a ride with Sue Bello at 12.45
    Or 1pm
    Chris Mungall
    @cmungall
    Shall we send an extra reminder for people to install Docker?