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    Nico Matentzoglu
    @matentzn
    I will put it on the list
    Chris Mungall
    @cmungall
    Unfortunately a lot of the wiki docs did not transfer well from googlecode to github. I would love to kill the buffering has relation in subQ but we would need the existing ontologies to stop is-a overloading, or buffer some other way
    the plant trait ontology is nice as it doesn't is-a overload, it uses part-of as in OBA.
    Nico Matentzoglu
    @matentzn
    @cmungall Perfect that was what I was looking for. I think we need to enumerate the pros and cons of all different approaches, and zone in on one before the meeting happens. I just hacked an extended abstract for ICBO and just in one minute of looking through definitions, found a few weirdness that need to be considered. In particular, you cant really omit the entity (bearer) in the definition (which often happens), even if a superclass specifies it, because you lose the fact that it is exactly that "part" quality that has a specific bearer rather than any. For example HP:Unilateral deafness does not specify the entity:
    has part some (’lacking processual parts’ and (towards some ’sensory perception of sound’) and has modifier some abnormal and has modifier some unilateral), one of its superclasses does (abnormal ear physiology). This does not, however, using the has part pattern, mean, that unilateral deafness has a part that inheres in the eye AND has modifier some unilateral (with an emphasis on the AND). And I think there are a bunch of those misconceptions.
    Nicole Vasilevsky
    @nicolevasilevsky
    Hi - Pankaj asked if we wanted to send out an email to the ICBO email list about our Phenotype workshop. Day 1 is invite only but day 2 is open to everyone, right?
    So I think I should say yes, right? I can draft an announcement
    Melissa Haendel
    @mellybelly
    yes for day 2
    we also need more time on the agenda
    i told pankaj we needed more than 2 hrs
    has that been fixed yet?
    Nicole Vasilevsky
    @nicolevasilevsky
    Oh- let me check
    doesn’t look like it - looks like we just have time scheduled from 4-5:30pm on Tues
    I’ll email Pankaj about that
    Melissa Haendel
    @mellybelly
    i think we need at least 3 hrs don’t you think?
    Nicole Vasilevsky
    @nicolevasilevsky
    yes, 1.5 hrs is very short
    Nicole Vasilevsky
    @nicolevasilevsky
    If there isn’t any extra room on the schedule for extra time for the phenotype meeting, we could consider making the ontologies 101 workshop shorter (1.5 hours instead of the currently scheduled 3 hours) and using some of that time?
    Nicole Vasilevsky
    @nicolevasilevsky
    Ok - Pankaj gave us 2 hours on day 2, but said we could go past 6pm, into the social and mixer/poster demo time
    Melissa Haendel
    @mellybelly
    what do you want to do nicole?
    ontology 101 needs time too
    Nicole Vasilevsky
    @nicolevasilevsky
    Yes, I agree, ontology 101 needs time.
    I think it’s okay if we just plan to go back 6pm.
    maybe we can advertise that as such?
    Melissa Haendel
    @mellybelly
    i guess so
    doesnt make me happy though
    Nicole Vasilevsky
    @nicolevasilevsky
    sorry!
    I’m not sure of a better solution, the schdule is pretty packed
    Nicole Vasilevsky
    @nicolevasilevsky
    Here is a draft email to Pankaj about the phenotype workshop - he can send this out to the ICBO mailing list:

    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.