by

Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Activity
    Nicole Vasilevsky
    @nicolevasilevsky
    I don’t understand Pankaj’s schedule - I don’t know what workshops group-1, etc. are - are those other workshops that people submitted?
    I’m fine with however we want to do it, I just can’t be in Corvallis on Friday, I need to leave on Thursday evening
    Nico Matentzoglu
    @matentzn

    @nicolevasilevsky I agree we should schedule a meeting soon, also to discuss workshop programme proposals.

    Did anyone ever write a piece on the implications of having multiple definitions on the same class? Blog, paper or otherwise? I explained the issue this morning to some ontology developers, and I was wondering whether there is anything I can send him to read up on it. @cmungall

    Melissa Haendel
    @mellybelly
    RE scheduling, did you look at the schedule that pankaj had suggested? The plan was to have workshops/tutorials in the afternoon
    one thing we could do is to have the full day before, next day half day obo tutorial, and then the next day half day phenotype workshop open to all?
    not sure if that fits Nico’s schedule though, and they wouldn’t be back to back.
    here is the draft program
    David Osumi-Sutherland
    @dosumis
    I think the new draft looks fine. A full day on the 6th + afternoon of 7th, after the ontologies 101 is what we wanted isn’t it?
    Melissa Haendel
    @mellybelly
    Yes!
    i kinda liked the workshops spread out over the afternoons instead of on one day, but this works best for our needs and its really fine either way.
    i think the challenge will be for the obo tutorial to be only a half day, and also there will be a lot of competing sessions.
    Nicole Vasilevsky
    @nicolevasilevsky
    Hi all,
    I don’t understand how this schedule is laid out
    I see we will have the phenotype ontologies workshop all day on Monday
    But is Ontologies 101 only for 1 hour on Tuesday?
    And then when are the other phenotype ontology workshop sessions? I only see ~30 min on Tuesday
    Leigh Carmody
    @LCCarmody
    I’m a little late to the game—but at my college, we had these gag talks called ‘Potato lectures’ forcing freshman to listen to potato-themed lectures. Ex. "The Potato as a Foundation for Renaissance Art and Architecture,” "The Tao of Tater Tots,” and "Networking the Potato: Ethernet and Spuds.” So I appreciate that I will have a day and half of ‘POTATO’ lectures. :)
    Nico Matentzoglu
    @matentzn
    Does someone know whether the introduction of 'has_part' penotype patterns is documented anywhere? Including some details regarding the motivation?
    (i.e. why is a phenotyope defined as having a quality as a part rather than simply being that quality)
    Jim Balhoff
    @balhoff
    I think there used to be a wiki page somewhere. It has been called the ‘sub-Q’ model. It introduced an indirection which avoided some unsatisfiable classes, but I don’t remember the examples. In Phenoscape I was using just qualities, but eventually added the has_part to be consistent with Upheno.
    Nico Matentzoglu
    @matentzn
    Thanks Jim. What I good find now that you pointed is this wiki page: https://github.com/obophenotype/upheno/wiki/OWL-Axiomatization. It would be good probably to extend the quite limited description there to motivate every component of the EQ definition template
    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