WBConfCall 2018.06.07-Agenda and Minutes

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Agenda

SAB

Link to SAB meeting wiki page http://wiki.wormbase.org/index.php/2018_Advisory_Board_Meeting

  • Need to form our agenda for day 2. Who is giving what talks?

Ontologies in WB

  • Plan is to include RO (and possibly also ECO) for WS267
  • Working on data model for RO led to a discussion at Caltech about how much associated data for each ontology we should include in WB
    • For example, RO also has terms from other ontologies:
    [Term]
    id: GO:0003674
    name: molecular_function
    is_a: BFO:0000015 ! process
    property_value: IAO:0000589 "molecular process" xsd:string
  • And extensive metadata about terms in the form of property_value tags (IAO = Information Artifact Ontology):
    • For example:
    [Typedef]
    id: BFO:0000050
    name: part of
    def: "a core relation that holds between a part and its whole" []
    property_value: IAO:0000111 "is part of" xsd:string
    property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string
    property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string
    property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string
    property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string
    property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at 
    certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string
    property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an 
    independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically 
    dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A 
    material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent 
    continuant: use 'bearer of'." xsd:string
    property_value: IAO:0000118 "part_of" xsd:string
    property_value: RO:0001900 RO:0001901
    property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections
    property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf
    property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string
    is_transitive: true
    is_a: RO:0002131 ! overlaps
    inverse_of: BFO:0000051 ! has part
  • For curation, we could import only the BFO and RO ID spaces of RO, but include all of the tag-value pairs (the usage examples might be helpful)
  • For WB, though, we could injest only the BFO and RO ID spaces of RO, and only include in the model: id, name, def, is_a, domain, range, and inverse_of tags
    • We can always link out from WB to pages with more detail on RO terms

modENCODE tracks mapped to older version of genome

  • There are apparently many modENCODE genome browser tracks that are not aligned properly, i.e. they are aligned to an older genome version
  • This can be quite misleading to users who aren't aware of the issue (probably most users)
  • We would like to correct this, but remapping won't be possible in the near term
  • Scott has offered to build a stand alone instance of JBrowse for these tracks (it exists: dev.wormbase.org:9019)
  • We need to assess the extent of the problem: which tracks are affected?
  • Chromosomes affected:
    • The total changes, by the time you reach the right end of the chromosome, are:
chr I   : 11bp off
chr II  : 76bp off
chr III : 101bp off
chr IV  : 36bp off
chr V   : 31bp off
chr X   : 76bp off
  • On the web-dev call, we discussed asking Mike Cherry (PI of ENCODE) about mapping it forward

Help Desk

Alliance Working Group on Literature Curation Pipelines

  • Are WormBase and Textpresso Central represented on this group?

Minutes

SAB

Link to SAB meeting wiki page http://wiki.wormbase.org/index.php/2018_Advisory_Board_Meeting

  • Need to form our agenda for day 2. Who is giving what talks?
    • Dow have Parasite? -> not on the schedule but Kevin can talk about it (overview) Data management and workflow
    • SAB will be worm people and other MODs
    • Todd: schedule light on curation
    • PS -> what do we want advice on; Kevin -> advice on tools that we don't have?; Raymond -> Trends on data? Curation and UI; Paul -> community annotation, GOCAM, Metabolomics
    • Advisors are new -> need to give an overview on WormBase
    • Raymond -> need to produce a progress report document so that when we make oral presentations we don't need to go into much detail.
    • Send out the MIMB paper to funders to give them an overview
    • PS: everyone should write a short page stating what they do -> start doing it now. Give big picture, what we will be doing in 5 years. Kevin-> should be half a page/ 1 page; Raymond -> present on a per topic page; Paul -> status of current data, what has been done, what's missing. Mention the Alliance data model (e.g. orthology is good but does not cover other nematodes)
    • PS will be talking about the Alliance -dataflow, curation tools, displays. What are we going to do to serve our community
    • Advisors are new -> need to give an overview on WormBase
    • Put together the doc pretty quickly and decide next steps once ready
    • Good to have a template? Yes: what is the data, why it's important, who are the users, what's the data model (important aspects of the data model) curation process, curation status, future plans (including community curation), name of the people involved. Not too heavy. Ranjana will send out the template (headers). How about user interface? PS -> good to have a description of tools (table display, figures). Stand alone tools (JBrowse, Spell, Simplemine, etc..) should be described separately. What kind of killer app is in the wish list and/or where is Alliance presenting this. Get down the basics for each data type, for the SAB we need the big picture. Prepare by Monday.
    • We will distribute this doc also to other people in the Alliance for transparency
    • Lincoln: meeting rooms are set up and working on meals and accommodation. The SAB members have been invited -7 confirmed SAB attendees, many are one off from the Toronto area. If you haven't booked flights contact Melissa Torres (Lincoln's assistance). For Agenda and wiki Sibyl is in charge. Let Melissa know if you have food restriction.

Ontologies in WB

  • Ontologies: What we import and store in WB
  • RO will go into WS267. Kimberly was working on parsing scripts for the relations to go into WB
  • RO should not be imported in WB in its entirety -> restrict to GO
  • Extensive metadata attached to some of the terms and is captured through the property value tag (usage examples). Kimberly preference is not to import this into WB. Can be useful for curation -> keep into caltech curation
  • Be selective about the tags and values of RO that we import in WB
  • Raymond -> how much info do we want to display and operate on in term of search tools in WB? Are we going to have an ontology browser for that given ontology? Will be included in Wobr? That should dictate how much info we want. Are we importing only the terms we are using? Kimberly: For GO important to import all of them, for RO not so much.
  • Raymond: we could import only the terms that we use we don't import the hierarchy, are we going to link out?. Kevin: if the structure of the ontology is not going to be used than we don't need to import it all.
  • Kimberly will continue to work on the RO model importing only the values (and external URLS) that will be useful to datomic, WB

modENCODE tracks mapped to older version of genome

  • The issue is that the MODENCODE data was mapped to pre WS235. On WS235 there were corrections made to the genome and some tracks went off sync
  • This is probably affecting all the tracks. Chromosome I is 11 bp off by the time you get to the end of the Chromosome. Chromosome III is 100bp off. Others are something in between.
  • We don't have the resources to do all the remapping of the data. Scott made a stand alone instance of JBrowse to deal with this issue.
  • Scott: That JBrowse instance can be incorporated to the main JBrowse.
  • From JBrowse perspective this will look like a separate species (C elegans WS234)
  • Raymond -> can we make the mod encode tracks look like that they have a problem so users will know that there is a problem? Lincoln thinks this should be corrected. We should have legacy data available (on WB or a pointer to the Modencode site) and whatever we show in the new build should map to the correct version. Better not to show it than show it incorrectly. PS -> possible to remap everything? Kevin -> this is what MODern has done, Kevin started but very time consuming. The original data is available at the MODENCODE browser, we could create a browser on the old assembly. Kevin suggests these tracks should be removed from the current browser.
  • Scott will look into what it will take to bring in the MODern data
  • Can have a banner at the top of the Browser? "Looking for MODENCODE? click here"
  • Chris: whenever the Modencode tracks are displayed put a disclaimer so that users know
  • Modencode GFP Chip data -> peaks that looked good. In intestine Chris opened up many tracks at the same time and it seemed that many TF that have binding sites that look identical. It looks like an artifact. They do not like hotspots but rather duplicates. Lincoln: that was one of the initial Modencode finding -> hot regions, they are not identical but look like duplicated tracks.
  • Scott will look into the data and see if they are duplicated files. Lincoln thinks that this should not be an artifact, it is what the data says.
  • Lincoln: UCSC has most of the mod encode data. Raymond: can we fetch UCSC tracks and display in JBrowse?. Scott: possible to do.

Help Desk

  • Mutant validation https://github.com/WormBase/website/issues/6452
  • gk448, ok195
  • on WB is a 355bp deletion
  • Chris will look into the issue and respond to the user.
  • On the page there is a list of the oligos and it is stated that is for sequence only assays.
  • Paul D will also look into it

Alliance Working Group on Literature Curation Pipelines

  • Has anyone in WB got back to Carol Bult wrt this?
  • We will discuss it at the Caltech call