[gensc-biodiversity-wg] [Gensc-developers] GSC 14 hackathon Sept 20-21

John Deck jdeck at berkeley.edu
Mon Mar 19 17:52:47 UTC 2012 

Coming in May is a Semantics of Biodiversity Workshop with Barry Smith,
sponsored by RCN4GSC.   The goal for this workshop is to clarify some
troublesome terms in Darwin Core, as they relate to the intersection to
lab/genomics and ecological/environmental domains.

Building on that (and the Jan/Feb hackathons), I'd like to see a
"Relationship Terms" hackathon breakout at GSC14 focused on implementing
relationship terms that work between domains to solve a set of problems
(somewhere between 3 to 5 problems?).  A couple of examples of cross-domain
problems (and we can certainly find more):

1) tracking identifiers between Genbank and GBIF, building and storing
relationships between related objects.
2) how do we describe the environmental space of metagenomic gut samples.
 (e.g. Sample from Gut of Fish that lives in a Coral reef, captured at
depth of X meters, water temperature of X deg Celsius).  Data coming from
a) weather stations, b) collecting event database, c) specimen database,
and from d) lab database.

Some good questions to consider in this session could also include:  When
is an object the sameAs another object?  What is the difference
and similarities between OBO relationship terms and DwC
ResourceRelationship and other standards?


John
On Mon, Mar 19, 2012 at 8:13 AM, Dawn Field <fiedawn at googlemail.com> wrote:

> Okay - I'll just say that we keep coming round to the semantics of
> using these standards - it would be a great topic for the hackathon.
>
> MixS clearly states use of several ontologies (including OBI) in the
> 2088 paper, but our hurdle is always needing ontology aware software
> and relevant terms in the right ontologies
>
>
>
> On Mon, Mar 19, 2012 at 3:06 PM, Philippe <proccaserra at gmail.com> wrote:
> > Well, I am trying to connect the threads of several discussions  :)
> >
> >
> > P
> >
> >
> > On 19/03/2012 15:00, Dawn Field wrote:
> >>
> >> are you suggesting a term/ontologies 'centre of gravity' at the
> >> hackathon? this would be brilliant!
> >>
> >>
> >>
> >> On Mon, Mar 19, 2012 at 2:58 PM, Philippe<proccaserra at gmail.com>
>  wrote:
> >>>
> >>> Hi Wim, Dawn,
> >>>
> >>> Thanks for circulating the minutes. The one thing I noticed in the note
> >>> is
> >>> the creation of a CV.
> >>> Is there a google spreadsheet where things are discussed and where it
> is
> >>> possible to contribute?
> >>> As GSC relies on ENVO, I was wondering if any decision had been made as
> >>> to
> >>> which ontological framework that CV could be anchored and where this
> >>> could
> >>> be discussed ?
> >>> There are several reasons why this could matter.
> >>> 1/ the interplay with existing OBO Foundry resources (I mentioned ENVO)
> >>> but
> >>> since Mimarks mentions OBI, it points to several contact points and
> >>> potential synergies
> >>> 2/ owing to the growing interest in RDF/OWL, again it seems to be
> >>> important
> >>> to look at the amount of work that has been done in OBI (library
> >>> preparation, nucleic acid extraction, assay, paired end
> sequencing.....).
> >>> It
> >>> seems that a lot of time could be saved and again community cross talk
> >>> enabled.
> >>>
> >>> The key points here are the following:
> >>> 1. OBI allows the creation of Views:
> >>> There is tooling available to extract just the classes you need from
> OBI
> >>> to
> >>> serve your needs. So no need to be spooked by the size of OBI.
> >>> 2. Template creation of metadata loading and creation of defined
> classes.
> >>> Again, this can save a lot of time as spreadsheet based tools exist to
> >>> augment OBI with GSC specific classes while ensuring that enough
> >>> information
> >>> about each new class is supplied (typically, a definition, a example of
> >>> usage, a source for the definition, synonyms and so forth).
> >>>
> >>> I would urge looking into all these elements
> >>>
> >>> All the best
> >>>
> >>> Philippe
> >>>
> >>>
> >>>
> >>> On 19/03/2012 14:46, Dawn Field wrote:
> >>>>
> >>>> A key point being to remember that these aren't the only potential
> >>>> topics (GCDML and MixS/DwC)...just the first two to have
> >>>> nucleated...For GSC 14 we are talking about a range of ideas -
> >>>> including high level things like considering website content.  So all
> >>>> ideas welcomed but let's sort out as soon as possible how the Oxford
> >>>> and NESCent interests dovetail...
> >>>>
> >>>>
> >>>>
> >>>> On Mon, Mar 19, 2012 at 2:41 PM, Wim De Smet<Wim.DeSmet at ugent.be>
> >>>>  wrote:
> >>>>>
> >>>>> Yes, caveats certainly apply! Thar be dragons 'ere, etc.
> >>>>>
> >>>>> Obviously there is some overlap between both hackatons and groups. In
> >>>>> reference to Hilmar's email, I think a larger hackaton at NESCent is
> a
> >>>>> good
> >>>>> idea and it should merge both groups in one longer event.
> >>>>>
> >>>>> regards,
> >>>>> Wim
> >>>>>
> >>>>>
> >>>>> On 19-03-12 14:38, Dawn Field wrote:
> >>>>>>
> >>>>>> Thanks Wim!  I think there is also a final report being made  - the
> >>>>>> 'live report' still contains many early notes that could be
> misleading
> >>>>>> - as they describe issues that were resolved by further
> >>>>>> talking/actions at the meeting.
> >>>>>>
> >>>>>> GBIF have also posted a news item on the Oxford hackathon
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> http://www.gbif.org/communications/news-and-events/showsingle/article/genomic-data-in-gbif-moves-a-step-closer/
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> On Mon, Mar 19, 2012 at 1:34 PM, Wim De Smet<Wim.DeSmet at ugent.be>
> >>>>>>  wrote:
> >>>>>>>
> >>>>>>> Hi,
> >>>>>>>
> >>>>>>> The live notes that we used at the (GCDML) mini-hackaton are here:
> >>>>>>> http://tinyurl.com/7x6v3vm
> >>>>>>>
> >>>>>>> I can fill in details on the java bindings (which are started but I
> >>>>>>> really
> >>>>>>> need to continue work on). Everybody sort of has their own projects
> >>>>>>> going,
> >>>>>>> so ideally we'd all contribute alike to the overview.
> >>>>>>>
> >>>>>>> I would propose tying this in with a developer call in a couple of
> >>>>>>> weeks
> >>>>>>> and
> >>>>>>> using that to consolidate a (non-definitive) list of projects for
> the
> >>>>>>> next
> >>>>>>> meeting. Off the top of my head we could use: central documentation
> >>>>>>> on
> >>>>>>> getting the various tools running, XML documentation, (functional)
> >>>>>>> tests
> >>>>>>> of
> >>>>>>> bindings, extra utility code, tutorials.
> >>>>>>>
> >>>>>>> Apologies for cross-posting, should we keep this discussion on
> >>>>>>> -developers?
> >>>>>>>
> >>>>>>> regards,
> >>>>>>> Wim
> >>>>>>>
> >>>>>>>
> >>>>>>> On 18-03-12 11:43, Dawn Field wrote:
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> We need to get both up and advertised and will do so with high
> >>>>>>>> priority!
> >>>>>>>>
> >>>>>>>> We propably need a new 'hackathon' page in the Gsc website...
> >>>>>>>>
> >>>>>>>> Volunteers from the past hackathons willing to help please come
> >>>>>>>> forward
> >>>>>>>> ... I will talk with Peter to get something started
> >>>>>>>>
> >>>>>>>> Sent from my iPhone
> >>>>>>>>
> >>>>>>>> On 18 Mar 2012, at 02:21, Trish Whetzel<plwhetzel at gmail.com
> >>>>>>>> <mailto:plwhetzel at gmail.com>>      wrote:
> >>>>>>>>
> >>>>>>>>> Excellent news! Is there a write-up or wiki page with the
> projects
> >>>>>>>>> from the last hackathon?
> >>>>>>>>>
> >>>>>>>>> Trish
> >>>>>>>>>
> >>>>>>>>> On Fri, Mar 16, 2012 at 5:12 PM, Dawn Field
> >>>>>>>>> <<mailto:fiedawn at googlemail.com>fiedawn at googlemail.com
> >>>>>>>>>
> >>>>>>>>> <mailto:fiedawn at googlemail.com>>      wrote:
> >>>>>>>>>
> >>>>>>>>>    Dear All,
> >>>>>>>>>
> >>>>>>>>>    Just a heads up that due to the success of the recent GSC
> >>>>>>>>>    hackathon/small group meeting within biodiversity, we will be
> >>>>>>>>> planning
> >>>>>>>>>    to keep 2 days open after the GSC 14 meeting in Oxford (Sept
> >>>>>>>>> 17-19,
> >>>>>>>>>    with hackathon booked for 20-21).
> >>>>>>>>>
> >>>>>>>>>    If you would like to use the time to tackle specific
> development
> >>>>>>>>>    projects just let us know and we can start to build it into
> the
> >>>>>>>>>    planning process for these two days.
> >>>>>>>>>
> >>>>>>>>>    We are working on a range of ideas, but we are looking for
> >>>>>>>>> 'champions'
> >>>>>>>>>    to put forward specific projects (small or larger) and help
> >>>>>>>>> organize
> >>>>>>>>>    getting the right people to the table to make real progress.
> >>>>>>>>>
> >>>>>>>>>    best to all,
> >>>>>>>>>    Dawn
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>    --
> >>>>>>>>>    Professor Dawn Field
> >>>>>>>>>    Molecular Evolution and Bioinformatics Group, Head
> >>>>>>>>>    Centre for Ecology&      Hydrology
> >>>>>>>>>
> >>>>>>>>>    Maclean Building
> >>>>>>>>>    Benson Lane
> >>>>>>>>>    Crowmarsh Gifford
> >>>>>>>>>    Wallingford
> >>>>>>>>>    Oxfordshire
> >>>>>>>>>    OX10 8BB
> >>>>>>>>>    T: +44 (0)1491 838800<tel:%2B44%20%280%291491%20838800>
> >>>>>>>>>    F: +44 (0)1491 692424<tel:%2B44%20%280%291491%20692424>
> >>>>>>>>>    Direct x2652
> >>>>>>>>>    Email:<mailto:dfield at ceh.ac.uk>dfield at ceh.ac.uk
> >>>>>>>>>    <mailto:dfield at ceh.ac.uk>
> >>>>>>>>>    _______________________________________________
> >>>>>>>>>    gensc-developers mailing list
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>  <mailto:gensc-developers at lists.gensc.org>
> gensc-developers at lists.gensc.org
> >>>>>>>>>    <mailto:gensc-developers at lists.gensc.org>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>  <http://lists.gensc.org/mailman/listinfo/gensc-developers>
> http://lists.gensc.org/mailman/listinfo/gensc-developers
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>> _______________________________________________
> >>>>>>>> gensc-biodiversity-wg mailing list
> >>>>>>>> gensc-biodiversity-wg at lists.gensc.org
> >>>>>>>> http://lists.gensc.org/mailman/listinfo/gensc-biodiversity-wg
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> --
> >>>>>>> Wim De Smet
> >>>>>>> http://www.straininfo.net/
> >>>>>>>
> >>>>>>> _______________________________________________
> >>>>>>> gensc-developers mailing list
> >>>>>>> gensc-developers at lists.gensc.org
> >>>>>>> http://lists.gensc.org/mailman/listinfo/gensc-developers
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>> --
> >>>>> Wim De Smet
> >>>>> http://www.straininfo.net/
> >>>>
> >>>>
> >>>>
> >>
> >>
> >
>
>
>
> --
> Professor Dawn Field
> Molecular Evolution and Bioinformatics Group, Head
> Centre for Ecology & Hydrology
> Maclean Building
> Benson Lane
> Crowmarsh Gifford
> Wallingford
> Oxfordshire
> OX10 8BB
> T: +44 (0)1491 838800
> F: +44 (0)1491 692424
> Direct x2652
> Email: dfield at ceh.ac.uk
> _______________________________________________
> gensc-biodiversity-wg mailing list
> gensc-biodiversity-wg at lists.gensc.org
> http://lists.gensc.org/mailman/listinfo/gensc-biodiversity-wg
>



-- 
John Deck
(541) 321-0689
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