all right so talk a bit about our crate
and how we go ahead of
moving these things out of the PID
record and into a separate object to
keep the collection
so
we our motivation is for Gathering all
kind of research outputs and not the
collection of just one thing but having
collection of different types of things
mainly if you have research output you
have often many different types of
objects coming out that maybe publishing
all kind of repositories like fake hair
or very domain specific
repositories for protein sequences and
so on and the idea of the research
ability is to gather these in a kind of
virtual package it may include some
actual files but in my inclusion
references out there and then these are
related together giving brief
description so we know what they are and
why they are in this collection
so this is our main Aim so we're trying
to be fairly platform independent and
we're not too tied into a particular way
of storing or identifying uh these
components uh we do want to have enough
information for reproducibility and to
support data that are coming in from
different sources it may not even be
accessible directly because they require
uh authorization and so on
and so our purchase called our crate
it's uh
a way to reuse the existing standards
and uh that is fairly web-based or when
I say web-based we as I said we're
platform Independence we're not
requiring our requests to be stored and
we're using those Technologies to our
advantage because we think that's fairly
well known by many developers they can
deal with Json objects as we saw before
uh it's become quite uh lingual fund
right in describing objects now but we
know there are a diverse set of projects
people want to describe so we want us to
have some extension sensibility so we
don't want to mandate only certain
properties people can use
so has schematically what I mean when I
say in our career so our create is a
collection it has its own metadata and
most fit fairly straightforward like the
author uh licensed State and so on
but then you have a set of content and
the content could be traditional files
as I said it could be references to a
more complex subject using handles the
dois it could be something on the web
but it could be software act more active
things like I'll come back into
and then each of those can be described
so I'm gonna have to jump straight into
Jason Lam to show you this so that's why
I have a little warning triangle but I
think this is a safe space so we can all
uh have a quick look so we're using Json
link data which is of a way of using
Json where the keys have meaning so they
have to find already what the keys mean
based on the mapping of the context
and
cut especially the magic bit we insert
on the top there and the way we have
documented this is that you shouldn't
normally care too much about the link
data aspect instead that provide the
links if you have them
but it doesn't mean we can process this
and make knowledge graphs and so on if
we want to
so our request always self-declare
because we want to if you just find one
in a while you can know that it SNR rate
and in fact it's this particular version
so you know which conventions we are
following
all right and then you have this
metadata about of the crate itself so
that's the outer box you saw before so
it maybe has some identifier order and
so on you see these are all mostly full
uh identifiers could be your voice we
use existing Registries for people and
organizations
and then the content is listed as part
so there you go it's the same as part as
we saw before uh but they can be mixed
so here you see there could be local
files as well as handles and so on in
here so because uh as I said there are
flexible and how you stored our required
so the base assumption is you have a
folder and you put in our create
metadata file into it now you can
describe those files and then you can
deposit this variable one
and it could be that all of these are
persistent there are no such files
and then the thing is that we have
additional entities to describe each of
you so each of these can kind of get
unrolled below so we include some core
metadata for each of the items you don't
have to follow the links to see what
that individual item is described as and
that is important because many of them
don't have any federal objects like I
said they could be in all kind of
repositories they maybe just have a web
page or it could be files that are are
fresh and don't have anywhere to go
so each of those can be described in the
same way and then you keep adding nested
links in this case this is from the
contextual entity so it's an entity that
you basically can't download like a
person you can't download a person so it
could be digital twins so that
and of course these are linked onwards
so this is fairly basic for anyone who
knows link data but the thing is you
shouldn't need to know link data to do
now because we only have this very flat
list of approaching so we have a kind of
profile adjacently there's more guided
than having all kind of possibilities
the first one is a good example because
it's a file that has been localized
based on a had a persistent identifier
but if you go to that sonoda page you
just get the landing page you don't get
to actually move so we have to kind of
unroll it in this way
so in a collection you can have
different kinds of focus
and typically there's some objects in
that are more important so the most
basic thing is just using has path like
that and it's just a flat collections of
things and although it could be nested
you could have a hierarchy as well and
that could be even through other
creators so you have then you follow the
links to see the content of that query
you can indicate a particular subject or
context context of a trade so that would
be the about so it would be a topic it
could be a species or it could be
whatever is the identifier for the thing
that this our crate is about this is
typically a real world object right so
it's not something you can download in
fact it's our great represented somehow
if it is a digital train you promote
adopt the main entity because
then it is the main thing that is about
and that could also be one of your data
so this is a crate that describes the
output of analysis that output is the
main entity but there could be
additional things to describe how it
came to be
in order to mention things that kind of
are just added in on the side I kind of
see also a thing I mentioned so so that
this could be a way to bring in things
to the collections that are not strictly
member because they're not
as something you consider part of the
collection but they're still important
to understand it
and it could even be that your creators
only those that is like a metadata
aggregator in which case there is no
downloadable parts to the oracle
except for the metadata so we use the
common vocabularies but only extend
where we need to so the most common
vocabulary we use is schema.org because
we use web technology so the core entry
is the data set which is based on decaf
and it has lots of those useful
properties we talked about like water
and so on but there's lots of types in
schema oil for Real World objects and
that's also it's quite important for
connecting that context so as you can
describe organizations or places
uh different instruments and so on
we also have rendering to HTML because
we know the JS not everyone speaks Json
so we have a way to
show each of these entries and this goes
back to what I said that not everything
is already at its login because if I
made here now uh an entry for a person
you can click this in the previewer and
you can see uh a rendering just like
this even if it doesn't already exist
within an identifier you have made a
local identifier for that digital object
that only exists within that crate
and the kind of there's no
differentiation between those that are
cited like this one and those that are
embedded the thing when you cite we only
have the minimal information that is
relevant for this collection
okay so I'll have a bit of taste of
different ways people are using our
crate and thinking about it from a
collection point of view so most of this
collection is people doing language
status so this is the Australian
co-chair Peter saffron who's working
with the language data common so the
collection large copy of uh Opera I'm
not sure how you pluralize Corpus and
often language records right so you have
a collection of collections in this case
right of course you have lots of
interviews with people speaking uh lots
of different Native languages and so on
and you have video recordings
transcriptions and so on so there's a
collection of collection of compound
objects and using our crate with this
particular profile for navigating this
and here's kind of really used for
filling in that kind of information
and the same GUI is used by this CS3
mesh project for connecting many
different repositories we're kind of
doing that Gathering I mentioned before
when you have resources from many
different phases and maybe deposited in
one of the more traditional uh
repositories but then added in the
metadata and the identifiers
so you don't lose that on the way this
is uh
one from plant scientists where you do
lots of studies like growing things with
certain uh
preparations and fertilizers and so on
and then you do maybe some sequencing
and sort of it's a mix of many different
Sciences coming together and they
organize the data uh pretty simply us
they still use good old files and they
manage them in git lab repositories in a
fixed folder structure
with data filled in along the way then
even a tool that kind of combine all of
this to make the hour crate for you so
you can kind of gather them at the data
a bit of it and then publish it in one
single Fair object
so here you have this mixture of a live
object that keeps changing and then the
publish artifact we have kind of uh
Frozen things and maybe added additional
formats
and this one is more closer to my heart
is a very hard that we run from
Manchester and many of these projects
remaining computational refers here the
main entity is a workflow it's a program
you can execute and of course you need a
certain engine to run it and so on so
there's lots of context around the
workflow as well and that's what we
capture in the workflow crate so there's
a type of our crate that is mainly
focused on workflows and that fits into
an ecosystem so ahead of the credit is a
unit of exchange it's for publishing in
the hub but it's also for things
happening during execution time
and during execution time we try to
attract the provenance but as you see
fairly light face if you follow the red
arrow you can see the
provenance chain be emerging from the
final results and going back to the
individual steps of the workflow and it
might be there is no actual Road flow
it's just someone running it manually
and you can describe it in exactly the
same way
so we have this kind of gradual approach
to describing how something came to be
so this is some optional thing that you
can add for when you have done
computation analysis and particularly
when you have reused data from other
digital object to connect up those
identifiers it may be through some
indirection like in this case
and
one new project we have another free
effects is doing uh secure our crates so
here is running interested research
environments so this there's our data
access agreement to get access to health
data and only approved workflows can run
so here are created more like a
access tokens so because it includes the
uh one of the metadata by who you are
and what you have access to and it gets
checked if you are allowed to run
certain workflows and so on
so here again it was important to bring
along their context along the journey so
we don't lose it and we can also when we
finish we can keep track of all the
things that are attributed to a
particular research project
I've also been doing some biodiversity
thing this is one from the synthesis
plus project which was doing a kind of
combination of the two especially a verb
for execution in a digital specimen
Refinery to build Fair digital objects
and in this case it's a digital train so
it's describing species in the wild in
this case discovered in 1952 and so you
have all these lovely texts mining on
handwritten labels to happening
so in this case we have you can read on
these papers about how we did
incremental digital objects to develop
this but here to our crate is capturing
that whole execution and we're moving on
the nudity biodiversity projects here we
should also hear about that are more on
the
very first side and also for digital
objects right
but all these things to describe are
like different ways of using our crate
and they're all kind of slightly
different so they're all special except
there's one person in the back who's not
special
and so what we use to describe this are
called profiles so the kind of a typing
system but it's more lightweight because
it could be uh textual guidance for
humans or it could be more structures we
have some structure that we added now
for computational validation and so on
and it's called the profile create so
you can add in additional terms things
through the northern schema.org that you
can Define in your profile and then
maybe use for themes for validation so
you can check the certain property
success it could be things like Json
schema and so on and so in this case
we're eating our own dog food so the
profile itself is also a collection
because it's not just one thing there
could be human guidance it could be as I
said this vocabularies and so on and to
to to do that we need this in-between
thing because just the Green Bay doesn't
tell you which is straight so we have
the concept of roles being added in here
so here you see different roles for
things in this collection so the one on
the left is a vocabulary the one on the
right is the constraint or mapping and
so the the kind of break apart at House
part into also deciding the role it has
in the collection was quite important to
do that
and this is my quick argument about I
fitted little objects this you probably
have already seen something like this
about what is conceptual idea of federal
objects but in case you were neutral
update this quick intro so we know we
have a persistent identified to some TLD
records some recordable what is inside
and then you can get to the data animate
the data and the collection is just a
type of these objects
and when I recreate we kind of realized
it in very much the same way but we use
Fair sign posting and URLs as the entry
point so it doesn't have to be in the
handle system and you will know the dois
are technically in the handle system but
you can be more flexible and using this
uh sign posting over here to follow that
same navigation so here you see how you
can find it it is an arcade and it's not
just any other crate it's a verb for our
crate and you can also find a direct
downloads so if you take away nothing
else from this I hope that you just add
these headers to your web server because
standing can programmatically follow the
digital update I did wouldn't need to do
that in Direction I did with the
scenario image because if Sonora did
include that kind of download link for
this I could already follow it
programmatically
and it's more about design posting which
I won't go into now
I have some discussion points but I can
lift them later so I just want to remind
about some Shameless plug that we have
so many of you are in Germany so this in
July are a nice open science Workshop
that could be interesting and also we
have Fair impact we have some calls for
open calls if you want to have a go
we're trying either side posting on our
crate you can get a tiny bit of support
and and I'm sure help with that