Hi Joshua,
On 14/07/14 06:30, Joshua Dunham wrote:
In reading the docs at the LMF site (invaluable), it seems that most
of the usage of Marmotta is more along the lines of users/admins
upload data manually with a cleaning/reconciliation step. I have a
bio lab information manager I'd like to integrate into Marmotta and
am wondering if there are published use cases that can help guide
me.
Although the LMF documentation is very relevant and there are still many
things we have to port, please take into account that with the move to
Marmotta the project has done a pivot toward more pure linked data
things, while linked media stuff keeps in LMF.
The basics of what I'm trying to do is define some more or less
static resources (let's say a cell type and associated meta data) and
> have a webapp query the store for all resources of type=cell (or the
> like) and then let system users describe what they did by filling in
> forms with this controlled meta-data lists. In this scenario I could
> have a list of cells, cell stains, some labware, some structured
> description of what I did (lab prep, imaging, etc). I would like to
> update the RDF store on every webapp form submit, so to speak. Since
> I have the luxury of being able to send along any property for any
> 'thing' I want to describe (I'm making the webapp), I can make the
> RDF store as granular as I wish.
1: Does it sound feasible that I define semantic searches for REST
and just return json for the list dropdowns etc when my webapp loads? > Is
there a better bay?
2: I would obviously like to capitalize on some public stores for
cell types and their meta-data, but how would I do this? I guess I
> would like to link cache the data ahead of time.
>
3: Should I make a different LD container, or context for different
> groups of things, like a container for chemistry related things and
> one for biology related ... etc etc?
>
4: Even starting small means I would need (want) to integrate in a
> bunch of external bio/chem/physics stores ... but how does the
> community integrate with this? Do I have to grab their ontology and
> integrate it into my store before I start? It seems pretty difficult
> to wrangle the nomenclature of each store especially since I haven't
> been able to find much written about the methodology by which they
> followed to create ontologies. The dc and rdf ontologies are really
> simple, but the BioPhysics at the OBO is a far departure from those.
> So far I'm thinking to create my own terms based on what I want to do
> with my webapp and downstream analytics, and then use sameAs to hook
> into the external metadata if that sounds OK.
Any tips and guidance would be greatly appreciated!
Taking into account your requirements, I'd say the best way you can
start is creating your own Marmotta module that you can include in a
custom WAR launcher.
You can use the maven archetype marmotta-archetype-module to generate
new modules for Marmotta, or just take any of the current modules of the
platform as example.
In your custom module you could add custom JAX-RS web services (for 1)
and custom CDI services (for 2 & 3). Unfortunately the 4th point is
about a vertical domain we have no experience, so I cannot help much more.
p.s. I followed the LMF videos on using google refine, importing
data, view it at the REST resource endpoint, and configure the LMF
server to create custom searches. Good stuff!
Thanks!
--
Sergio Fernández
Partner Technology Manager
Redlink GmbH
m: +43 660 2747 925
e: sergio.fernan...@redlink.co
w: http://redlink.co
