Module or view for semantic relationships

[Giancarlo Birello]

Just an idea:
our new project is about agriculture and food objects as microscopy images, virus, plants, laboratory notes, grey literature, so we think to adopt custom relationships as "is virus of", "is leaf of", "is cause of", ecc.
What about a module or custom view for repository objects to list "references" based on this relationships? for example below image after metadata in object view?

Giancarlo

[Mark Leggott]

Hi Giancarlo,

I think this is a sound approach, especially if there is an ontology you can use, thereby making the relationships accessible at some point in the future as a standards-based external endpoint using an established vocabulary. We have been looking at adding similar functionality to the Digital Humanities Solution Pack using the Fabio FRBR ontology [1]. At the end of the day we wanted to be able to "publish" an exhibit page which would list and group all the concepts and resource objects related to the chosen object. This is also part of the goal with the Smithsonian's research data Sidora application, which does have an Exhibit tool. Would you be using a vocabulary based on AGROVOC [2] or something along those lines? It would also be nice as we get a few people working on similar requirements to establish a best practice for how one integrates an ontology into Islandora for this kind of use.

I'm always interested in efforts that can be rolled into distributable Solution Packs, and this sound like one :-)

1. http://speroni.web.cs.unibo.it/cgi-bin/lode/req.py?req=http:/purl.org/spar/fabio

2. http://aims.fao.org/website/AGROVOC-Thesaurus/sub

Mark

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[Giancarlo Birello]

Hi Mark,

many thanks for you answer.
At the moment we are working to get a full list of every type of objects we will ingest in repository and what kind of information we would like.
The next step will be choose metadata, vocabulary and semantic.
Yes, my idea is something like a solution pack, a module or a block (as for islandora search) to be plugged into drupal to friendly exhibit related objects.

Giancarlo

[Rosemary Le Faive]

Hi, 

I am very interested to see how this goes. I've no clue how to incorporate a standard ontology into Islandora, but it's something I hope catches on. Semantic web FTW! 

But here's a module I wrote a while back - it's proof-of-concept, but it might be of use to you as a starting point.  It provides an interface to add relationships to your objects under the "Manage" tab. It also throws links to the related items into the object view, though you'll probably want to tweak how they display, or else incorporate the related items call into your own object view theme. 

https://github.com/rosiel/islandora_relationship_editor

[Giancarlo Birello]

Wow !! Great! This is a very good starting point, many thanks!
Giancarlo

[Giancarlo Birello]

Hi Rosie,

what do you think about include a complete ontology as AOS (http://aims.fao.org/aos/)?
I will try to populate return array of function get_possible_relationships($object_pid) with AOS.

The next step will be add a configuration parameter to module setting page for custom link to ontology site.

Giancarlo

On Monday, April 22, 2013 11:01:11 PM UTC+2, Rosemary Le Faive wrote:

[Rosemary Le Faive]

Cool!

Rosie

[Giancarlo Birello]

I started a github project https://github.com/giancarlobi/islandora_relationship_editor .

First change was move related objects view to block (so I can put it anywhere).

I choose to store ontology in a datastream, i.e. PID islandora:ontology DSID ONTOLOGY, these parameters can be configured by block conf page.
At the moment I have to create manually this object, I think can be a good solution add it to solution packs models, or something like this.
Now I will try to browse xml ontology and extract relationships and opposite.

Well, any suggestions are welcome.
Giancarlo

[Giancarlo Birello]

I'm working on parse different ontology files (OWL RDF/XML), I have started with PHP Domdocument and Xpath.
I know there are interesting PHP/java libraries for parsing this type of files.
Has anyone experience about this kind of tools/library as RAP(http://wifo5-03.informatik.uni-mannheim.de/bizer/rdfapi/), ARC2(https://github.com/semsol/arc2/), grapgite(http://graphite.ecs.soton.ac.uk/), Jena, Neologism ... ?
The idea is integrating module/block islandora_relationship_editor with tools.

Best,
Giancarlo

[Giancarlo Birello]

Added namespace management e some more features to module.
I opted for ARC2 library and some relx function.
I used tuque function for add namespace and manage RELS-EXT reltionships.
I added a first draft delete function.
I added a lightbox to show ontology.

Ontology must be in OWL RDF/XML format and stored in a datastream of an object of repository (PID and DSID configured in block configuration).

Ref: https://github.com/giancarlobi/islandora_relationship_editor

Best,
Giancarlo

[Don]

Giancarlo ... this is really interesting. We've been looking at enhanced content models ( http://sourceforge.net/apps/mediawiki/ecm/index.php?title=Main_Page ) but haven't had the time to investigate deeply.

I've got the relationship module and its dependencies installed. 

I've created an islandora:ontology object with DC and ONTOLOGY datastreams. The ONTOLOGY datastream contains the fedora ontology expressed as OWL-LITE ( https://wiki.duraspace.org/display/DEV/fedora-model+Ontology ). Not sure if that works, but could swap something else in.
I'm not seeing any configuration options, so I may have missed installing something.  Is there a default block ?

Thanks,
Donald

[Giancarlo Birello]

Hi Don,
yes, there is a block configuration page where you configure PID and DSID and you can see ontology.
Then there is a tab "Relationships" where you add relationships to object from previously defined ontology.
Then in the block view there is a link to lightbox to see current ontology (see here http://v2p2.to.cnr.it/ at the end on the left side).
For relationships I use objectproperty tag from owl in rdf/xml format like this one http://aims.fao.org/aos/
I hope this is some useful for islandora community.
Best,
Giancarlo

[Don]

Thanks Giancarlo !

Have that working except for the colorbox display ... I'll work on that. Could be my config.
I'm able to add/manage a relationship based on the ontology I've specified.

I notice that in your collection you've got some microscope slides ... we're hoping to create a solution pack based on that use case this summer. We've got a number of slides in the Aperio (.svs) format.  If you (or anyone else on the list) are interested in collaborating  on that let me know and I'll share the requirements document I've started.

Thanks again,
Don.

[Giancarlo Birello]

On Sunday, May 19, 2013 9:20:51 PM UTC+2, Don wrote:

Thanks Giancarlo !

Have that working except for the colorbox display ... I'll work on that. Could be my config.
I'm able to add/manage a relationship based on the ontology I've specified.

 

Great! I'm happy for this. I apologize the code is not commented well but I will add comments and there some things to change. It is a very beta version.

I notice that in your collection you've got some microscope slides ... we're hoping to create a solution pack based on that use case this summer. We've got a number of slides in the Aperio (.svs) format.  If you (or anyone else on the list) are interested in collaborating  on that let me know and I'll share the requirements document I've started.

Good, I'll talk about this with my biologist colleagues. 

[Mark Leggott]

This is an awesome contribution - kudos to Rosie and Giancarlo! I haven't had a chance to see this in action yet, but the design and feature set seems to scratch a significant itch in the community. Would it be feasible to implement this is a test site like sandbox, or do up a quick video of how this works Giancarlo? 

Mark

[Giancarlo Birello]

Many thanks Mark!

I'll try to record a short video or some screenshots in next days.
You can see public side of new project here http://v2p2.to.cnr.it/ , at the end on the left side click on Current ontology to see lightbox with relations fron Avoc.
Consider that presentation block is very basic for now, it show only related objects, I would like to show objects grouped by relations.

Best,
Giancarlo

[Giancarlo Birello]

Mark,

here http://devbioinfo.to.cnr.it/out.ogv a first quick video about module.
Anyway, I know Don installed it a week ago.

Best,
Giancarlo

[Michael Haft]

I should mention that we’ve been working on something similar here at the FBA, our module allows for you to add any semantic relationship between any two objects using a predefined set of relationships created by an administrator, it also uses the autocomplete function in drupal forms to link objects, so if you had for example a field in your form for MODS <subject><topic>MyKeyword</topic></subject> could autocomplete over a list of MADS objects and once you select one our object linker writes the appropriate relationship in the RELS-EXT of the two objects.

 

We’re finishing off some parts of our code and adding it to github in the next few weeks.

 

Mike

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[Peter Murray]

This is great work, Giancarlo. Thanks for the video that walks through the module. I can see this being more generally useful. One thing I'd add to it is an explanation of why an object is related in the "Related Objects" block. That would be a great way to take advantage of the ontology vocabulary to lead the user through to related objects. If I find I need to scratch that itch before anyone else, I'll be happy to contribute back.


Peter

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[Giancarlo Birello]

Yes, Peter, the block is not completed, my next step wiil be show related objects grouped by relations and describe relations, I agree with you that is an important step.
I have some tasks to close before I can work on it, so any your contributions will be a great help for me.

Best,
Giancarlo