[permaculture] the next generation of Pc Design resources.

Lawrence F. London, Jr. venaurafarm at bellsouth.net
Tue Nov 24 01:55:55 EST 2009


christophe mckeon gonzalez de leon wrote:
> hi,
> 
> there seems to be recurring interest in the db project, maybe there
> will be a critical mass reached. a lot of the below links and stuff i
> was hoping to post to the pcdb list in a more organized fashion in a
> month or two but here it is a bit prematurely.
> 
>>> a social network for instance, you just load up the foaf ontology over
>>> the wire. if you
>>> need to work with plant systematics you load up the relevant ontology
>>> that some domain
>>> experts have already done all the hard work writing. there are many
>> Where is an example or further explanation of this?
> 
> i'll try to cook up a quick example. say we wrote a pfaf ontology and
> had an rdf interface to the pfaf db. we can now load up the ontology
> into a model object with an attached reasoner. the reasoner is capable
> of making deductions based on our ontology. so for instance if in our
> ontology we declared that all instances of the class plant are living
> things, then when we ask the model for all living things, it will give
> us all the plants in the db. there is no need for any application code
> to do this, or any extra fields or data added to any plant instances
> in the db.

In the case of PFAF (what an incredible resource - you should subscribe 
to their mailing list) would a user seeking information from that 
resource have access to the same search options with an OWL - PC DB that 
they would through direct access to PFAF? As I understand it PFAF offers
a RBD user interface/front end. How would this be accessed through an 
OWL interface?
And.....
As with Amazon's message to shoppers Ex.: "people who bought this 
Perotin CD also bought the Machaud Notre Dame Mass CD"
- this seems like an opportune time to utilize the added capability of 
OWL to go beyond the PFAF user interface and database engine to relate 
and integrate PFAF data with that in other DB datasets on the Web or 
other data sources in text format or some other media type, graphics, 
video, sound, etc. Linking knowledge contained in sites around the Web 
with an OWL knowledge center could be as easy to build and use as a wiki 
or blog but much more effective with greater long term possibilities for 
building a cohesive, robust Permaculture Knowledgebase.
In other words, a user searching PFAF could be presented, along with his 
search results, with the option to look at other pertinent data or 
potential sources of data, as with "see also the eleagnus entry at such 
and such website or database", with a brief sample of text existing 
there, or "you might want to look at such and such website or database".
Like the PC OWL (that's a great name for this project!) could use a 
Google-like indexer or web crawler or spyder to uncover useful sources 
of data; actually just use Google for this. How would you integrate that 
function into PC OWL so that Google searches (possibly using a Google 
Custom Search Engine [I have set up one of these] return results 
alongside PFAF database search results. Lots of possibilities here.
This discussion should occur or also occur in the PCDB list. Anyone 
seriously interested in being on that list let me know and I will add 
you or subscribe here: http://lists.ibiblio.org/mailman/listinfo/pcdb
Archives are public and here: http://lists.ibiblio.org/pipermail/pcdb/.

  where this gets very interesting is that we can load up
> several ontologies & rdf datasets with a 'glue' ontology between them
> which the reasoner uses to deal with both datasets. say we have access
> to a new dataset through a sparql endpoint over the wire, which has
> animals in it. if we declare all animals to also be living things then
> the model will now return all plants and animals if we ask for all
> living things. lets say that plants have a field 'commonName' and
> animals just use the field 'name' to mean the same thing, we can
> declare that they are equivalent properties in the glue ontology and
> our model and db queries will reflect that equivalence. the main gist
> is that our 'schemas' are now semantically rich (we can declare that
> name and commonName *mean* the same thing) and are no longer
> firewalled silos but can be usefully shared and recombined, and
> queries aren't necessarily made to one db, but to a smart data
> aggregator with semantic knowledge. we can also write different
> ontologies which encode different semantics to be attributed to the
> underlying datasets for different views and applications on the data.

"for different views and applications on the data"
Before, there was interest in a |permaculture relationships database|
which would (I assume, using RDB technology) explore, uncover, discover
and display, with text and graphics all possible relationships between
elements in the dataset, hopefully identifying and documenting guilds 
this way. The project was about guilds or put differently, plant-animal 
relationships, useful to know about when creating permaculture site designs.

My particular interest was in its agricultural use involving GPS/GIS to 
take a detailed site inventory and use the gathered data in the PC 
Relationships Database. This way a homesteader, gardener, orchardist, 
nurseryman or farmer could catalog all existing elements on his property
that were part of some guild or could become part of one. This data 
would be tracked year to year, used seasonally and updated regularly.
All plantings could be identified and tracked season to season. For a 
market farmer, tracking crops through the DB could be a useful planning 
tool correlating the features and microclimatic information of any 
particular garden plot on site with crops suitable or not suitable for 
that location on the site, and of course, proximity to and compatibility 
with any existing guilds or guilds desired for the location.

Think of an online knowledge system that becomes a global tool for 
anyone to use for site development and maintenance, one that allows them 
to enter, store, process and retrieve data about their site and region,
i.e. their homestead or farm, their community or town and their 
bioregion. This could become quite a project. I would like to see Google 
give it special attention (wonder how many others involved in special 
projects would like that also).


It seems that your system might make it easier to track, store and 
process site data to be used in multiple ways, not just guild 
identification, preservation and creation but overall site planning and 
systems design implementation, use and maintenance.

> 
> the best no nonsense, practical, high level overview of semantic tech and what
> it can and can't presently do, that i have read, is the first chapter of this:
> 
> http://www.amazon.com/Semantic-Web-Programming-John-Hebeler/dp/047041801X
> 
> these two aren't bad either
> 
> http://www.amazon.com/Semantic-Web-Working-Ontologist-Effective/dp/0123735564
> http://www.amazon.com/Semantic-Primer-Cooperative-Information-Systems/dp/0262012421
> 
> i'm currently working through all 3 of them, and still have quite a
> bit to learn.
> 
> here are some tool sets. almost everything semweb is written in java:
> 
> http://jena.sourceforge.net/
> http://www.openrdf.org/
> http://clarkparsia.com/pellet/
> 
> this is the implementation language i am currently using and which i
> think is a perfect fit for this kind of work, because i love lisps and
> this is the nicest one i've seen, and because i don't like java much &
> clojure is fast and sits snuggly on th JVM, but also because clojure's
> approach to polymorphism and taxonomies independent of type i think
> will play very well with owl's class hierarchies in which an instance
> can be of many types:
> 
> http://clojure.org/
> 
> here is the specification for the FOAF (friend of a friend) ontology
> as an example:
> http://xmlns.com/foaf/spec/#sec-intro
> 
> here are some biological ontologies, some in owl:
> http://www.obofoundry.org/
> 
> these are some sites using the technology today:
> 
> http://dbpedia.org/
> http://en.wikipedia.org/wiki/DBpedia
> http://www.freebase.com/
> http://en.wikipedia.org/wiki/Freebase
> 
>> I would be interested in hearing more about owl and possibly
>> contributing to a PC knowledgebase project using owl as a starting point.
> 
> great! a good way to get a hands on start is to read/work through protege
> manual: http://www.co-ode.org/resources/tutorials/ProtegeOWLTutorial.pdf
> using the latest owl protege 4:
> http://protege.stanford.edu/download/registered.html#p4
> 
> the learning curve is relatively steep but i see rich rewards at the top of it.
> i think that in a month or so i will be ready to start collaborating on
> ontologies and another month or two after that to start developing some
> code for a social network/pcdb project.
> 
>> This is fascinating. Googling ontology gave me some ideas. I will share
>> these in another post after I have absorbed the following:
> 
> i look forward to hearing your thoughts.
> 
>>  From Wikipedia:
>> "Ontology ...
> 
> the philosophical basis is fascinating as you say but this is another
> one of those terms
> hijacked by computer science which has taken on a more specific
> concrete meaning.
> i think one reason for slow adoption of semantic web technologies is
> that things like
> ontologies are made to seem more impenetrable than they need to be.
> the first book i
> listed above really clears things up nicely. so far i find OWL &
> SPARQL much more
> intuitive & satisfying on a practical level than DDLs and SQL.
> 
> http://en.wikipedia.org/wiki/Ontology_%28information_science%29
> http://en.wikipedia.org/wiki/Web_Ontology_Language
> http://en.wikipedia.org/wiki/SPARQL
> 
> cheers,
> _c
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