Hi,
Did they use WebProtege for this? Can you suggest something different?
BioPortal is older, it had limited editing functionality since
2008-2009, they included a stripped down version of webProtege about ~ a
year ago. It has a lot of added functionality like creating mappings
between different ontologies and recommending mappings. It is open
source [3] but it's a monster, hence they offer it as a preconfigured VM
(a lot of rails code...). I'm not suggesting we use it but it's good to
look at it for ideas, they have a huge community (for SW standards) that
develops some of the largest ontologies.
We can use a webProtege gui for this that shows only e.g. labels and
comments. Experts can use the usual protege tabs.
An alternative is to use OntoWiki
Limiting the functionality for novices is a good approach. I'd also
like to keep the option of editing the ontology from Mediawiki, if possible.
WebProtege is on a short notice and maybe we should give an extra
thought about it.
Mappings and ontology is a lot of work for a student and maybe we
should break it into safe independent tasks.
I have a student digging trough the medawiki API in order to add batch
updates for the labels and mappings, we're almost done with label
updates. We'll document what we find in order to make reduce the
workload on GSoC students. If the API isn't to badly designed, we can
try to integrate WebProtege by API calls. Alternatives would be to do it
directly by editing the database or move everything to something like
OntoWiki (which I don't know how long it will take), or make our own
mappings/ontology service and extend the webProtege interface to handle
everything.
Cheers,
Alexandru
[1] https://bioportal.bioontology.org/
[2] http://www.bioontology.org/BioPortal
[3]
http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance
On 02/20/2014 09:15 PM, Dimitris Kontokostas wrote:
On Thu, Feb 20, 2014 at 2:03 PM, Alexandru Todor
<[email protected] <mailto:[email protected]>> wrote:
Hi,
I've been working with BioPortal for a couple of years, and they
implement a similar approach to webProtege which has been quite
successful.
Did they use WebProtege for this? Can you suggest something different?
We will definetly have to go the way of an online, collaborative
ontology editor one way or another, either by improving the
mappings wiki or adopting a full blown ontology editor. However I
fear that webProtege has too many features and should prove hard
for novices to use, which might increase the learning curve.
We can use a webProtege gui for this that shows only e.g. labels and
comments. Experts can use the usual protege tabs.
An alternative is to use OntoWiki
i agree with JC that this is a lot of work and we should focus on
tests but we are short on hands and GSoC is a chance to get at least
something done.
WebProtege is on a short notice and maybe we should give an extra
thought about it.
Mappings and ontology is a lot of work for a student and maybe we
should break it into safe independent tasks.
1) move only the ontology in WebProtege or OntoWiki (or something
better than Wikitext): Basically set up an ontology editing service
with a couple of simple interfaces for editing. Also create a mw bot
that updates the mappings wiki only with the basic stuff we have
already (labels, comments, hierarchy, equivalent class/property). If
there is time (which probably will be) change the ontology generation
code to read both from RDF.
This keeps us compatible with the existing infrastructure if we see
that it doesn't work out.
2) Extend the server module to generate rdf for the existing mappings
/ statistics and build a few visualizations / stats around it
(basically extend Andrea's idea)
If we see that this performs well we can consider maintaining the
mappings in RDF.
Comments?
Cheers,
Alexandru
On 02/20/2014 10:07 AM, Dimitris Kontokostas wrote:
Hi,
Jens Lehmann suggested to move the ontology editing to webProtege
[1].
It will save a lot of effort trying to support more owl axioms
(defining new wiki syntax, parsing it properly etc.)
This solves many problems but creates a few more, like
integration with the core module and syncing with the mappings
definitions (server module). However, this has some good potential.
Taking this a little further we could also use web protege for
the mappings DB. I haven't looked at it in too detail but we can
define custom editing forms [2] which also solves the mappings
web editor problem.
The plus to that is that we have the mappings directly in RDF and
if we publish the server statistics in rdf too, we can have many
cool visualizations & reports through SPARQL.
(This also creates some syncing problems with Live but we can
probably overcome them with some effort)
WDYT?
[1] http://protegewiki.stanford.edu/wiki/WebProtege
[2] http://protegewiki.stanford.edu/wiki/WebProtegeLayoutConfig
--
Dimitris Kontokostas
Department of Computer Science, University of Leipzig
Research Group: http://aksw.org
Homepage:http://aksw.org/DimitrisKontokostas
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