The PSM Librarian:
Download Area
The core PSM Librarian tab plugin
PSM reuse experiments
Additional PSM libraries
The core PSM Librarian Tab plugin
New: Release for Protégé version
3.1
Download the PSM Librarian Tab plugin archive for Protégé
version 3.1: edu.stanford.smi.protegex.psm.zip.
- Unzip the archive in your plugins directory.
- Instructions and base projects are included in the archive.
- Note that the default
<psm_tab> folder is now
C:\Program Files\Protege_3.1\plugins\edu.stanford.smi.protegex.psm\psm_tab_projects
on Windows, or
/Applications/Protege_3.1/plugins/edu.stanford.smi.protegex.psm/psm_tab_projects
on Mac OSX).
Release for Protégé version 3.0
Download the PSM Librarian Tab plugin archive for Protégé
version 3.0: edu.stanford.smi.protegex.psm.zip.
- Unzip the archive in your plugins directory.
- Instructions and base projects are included in the archive.
- Note that the default
<psm_tab> folder is now
C:\Program Files\Protege_3.0\plugins\edu.stanford.smi.protegex.psm\psm_tab_projects
on Windows, or
/Applications/Protege_3.0/plugins/edu.stanford.smi.protegex.psm/psm_tab_projects
on Mac OSX).
Release for Protégé version 2.1
Download the PSM Librarian Tab plugin archive for Protégé
version 2.1: edu.stanford.smi.protegex.psm.zip.
- Unzip the archive in your plugins directory.
- Instructions and base projects are included in the archive.
- Note that the default
<psm_tab> folder is now
C:\Program Files\Protege_2.1\plugins\edu.stanford.smi.protegex.psm\psm_tab_projects
on Windows, or
/Applications/Protege_2.1/plugins/edu.stanford.smi.protegex.psm/psm_tab_projects
on Mac OSX).
Release for Protégé version 1.9
This version of the PSM Librarian tab plugin is compatible with Protégé-2000 version
1.7 and higher, and has been tested on Mac OS X and Windows XP platforms. The
plugin is bundled in an archive file (psmtab_1.9.zip)
that contains:
- A set of Java archive files, to run the PSM Librarian tab
itself and the domain-to-PSM mapping interpreter;
- A set of Protégé projects, that are needed to operate the PSM Librarian
tab, including the UPML
library-modeling ontology and the generic domain-to-PSM mapping ontology;
- Customized Protégé execution scripts (for Mac OS X
and for Windows) to run Protégé with parameters appropriate
for operating the PSM Librarian tab (note that you will not be able to operate
the domain-to-PSM mapping interpreter from within the PSM Librarian tab if
you run Protégé using the regular
protege-2000
executable file).
To install the PSM Librarian tab, simply unzip the contents of the archive and
copy the whole file structure into your Protege-2000 installation folder or follow
the step-by-step instructions given in the installation
notes (also included in the archive). In particular, note that because of
the current way in which Protégé handles project inclusion, ALL Protégé files
related to the PSM tab need to be saved in the same <psm_tab>
folder.
To enable and use the PSM Librarian tab on one of your Protégé projects,
run Protégé using the above-mentioned execution script that corresponds
to your operating system, open your project, go to the Project|Configure
panel and add a checkmark on the PSMTab line. After you close the
configuration panel, you should see the PSM tab displayed next to the other Protégé
tabs. See the PSM tab documentation for
details about using the PSM tab.
Important notes about the PSM Librarian tab:
- It is intended for users who have a relatively good practice of Protégé
and who understand the principles of the domain-to-PSM mapping activity, as
outlined in the documentation and
detailed in related publications.
- It assumes that problem-solving methods and other knowledge components are
modeled in libraries with the Unified
Problem-solving Method development Language (UPML). See the documentation
for more details.
- It does not yet comply with the latest version of our recently reworked
domain-to-PSM mapping ontology, although this enhancement is the highest on
our priority list. Serious users should remain aware that next versions of
the PSM Librarian tab will support the new mapping ontology instead of the
current one, although backwards compatibility will be provided as much as
possible. (Note that the mapping interpreter shipped with the releases actually
already processes the current and new mapping ontologies transparently.)
- It does not yet support the actual activation (i.e., execution) of the configured
PSM with case data. The configured PSM can be executed outside of the PSM
Librarian tab, using a console window or execution environment that is appropriate
for the PSM's implementation.
The source code of the PSM Librarian tab is available on request at crubezy@smi.stanford.edu.
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PSM reuse experiments
As a primary resource, we have created a sample PSM library, the Protégé
PSM Library, that contains (partial) UPML descriptions of the PSMs that
we have studied as part of our research on PSM reuse. In particular, we have
conducted several experiments with the propose-and-revise
and protean PSMs, applying them for different
domain tasks. The PSM Librarian tab allows you to load the Protégé
PSM Library, as well as inspect and replay some of our experiments. See
also related publications for published
details of our experiments.
Download the Protégé PSM library (see installation
notes for details about making those files available to the PSM Librarian tab):
Note: We are currently updating the PSM experiments
with a re-worked version of the mapping ontology. We will make these files available
as soon as possible (for Protégé version 3.1).
The propose-and-revise PSM
A well-known
PSM is propose-and-revise, a generic constraint-satisfaction method
that has been used to tackle domain tasks as diverse as: computing a viable
elevator design, managing mechanical-ventilator therapy, prescribing antiretroviral
drug therapy for HIV, and predicting plausible configurations of helices in
a ribosome strand.
The PSM Librarian tab allows you to inspect and re-play our experiments in configuring
the generic propose-and-revise PSM both for elevator configuration
and for ribosome-conformation prediction. To run these demo experiments, you
need to download the PnR_psm.zip
archive that contains additional Protégé project files, namely:
- The method ontology of the propose-and-revise
PSM (separate from the UPML-modeled Protégé PSM Library)
- The domain knowledge bases of elevator design
and of ribosome topology
- The 2 mappings projects that define the mapping relations
between elevator-design / ribosome-topology concepts to
propose-and-revise concepts
- The 2 method knowledge bases (i.e., instances of the propose-and-revise
concepts) that result from running the mapping interpreter with the above
files
Download the propose-and-revise experiments archive
(see installation notes for details about making those files available to the
PSM Librarian tab):
The protean PSM
The protean method also encodes a generic constraint-satisfaction algorithm
that was developed originally for the domain task of predicting plausible configurations
of helices in a ribosome strand. Using our generic domain-to-method mapping
approach, we were able to compare it to the propose-and-revise PSM.
The PSM Librarian tab allows you to inspect and re-play our configuration of
the protean PSM for ribosome-conformation prediction. To run this demo
experiment, you need to download the protean_psm.zip
archive that contains additional Protégé project files, namely:
- The method ontology of the protean PSM (external
to the UPML-modeled Protégé PSM Library)
- The domain knowledge base of ribosome topology
(same as for propose-and-revise)
- The mappings project with mapping relations from ribosome-topology
concepts to protean concepts
- The method knowledge base (i.e., instances of the protean
classes) that results from running the mapping interpreter with the above
files
Download the protean experiments archive (see installation
notes for details about making those files available to the PSM Librarian tab):
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Additional PSM libraries
A few additional libraries have been studied within the PSM Librarian/UPML framework:
If you want to add your own PSM library to the list of libraries that are available
to the PSM Librarian tab, you need to model your library with the UPML
editor and save it as <your-library-name>-library.pprj
under your <psm_tab>
folder.
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