Open Semantic Framework 3.2 Released

Frederick Giasson
Structured Dynamics is happy to announce the immediate availability of the Open Semantic Framework version 3.2. This is the second important OSF release in a month and a half. triple_120

This new major release of OSF changes the way the web services communicate with the triple store. Originally, OSF web services were using a ODBC channel to communicate with the triple store (Virtuoso). This new release uses the SPARQL HTTP endpoints of the triple store to send queries to it. This is the only changes that occurs in this new version, but as you will see bellow, this is a major one.

Why switching to HTTP?

The problem with using ODBC as the primary communication channel between the OSF web services and the triple store is that it was adding a lot of complexity into OSF. Because the UnixODBC drivers that are shipped with Ubuntu had issues with Virtuoso, we had to use the iODBC drivers to make sure that everything was working properly. This situation forced us to recompile PHP5 such that it uses iODBC instead of UnixODBC as the ODBC drivers for PHP5.

This was greatly complexifying the deployment of OSF since we couldn’t use the default PHP5 packages that shipped with Ubuntu, but had to maintain our own ones that were working with iODBC.

The side effect of this is that system administrators couldn’t upgrade their Ubuntu instances normally since PHP5 needed to be upgraded using particular packages created for that purpose.

Now that OSF doesn’t use ODBC to communicate with the triple store, all this complexity goes away since no special handling is now required. All of the default Ubuntu packages can be used like system administrators normally do.

With this new version, the installation and deployment of a OSF instance has been greatly simplified.

Supports New Triple Stores

Another problem with using ODBC is that it was limiting the number of different triple stores that could be used for operating OSF. In fact, people could only use Virtuoso with their OSF instance.

This new release opens new opportunities. OSF still ships with Virtuoso Open Source as its default triple store, however any triple store that has the following characteristics could replace Virtuoso in OSF:

  1. It has a SPARQL HTTP endpoint
  2. It supports SPARQL 1.1 and SPARQL Update 1.1
  3. It supports SPARQL Update queries that can be sent to the SPARQL HTTP endpoint
  4. It supports the SPARQL 1.1 Query Results JSON Format
  5. It supports the SPARQL 1.1 Graph Store HTTP Protocol via a HTTP endpoint (optional, only required by the Datasets Management Tool)

Deploying a new OSF 3.2 Server

Using the OSF Installer

OSF 3.2 can easily be deployed on a Ubuntu 14.04 LTS server using the osf-installer application. It can easily be done by executing the following commands in your terminal:

[cc lang=”bash”]
[raw]
mkdir -p /usr/share/osf-installer/

cd /usr/share/osf-installer/

wget https://raw.github.com/structureddynamics/Open-Semantic-Framework-Installer/3.2/install.sh

chmod 755 install.sh

./install.sh

./osf-installer –install-osf -v
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[/cc]

Using a Amazon AMI

If you are an Amazon AWS user, you also have access to a free AMI that you can use to create your own OSF instance. The full documentation for using the OSF AMI is available here.

Upgrading Existing Installations

It is not possible to automatically upgrade previous versions of OSF to OSF 3.2. It is possible to upgrade a older instance of OSF to OSF version 3.2, but only manually. If you have this requirement, just let me know and I will write about the upgrade steps that are required to upgrade these instances to OSF version 3.2.

Security

Now that the triple store’s SPARQL HTTP endpoint requires it to be enabled with SPARQL Update rights, it is more important than ever to make sure that the SPARQL HTTP endpoint of the triple store is only available to the OSF web services.

This can be done by properly configuring your firewall or proxy such that only local traffic, or traffic coming from the OSF web service processes, can reach the endpoint.

The SPARQL endpoint that should be exposed to the outside World is OSF’s SPARQL endpoint, which adds an authentication layer above the triple store’s endpoint, and restricts potentially armful SPARQL queries.

Conclusion

This new version of the Open Semantic Framework greatly simplifies its deployment and its maintenance. It also enables other triple stores that exist on the market to be used for OSF instead of Virtuoso Open Source.

Open Semantic Framework 3.1 Released

Frederick Giasson
Structured Dynamics is happy to announce the immediate availability of the Open Semantic Framework version 3.1. This new version includes a set of fixes to different components of the framework in the last few months. The biggest change is deployment of OSF using Virtuoso Open Source version 7.1.0. triple_120

We also created a new API for Clojure developers called: clj-osf. Finally we created a new Open Semantic Framework web portal that better describes the project and is hopefully easier to use and more modern.

Quick Introduction to the Open Semantic Framework

What is the Open Semantic Framework?

The Open Semantic Framework (OSF) is an integrated software stack using semantic technologies for knowledge management. It has a layered architecture that combines existing open source software with additional open source components. OSF is designed as an integrated content platform accessible via the Web, which provides needed knowledge management capabilities to enterprises. OSF is made available under the Apache 2 license.

OSF can integrate and manage all types of content – unstructured documents, semi-structured files, spreadsheets, and structured databases – using a variety of best-of-breed data indexing and management engines. All external content is converted to the canonical RDF data model, enabling common tools and methods for tagging and managing all content. Ontologies provide the schema and common vocabularies for integrating across diverse datasets. These capabilities can be layered over existing information assets for unprecedented levels of integration and connectivity. All information within OSF may be powerfully searched and faceted, with results datasets available for export in a variety of formats and as linked data.

A new Open Semantic Framework website

The OSF 3.1 release also triggered the creation of a new website for the project. We wanted something leaner and more modern and that is what I think we delivered. We also reworked the content, we wrote about a series of usecases 1 2 3 4 5 6 and we better aggregated and presented information for each web service endpoint.

A new OSF sandbox

We also created an OSF sandbox where people can test each web service endpoint and test how each functionality works. All of the web services are open to users. The sandbox is not meant to be stable considering that everybody have access to all endpoints. However, the sandbox server will be recreated on a periodic basis. If the sandbox is totally broken and users experiment issues, they can always request a re-creation of the server directly on the OSF mailing list.

Each of the web service pages on the new OSF portal has a Sandbox section where you see some code examples of how to use the endpoint and how to send requests to the sandbox. Here are the instructions to use the sandbox server.

A new OSF API for Clojure: clj-osf

The OSF release 3.1 also includes a new API for Clojure developers: clj-osf.

clj-osf is a Domain Specific Language (DSL) that should lower the threshold to use the Open Semantic Framework.

To use the DSL, you only have to configure your application to use a specific OSF endpoint. Here is an example of how to do this for the Sandbox server:

[cc lang=”lisp”]
[raw]
;; Define the OSF Sandbox credentials (or your own):
(require ‘[clj-osf.core :as osf])

(osf/defosf osf-test-endpoint {:protocol :http
:domain “sandbox.opensemanticframework.org”
:api-key “EDC33DA4D977CFDF7B90545565E07324”
:app-id “administer”})

(osf/defuser osf-test-user {:uri “http://sandbox.opensemanticframework.org/wsf/users/admin”})
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Then you can send simple OSF web service queries. Here is an example that sends a search query to return records of type foaf:Person that also match the keyword “bob”:

[cc lang=”lisp”]
[raw]
(require ‘[clj-osf.search :as search])

(search/search
(search/query “bob”)
(search/type-filters [“http://xmlns.com/foaf/0.1/Person”]))
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A complete set of clj-osf examples is available on the OSF wiki.

Finally the complete clj-osf DSL documentation is available here.

A community effort

This new release of the OSF Installer is another effort of the growing Open Semantic Framework community. The upgrade of the installer to deploy the OSF stack using Virtuoso Open Source version 7.1.0 has been created by William (Bill) Anderson.

Deploying a new OSF 3.1 Server

Using the OSF Installer

OSF 3.1 can easily be deployed on a Ubuntu 14.04 LTS server using the osf-installer application. It can easily be done by executing the following commands in your terminal:

[cc lang=”bash”]
[raw]
mkdir -p /usr/share/osf-installer/

cd /usr/share/osf-installer/

wget https://raw.github.com/structureddynamics/Open-Semantic-Framework-Installer/3.1/install.sh

chmod 755 install.sh

./install.sh

./osf-installer –install-osf -v
[/raw]
[/cc]

Using a Amazon AMI

If you are an Amazon AWS user, you also have access to a free AMI that you can use to create your own OSF instance. The full documentation for using the OSF AMI is available here.

Upgrading Existing Installations

Existing OSF installations can be upgraded using the OSF Installer. However, note that the upgrade won’t deploy Virtuoso Open Source 7.1.0 for you. All the code will be upgraded, but Virtuoso will remain the version you were last using on your instance. All the code of OSF 3.1 is compatible with previous versions of Virtuoso, but you won’t benefit the latest improvements to Virtuoso (in terms of performances) and its latest SPARQL 1.1 implementations. If you want to upgrade Virtuoso to version 7.1.0 on an existing OSF instance you will have to do this by hands.

To upgrade the OSF codebase, the first thing is to upgrade the installer itself:

[cc lang=”bash”]
[raw]
# Upgrade the OSF Installer
./usr/share/osf-installer/upgrade.sh
[/raw]
[/cc]

Then you can upgrade the components using the following commands:

[cc lang=”bash”]
[raw]
# Upgrade the OSF Web Services
./usr/share/osf-installer/osf –upgrade-osf-web-services=”3.1.0″

# Upgrade the OSF WS PHP API
./usr/share/osf-installer/osf –upgrade-osf-ws-php-api=”3.1.0″

# Upgrade the OSF Tests Suites
./usr/share/osf-installer/osf –upgrade-osf-tests-suites=”3.1.0″

# Upgrade the Datasets Management Tool
./usr/share/osf-installer/osf –upgrade-osf-datasets-management-tool=”3.1.0″

# Upgrade the Data Validator Tool
./usr/share/osf-installer/osf –upgrade-osf-data-validator-tool=”3.1.0″
[/raw]
[/cc]

Major UMBEL Release: 1.10

Frederick Giasson
After more than 2 years, we are now finally releasing a new version of the UMBEL ontology and reference concept structure. One might think that we haven’t worked on the project all that time, but it is not strictly true. umbel_logo_260_160

We did improve the mapping to external vocabularies/ontologies, we worked much on linking Wikipedia pages to the UMBEL structure, but we haven’t had time to release a new version… until now!

For people new to the ontology, UMBEL is a general reference structure of about 28,000 reference concepts, which provides a scaffolding to link and interoperate other datasets and domain vocabularies. Its main purpose is to have a coherent conceptual structure that we can use to link and interoperate unrelated data sources. But it can also be used as a conceptual structure to be used to describe information like any other ontologies.

What is new with the ontology?

The major change in UMBEL is not the structure itself, but the piece of software used to generate it. In fact, the previous system we developed for generating UMBEL was about 7 years old. It was a bit clunky and really not that easy to work with.

Based on our prior experience with UMBEL, we choose to dump it and to create a brand new UMBEL reference structure generator. This new generator has been developed in Clojure and uses the latest version of the OWL API. It makes the management of the structure much simpler, which means that it will help in releasing new UMBEL version more regularly. We also have a suite of tools to analyze the structure and to pinpoint possible issues.

Other than that, we updated the Schema.org, DBpedia Ontology and Geonames Ontology mappings to UMBEL. This is a major effort undertaken by Mike for this new version. The mappings are composed of:

  • 754 rdfs:subClassOf relationships between Schema.org classes and UMBEL reference concepts
  • 688 rdfs:subClassOf relationships between DBpedia Ontology classes and UMBEL reference concepts
  • 682 rdfs:subClassOf relationships between Geonames Ontology classes and UMBEL reference concepts

These new mappings will help manage data instances that use these external ontologies/schemas in a broader conceptual structure (which is UMBEL). This enables us to be able to reason over this external data using the UMBEL conceptual structure even if these external data sources didn’t originally use UMBEL to describe their data. That is one of the main features of UMBEL.

We also managed to add a few hundred UMBEL reference concepts. Most of them were added to create these new linkages with the external ontologies. Others have been added because they were improving the overall structure.

A few weeks back, we found an issue with the umbel:superClassOf assignations, which has also now been resolved in version 1.10.

In the previous versions of UMBEL, the preferred labels were not unique. There were a few hundred of the concepts that were having the same preferred labels. This was not an issue in itself, but this was not a best practice to create an ontology. We managed to remove all these non-distinct preferred labels and to make all of them unique.

We added a few skos:broader and skos:narrower relationships between some of the reference concepts. In the previous versions, all the relationships were skos:broaderTransitive and skos:narrowerTransitive properties only.

Finally we made sure that the entire UMBEL reference structure (Core + the Geo module) was absent of any inconsistencies and that it was satisfiable.

What is new with the portal and web services?

This new version of UMBEL also led us to create a few new features to the UMBEL website. The most apparent feature is the new External Linkage section that may appear at the top of a reference concept page (obviously, it will not appear if there are no external links for a given reference concept). This section shows you the linkage between the UMBEL reference concept and other external classes:

umbel_linkage_module

Another feature that you will notice on this screenshot is the Core blue tag at the right of the URI of the reference concept. This tag is used to tell you from where the reference concept is coming. Another tag that you may encounter is the green Geo tag, which tells you that the reference concept comes from the UMBEL Geo module. The same tags appear in the search resultsets:

search_modules

What is next?

Because UMBEL is an ontology, by nature it will always evolve over time. Things change, and the way we see the World can always improve.

For the next version of UMBEL, we will analyze the entire UMBEL reference concept structure using different algorithms, heuristics and other techniques to analyze the conceptual structure and to find conceptual gaps in it. The goal of this analysis is to tighten the structure, to have a better conceptual hierarchy and a more fine-grained one.

Other things we want to do in other coming versions are to improve the Super Types structure of UMBEL. As you may know, many of the Super Types are non disjoint because some of the concepts belong to multiple Super Type classes. What we want to do here is to create new Super Types classes that are the intersection between two, or more, Super Types that will be used to categorize these concepts that belong to multiple Super Types. That way, we will end-up with a better classification of the UMBEL reference concepts from a Super Types standpoint.

Another thing we want to do related to the UMBEL web services is to update them such that you can query the linkage to the external ontologies. For now, you can see the linkage when querying the sub-classes and super-classes of a reference concept. But you cannot query the web services this way: give me all the sub-classes-of the http://schema.org/FireStation class, for example.

As you can see, the UMBEL ontology and web services will continue to evolve over time to enable new ways to leverage the conceptual structure and external data sources.

Open Semantic Framework 3.0.1 Released

Frederick Giasson
I am happy to announce the immediate availability of the Open Semantic Framework version 3.0.1. This new version includes a set of fixes to different components of the framework in the last few months.The biggest addition is the new OSF Installer which will deploy OSF on Ubuntu LTS 14.04 servers. triple_120

A Community Effort

This new release of the OSF Installer is an effort of the growing Open Semantic Framework community. The upgrade of the installer to deploy the OSF stack on the lastest Ubuntu Long Term Support (LTS) version 14.04 has been created by William (Bill) Anderson.

Samar Acharya also suggested to decouple the PHP5 Debian packages from the core OSF Installer repository to cope with the support of future version of Ubuntu or other Linux distributions. This led to the creation of the new OSF-Installer-Ext repository, which is only used to host these distribution specific files like the PHP5 Debian files.

Upgrading Existing Installations

Existing OSF installations can be upgraded using the OSF Installer. The first thing is to upgrade the installer itself:

[cc lang=”bash”]
[raw]
# Upgrade the OSF Installer
./usr/share/osf-installer/upgrade.sh
[/raw]
[/cc]

Then you can upgrade the components using the following commands:

[cc lang=”bash”]
[raw]
# Upgrade the OSF Web Services
./usr/share/osf-installer/osf –upgrade-osf-web-services=”3.0.1″

# Upgrade the OSF WS PHP API
./usr/share/osf-installer/osf –upgrade-osf-ws-php-api=”3.0.1″

# Upgrade the OSF Tests Suites
./usr/share/osf-installer/osf –upgrade-osf-tests-suites=”3.0.1″

# Upgrade the Datasets Management Tool
./usr/share/osf-installer/osf –upgrade-osf-datasets-management-tool=”3.0.1″

# Upgrade the Data Validator Tool
./usr/share/osf-installer/osf –upgrade-osf-data-validator-tool=”3.0.1″
[/raw]
[/cc]

Big Structures: Where the Semantic Web Meets Artificial Intelligence

Frederick Giasson

Mike Bergman just published the second part1 of his series of blog posts that summarize the evolution of the Semantic Web in the last decade, and how our experience of the last 7 years of research in that field has led to these observations.

The second part of that series is: Big Structure: At The Nexus of Knowledge Bases, the Semantic Web and Artificial Intelligence.

He continues to outline some issues with the Semantic Web, but more importantly how it fits in a much broader ecosystem, namely KBAI (Knowledge Based AI). He explains the difference between data integration and data interoperability and how these problems could benefit leveraging a sub-set of the Artificial Intelligence domain related to data interoperability:


ai_data_interoperability
These two blog posts set the foundation and the direction where Structured Dynamics is heading in the coming years and where we will focus our research projects and how we will help our clients with their data integration and interoperability issues.

We welcome hearing from you!