Tag: RDF

How to (properly) publish a vocabulary or ontology in the web (part 5 of 6)

This week I want to quickly introduce how and why you should include a license in your vocabulary and documentation. Since this subject has been already dealt with, I am mainly going to be providing links to posts describing these matters in detail.

Why should you add a license to your ontologies? Because if others want to reuse your vocabulary or ontology, the license will clarify what are they allowed doing with it according to the law (for instance, if they have to give attribution to your work). Remember that you are the intellectual author and you have the rights over the resource being published. See more details and types of licenses here.

How can you specify a license? You can add it as a semantic description to the ontology/vocabulary. Two widely used properties are dc:rights and dc:license, from the Dublin Core vocabulary. These properties can be used to describe the OWL file being produced, or in the documentation itself with annotations in RDF-a or microdata. See how it can be done here.

Spend some time analyzing which is the most appropriate license for your work. It may help you and many others in the future! If you are confused on which license to use, this is the one which we use on our vocabularies: http://creativecommons.org/licenses/by-nc-sa/2.0/.

This is part of a tutorial divided in 7 parts:

  1. Overview of the tutorial.
  2. (Reqs addressed A1(partially), A2, A3, A4, P1) Publishing your vocabulary at a stable URI using RDFS/OWL.
  3. (Reqs addressed P2, P3). How to design a human readable documentation.
  4. Extra: A tool for creating html readable documentation
  5. (Reqs addressed P4). Derreferencing your vocabulary
  6. (Reqs addressed A1 (partially)). Dealing with the license. (this post)
  7. (Reqs addressed A5, P5). Reusing other vocabularies. (To appear)
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How to (properly) publish a vocabulary or ontology in the web (part 4 of 6)

(Update: purl.org seems to have stopped working. I recommend you to have a look at my latest post for doing content negotiation with w3id)

After a long summer break in blogging, I’m committed to finishing this tutorial. In this post I’ll explain why and how to dereference your vocabulary when publishing it in the Web.

But first, why should you dereference your vocabulary? In part 2 I showed how to create a permanent URL (purl) and redirect it to the ontology/vocabulary we wanted to publish (in my case it was http://purl.org/net/wf-motifs). If you followed the example you would have seen that now when you enter the purl you created in the web browser it redirects you to the ontology file. However if you enter http://purl.org/net/wf-motifs you will be redirected to the html documentation of the ontology. When entering the same URL in Protégé, the ontology file will be loaded in the system. By dereferencing the motifs vocabulary I am able to choose what to deliver depending on the type of request received by the server on a single resource: RDF files for applications and nice html pages for the people looking for information about the ontology (structured content for machines, human readable content for users).

Additionally, if you have used the tools I suggested in previous posts, when you ask for a certain concept the browser will take you to the exact part of the document defining it. For example, if you want to know the exact definition for the concept “FormatTransformation” in the Workflow Motif ontology, then you can paste its URI (http://purl.org/net/wf-motifs#FormatTransformation) in the web browser. This makes the life easier for users when browsing and reading your ontology.

And now, how do you dereference your vocabulary? First, you should set the purl redirection as a redirection for Semantic Web resources (add a 303 redirection instead a 302, and add the target URL where you plan to do the redirection). Note that you can only dereference a resource if you control the server where the resources are going to be delivered. The screenshot below shows how it would look in purl for the Workflow Motifs vocabulary. http://vocab.linkeddata.es/motifs is the place our system admin decided to store the vocabulary.

Purl redirection
Purl redirection

Now you should add the redirection itself. For this I always recommend having a look into the W3C documents, which will guide you step by step on how to achieve this. In this case in particular we followed http://www.w3.org/TR/swbp-vocab-pub/#recipe3, which is a simple redirection for vocabularies with a hash namespace. You have to create an htaccess file similar to the one pasted below. In my case the index.html file has the documentation of the ontology, while motif-ontology1.1.owl contains the rdf/xml encoding. If a ttl file exists, you can also add the appropriate content negotiation. All the files are located in a folder called motifs-content, in order to avoid an infinite loop when dealing with the redirections of the vocabulary:

# Turn off MultiViews
Options -MultiViews

# Directive to ensure *.rdf files served as appropriate content type,
# if not present in main apache config
AddType application/rdf+xml .rdf
AddType application/rdf+xml .owl
#AddType text/turtle .ttl #<---Add if you have a ttl serialization of the file

# Rewrite engine setup
RewriteEngine On
RewriteBase /def

# Rewrite rule to serve HTML content from the vocabulary URI if requested
RewriteCond %{HTTP_ACCEPT} !application/rdf\+xml.*(text/html|application/xhtml\+xml)
RewriteCond %{HTTP_ACCEPT} text/html [OR]
RewriteCond %{HTTP_ACCEPT} application/xhtml\+xml [OR]
RewriteCond %{HTTP_USER_AGENT} ^Mozilla/.*
RewriteRule ^motifs$ motifs-content/index.html

# Rewrite rule to serve RDF/XML content from the vocabulary URI if requested
RewriteCond %{HTTP_ACCEPT} application/rdf\+xml
RewriteRule ^motifs$ motifs-content/motif-ontology1.1.owl [R=303]

# Rewrite rule to serve turtle content from the vocabulary URI if requested
#RewriteCond %{HTTP_ACCEPT} text/turtle
#RewriteRule ^motifs$ motifs-content/motifs_ontology-ttl.ttl [R=303]

# Choose the default response
# ---------------------------

# Rewrite rule to serve the RDF/XML content from the vocabulary URI by default
RewriteRule ^motifs$ motifs-content/motif-ontology1.1.owl [R=303]

Note the redirections when the owl is being requested. If you have a slash vocabulary, you will have to follow the aforementioned W3C document for further instructions.

Now it is time to test that everything works. The easiest way is just to paste the URI of the ontology in Protégé and in your browser and check that in one case it loads the ontology properly and in the other you can see the documentation. Another possibility is to use curl like this: curl -sH “Accept: application/rdf+xml” -L http://purl.org/net/wf-motifs (for checking that the rdf is obtained) or curl -sH “Accept: text/html” -L http://purl.org/net/wf for the html.

Finally, you may also use the Vapour validator to check that you have done the process correctly. After entering your ontology URL, you should see something like this:

Vapur validation
Vapur validation

Congratulations! You have dereferenced your vocabulary successfully 🙂

This is part of a tutorial divided in 7 parts:

  1. Overview of the tutorial.
  2. (Reqs addressed A1(partially), A2, A3, A4, P1) Publishing your vocabulary at a stable URI using RDFS/OWL.
  3. (Reqs addressed P2, P3). How to design a human readable documentation.
  4. Extra: A tool for creating html readable documentation
  5. (Reqs addressed P4). Derreferencing your vocabulary (this post)
  6. (Reqs addressed A1 (partially)). Dealing with the license. (To appear)
  7. (Reqs addressed A5, P5). Reusing other vocabularies. (To appear)

How to (properly) publish a vocabulary or ontology in the web (part 2 of 6)

This part of the tutorial explains how to publish your vocabulary at a stable URI using RDFS/OWL. In order to make things easier, I’ll illustrate each step of this part of the tutorial with an example. The steps to follow are further described below:

1)      Select the name of your vocabulary/ontology. Easy, right? In my case I want to publish an ontology encoding the workflow motif catalogue we describe in this paper, so the name I have chosen is “The workflow motif ontology” (wf-motifs to keep it short).

2)      Select the proper URI to publish your vocabulary. Now that we know how we want to name our vocabulary, things start to get trickier. Which URI do we choose? How do we ensure that it is not going to change?
The URI you choose for your ontology should be permanent and defined in a domain you control. The rationale behind this is simple: imagine that somebody is reusing the concepts defined in your ontology and you change its URI. The person reusing your ontology will no longer know the proper definitions and semantics of the reused term.
Since I assume that most of the people reading this are not willing to pay for a new domain each time a new ontology is published, I recommend defining the URI of your vocabularies/ontologies in http://purl.org. PURL stands for “persistent uniform resource locator”, and they are widely used to give persistent URIs to resources. Once you register in the page, the process is really simple. You define a new domain, wait for the approval and create the URI for your ontology. In my case it is: http://purl.org/net/wf-motifs.

EDIT: If you are interested in having more control on your redirections, w3id is a better alternative to purl. Have a look at my post for more information on how to set it up.

Note 1: If you create the name under the /net/ domain things will go faster, since it is the default domain. Otherwise they’ll have to approve the domain AND the name of your vocabulary/ontology.

Note 2: Someone could argue that by speaking to the system admin of your enterprise/university you can obtain the vocabulary URI as well. However, depending on who you are and the ontology you are working on, the URI they suggest could be something like: mayor2.dia.fi.upm.es/oeg-upm/files/dgarijo/wf-motifs. This is perfectly fine, but this looks more like the place where my .owl will finally be stored. If my file has to be moved, my URI will change. Using purl ensures the URI will be permanent, and that I have control over it.

3)      Create the ontology in RDF/OWL: There are several editors to create vocabularies/ontologies and their properties according to the W3C standards: Protégé, the NeOn Toolkit, TopBraid Composer, etc. The one I’m most familiar to is Protégé, which is free to install and use (they say that TopBraid is very good, but since the license is quite expensive I haven’t been able to test it).  Once you have installed your editor you just have to change the base URI of the ontology (Ontology IRI in Protégé) with the one you registered as a PURL. Protégé will use a hash (“#”) by default to identify the classes and properties you declare in the vocabulary/ontology. You can use a slash (“/”) for this purpose as well.

Hash versus slash debate: There has been a long discussion regarding the usage of “/” vs “#”. If you are not sure about which one is the best for your vocabulary/ontology, here is a tip: if your ontology will be huge and will be divided in many different modules, use “/”. Otherwise use “#”. It is easier to set up and will make it easier to point to the right spot in the documentation.

Returning back to the example, this is how my ontology IRI looks like:
http://purl.org/net/wf-motifs#
and a sample class will be
http://purl.org/net/wf-motifs#Motif

4)      Redirect your permanent URI to your vocabulary/ontology file. Once you are done editing your vocabulary/ontology, you have to host the .owl file somewhere. It is not important where you host it, as long as you know that it won’t be deleted. It’s fine if it gets moved, as long as you know where. In my case, I talked to the system admin and he stored the owl file here:
http://vocab.linkeddata.es/motifs/motif-ontology1.1.owl
Finally, we go back to the purl page and we add the basic redirection to the target URL we have just set up. The form looks like this:purl

Now whenever we enter the URI of our ontology, it will be redirected to the OWL file. Congrats!
Note: In my case http://purl.org/net/wf-motifs will take you to the ontology if you load it in Protégé and to the documentation if you load it from the web browser. I’ll explain how to achieve that in part 4 of the tutorial, so don’t worry for the moment.

Note: the steps I propose here are not normative. There may be other ways to achieve what is covered here. This is just a possible way to do it.

This is part of a tutorial divided in 7 parts:

  1. Overview of the tutorial.
  2. (Reqs addressed A1(partially), A2, A3, A4, P1) Publishing your vocabulary at a stable URI using RDFS/OWL. (this post)
  3. (Reqs addressed P2, P3). How to design a human readable documentation.
  4. Extra: A tool for creating html readable documentation.
  5. (Reqs addressed P4). Derreferencing your vocabulary.
  6. (Reqs addressed A1 (partially)). Dealing with the license.
  7. (Reqs addressed A5, P5). Reusing other vocabularies.

How to (properly) publish a vocabulary or ontology in the web (1 of 6)

Vocabularies and ontologies have been developed in the last years for modeling different use cases in heterogeneous domains. These vocabularies/ontologies are often described in journal publications and conferences, which reflect the rationale of the design decisions taken during their development. Now that everyone is talking about Linked Data, I have found myself looking for guidelines to properly publishing my vocabularies on the web, but unfortunately the required documentation is scattered through many different places.

First things first. What do I mean by properly publishing a vocabulary? By that I refer to making it an accessible resource, both human and machine readable, with documentation with examples and with its license specified. In this regard, there have been two initiatives for gathering the requirements I am trying to address in this tutorial: the 5-Star Vocabulary requirements by Bernard Vatant and the AMOR manifesto by Raúl García-Castro. Both of these approaches are based in Tim Berners Lee’s Linked Data 5 star rating, and complement each other. In this tutorial (which will be divided in 5 parts), I will cover possible solutions to address each of their requirements, further described below (quoting the original posts).

Requirements of the AMOR manifesto (A):

  • (A1) The ontology is available on the web (whatever format) but with an open licence
  • (A2) All the above, plus: available as machine-readable structured data (e.g., CycL instead of image scan of a table)
  • (A3) All the above, plus: non-proprietary format (e.g., OBO instead of CycL)
  • (A4) All the above, plus: use open standards from the W3C (RDF Schema and OWL)
  • (A5) All the above, plus: reuse other people’s ontologies in your ontology

– Requirements of the 5 start vocabulary principles (P)

  • (P1)Publish your vocabulary on the Web at a stable URI
  • (P2) Provide human-readable documentation and basic metadata such as creator, publisher, date of creation, last modification, version number
  • (P3) Provide labels and descriptions, if possible in several languages, to make your vocabulary usable in multiple linguistic scopes
  • (P4) Make your vocabulary available via its namespace URI, both as a formal file and human-readable documentation, using content negotiation
  • (P5) Link to other vocabularies by re-using elements rather than re-inventing.

The tutorial will be divided in 5 parts (plus this overview):

  1. Overview of the tutorial.
  2. (Reqs addressed A1(partially), A2, A3, A4, P1) Publishing your vocabulary at a stable URI using RDFS/OWL. (this post)
  3. (Reqs addressed P2, P3). How to design a human readable documentation.
  4. Extra: A tool for creating html readable documentation.
  5. (Reqs addressed P4). Derreferencing your vocabulary.
  6. (Reqs addressed A1 (partially)). Dealing with the license.
  7. (Reqs addressed A5, P5). Reusing other vocabularies.

Annotating your personal page with RDF-a

A couple of weeks ago some members of the OEG and me organized a small tutorial about RDF-a  to the rest of the group (also known as the First OEG RDF-a Collaborative Tripleton). The final goal was to provide an overview and eat our own dog food by annotating our personal web pages with some simple RDF-a statements. The bait, some free pizza:

Participantes enjoying their pizza. It always works
Participants enjoying their pizza. It always works

People were very participative, and we discussed some examples during the tutorial. Given the fact that nobody was an expert in RDF-a, I think that the overall experience was very useful for everyone.
Therefore, if you want to annotate your page with some RDF-a statements, I have prepared a small guideline below listing the main common steps to take into consideration. The guidelines are based on what we discussed on the tutorial and later:

1)      Distinguish your web page from yourself: Don’t use the URL of your home page as your URI. Instead, create a URI for yourself. For example, my personal page is: http://delicias.dia.fi.upm.es/members/DGarijo/. If I want to describe the page (title, creation date, etc), I would use that URL. If I want to add some descriptive statements about myself (name, email, phone, etc.) then I can use http://delicias.dia.fi.upm.es/members/DGarijo/#me. This is a recognized good practice, although you can use any identifier for yourself as long as you control the domain where you create it. Another could have been: http://delicias.dia.fi.upm.es/members/DGarijo/#DanielGarijo

2)      Provide at least a minimum set of statements about yourself: If you provide some information in html for users, why not in RDF-a for machines? Add your name, an image, phone, email, institution, a link to your publications, the institutions you are working for, past and present projects, etc.

3)      Use widely used vocabularies like schema and foaf for describing yourself, Dublin Core to describe the document and, if you want to state the provenance of the document itself, you may even use the PROV standard.

4)      Try to use existent authoritative URIs for the resources you are describing. Linking to other resources is always better than creating your own URIs. If you don’t know the URI for an institution or a project you can always create your own and add an owl:sameAs once you know the good one. But you can try looking up in DBpedia or Sindice for existent ones.

5)      Validate your RDF-a! Before publishing, be sure to test the statements you have produced with an RDF validator like this one.

Do you want to know more? Check out the RDF-a Primer! It’s full of examples and it is very easy to follow.