Linking Research

Posts Tagged ‘publishing’

Permanent identifiers and vocabulary publication: purl.org and w3id

Posted by dgarijov on January 17, 2016

Some time ago, I wrote a tutorial with the common practices for publishing vocabularies/ontologies on the Web. In particular, the second step of the tutorial addressed the guidelines for describing how to set a stable URI for your vocabulary. The tutorial referred to purl.org, a popular service for creating permanent urls on the web. Purl.org had been working for more than 15 years and was widely used by the community.

However, several months ago purl.org stopped registering new users. Then, only a couple of months ago the website stopped allowing registering or editing the permanent urls from a user. The official response is that there is a problem with the SOLR index, but I am afraid that the service is not reliable anymore. The current purl redirects work properly, but I have no clue on whether they intend to keep maintaining it in the future. It’s a bit sad, because it was a great infrastructure and service to the community.

Fortunately, other permanent identifier efforts have been hatched successfully by the community. In this post I am going to talk a little about w3id.org, an effort launched by the W3C permanent identifier community group that has been adopted by a great part of the community (with more than 10K registered ids). W3id is supported by several companies, and although there is no official commitment from the W3C for maintenance, I think it is currently one of the best options for publishing resources with a permanent id on the web.

Differences with purl.org: w3id is a bit geekier, but way more flexible and powerful when doing content negotiation. In fact, you don’t need to talk to your admin to do the content negotiation because you can do it yourself! Apart from that, the main difference between purl.org and w3id is that you don’t have a user interface to edit you purls. You do so through Github by editing there the .htaccess files.

How to use it: let’s imagine that I want to create a vocabulary for my domain. In my example, I will use the coil ontology, an extension of the videogame ontology for modeling a particular game. I have already created the ontology, and assigned it the URI: https://w3id.org/games/spec/coil#. I have produced the documentation and saved the ontology file in both rdf/xml and TTL formats. In this particular case, I have chosen to store everything in one of my repositories in Github: https://github.com/dgarijo/VideoGameOntology/tree/master/GameExtensions/CoilOntology. So, how to set up the w3id for it?

  1. Go to the w3id repository and fork it. If you don’t have a Github account, you must create one before forking the repository.
  2. Create the folder structure you assigned in the URI of your ontology (I assume that you won’t be rewriting somebody else’s URI, as if that is the case, the admins will likely detect it). In my example, I created the folders “games/spec/” (see in repo)
  3. Create the .htaccess. In my case it can be seen in the following url: https://github.com/perma-id/w3id.org/blob/master/games/spec/.htaccess. Note that I have included negotiation for three vocabularies in there.
  4. Push your changes to your local repository.
  5. Create a pull request to the perma-id repository.
  6. Wait until the admins accept your changes.
  7. You are done! If you want to add more w3id ids, just push them to your local copy and create additional pull requests.

Now every time somebody accesses the URL https://w3id.org/games/spec/coil#, it will redirect to where the htaccess file points to. In my case, http://dgarijo.github.io/VideoGameOntology/GameExtensions/CoilOntology/coilDoc/ for the documentation, http://dgarijo.github.io/VideoGameOntology/GameExtensions/CoilOntology/coil.ttl for TTL and http://dgarijo.github.io/VideoGameOntology/GameExtensions/CoilOntology/coil.owl for rdf/xml. This works also if you want to do simple 302 redirections as well. W3id administrators are usually very fast to review and accept the changes (so far I haven’t had to wait more than a couple of hours before having everything reviewed). The whole process is perhaps slower than what purl.org used to be, but I really like the approach. And you can do negotiations that you were unable to achieve with purl.org.

Http vs https: As a final comment, w3id uses https. If you publish something with http, it will be redirected to https. This may look as an unimportant detail, but is critical in some cases. For example, I have found that some applications cannot negotiate properly if they have to handle a redirect from http to https. An example is Protégé: if you try to load http://w3id.org/games/spec/coil#, the program will raise an error. Using https in you URI works fine with the latest version of the program (Protégé 5).

Posted in Tutorial | Tagged: , , , , | 9 Comments »

How to (properly) publish a vocabulary or ontology in the web (part 3.5 of 6)

Posted by dgarijov on July 20, 2013

This is a short post that I want to write to expand on my previous part of the tutorial (how to create a nice human readable documentation for your vocabulary/ontology). Since I have been releasing some vocabularies lately, I have developed a simple tool that generates the main structure of an html document describing the resource with the 11 parts I introduced on my previous post (title and date, metadata, abstract, table of contents, introduction, namespace declarations, overview of classes and properties, description, Cross reference section, references and acknowledgements).

This tool does not intend to replace any of the other tools designed to describe the properties and classes of an ontology. In fact, it rather acts as wrapper using LODE for that very purpose in one of the sections (the cross reference section). So, why should you use it?

  1. It saves time by providing the whole structure of the html document.
  2. It doesn’t require you to add any RDF metadata to the ontology being described. The URI of the ontology itself is optional. All metadata can be configured in the config.properties file of the project (see readme for more info).
  3. It automatically adds the metadata as rdf-a annotations to the document, which makes it easier to parse by machines.

I have uploaded the tool to Github, and it’s available here, along with the code I used.

As stated, I have used LODE for one of the sections of the document. I have already added LODE in the acknowledgements. If you use this tool please make sure to acknowledge any tool you use to generate your documentation.

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 (this post)
  5. (Reqs addressed P4). Derreferencing your vocabulary.
  6. (Reqs addressed A1 (partially)). Dealing with the license. (To appear)
  7. (Reqs addressed A5, P5). Reusing other vocabularies. (To appear)

Posted in Linked Data, Miscellaneous | Tagged: , , , , , | 8 Comments »

How to (properly) publish a vocabulary or ontology in the web (part 3 of 6)

Posted by dgarijov on July 7, 2013

This part of the tutorial explains how to design a human readable documentation. When browsing an ontology, it is very important to provide accurate definitions and examples of how to use it. If these are not provided, the ontology will be very difficult to reuse. Having a documentation easy to navigate, which explains every concept and relationship separately and which presents an overview and examples improves the understandability of the whole ontology to other people.

Some people address this step by pointing to a report/deliverable/paper where the ontology is described. Although this helps, it is not easy to navigate and will drive crazy any final user. I don’t recommend it. Furthermore, according to my experience, if the ontology is documented in a paper then the information will be of little use.

Making a proper documentation is difficult and takes time. Fortunately, there are some tools to help you overcome this task, like LODE, Parrot, OWLDoc, neologism, Ontospec, etc. I have worked with LODE, Parrot and OWLDoc, so I will only cover these here:

  • LODE: For me it’s the best of the tools I’ve tried. It is a web service that takes as input an owl file and generates an html. The html is W3C-style with the definition of each of the terms extracted from the domain, ranges and metadata of your owl file. If you extract the appropriate bits you can automatically create templates to customize your documentation with additional images, explanations and examples (like this one).
  • Parrot: Very similar to LODE, although the styles used are different and you have to clean some of the properties not defined within the namespace of your ontology (like the ones used to add metadata). It works really well, and my choice picking LODE instead of Parrot is a matter of styles.
  • OWLDoc: NeOn Toolkit plug-in that generates an owl documentation javadoc style from your .owl file. I don’t personally like it much, as customizing it is a bit of a pain.

Once you have your html template from one of these tools (with all the concepts of the ontology fully covered), you should add sections describing an overview of the model and examples. My suggestion is to follow the structure of W3C documents, namely:

  1. Title and date of the release.
  2. Metadata: Authors, contributors, version, imported ontologies, license, link to previous version, link to the latest version.
  3. Abstract: small summary of your ontology in 2 lines. I recommend pointing to the owl file here as well.
  4. Table of contents of your html document.
  5. Introduction: provide context to the ontology. What are its goals and the benefits of using it?.
  6. Namespace declarations: Namespace URIs of all the vocabularies used within the document (this could be found at the end as well).
  7. Overview of classes and properties: Very small section with the list of tables and properties of the ontology, for making the navigation easier to the reader.
  8. Description: Diagram of the ontology concepts, relationships and how they are related to each other. Usage examples might help clarifying things as well.
  9. Cross reference section: this is the section automatically generated by the tools covered above. Just copy what they generated J
  10. References.
  11. Acknowledgements, specially remember to include the developers of the tools you have used.

Want to see some examples? Check PROV (W3C), some commonly used vocabularies like foaf or Dublin Core (which cover the points listed above with their own structure) or some of the ontologies I’ve been publishing, like p-plan or wf-motifs. Note that the order in which the points of the list appear is not mandatory. Modify it in order to make your ontology easier to use to the final user!

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.  (this post)
  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. (To appear)
  7. (Reqs addressed A5, P5). Reusing other vocabularies. (To appear)

 

Posted in e-Science, Linked Data | Tagged: , , , , | 11 Comments »

Science, Semantic Web and Excuses

Posted by dgarijov on May 10, 2013

We have just published our proposal for the “Call for Polemics” at Sepublica 2013 (ESWC). Check it out here!: http://www.oeg-upm.net/files/polemics/

The document critizices the actual semantic publishing practices and proposes a set of requirements that all authors should accomplish when submitting a research work. In the near future we would like to include examples from our environment (complete and incomplete) in order to illustrate our proposal.

If you wish to contribute with additional ideas/suggestions, please do it in this thread.

Posted in Conference | Tagged: , , , , , , | Leave a Comment »