Difference between revisions of "FAQ"

Revision as of 16:59, 16 February 2014

FAQ about Ontohub

The FAQ page is result of an interaction between the Ontohub users and the Ontohub team who is providing technical support to the users by giving accurate and up-to-date information about the Ontohub utilities. An active contribution and feedback of the Ontohub users is more than welcome!

What is Ontohub?

Ontohub is an open ontology repository which enables communities to share, exchange, and manage their ontologies easily.

As a member of of the OOR initiative, Ontohub supports interoperability across distributed ontology repositories.

The Ontohub engine is providing tools for

• organising ontology collections
• ontology retrieval
• ontology management (reuse, editing, creation, formal mapping, evaluation)

Moreover, the Ontohub technology provides a web-based system for

• working with multiple logical formalisms
• management of distributed heterogeneous ontologies

What are the unique features of Ontohub?

Ontohub provides several unique features for searching, evaluating, and managing the repository content. The heterogeneous nature of Ontohub makes it possible to integrate ontologies written in various ontology languages.

Start

The home page of Ontohub provides access to all public repositories, ontologies, symbols, logics and ontology mappings stored in this hub of distributed, and yet interconnected, ontology repositories. Recently updated repositories and ontologies are listed as well.

Sign In

The full functionality of Ontohub (ontology and repository, creation, collaborative editing and development of ontologies, mapping across ontologies, visualisation, and evaluation) is available upon sign in. Every registered Ontohub user can modify and adjust its own version of interface, i.e. specific and highly personalised access to the repository content.

How to submit an ontology?

The submission of a new ontology into Ontohub consists of the following steps:

a. Register/sign in ontohub.org

b. Select an existing repository that fits best your specific target domain, task, and ontology type; All public repositories are listed upon clicking on the 'Repository' button in the main menu; alternatively, it is possible to create a new repository (as described in the section below); certain repositories are 'read-only' while others allow editing of the repository content;

c. If uploading an ontology to the existing repository you will need to get a permission via requesting the editing rights; the permission is provided by the administrator of the repository ('owner'); After selecting (or creating) an appropriate ontology repository and acquiring the editing rights, the ontology upload can proceed through the use of file system.

d. The 'Edit' button appears on the page of each repository for which you have the editing rights. 'Edit' button leads to the interface with the editing option. So, the first step in editing is to to confirm that you want to 'Update repository'. The next step is to go to the file browser, where you can upload your ontology as a new file. The information provided there in gets stored into the file system, which can afterwords be accessed in the file browser. You might want to upload your ontology into an already existing folder that stores ontologies of your interest. In that case, in the section 'Target directory' you will need to type the exact name of the directory in which you want to store your ontology file. Into the section 'Target file name' you will need to type the ontology name together with its correct extension, e.g. name.owl, name.clif etc. A message that accompanies upload is optional but desirable as it can be helpful in tracking the history of activities and changes in repository. The next step is to 'Upload file'.

e. Since your submitted file is recognised as an ontology (via its extension), you will need to provide metadata that describe your ontology: ontology name, category (domain), ontology type, formality level, and a specific description. The inserted metadata are helpful in classification of ontologies in repository and their easier, a task specific retrieval.

When selecting metadata that describe the domain of your ontology you can select multiple fields ('Categories') that will help to characterise your ontology as specific as possible. For instance, if an ontology is about anatomy of a biological species, then the appropriate categories would be 'biology' and 'space', while a geospatial ontology can be associated with the domains 'geography' and 'space', an ontology that describes chemical structures would be associated with 'chemistry' and 'space'.

'Ontology type' and 'Formality level' provide specification of your ontology as a domain ontology, an upper level ontology etc. Please note that the classification of ontology types and formality levels mostly follows the OMV specifications. Modifications and revisions to this classification are work in progress.

'Description' of ontology provides an important narrative, i.e. information that will additionally help users (people and machines) to capture the targets and aims of the ontology designer.

How to search for an ontology?

Ontology search can be performed either over whole Ontohub content ('Ontology' tab on the menu bar) or over ontologies stored within a particular Ontohub repository (Ontology browser on the page of a particular Ontohub repository).

Ontology retrieval is done by typing into the ontology browser one or many of the available search criteria:

• Ontology name
• ontology acronym
• ontology language
• a symbol or a label that an ontology contains
• a particular domain (category) that an ontology belongs to (e.g. space, biology, etc.)
• ontology type (e.g. upper, domain, task, etc.) Please note that this feature has not been implemented yet.

Since the search engine uses metadata to retrieve an ontology, all Ontohub users are encouraged to specify metadata about their ontology during the ontology upload. Having described an ontology domain, type, task, etc. increases findability of an ontology.

What is a category?

Ontologies can be categorised. Ontohub's category system is maintained as an OWL ontology in Ontohub itself, see [1].

For more details see Category.

How to edit an ontology?

How to evaluate an ontology?

How to create an ontology repository?

Every registered Ontohub user can create a new repository via the button 'Create repository'. The repository creator acquires administrative rights, i.e. management of repository, editing permissions, and visibility of repository (public or private).

While considering creation of a new repository, every Ontohub user should mind knowledge sharing as the driving force in ontology development. In oder words, private repositories are designed to serve the research purposes only. Accordingly, private repositories can be used to store work in progress. As soon as work on ontology development and mappings reach the stage to be published, it is recommended to make private repository and/or its content publicly available. It is also advisable to publish ontologies in already existing repositories that are domain or problem oriented, e.g. geospatial ontologies can be published in SOCoP or SpacePortal; biomedical ontologies in BioPortal etc. By following this policy, Ontohub users support joint efforts of ontology community in knowledge sharing and ontology reuse.

Besides serving as an ontology repository, Ontohub is also a hub that links other ontology repositories. Ontohub provides a single web interface to access various ontology repositories, either hosted or mirrored on Ontohub. The button Repositories (on the menu-bar) leads to the page where all public repositories are listed and the access to their content provided. In addition, Ontohub allows creation and hosting of new repositories, the function available to all registered Ontohub users. Along the opportunity of creating a new repository, Ontohub users can get advantage of the Ontohub collaborative environment in order to develop ontologies and/or repositories in either problem or domain oriented manner. Thus, Ontohub supports reuse of ontologies stored in other ontology repositories and creation of new repositories that organize ontologies resulting from the activities of a team focused around a particular project or a specific task.

Ontohub repositories are stored as git repositories. Git provides a persistent storage and version control for ontologies, as weill as access to Ontohub repositories via the usual git tools.

It is also possible to create private repositories. These are visible only for users who have read-permission for the repository.

Which logical formalisms (languages) are supported by Ontohub?

Ontologies can be formulated in various logic. Ontohub supports a number of different logics, among them OWL, RDF and Common Logic.

Why does Ontohub support multiple (onto)logical formalisms?

Ontohub supports multiple (onto)logical formalisms in order to admit inclusion and interoperability of ontologies distributed across various repositores. A variety of languages is used for formalising ontologies. Some of these, such as RDF (mostly used for data), OBO and certain UML class diagrams, can be seen more or less as fragments and notational variants of OWL, while others, like F-logic and Common Logic (CL), clearly go beyond the expressiveness of OWL. ^[1]

In other words, Ontohub respects the existing plurality of formalisms, expressivities and aims, as they are found across diverse scientific communities. While accepting the plurality of formal languages and tools (e.g. CL, OWL, RDF, etc), methodologies and perspectives, Ontohub provides interoperability of domain needs and exchange of knowledge on a formal level. Thus, Ontohub supports linking ontologies across ontology languages, and creating distributed ontologies as sets of basic ontologies and links among them. The links (mappings) in Ontohub have formal semantics, and therefore enable new reasoning and interoperability scenarios between ontologies. ^[1]

What is a single ontology?

A single ontology, also labeled as 'basic' ontology (DOL terminology), is any ontology that is written in a single ontology language and it does not include any other ontology (or ontology module) within its content.

What is a distributed ontology?

A distributed ontology is an ontology which is composed of two or more ontologies (modules). A distributed ontology can be written in a single (homogeneous) or diverse (heterogeneous) ontology languages. The content of a distributed ontology may be distributed across diverse ontology sources and repositories. Ontohub allows storage and management of heterogeneous and distributed ontology content. (Note: currently, Ontohub still uses distributed ontology for what should be called an ontology library (see below) - sorry for the confusion, we will fix this soon.)

What is a heterogeneous ontology?

A heterogeneous ontology is an ontology which is composed of more than one ontology (module) and its content and structure are formalised in more than one ontology language.

What is an ontology library?

An ontology library is a collection of ontologies and mappings, written in DOL.

What is a mappings

Mappings have a source and a target ontology, and provide mappings or relations between the symbols of these ontologies. Under the mappings tab, you can see all mappings.

Currently, new mappings can only be created using e.g. an interpretation or an alignment in a DOL file, and uploading that DOL file.

References

1. ↑ ^{1.0 1.1} Mossakowski, Till, Christoph Lange, and Oliver Kutz. "Three Semantics for the Core of the Distributed Ontology Language." FOIS. 2012. PDF