Ontohub - New pages [en]

Atom

2018-06-21T09:03:41Z

Tillmo:

We will use the [http://atom.io/ Atom editor] for working with DOL, OWL, CommonLogic, CASL etc. We aim at a neat integration of Atom into [[Hets]].

Useful Atom packages:
* LaTeX
* git-plus

Hets

2017-05-04T20:18:35Z

Tillmo: start

The heterogeneous tool set (Hets) is a parsing, static analysis and proof management tool incorporating various provers and different logical languages, thus providing a tool for heterogeneous ontologies, models and specifications. Logic translations are first-class citizens. Hets is the central analysis tool for [[DOL]].

Find more about Hets on the [http://hets.eu/ Hets homepage].

Axiom names

2017-05-04T20:06:31Z

Tillmo: /* OWL */ other syntaxes

It is useful to label axioms and conjectures with self-explanatory names. This pays off especially when using a theorem prover with [[Hets]] or [[Ontohub]], because then these names can be used to quickly select both axioms and conjectures (proof goals).
==DOL==
In DOL, axiom labels are written as follows:
. axiom %(axiom_label)%
==OWL==
In OWL, axioms can be annotated with labels, using an rdfs:label annotation. Protégé has an editing facility for this. These labels will be stored together with the ontology in any syntax.

For example, in OWL Manchester syntax, this looks as follws:
Class: Woman SubClassOf: Annotations: rdfs:label "WomanSubClassOfPerson" Person
see also [https://ontohub.org/appliedontologyontohubpaper/familyRelations.omn some example OWL file] [https://ontohub.org/appliedontologyontohubpaper/scenario.omn another sample OWL file] [https://ontohub.org/appliedontologyontohubpaper/competencyQuestion.dol sample DOL file]

Emacs mode

2016-08-16T06:18:05Z

Tillmo: running Hets

* Download [https://raw.githubusercontent.com/spechub/Hets/f93990c928a2b0b8f970b86d0fbd18d604147af6/utils/el/dol-mode.el dol-mode.el] and [https://raw.githubusercontent.com/spechub/Hets/f93990c928a2b0b8f970b86d0fbd18d604147af6/utils/el/dol.el dol.el] and save them locally (e.g. in .emacs.d, or elsehwere)
* in the .emacs file in your home folder, add
(load-file "<path-to>/dol.el")
* For running Hets on a DOL file, type C-c C-r
* For running Hets on a DOL file and starting the GUI, type C-c C-c

Tutorial

2016-03-15T21:16:26Z

Eugenk:

Here we collect some tutorials for the Ontohub usage.

* [https://youtu.be/VagEH8-67Hs Basic usage of Ontohub]
**This video tutorial describes some basic usage steps of Ontohub:
*** Creating a repository
*** Uploading an ontology file
*** Changing an ontology file via the web interface
*** Visualizing ontology contents
*** Proving Theorems in an ontology

How to test Ontohub

2015-09-28T12:37:07Z

E.bolloff:

If you want to test Ontohub, you can use [http://www.seleniumhq.org/ Selenium] (to be exact the Selenium IDE Plugin for Firefox) and the [http://www.test.ontohub.org Ontohub test platform]. This site is in an similiar status like Ontohub, but it has a few test data for you to play with. May you want to check on some infos about Selenium and Cucumber before you test our site.

With Selenium you can record test on [http://www.test.ontohub.org test.ontohub.org] and translate them with this gem called [https://github.com/ebolloff/featurecorder featurecorder] for us developer. In the readme ([https://github.com/ebolloff/featurecorder featurecorder]) you'll find instructions what to install and how to test Ontohub. You'll find these instructions also below.

== Installation and Configuration ==

The translation gem feaeturecorder is not hosted on rubygems.org, so to install it you need to download it from [https://github.com/ebolloff/featurecorder here] and run ''bundle'' and ''rake install''.

What you need to do next is to install Mozilla Firefox (currently version 39.0), if you haven't yet. After that you need to install the Firefox plugins 'Selenium IDE' (currently version 2.9.0), 'Selenium XML Formatter' (currently version 1.5.1), which allows you to export the recorded test as XML, and 'Selenium IDE Button'(currently version 1.2.0.1) to start Selenium with an easy button click next to your address bar in Firefox.

After that you need to change some options in Selenium. Start Selenium and click on Options -> Options. In the opened window you select the tab 'Locator Builders'. These handle the locators to find your selected elements in your tests. With drag & drop you can arrange the locators like this:

ui
id
link
name
dom:name
xpath:link
xpath:img
xpath:attributes
xpath:idRelative
xpath:href
dom:index
xpath:position
css

Now Selenium will record the elements with the ID, not the css selector because that could be unexcact.

== Recording ==

So let's record some tests. Please check in the Ontohub project that the test you want to record doesn't exist already. Also notice, that Selenium will record every input as plaintext, so create a new account with a different password on test.ontohub.org. Start Selenium, go to test.ontohub.org and click the record button. Everything you interact with the site now will be recorded. With a right click you can add commands like assertText or verifyTitle so check, if a expected element is present. Please just use the assert* and verify* commands, because the other ones aren't supported. If you're done just click the record button again and the record will stop. Now you can export the test as XML via File -> Export Test Case As... -> XML Formatter.

== Translation ==

Now you can translate your recorded XML tests to Cucumber. With ''featurecorder -h'' you can see the options of this gem.

Usage:
featurecorder [options] <file>
Options:
-s --scenario-name=<scenario> Name of the scenario.
-f --feature-name=<feature> Name of the feature.
-o --output-directory=<dir> Output directory for generated files.
Default is current directory.
-h --help Show this screen.

With the option -s/--scenario-name you can choose the name for the scenario, with -f/--feature-name the name for the feature. -o/--output-directory lets you decide where you want to save the generated files for Cucumber. If you call featurecorder you need to state the XML file. If you're ready, fork the Ontohub project and you can post the files in a pull request.

Ontohub team

2014-03-29T17:55:13Z

Tillmo: /* Implementation */ Sascha -> Tom

==Project Leader==

* [http://iws.cs.uni-magdeburg.de/~mossakow/ Till Mossakowski]

==Ontological background==

* [http://www.informatik.uni-bremen.de/~okutz/ Oliver Kutz]
* [http://iws.cs.uni-magdeburg.de/~fneuhaus Fabian Neuhaus]
* [http://iws.cs.uni-magdeburg.de/~codescu/ Mihai Codescu]
* [https://sites.google.com/site/aleksandrasojic/ Aleksandra Sojic]
* [http://www.cs.bham.ac.uk/~langec/ Christoph Lange]

==Implementation==
* Eileen Bolloff
* Tom Gehrke
* Eugen Kuksa

====Former members of the programming team====
* Hardik Balar
* Ingo Becker
* Christian Clausen
* Sascha Graef
* Timo Kohorst
* Tim Reddehase
* Daniel Vale

==Consulting Ruby on Rails==

* Julian Kornberger (Digineo complex web solutions, http://www.digineo.de/)
* Henning Müller (dto.)

==Source code (Affero GNU Pulic License)==
https://github.com/ontohub/ontohub/

SpacePortal

2014-02-27T16:20:15Z

Asojic: Created page with "SpacePortal is a specialised ontology repository which supports the collection and re-use of ontologies that formally represent the large array of the space-related domains. T..."

SpacePortal is a specialised ontology repository which supports the collection and re-use of ontologies that formally represent the large array of the space-related domains. The infrastructure of SpacePortal is based on the Ontohub technological platform which supports multiple (onto)logical formalisms (e.g. OWL, CL, OBO, RDF, CASL, etc) and various mappings between ontologies.

The repository engine is designed to manage distributed and heterogeneous ontologies. The distributed nature enables communities to share and exchange their contributions easily. The heterogeneous nature makes it possible to integrate ontologies written in various ontology languages. Note that spatial ontologies are being written in OWL (e.g. GUM-Space), but also in first-order logic (e.g. GFO spatial ontology).

The instructions for new users of SpacePortal are available within this wiki which provides general guidelines for the Ontohub platform. A new space-related ontology can be uploaded at [http://ontohub.org/spaceportal http://ontohub.org/spaceportal]. Ontologies can be submit in any of the [http://wiki.ontohub.org/index.php/Logic supported formats].

Ontohub

2014-02-11T10:27:11Z

Tillmo: /* LoLa Ontology */ removed dead link

==Ontohub web portal==
Ontohub is available at [http://ontohub.org http://ontohub.org].

==Ontohub architecture==

The Ontohub infrastructure is powered by the open-source web framework [http://ruby.railstutorial.org/ruby-on-rails-tutorial-book Ruby on Rails] for building dynamic web applications. The source code is available at [https://github.com/ontohub/ontohub/ github]. The
Ontohub git repository has separate branches development, staging and master. Software developers are introducing new features of Ontohub on its develop branch. After going through all necessary tests for stability, new features are merged to the staging (and master, i.e. visible website). In that way, the UI on the main page is always stable.

==HETS==

The parsing and inference backend of Ontohub is the [[Hets|Heterogeneous Tool Set]]. you can find a detailed architecture of Ontohub on page 8 of [http://ontolog.cim3.net/file/work/OpenOntologyRepository/Ontohub/ontohub--TillMossakowski-et-al_20130621a.pdf Ontohub preprint paper] <ref name="Mossakowski">Mossakowski, Till, Oliver Kutz, and Mihai Codescu. "Ontohub - a repository engine for heterogeneous ontologies and alignments." preprint. [http://ontolog.cim3.net/file/work/OpenOntologyRepository/Ontohub/ontohub--TillMossakowski-et-al_20130621a.pdf PDF] </ref>

Ontohub accesses the Heterogeneous Tool Set Hets via a RESTful web service interface for having the structure of ontologies analyzed. Hets already supports a large number of basic ontology languages and logics, and is capable of describing the structural outline of an ontology from the perspective of DOL, which is not committed to one particular logic.

==DOL==

The '''D'''istributed '''O'''ntology, Modelling and Specification '''L'''anguage ([[DOL]]) covers all state-of-the-art ontology languages, and provides a meta level on top of these. This meta level allows for the representation of logically heterogeneous ontologies. DOL ontologies may comprise of modules written in ontology languages with different underlying logics. Moreover, the DOL meta level constructs allow for links between ontologies such as relative interpretations or conservative extensions. <ref name="Mossakowski2">Mossakowski, Till, Christoph Lange, and Oliver Kutz. "Three Semantics for the Core of the Distributed Ontology Language." FOIS. 2012. [http://www.informatik.uni-bremen.de/~till/papers/DOLsemantics.pdf PDF] </ref>

Since the Ontohub infrastructure supports DOL, it allows the Ontohub users
* to relate ontologies that are written in different formalisms;
* to re-use ontology modules even if they have been formulated in a different formalism;
* to re-use ontology tools like theorem provers and module extractors along translations between formalisms.

DOL has been standardised at OMG.

==LoLa Ontology==

LoLa is an ontology of (ontology) '''Lo'''gics and '''La'''nguages. Onthub implements LoLa for structuring the repository content. The OWL core of the LoLa ontology comprises classes for ontology languages, logics, mappings (translations or projections) between ontology languages and between logics, as well as serialisations. The LoLa properties relate all of the former classes to each other. Besides its OWL module, LoLa includes additional FOL axioms for closure rules not expressible in OWL, such as non-expressible role compositions and circumscription rules for minimising the extension of default translations. <ref name="Lange">Lange, Christoph, Till Mossakowski, and Oliver Kutz. "LoLa: A Modular Ontology of Logics, Languages, and Translations." Workshop on Modular Ontologies (WoMO) 2012. 2012. [ftp://ceur-ws.org/pub/publications/CEUR-WS/Vol-875.zip#page=60 PDF] </ref>

----

== References ==
<references/>

Glossary

2014-02-11T10:13:23Z

Tillmo: Created page with "{|class="wikitable sortable" ! data-sort-type="Term" | Term!!Description |- |Logical theory||set of expressions (like non-logical symbols, sentences and structuring elements) ..."

{|class="wikitable sortable"
! data-sort-type="Term" | Term!!Description
|-
|Logical theory||set of expressions (like non-logical symbols, sentences and structuring elements) in a given [[logic|logical language]]
|-
|Alignment||flexible, relational link that does not always have a formal, logic-based semantics
|-
|Matching||algorithmic procedure that generates an alignment for two given logical theories
|-
|[[Logic|Logical language]]||language that is used for writing down logical theories (e.g. formal ontologies, models and specification), equipped with a formal, declarative, logic-based semantics, plus non-logical annotations
|-
|[[Mapping]]||relationship between two logical theories, relating their non-logical symbols
|-
|Language translation||mapping from constructs in the source logical language to their equivalents in the target logical language
|-
|Interpretation||logical link that postulates a relation between two logical theories
|-
|Combination||aggregation of several logical theories along links to a new logical theory where (only) the linked non-logical symbols of the involved logical theeories are identified
|-
|Conservativity||property of an extension of theories, ensuring that the extension does not add new logical context
|-
|Basic logical theory||set of non-logical symbols, sentences, annotations about them, which is used as a building block for a larger logical theory
|-
|[[Axiom]]||sentence postulated to be valid (i.e. true in every model), party of a logical theory
|-
|[[Theorem]]||sentence that has been proven (in some logical theory) from other axioms and theorem
|-
|Structured logical theory||logical theory that results from other logical theories by import, union, combination, renaming or other structuring operations
|-
|[[Sentence]]||term that is either true or false in a given model, i.e. which is assigned a truth value in this model
|-
|Satisfaction relation||relation between models and sentences indicating which sentences hold true in the model
|-
|Non-logical [[symbol]]||atomic expression or syntactic constituent of a logical theory that requires an interpretation through a model
|-
|Module extraction||activity of obtaining from anlogical theory concrete modules to be used for a particular purpose (e.g. to contain a particular sub-signature of the original logical theory)
|-
|Module||subtheory that conservatively extends to the whole logical theory
|-
|Model||semantic interpretation of all non-logical symbols of a logical theory, satisfying the theory's axioms
|-
|Approximation||reduction of a theory to a less expressive logical language, such that the original theory implies the approximation
|}

User

2014-02-11T09:46:59Z

Tillmo: Created page with "If you want to use certain features of Ontohub, like creating repositories of uploading ontologies, you have to register as a '''user'''. Registrat..."

If you want to use certain features of Ontohub, like creating [[repository|repositories]] of uploading [[ontology|ontologies]], you have to register as a '''user'''. Registration is quite easy: just enter your name, email address and a password at the Ontohub main page.

==User settings==
You can change your user settings at the right top corner of the Ontohub page:
*edit the details of your account (like email address and password)
*manage your [[team]]s
*manage your [[SSH key]]s

Theorem

2014-02-11T09:43:08Z

Fabian: added navigation instruction for theorem

A '''theorem''' is a [[sentence]] that is postulated to logically follow from the [[axiom]]s of an [[ontology]]. Theorems help documenting the (intended or unintended) consequences of an ontology. Theorems can be proved with a [[theorem prover]].

A DOL file may associate an ontology with one ore more theorems. The theorems that are associated with a given ontology can be found as follows:
In a given repository select an ontology. (If it is a heterogenous ontology, you may need to select a child ontology). The theorems are displayed in the "Theorem" subtab under the "Content" tab.
Here is an example [https://ontohub.org/appliedontologyontohubpaper/competencyQuestion//CCbase///theorems].

Axiom

2014-02-11T09:41:28Z

Tillmo: Created page with "An '''axiom''' is a sentence of an ontology that is postulated to be true. It is used to define the ontology by constraining its models, i.e. its possible interpretati..."

An '''axiom''' is a [[sentence]] of an [[ontology]] that is postulated to be true. It is used to define the ontology by constraining its models, i.e. its possible interpretations of [[symbol]]s.

Symbol

2014-02-11T09:30:02Z

Tillmo: Created page with "In Ontohub, an ontology consists of '''symbols''' and sentences. The possible kinds of symbols depend on the logic: *OWL: classes, individuals, object properties, ..."

In Ontohub, an [[ontology]] consists of '''symbols''' and [[sentences]]. The possible kinds of symbols depend on the [[logic]]:
*OWL: classes, individuals, object properties, data properties
*Propositional logic: propositional letters
*Common Logic: names, sequence markers
*CASL: sorts, predicate symbols, operation symbols

==Ontohub page==
On an [http://ontohub.org/repositories/bioportal/ontologies/279 ontology page], you get an overview of the symbols in an ontology.

Single ontology

2014-02-10T22:21:30Z

Tillmo: Created page with "A '''single ontology''' is just an ontology, in contrast to an ontology library."

A '''single ontology''' is just an [[ontology]], in contrast to an [[ontology library]].

Ontology library

2014-02-10T22:18:06Z

Fabian: added info about URIs of children of ontology library

An '''ontology library''' (currently also called ''distributed ontology'' on Ontohub) is a collection of [[ontology|ontologies]] and [[mappings]] (these are called the '''children''' of the ontology library). Ontology libraries can be written in [[DOL]] and uploaded to Ontohub.

The URI of a child of an ontology library consists of the URI of the library, two slashes, and the name of the ontology. E.g.,
http://ontohub.org/myRepository/myOntologyLibrary//myOntology

Individual ontologies are sometimes called [[single ontology|single ontologies]] in order to distinguish them from ontology libraries.

Mirror

2014-02-10T22:14:10Z

Tillmo: Created page with "Normally, repositories are hosted at Ontohub. However, it is also possible to '''mirror''' an existing git or subversion repository, which is copied once a day to Ontohub...."

Normally, [[repositories]] are hosted at Ontohub. However, it is also possible to '''mirror''' an existing git or subversion repository, which is copied once a day to Ontohub. At Ontohub, mirrored repositories are read-only - you should alter the original, not the copy.

Teams

2014-02-10T21:34:31Z

Tillmo:

[[User]]s can be grouped into teams. The advantage is that [[permissions]] (for [[repositories]]) can be given to a whole team at once, so there is no need to give permissions to each invidual team member separately.

==Ontohub pages for teams ==
* [http://ontohub.org/teams http://ontohub.org/teams] This page lists your teams. You also can create new teams.
* [http://ontohub.org/teams/1 A team page] displayes details of a team. With the members tab, you can add new members to the team by typing (at least) the first three letters of a username.

Sentences

2014-02-10T21:24:31Z

Tillmo: Tillmo moved page Sentences to Sentence: uniform singular

A sentence in an [[ontology]] expresses some logical information about the ontology, e.g. some subclass relationship, or some constraint on certain [[symbol]]s. Sentence can be
*[[axiom]]s, which are postulated to be true, or
*[[theorem]]s, which are postulated to follow from the axioms.

==Ontohub page [http://ontohub.org/repositories/bioportal/ontologies/269/sentences listing sentences]==
All sentences of an ontology are listed.

Mappings

2014-02-10T21:19:31Z

Tillmo: Tillmo moved page Mappings to Mapping: uniform singular

A mapping relates two [[ontology|ontologies]]: a source and a target ontology. It consists of a set of correspondences, where each correspondence relates a [[symbol]] of the source ontology with a symbol of the target ontology. There are various different types of mapping, which all can be written down in [[DOL]]:
* '''Imports''': If an ontology imports another one, the inclusion is automatically a mapping.
* '''Views''', or '''interpretations''': one ontology is mapped into another one, such that [[axiom]]s of the source ontology are translated into [[theorem]]s of the target ontology.
* '''Alignments''': two ontologies are related (in contrast to the other kinds of mappings, this need not be functional). The [[DOL]] notation for alignments follows the [http://alignapi.gforge.inria.fr/ Alignment API].

==Ontohub pages for mappings==
* [http://ontohub.org/links http://ontohub.org/links] lists all existing mappings among all ontologies.
* [http://ontohub.org/repositories/bioportal/ontologies/307/links Ontology-specific pages] list only the mappings belonging to one particular ontology.
* [http://ontohub.org/links/1 Mapping-specific pages] showing one specific mapping. Here, the status of the mapping is shown. E.g. an interpretation needs to be proven, and is open as long as that has not been done.

Graphs

2014-02-10T21:06:43Z

Tillmo: Tillmo moved page Graphs to Graph: uniform singular

The graph for an ontology or ontology library shows [[ontology|ontologies]] as nodes and [[mappings]] as edges. Typically, the graph shows all the imported ontologies, but it can also contain other kinds of mappings.

==Ontohub graph page, for example [http://ontohub.org/repositories/bioportal/ontologies/307/graphs this one]==
By clicking on nodes and edges, you can obtain more details about the respective ontologies and mappings.
You can restrict the shown mappings to import mappings (see the [[mappings]] page for more information). Also, you can select a radius that determines how much of the graph is shown.

Ontology versions

2014-02-10T21:00:32Z

Tillmo: Created page with "An ontology has different versions, corresponding to the different version of the underlying file, identified by its git commit id. A specific version..."

An [[ontology]] has different versions, corresponding to the different version of the underlying [[File browser|file]], identified by its [[git]] commit id.
A specific version is analysed by Ontohub and marked as pending, processing, done or failed (in the latter case, an error can be displayed). A failed ontology can be retried by its owners.

List comments

2014-02-10T20:50:18Z

Tillmo: Created page with "You can add comments to ontologies. Comments can be viewed by anyone."

You can add comments to ontologies. Comments can be viewed by anyone.

Permissions

2014-02-07T12:22:19Z

Tillmo: What to do if I do not have the needed permissions?

Permissions in Ontohub are given per [[repositories|repository]] and are inherited to the [[ontology|ontologies]] of the respective repository.
If you are owner of a repository, you can give permissions to other people and [[teams]]:
* '''read permission''' - this is applicable only for private repositories
* '''edit permission''' - this gives read and write access to the repository.
* '''owner permission''' -by default,one who creates a new repository at Ontohub gets owner permission over it.Anyone with owner permissions can read, write and assign different permissions to other people or teams.People having owner permission can also edit repository's metadata and delete the repository.It is possible that more than one person or team has an owner permission over a repository.

There are three different roles a user can have in relation to the specific repository:
*'''Owner'''-This is the default role for the user who create a repository on Ontohub. Owner of the repository can assign different permission to other people and teams.
*'''Editor'''-This role is for people who has been assigned 'edit permission' by the owner of the repository.Editor can read and update a repository but can not delete it.
*'''Reader'''-Reader of the repository can only view/read the specific repository for which they have 'read permission'.

In search box, while typing in the first three letters of a user or team name, Ontohub will suggest different possible completions to full names.
In order to respect privacy of users, it is not possible to select users from a list.

Sample permission page on Ontohub: [http://ontohub.org/repositories/sandbox/permissions http://ontohub.org/repositories/sandbox/permissions]

==What to do if I do not have the needed permissions?==
* Ask an owner of the repository (or of the team owning the repository) to give you access rights (in the future, ontohub will provide a means for requesting this)
* fork the repository by creating a new one and git pushing the old one into it (also for this, ontohub will provide a means in the future)

Metadata

2014-02-03T16:37:07Z

Tillmo: formatting

Each ontology can be associated with metadata:
* '''projects''' that use the ontology. You can add a new project by specifying its name, URL, institution and contact person, or select one from a list of existing projects.
* '''categories''': the subject field of an ontology can be specified using one or more [[categories]]
* '''tasks'''
* '''license models''': you can select among various licences
* '''formality levels''': you can select among different formality levels:
** vocabulary (list of words)
** terminology (list of concepts with definitions)
** taxonomy (terminology with subsumption hierarchy)
** axiomatization (ontology with axioms beyond a pure subsumption hierarchy)

Ontology

2014-02-03T16:30:20Z

Tillmo: wikilinks, Ontohub pages

In Ontohub, an ontology consists of a set of [[symbol]]s and a set of [[sentence]]s:
* A symbol is an atomic expression or syntactic constituent that may be used in axioms. (Moreover, an semantic interpretation or model of an ontology usually consists of an interpretation of all the symbols.)
:Symbols have different kinds, for example, in OWL, there a classes, object properties, individuals etc. (In other [[logics]], there are other kinds of symbols.) For each symbol, there is a tab displaying the symbols of that kind.
kind, there is a
* A [[sentences|sentence]] (formula) is a logical expression constraining the meaning (interpretation) of the ontology and often thereby linking different symbols.
:A sentence may be an [[axiom]] (i.e. it is postulated to be true) a conjecture (i.e. it is postulated to follow from the axioms), or a [[theorem]] (i.e. it has been proven to follow from the axioms).

Ontologies are defined in [[File browser|files]]. An ontology may be defined as [[single ontology]] in one file,
or it may be part of an [[ontology library]], which in turned is defined in a file.

Ontologies can be annotated with comments and [[metadata]]. You can browse their versions, and show a [[graphs|graph]] of [[mappings]] to other ontologies.

==Ontohub pages for ontologies==
*[http://ontohub.org/repositories/bioportal/ontologies/270 Overview of an ontology]
*[[metadata]] of an ontology
*[[file browser]]

Search

2014-02-03T13:31:46Z

Fabian: Created page with "You can search by name of the ontology, names of symbols that occur in ontologies (e.g., "town" or "part_of"), the logic that is the ontology is written in (e.g, "OWL" or "Com..."

You can search by name of the ontology, names of symbols that occur in ontologies (e.g., "town" or "part_of"), the logic that is the ontology is written in (e.g, "OWL" or "CommonLogic") or any combination of search strings.

Some tips:
* Capitalization is irrelevant (e.g. "CommonLogic" or "commonlogic" are treated the same)
* Whitespace matters (e.g., "Common Logic" and "CommonLogic" are treated differently)
* If you want to enter more than one search string, then you need to use the <return> key on your keyboard to ensure that they are treated as separate strings . (E.g., if you want to search for an ontology written in OWL which contains the class Spine, you need to first enter "OWL <return> spine <return>". Otherwise, OntoHub will search for an ontology that contains the symbol "OWL spine".)

Version history

2014-02-03T11:17:42Z

Tillmo: Created page with "This page lists the version history of a repository, as maintained by the git version control system. Each git version is marked with a commit id like 175ff44. (Note that..."

This page lists the version history of a repository, as maintained by the [[git]] version control system.
Each git version is marked with a commit id like 175ff44. (Note that these are shorthand ids, full
git commit ids are even longer.)

If you click on a commit id (on the right) or on the commit message
(on the left), you get the list of changes to files in the repository
that have been introduced by this commit. If you click on the corresponding "Browse files" button,
you will get a [[file browser]] for a past version of the repository, namely that specified by
the commit. In order to remind you of the fact that not the latest version is being
displayed, the commit will always be displayed in the file browser.

Linked data

2014-02-03T11:16:37Z

Tillmo: Created page with "Ontohub is linked data compliant. That is, the raw text of an ontology and the HTML page containing a conceptual overview of the ontology can be accessed with one and the ..."

Ontohub is [[linked data]] compliant. That is, the raw text of an ontology and the HTML page
containing a conceptual overview of the ontology can be accessed with one and the same URL.
If you enter the URL into a browser, a nice HTML page will be shown. If you enter the URL
into a tool like Protege, Hets or wget, the raw ontology text will be delivered. It is
also possible to request an xml or json representation, useful for machine processing.

File browser

2014-02-03T11:16:22Z

Tillmo:

Each [[repositories|repository]] consists of a tree of files, structured into folders.

==Ontohub file browser, e.g. at [http://ontohub.org/colore http://ontohub.org/colore]==
This page provides a file browser for the repository.
Initially, the root folder of the repository is displayed. In order to find a particular file, you can navigate through the file system.

The files and folders are displayed in the left column. Note that not
all files contain [[ontology|ontologies]]. For those that do, the corresponding
ontology is displayed in the right column. Note that one file may
contain several ontologies (this then is an [[ontology library]]), but
also several files may be associated to the same ontology (these are
then different [[serialization]]s of the ontology).

While on this page, ontologies and their files are displayed as different but related objects,
generally, Ontohub is [[linked data]] compliant. That is, the raw text of an ontology and the HTML page
containing a conceptual overview of the ontology can be accessed with one and the same URL.

You can also browse through the [[version history]] of the repository.

URL catalog

2014-02-03T11:14:42Z

Tillmo: Created page with "With an URL catalog, you can substitute URLs by other URLs. This may be necessary if you mirror a repository. For example, the COLORE repository contains a lot of references (..."

With an URL catalog, you can substitute URLs by other URLs. This may be necessary if you mirror a repository.
For example, the COLORE repository contains a lot of references (ontology imports) of the form http://colore.oor.net/path-to-some-onotology.
Now you want that these references to point to ontohub. Therefore, you add an URL map from http://colore.oor.net to
http://ontohub.org/colore

Logics

2014-02-03T11:13:34Z

Tillmo: Tillmo moved page Logics to Logic: uniform singular

Ontohub supports a wide range of formal logical and ontology languages building on the OntoIOp.org project and allows complex inter-theory (concept) mappings and relationships with formal semantics.
{| class="wikitable" style="color:green; background-color:#ffffcc;" cellpadding="10"
!colspan="3"|List of formal logical and ontology languages supported by Ontohub
|-
! scope="col"| Language
! scope="col"| Description
! scope="col"| Serialisation
|-
| OWL 2 DL
| OWL 2 Web Ontology Language, Description Logic semantics (W3C Recommendation) http://purl.net/dol/languages/OWL2/DL
|
|-
| Common Logic
| Common Logic (ISO/IEC 24707) http://purl.net/dol/languages/CommonLogic
|
|-
| OBO 1.4
| Open Biomedical Ontologies (OBO) 1.4 http://purl.net/dol/languages/OBO/1.4
|
|-
| RDF
| Resource Description Framework (W3C Recommendation) http://purl.net/dol/languages/RDF
|
|-
| SATLIB
| Propositional logic http://purl.net/dol/languages/SATLIB
|
|-
| TPTP
| First-order logic http://purl.net/dol/languages/TPTP
|
|-
| CASL
| Common Algebraic Specification Language (subsorted partial first-order logic with induction) http://purl.net/dol/languages/CASL
|
|-
| THF0
| Higher-order logic http://purl.net/dol/languages/THF0
|
|-
|}

Ontology overview

2014-02-03T11:12:07Z

Fabian:

(This wiki page is the documentation for [http://ontohub.org/ontologies].)

On this page you get an overview of all the ontologies in a repository. You can also [[search]] the ontologies in the repository under various aspects.

Note that the ontologies (whether all ontologies or the search result is displayed) are paginated. You can
browse through the different pages by clicking on the numbers or the arrows.

Git

2014-02-02T05:21:01Z

Tillmo: /* Access with permissions */ better explanation

[http://en.wikipedia.org/wiki/Git_%28software%29 Git] is a decentralised version control system. Ontohub uses Git for maintaining [[repositories]] of ontologies.

==Access to a Git repository==
===Access for anyone===
On the main page of a repository, you find a "clone with Git" URL for cloning the repository. At the command line, with
git clone <URL>
you can create a local copy of the repository on your computer. (If you have a graphical interface for Git, enter the URL at the appropriate place for cloning).
Note that you will have only limited access to the repository, depending on its access type (for private repositories, you won't have any access, for public readable repositories, you will have read access, for public readbale and writable repositories, you also will have write access).

===Access with permissions===
If you want to have also write access, then you have to uploaded an [[SSH keys|SSH key]], and use the "clone with git-ssh" URL for cloning. Then you will have access as specified by your [[permissions]]: e.g. you get write access to an otherwise read-only repository, or you get read access to an otherwise private repository. You will also get write access to all public writable repositories - you won't need any permissions for that, but you still need to upload your ssh key (this is needed for protection against Spam).

==Working with a Git repository==
The usual working cycle is:
* make some local changes
* add the new and changed files using "git add <files>". With "git add .", you add everything.
* if needed, remove files using "git rm <files>".
* commit your changes using "git commit" or "git commit -m <message>"
* push your changes to the ontohub server with "git push"
* if someone else has pushed in the meantime, you have to get his/her commits first, using "git pull". This will merge both commits. Note that nothing can get lost, you can always restore your commit if needed.

==Pushing to an empty repository==
In this case, you need to use "git push origin master"

==Read more==
Documentation of Git and a try-out tour can be found at [http://gitscm.com/].

SSH keys

2014-02-02T05:12:59Z

Tillmo: Tillmo moved page SSH keys to SSH key: uniform singular

OntoHub uses the Secure Shell (SSH) protocol for secure communication between your local working copy of a repository and the repository on the OntoHub server. If you want to use [[git]] to interact with the OntoHub server, you will need to upload your [http://en.wikipedia.org/wiki/Secure_Shell public SSH key] to OntoHub. A description of how to generate a public key can be found here:
http://git-scm.com/book/no-nb/Git-on-the-Server-Generating-Your-SSH-Public-Key

==Ontohub pages for SSH keys==
You reach these pages via the menu available below your user name (at the top-right corner of Ontohub)
* [http://ontohub.org/keys The list of your keys]
* [http://ontohub.org/keys/new Adding a key] - you need to provide a name (needed only for your own distinction between several keys), and the public key itself.

Repository details

2014-02-02T04:41:23Z

Tillmo:

This is the main page of a [[repositories|repository]]. You can
* edit or delete the repository (top-right buttons)
* view the ontologies, the files or the history of the repository
* add ontology URLs that should be substituted by other URLs
* list the errors that Ontohub has found in the repository's ontologies
* if you own the repository, view and change the [[permissions]] of the repository, i.e. who can edit it
* get a URL for cloning the repository with [[git]]. There are two URLs: one for read access, and one for read and write access. For deatils, see [[git]].

Create repository

2014-02-02T04:31:18Z

Fabian:

If you want to '''create''' a new [[repositories|repository]], you have to enter
* name: should be short and unique
* description: this will be displayed on the main page of the repository
* access: default is public read access, while write access can be specified in the [[permissions]]. You can also chose public read and write access, but then anyone can modify or delete files in your repository (this is useful e.g. for sandboxes). For private repositories, both read and write access is regulated by the permissions.
* source address: here, you can specify the URL of an existing [[git]] or [http://en.wikipedia.org/wiki/Apache_Subversion subversion] repository. Then your new repository will become a [[mirror]] of that repository. If you want a completely fresh repository, leave this field empty.

If you want to '''edit''' an existing repository, you can change the first three items. Beware that the repository's permissions are reset if you change its access mode.

Repositories

2014-02-02T04:20:04Z

Tillmo: Tillmo moved page Repositories to Repository: uniform singular

Ontohub ist organised in [[git]] repositories, which contain collections of ontologies. Each repository contains ontology files and other files. Git provides a version control, facilities for concurrent editing and merging in case that two people have edited the same document.

==Ontohub page [http://ontohub.org/repositories http://ontohub.org/repositories]==
This page provides an overview over and links to the public repositories that are currently available.

If you are logged into Onthohub, you can create your own repository by creating the "Create Repository" button.

Access permissions can be given per repository - all ontologies in a repository inherit its permissions.

Installation

2013-12-09T23:29:37Z

Tillmo:

The '''installation''' of Ontohub is described at the [https://github.com/ontohub/ontohub/ github page].

An '''automated script''' for installation under Ubuntu 12.04 can be found [https://github.com/ontohub/ontohub/blob/develop/script/install-on-ubuntu here].
Run the script with
bash install-on-ubuntu develop
for e.g. installing the develop branch.

A '''virtual machine image''' (based on a Ubuntu 12.04.3 server guest, for use with VirtualBoc or VMWare) can be found [http://libvirt.communtu.de here].
Username and password are ontohub. Start a rails server with
cd Workspace/Ontohub
rails s
Then you can see your Ontohub instance at http://localhost:3000. If you use the VirtualBox config file, some port redirections will ensure that your port 3000 will be redirected to the VM, and you can ssh to the VM with "ssh -p 2222 ontohub@localhost". If you want to set up a productive environment, see the [https://github.com/ontohub/ontohub/ github page] for Apache etc.

Problems? Please send us an email at ontohub-dev-l@ovgu.de

DOL

2013-12-09T10:12:32Z

Tillmo: /* Documents */ OMG url

=The Distributed Ontology, Modeling and Specification Language – DOL=

The Distributed Ontology, Modeling and Specification Language (DOL) has been adopted as [http://omg.org OMG] standard in October 2018.
DOL aims at providing a unified metalanguage for
* “as-is” use of ontologies, specifications, and models (OSMs), formulated in a specific language,
* OSMs formalised in heterogeneous logics,
* modular OSMs,
* mappings (interpretations, alignments, refinements, and others) between OSMs,
* networks of OMS and mappings.

[[Ontohub]] is a web-based repository engine speaking DOL. In order to upload a DOL file to Ontohub, go to some repository. Both in the 'Ontologies' tab and in the 'Ontology files and related files', you can upload files of different types, including DOL.

==Documents==
* [http://www.omg.org/dol/ official version of the DOL standard] (freely available)
* [http://iws.cs.uni-magdeburg.de/%7Emossakow/papers/DOL-Manifesto.pdf DOL manifesto (2015)] overview of DOL syntax and semantics, with examples
* [http://iws.cs.uni-magdeburg.de/%7Emossakow/papers/Ontology-Patterns-with-DOWL-The-Case-of-Blending.pdf Ontology Patterns with DOWL: The Case of Blending] DOL for OWL users
* [http://www.iks.cs.ovgu.de/~till/papers/womo2013.pdf invited paper about DOL (2013)] overview of DOL syntax, with examples

==Ontology==
* [https://www.omg.org/spec/DOL/DOL-terms.rdf Ontology of DOL terms]

==Slides==
* [http://iks.cs.ovgu.de/~till/papers/slides-augsburg.pdf Modular and heterogeneous logical theories in DOL], Augsburg, Jan 2018
* [http://iks.cs.ovgu.de/~till/papers/GI-Logic-2017.pdf Modular and heterogeneous logical theories in DOL], GI logic group, Nov 2017
* [http://esslli2016.unibz.it/?page_id=171 DOL tutorial] at ESSLLI 2016 [http://iks.cs.ovgu.de/%7Etill/papers/dol-esslli.pdf all ESSLLI slides at once]
* [http://iws.cs.uni-magdeburg.de/%7Emossakow/papers/2015-09-21-DOL-tutorial.pdf DOL tutorial] at FroCoS 2015

==DOL examples==
* [http://ontohub.org/dol-examples DOL examples at Ontohub]
* [https://github.com/spechub/Hets-lib/tree/master/DOL DOL examples at Hets-lib].

==DOL Tools==
* [[Hets|The Heterogneous Tool Set (Hets)]] parsing, static analysis and proof management for DOL
* [[Ontohub]] a web-based ontology, model and specification repository engine
* [[emacs mode]] for DOL

==Links==
* [https://github.com/tillmo/DOL DOL development page]
* [http://ontoiop.org OntoIOp page]

Ontohub - New pages [en]

Atom

Hets

Axiom names

Emacs mode

Tutorial

How to test Ontohub

Ontohub team

SpacePortal

Ontohub

Glossary

User

Theorem

Axiom

Symbol

Single ontology

Ontology library

Mirror

Categories

Teams

Sentences

Mappings

Graphs

Ontology versions

List comments

Permissions

Metadata

Ontology

Search

Version history

Linked data

File browser

URL catalog

Logics

Ontology overview

Git

SSH keys

Repository details

Create repository

Repositories

Installation

DOL