Reblogging 2013: Release of the (beta version of the) foundational ontology library ROMULUS

From the “10 years of keetblog – reblogging: 2013”: also not easy to choose regarding research. Here, then, the first results of Zubeida Khan’s MSc thesis on the foundational ontology library ROMULUS, being the first post of several papers on the theoretical and methodological aspects of it (KCAP’13 poster, KEOD’13 paper, MEDI’13 paper, book chapter, EKAW’14 paper) and her winning the award for best Masters from the CSIR. The journal paper on ROMULUS has just been published last week in the Journal on Data Semantics, in a special issue edited by Alfredo Cuzzocrea.

Release of the (beta version of the) foundational ontology library ROMULUS; April 4

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With the increase on ontology development and networked ontologies, both good ontology development and ontology matching for ontology linking and integration are becoming a more pressing issue. Many contributions have been proposed in these areas. One of the ideas to tackle both—supposedly in one fell swoop—is the use of a foundational ontology. A foundational ontology aims to (i) serve as a building block in ontology development by providing the developer with guidance how to model the entities in a domain, and  (ii) serve as a common top-level when integrating different domain ontologies, so that one can identify which entities are equivalent according to their classification in the foundational ontology. Over the years, several foundational ontologies have been developed, such as DOLCE, BFO, GFO, SUMO, and YAMATO, which have been used in domain ontology development. The problem that has arisen now, is how to link domain ontologies that are mapped to different foundational ontologies?

To be able to do this in a structured fashion, the foundational ontologies have to be matched somehow, and ideally have to have some software support for this. As early as 2003, this issue as foreseen already and the idea of a “WonderWeb Foundational Ontologies Library” (WFOL) proposed, so that—in the ideal case—different domain ontologies can to commit to different but systematically related (modules of) foundational ontologies [1]. However, the WFOL remained just an idea because it was not clear how to align those foundational ontologies and, at the time of writing, most foundational ontologies were still under active development, OWL was yet to be standardised, and there was scant stable software infrastructure. Within the Semantic Web setting, the solvability of the implementation issues is within reach yet not realised, but their alignment is still to be carried out systematically (beyond the few partial comparisons in the literature).

We’re trying to solve these theoretical and practical shortcomings through the creation of the first such online library of machine-processable, aligned and merged, foundational ontologies: the Repository of Ontologies for MULtiple USes ROMULUS. This version contains alignments, mappings, and merged ontologies for DOLCE, BFO, and GFO and some modularized versions thereof, as a start. It also has a section on logical inconsistencies; i.e., entities that were aligned manually and/or automatically and seemed to refer to the same thing—e.g., a mathematical set, a temporal region—actually turned out not to be (at least from a logical viewpoint) due to other ‘interfering’ axioms in the ontologies. What one should be doing with those, is a separate issue, but at least it is now clear where the matching problems really are down to the nitty-gritty entity-level.

We performed a small experiment on the evaluation of the mappings (thanks to participants from DERI, Net2 funds, and Aidan Hogan), and we would like to have more feedback on the alignments and mappings. It is one thing that we, or some alignment tool, aligned two entities, another that asserting an equivalence ends up logically consistent (hence mapped) or inconsistent, and yet another what you think of the alignments, especially the ontology engineers. You can participate in the evaluation: you will get a small set of a few alignments at a time, and then you decide whether you agree, partially agree, or disagree with it, are unsure about it, or skip it if you have no clue.

Finally, ROMULUS also has a range of other features, such as ontology selection, a high-level comparison, browsing the ontology through WebProtégé, a verbalization of the axioms, and metadata. It is the first online library of machine-processable, modularised, aligned, and merged foundational ontologies around. A poster/demo paper [2] was accepted at the Seventh International Conference on Knowledge Capture (K-CAP’13), and papers describing details are submitted and in the pipeline. In the meantime, if you have comments and/or suggestions, feel free to contact Zubeida or me.

References

[1] Masolo, C., Borgo, S., Gangemi, A., Guarino, N., Oltramari, A. Ontology library. WonderWeb Deliverable D18 (ver. 1.0, 31-12-2003). (2003) http://wonderweb.semanticweb.org.

[2] Khan, Z., Keet, C.M. Toward semantic interoperability with aligned foundational ontologies in ROMULUS. Seventh International Conference on Knowledge Capture (K-CAP’13), ACM proceedings. 23-26 June 2013, Banff, Canada. (accepted as poster &demo with short paper)

Article on the Repository of Ontologies for MULtiple Uses (ROMULUS) in print with JoDS

Yay, also the paper on my student’s implementation work of her MSc thesis made it into a journal paper: the Repository of Ontologies for MULtiple Uses (ROMULUS) populated with mediated foundational ontologies is now on online-first [1] with the Journal on Data Semantics. It will appear in a special issue on extended and revised papers of MEDI’13, edited by Alfredo Cuzzocrea.

http://link.springer.com/article/10.1007/s13740-015-0052-1

Although I have mentioned the beta release of the repository earlier and noted as well that the student, Zubeida Khan, has won the CSIR prize of best Masters, that was 1-2 years ago and more has happened in the meantime.

From the technological viewpoint, there are more features available now than in the beta and MEDI’13 releases, such as the automated foundational interchangeability [2], and there’s more detail on the technologies used as well as an extended EER diagram for ontology storage and annotation, and it has an updated comparison with other repositories and usage statistics. Overall, it is the first attempt to realise the vision of an ontology library that was posed some 12 years ago in WonderWeb Deliverable D18, and it thus ended up having more features than those D18 requirements for a foundational ontology library. Have a look at ROMULUS online.

From a theoretical viewpoint, besides now having a book chapter on the mappings between the foundational ontologies [3], the ‘storyline’ and need for it—known very well in ontology engineering already—has been framed into one where the repository of the foundational ontologies is also needed for ontology-driven conceptual data modelling. Why is that so? There is an increasing amount of results on ontology-driven conceptual modelling (see ER’15 proceedings), which avails of foundational ontologies, such as UFO. There are multiple extensions to the conceptual modelling languages based on insights from ontology, and when they are based on different foundational ontologies, one can’t pick-and-choose anymore as there may be incompatibilities in how things are represented. Likewise, choosing for one foundational ontology limits, or enables, one to model one thing but not another. For instance, some do have ‘substance’ or ‘amount of matter’ (wine, alcohol and the like), others do not, so that there is, in theory, no place for such things in one’s conceptual data model. That’s not good—or at least complicates matters—for an information system or database that needs to store data about, say, a food processing plant or animal fodder. The paper presents more of such issues and how ROMULUS helps addressing them. Also, just like that ROMULUS can help choosing the most appropriate foundational ontology for ontology engineering and help analysing the foundational ontologies without reading umpteen papers on it first, it can do so for the conceptual modeller. Be this though ONSET or the web-based querying of the ontologies and their alignments.

Finally, in case you think there are shortcomings to the repository to the extent you feel the need to develop your own one: the paper provides ample material on how to build one yourself. If you don’t want to go through that trouble, then contact Zubeida or me for the feature request, and we’ll try to squeeze it in with the other activities.

 

References

[1] Khan, Z.C., Keet, C.M. ROMULUS: a Repository of Ontologies for MULtiple USes populated with foundational ontologies. Journal on Data Semantics. DOI: 10.1007/s13740-015-0052-1 (in print)

[2] Khan, Z.C., Keet, C.M. Feasibility of automated foundational ontology interchangeability. 19th International Conference on Knowledge Engineering and Knowledge Management (EKAW’14). K. Janowicz et al. (Eds.). 24-28 Nov, 2014, Linkoping, Sweden. Springer LNAI 8876, 225-237.

[3] Khan, Z.C., Keet, C.M. Foundational ontology mediation in ROMULUS. Knowledge Discovery, Knowledge Engineering and Knowledge Management: IC3K 2013 Selected Papers. A. Fred et al. (Eds.). Springer CCIS vol. 454, pp. 132-152, 2015. preprint

Zubeida Khan awarded with best Master’s thesis from CSIR

Zubeida Khan

I’m delighted to highlight here that Zubeida Khan (Dawood) was awarded with a “Best Master’s Thesis” from the CSIR (South Africa’s Council for Scientific and Industrial Research), where she was based when she did her Msc (cum laude) from UKZN, with a scholarship from the UKZN/CSIR-Meraka Centre for Artificial Intelligence Research, and yours truly as her supervisor.

Her thesis was about realising that library of foundational ontologies that had been proposed since late 2003 (in that WonderWeb deliverable D18). The concrete library is the online Repository for Ontologies of MULtiple Uses, ROMULUS, which was described briefly in the MEDI’13 paper [1], and she has a CSIR “technology demonstrator” about it (file) that received an overall panel evaluation of 90%. The theoretical foundations principally had to do with aligning and mapping the foundational ontologies that are included in the library, which are, to date, the OWL versions of DOLCE, GFO, and BFO, which has appeared in a KCAP’13 poster [2] and KEOD’13 full paper [3] and an extended version is due to appear in a best-papers-of-KEOD book [4]. In case you want to have more details: check Zubeida’s thesis, and I have a few blog posts that informally introduce the material: the first announcement of ROMULUS and the KCAP poster.

ROMULUS also contains an online and extended version of the foundational ontology recommender ONSET [5] (which was mostly her Bsc(hons) project, and whose integration into ROMULUS was part of her MSc), various documentation and browse and search features, and the new SUGOI tool for automated foundational ontology interchangeability [6].

Zubeida recently started her PhD at UCT with me as advisor, on ontology modularity, but in case you have feedback on the work, suggestions, or perhaps also new mappings to/from your favourite foundational ontology, feel free to contact her (or me)!

p.s.: Engineering news has an item about the awards, and so will CSIR have one.

p.p.s.: The minimum requirements for the award was:
-Published more than one paper in a peer reviewed publication
-Excellent behavioural attributes as attested by fellow team members such as work ethic and developing a good personal and professional relationships and an active contribution as a team member
-Above average performance score
-The studies must have been completed on a record time
-Excellent academic achievement

References

[1] Khan, Z., Keet, C.M. The foundational ontology library ROMULUS. 3rd International Conference on Model & Data Engineering (MEDI’13). A. Cuzzocrea and S. Maabout (Eds.) September 25-27, 2013, Amantea, Calabria, Italy. Springer LNCS 8216, 200-211.

[2] Khan, Z., Keet, C.M. Toward semantic interoperability with aligned foundational ontologies in ROMULUS. Seventh International Conference on Knowledge Capture (K-CAP’13), ACM proceedings. 23-26 June 2013, Banff, Canada. (poster/demo)

[3] Khan, Z., Keet, C.M. Addressing issues in foundational ontology mediation. 5th International Conference on Knowledge Engineering and Ontology Development (KEOD’13), Vilamoura, Portugal, 19-22 September. Filipe, J. and Dietz, J. (Eds.), SCITEPRESS, pp5-16.

[4] Khan, Z.C., Keet, C.M. Foundational ontology mediation in ROMULUS. invited extended version of the KEOD’13 paper, to be published in Springer CCIS.

[5] Khan, Z., Keet, C.M. ONSET: Automated Foundational Ontology Selection and Explanation. 18th International Conference on Knowledge Engineering and Knowledge Management (EKAW’12), A. ten Teije et al. (Eds.). Oct 8-12, Galway, Ireland. Springer, Lecture Notes in Artificial Intelligence LNAI 7603, 237-251.

[6] Khan, Z.C., Keet, C.M. Feasibility of automated foundational ontology interchangeability. 19th International Conference on Knowledge Engineering and Knowledge Management (EKAW’14). K. Janowicz et al. (Eds.). 24-28 Nov, 2014, Linkoping, Sweden. Springer LNAI 8876, 225-237.

Release of the (beta version of the) foundational ontology library ROMULUS

With the increase on ontology development and networked ontologies, both good ontology development and ontology matching for ontology linking and integration are becoming a more pressing issue. Many contributions have been proposed in these areas. One of the ideas to tackle both—supposedly in one fell swoop—is the use of a foundational ontology. A foundational ontology aims to (i) serve as a building block in ontology development by providing the developer with guidance how to model the entities in a domain, and  (ii) serve as a common top-level when integrating different domain ontologies, so that one can identify which entities are equivalent according to their classification in the foundational ontology. Over the years, several foundational ontologies have been developed, such as DOLCE, BFO, GFO, SUMO, and YAMATO, which have been used in domain ontology development. The problem that has arisen now, is how to link domain ontologies that are mapped to different foundational ontologies?

To be able to do this in a structured fashion, the foundational ontologies have to be matched somehow, and ideally have to have some software support for this. As early as 2003, this issue as foreseen already and the idea of a “WonderWeb Foundational Ontologies Library” (WFOL) proposed, so that—in the ideal case—different domain ontologies can to commit to different but systematically related (modules of) foundational ontologies [1]. However, the WFOL remained just an idea because it was not clear how to align those foundational ontologies and, at the time of writing, most foundational ontologies were still under active development, OWL was yet to be standardised, and there was scant stable software infrastructure. Within the Semantic Web setting, the solvability of the implementation issues is within reach yet not realised, but their alignment is still to be carried out systematically (beyond the few partial comparisons in the literature).

We’re trying to solve these theoretical and practical shortcomings through the creation of the first such online library of machine-processable, aligned and merged, foundational ontologies: the Repository of Ontologies for MULtiple USes ROMULUS. This version contains alignments, mappings, and merged ontologies for DOLCE, BFO, and GFO and some modularized versions thereof, as a start. It also has a section on logical inconsistencies; i.e., entities that were aligned manually and/or automatically and seemed to refer to the same thing—e.g., a mathematical set, a temporal region—actually turned out not to be (at least from a logical viewpoint) due to other ‘interfering’ axioms in the ontologies. What one should be doing with those, is a separate issue, but at least it is now clear where the matching problems really are down to the nitty-gritty entity-level.

We performed a small experiment on the evaluation of the mappings (thanks to participants from DERI, Net2 funds, and Aidan Hogan), and we would like to have more feedback on the alignments and mappings. It is one thing that we, or some alignment tool, aligned two entities, another that asserting an equivalence ends up logically consistent (hence mapped) or inconsistent, and yet another what you think of the alignments, especially the ontology engineers. You can participate in the evaluation: you will get a small set of a few alignments at a time, and then you decide whether you agree, partially agree, or disagree with it, are unsure about it, or skip it if you have no clue.

Finally, ROMULUS also has a range of other features, such as ontology selection, a high-level comparison, browsing the ontology through WebProtégé, a verbalization of the axioms, and metadata. It is the first online library of machine-processable, modularised, aligned, and merged foundational ontologies around. A poster/demo paper [2] was accepted at the Seventh International Conference on Knowledge Capture (K-CAP’13), and papers describing details are submitted and in the pipeline. In the meantime, if you have comments and/or suggestions, feel free to contact Zubeida or me.

References

[1] Masolo, C., Borgo, S., Gangemi, A., Guarino, N., Oltramari, A. Ontology library. WonderWeb Deliverable D18 (ver. 1.0, 31-12-2003). (2003) http://wonderweb.semanticweb.org.

[2] Khan, Z., Keet, C.M. Toward semantic interoperability with aligned foundational ontologies in ROMULUS. Seventh International Conference on Knowledge Capture (K-CAP’13), ACM proceedings. 23-26 June 2013, Banff, Canada. (accepted as poster &demo with short paper)