Perspectives in Knowledge Formalization for Scientific Collaborative Research: the case of Plastic pollution in the sea

Tracking #: 1924-3137

Paolo Diviacco
Dmitry Pavlov
Alessandro Busato
Yury Emelianov
Ariadna Barinova
Tomaso Fortibuoni
Dmitry Mouromtsev
Francesca Malfatti

Responsible editor: 
Guest Editors Knowledge Graphs 2018

Submission type: 
Full Paper
Collaborative scientific research is based on sharing observations and resources. This implies some form of convergent cognition and mutual understanding, which is often not easy to achieve especially when researchers come from different disciplinary background, but also when they work in the same domain but live within different paradigms. To support and ease these activities, we propose to embed boundary objects into web based collaborative software. Boundary objects are artifacts, such as graphs, maps, software, abstract or concrete objects that being weakly structured in a common use, while strongly structured in individual use, facilitate communication between multiple social worlds. We report on how boundary objects can be implemented in a collaborative software by means of graphic maps derived from an ontology that at the same time formalise knowledge, allow implicit meaning to emerge from how data, information and communication is spontaneously organized by users, and link to controlled vocabularies widely recognized by the designated communities.
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Solicited Reviews:
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Review #1
Anonymous submitted on 06/Aug/2018
Review Comment:

Although the paper is well written, it is unclear what the contribution of the work is as a work of computer science. The introduction and context of the paper is very broad, investing in significant discourse explaining concepts that would be well-understood to the readership of the journal. Explanations of the differences between ontologies, controlled vocabularies, and 'graphical maps' are unnecessary, as is the lengthy description of the boundary object construct. The presentation of ontologies as boundary objects is hardly original and although some of the core concepts presented are presented in an intriguing way ('boundary objects are ... weakly structured in a common use and strongly structured in individual use'), there is insufficient formalization of these ideas as concrete experiments or investigations.

In particular, the technical contribution seems to be based on the development of a tool (COLLA), whose source code does not seem to be available online. The presentation of the tool's design in the paper revolves around the use of small (unreadable) screenshots. Again, it seems unclear what the scientific contribution of this work would be to the semantic web community since well-established, existing tools provide the same graphical functionality presented here.

The use case presented appears as a fairly simple mapping from a small conceptual diagram into a knowledge graph. The diagram itself is also difficult to read. It is not clear what the utility of the semantic representation is, who the target audience is or what data-driven tasks this would be applicable to.

Finally, the style of writing is reminiscent of philosophy rather than original research in computer science. For example: "The assonance with representation in the arts, is not only casual then, but reasonable, as in the arts the role of the artist is central in shaping reality and the product of art is the vision of the artist, but at the same time art consumers are free to construct their experience upon what they perceive." Although, I personally enjoyed the sophistication of the point being made, it is verbose, irrelevant, and not really suitable in a technical computer science research article.

I would suggest that the authors focus more heavily on the technical elements of their work, and identify a more urgent and immediate use case. If they are investigating pollution, for example, they should be able to demonstrate its utility to domain scientists working in the field. They should strive a little harder to make their work available for scrutiny (by publishing their code and data for reuse by other researchers).

Review #2
By Raul Alejandro Vargas-Acosta submitted on 16/Aug/2018
Major Revision
Review Comment:

This manuscript was submitted as 'full paper' and should be reviewed along the usual dimensions for research contributions which include (1) originality, (2) significance of the results, and (3) quality of writing.

This paper presents an ontology-based framework that aims to reach knowledge formalization among different disciplines. The authors present the concept of a “boundary object,” a simple artifact that can be used to interact with people from other culture, and propose to use an ontology as a boundary object so researchers from different disciplines or even among the same discipline but within different perspectives can come to an agreement.

For this purpose, the authors present COLLA, a web-based application that is able to receive as input an RDF and allows the user to generate graphs with different levels of granularity depending on the users’ requirements. This RDF contains a domain of discourse and has to be generated previously using third-party tools.

The paper gives a brief but concise definition for boundary object and the study case.
The authors give a good analysis of both the weaknesses and strengths of ontology-based solutions.

Related work
No information is given related to other approaches, or researchers using this approach for this context (boundary objects).
It needs to analyze evaluation of boundary objects and the effectiveness of a boundary object to allow effective communication. In [1, 2] they state that they may “be perceived or used differently over time”.


The challenge that the authors aim to solve is of recognized importance.

The authors give basic definitions of jargon used in the paper. (e.g., boundary object, Apache Jena Fuseki, ontology, triple)
Technical quality:

The paper does not show explicit details of the evaluation of COLLA (linked data used, number of members of the team, members’ background, experience on ontologies, etc.).

Future work
A comparison could be given concerning OWL visualization.
An evaluation could be made to use COLLA under different study cases.

• It is not clear if the authors developed COLLA or if it was developed by a third-party and they are just reviewing it.
• No PURL is given for COLLA.
• No evaluation of COLLA could be made by this reviewer given the fact that no PURL is found in the paper.
• No analysis is given for COLLA’s learning curve neither for researchers that have no experience of ontologies and have to use COLLA.
• As a conclusion, it is stated that the authors feel confident that their “collaborative environment approach can complement e-Research effectively,” this should also be addressed in future work.
• At the beginning of “conclusions,” the authors state that their proposal can be used to “ease collaborative work in scientific research.” How is “ease” measured?
• How is the ontology, that is used for this study-case, validated?
• No details are given on the output of COLLA, can the graphs be exported?

Given that the main research question tried to prove that an ontology-based framework can be used as a boundary object but lacked evidence of the proofs, it needs improvement.

To what extent can this solution be used in a different context? (e.g., languages, disciplines)

1. Pennington, D.: The dynamics of material artifacts in collaborative research teams. Computer Supported Cooperative Work. 19, 175–199 (2010)
2. Akkerman, S.F., Bakker, A.: Boundary crossing and boundary objects. Review of educational research. 81, 132–169 (2011)

Review #3
By Daniel Garijo submitted on 19/Aug/2018
Review Comment:

This paper present an extension to COLLA, a tool to develop, integrate and populate ontologies to ease discussion and collaboration in scientific research. The authors provide an example use case in the domain of plastic pollution.

The paper reads well and it's easy to follow. The topic addressed is not new, but it's very relevant to the Semantic Web community and in particular to the SWJ journal. We need more approaches and frameworks that help bridge the gap between knowledge engineers and domain scientists, and I like how the authors have tried to combine modeling and examples to do so. However, I don't think the paper meets the quality criteria to be accepted in the journal. I detail below the main reasons why I think the paper should be rejected.

- The contribution of the work is not clear: By reading the abstract and implementation, it is not clear what the authors are proposing in the paper. Is it a new framework? Is it a new model or methodology? By Section 3.4 I see that what the authors propose is to extend COLLA to facilitate collaboration of scientists when formalizing and populating a domain of interest. However it is not clear to me how this is related to collaboration, as it is not mentioned how a different team of researchers have used COLLA to build or populate an ontology/KG.

- Related work: There are plenty of works in environments for collaborative ontology development (or KG population), and none of them are mentioned in the paper. Some examples are Web Protege, OntoWiki, the Linked Earth Wiki, Moki, LexWiki, etc. Other work uses graph-based editors to create ontologies, such as WebVowl. I don't understand why the proposed extension to COLLA is new, or how is it different from all these existing systems. Most of these systems also use instances to illustrate what a concept means.

- Use case: A use case is presented with a lot of details on the specific domain, but not why these make it difficult or cumbersome to build it with existing tools. What are the challenges in the domain? In addition, the use case does not showcase at all the collaborative aspect of the tool, which is what the paper claims. Also, the methodology used to build the ontology is not clear, and the result of it (its URI) is not available in the paper.

- Evaluation: there is no evaluation of the tool/framework/approach. The statistics on the survey presented to users are completely opaque, without even showing the number of users who participated, or what were the main goals to achieve. How do we know that the tool was useful to reach consensus? How are boundary objects "facilitating communication between different social worlds"? All these aspects are not addressed in the paper.

- Availability of the tool: the tool is briefly described but not made available for review.

- COLLA: The diagrams look fantastic, but it's not clear to me what kind of assertions you can do in COLLA besides domain and ranges. What can you do in COLLA that you cannot do in other tools/approaches?


- Given that this is a journal about semantics, having sections 2.1 and 2.2 seem unnecessary, as most of the readers are familiar with the concept of ontologies and controlled vocabularies.

- Figure 4 cannot be read very well when zooming in.