CiTO + SWAN: The Web Semantics of Bibliographic Records, Citations, Evidence and Discourse Relationships

Paper Title: 
CiTO + SWAN: The Web Semantics of Bibliographic Records, Citations, Evidence and Discourse Relationships
Paolo Ciccarese, David Shotton, Silvio Peroni and Tim Clark
Most literature searching in biomedicine is now conducted via PubMed, Google Scholar or other web-based bibliographic search mechanisms. Yet until now a public, open, interoperable and complete web-adapted information schema for bibliographic citations, bibliographic references and scientific discourse has not been available. Such a schema, expressed in the form of a description logic compatible with current web semantics approaches, would provide the ability to treat bibliographic references and citations, and rhetorical discourse in scientific publications, as semantic metadata on the web, with all the benefits that implies for organization, search and mash-up of web-based scientific information. In this paper we present CiTO + SWAN, a set of fully harmonized ontology modules resulting from the harmonization of CiTO (the Citation Typing Ontology) with SWAN (Semantic Web Applications in Neuromedicine), which we have developed by jointly adapting and evolving version 1.6 of CiTO, the Citation Typing Ontology, and version 1.2 of the SWAN Scientific Discourse Ontology (v1.2). The CiTO + SWAN model is specified in OWL 2 DL, is fully modular, and inherently supports agent-based searching and mash-ups. Through the harmonization activity presented here, and previous work that harmonized SWAN with the SIOC (Semantically-Interlinked Online Communities) Ontology for describing blogs, wikis and discussion groups, we have construct the basis of a powerful new web framework for scientific communications.
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This is a revised version, now accepted, after an "accept with minor revisions". The reviews below are from the original submission.

Solicited review by John Westbrook:

The authors report on the harmonization of ontologies representing citation typing and discourse in the field of neuroscience. In describing their work the authors present a very high-level description of the importance of ontologies and semantic alignment, and then jump into the details of the particular semantic challenges in this domain. While the latter is the bulk of the hard work that has been done here, there is perhaps some room for additional examples to that have motivated this body of work.

The introductory section describing ontologies and importance of semantic harmonization is rather generic and not well associated to the topic at hand. One could easily begin this manuscript with the section that begins with "The ontology harmonization activity described in this paper…".

Rather than present this generic discussion, the manuscript would be strengthened with the inclusion of a broader set of use cases. For example, some of the following could be described:
• The mechanism for inking conventional and open source publications with blog and forum entities where a single URL may embody a range of opinions.
• Integration with emerging schemes for identifying individual contributors and researchers.
• The mechanics of handling the retraction of citations not accompanied by a body of literature describing the reason for the retraction.

Either the wrong version of Figure 7 is provided in the Conclusion section or this figure and its description add little to the discussion.

Solicited review by Cameron Neylon:

The effective harmonisation and integragtion of complementary and competitive ontologies is a key area for development if the promise of semantic web technologies in the sciences is to be realised. This paper describes the harmonisation of two suites of ontologies, both of which are gaining significant use, and which had the potential to become competing standards.

The paper offers two important contributions. The first is the harmonised suites of ontologies themselves, the second is a clearly described example of the process of such harmonisations. The process, challenges, and the conditions that made the harmonisation feasible are clearly described and this will be useful for future efforts.

The manuscript reads very clearly throughout and key issues are well described. A minor suggestion which may help the naive reader would be to signpost specific issues via subheadings. There are a number of key points made, distinction between citation as an act and the citation as the thing being cited, directionality of citation, importance of distinctions within FRBR and manifestations. My feeling is that incorporating those statements as subheadings could help guide the reader to the key points.

From my perspective I think it would have been helpful for one of "before and after" examples to appear in the main text. This might mean bringing the supplementary figure into the main text (the supplementary figure isn't included in the document I have reviewed) or alternately showing a before and after version of Figure 1. A visual representation of how this has changed and new connections have been forged would have been helpful for me to understand the changes.

Finally, it would be valuable, although I appreciate not straightforward, to see some more detail on the social processes by which agreement on issues was reached and in particular how disagreements were resolved. Was resolution through a purely consensus approach, reached by argumentation? Were rules of engagement or resolution agreed in advance? Are there suggestions on how best to approach harmonisation activities, particularly as the size of groups involved increases?



We have read and carefully considered the reviewers' suggestions for minor changes to our paper, and we thank them for their thoughtful ideas, many of which we have incorporated in a revised version of the paper which we now submit for publication.

The specific points raised, with our responses, are shown below.

Response to reviewers' suggestions for minor changes

1. Reviewer #1 suggested we delete the introductory material, replacing it with more use cases. However reviewer #2 did not request this change nor did he see a need for additional use cases. We think the introductory material should be kept, and have made no changes here, in agreement with the second reviewer.

2. The first reviewer suggested that Figure 7 was superfluous and added little to the discussion, with the implication that it may be confusing as well. We have accordingly dropped Figure 7.

3. Reviewer #2 asked us to add subheadings to highlight several issues he felt were important to call to the reader's attention. We have added 12 subheadings covering the key points he suggested we highlight, as well as several others of similar importance.

4. Reviewer #2 suggested we include more "before and after" examples in the main text. We feel that Tables 3, 4 and 5 sufficiently will cover the reviewer's suggestion if included in the main text. We did not choose to include an additional "before and after" version of Figure 1, as we felt it would be distracting to the reader.

5. Reviewer #2 also asked to see some more detail on the social processes by which agreement on issues was reached, with suggestions on how best to approach harmonisation activities in general. We have added a subsection with comments on the social process issues we felt were most important and generalizable.

Kind regards,

Tim Clark