Introducing metrics in the lattice to build ontology

Tracking #: 721-1931

Authors: 
My Thao Tang
Yannick TOUSSAINT

Responsible editor: 
Guest Editors EKAW 2014 Schlobach Janowicz

Submission type: 
Conference Style
Abstract: 
Formal Concept Analysis (FCA) (\cite{ganter99}) which is a formal conceptualisation method offers several advantages for building ontology. The hierarchical structure of the lattice resulting from FCA suits well the need for organizing classes in an ontology from general to most specific concepts. The lattice can be considered as the knowledge model from which, domain experts can select the concepts to build ontology. However, the task evaluation of the lattice can be impractical if domain experts have to evaluate all the concepts and it is not easy to handle if they want to change something in the lattice to make it more in accordance with their needs. In this paper, we conduct a study of using metrics in the lattice to build ontology. The metrics are introduced in the lattice to support domain experts in the tasks evaluation and refinement. In this work, firstly, we learn various metrics that are defined for ontology evaluation and lattice; secondly, we apply them to analyze the lattice, identify the set of metrics that can work for our goal and propose the way of using them to support efficiently evaluation and refinement of the lattice. The experiment results confirm that the use of the metrics is helpful to facilitate the lattice evaluation and refinement.
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Decision/Status: 
[EKAW] reject

Solicited Reviews:
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Review #1
Anonymous submitted on 24/Aug/2014
Suggestion:
[EKAW] conference only accept
Review Comment:

Overall evaluation
Select your choice from the options below and write its number below.

== 3 strong accept
== 2 accept
== 1 weak accept
=X= 0 borderline paper
== -1 weak reject
== -2 reject
== -3 strong reject

Reviewer's confidence
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== 5 (expert)
== 4 (high)
=X= 3 (medium)
== 2 (low)
== 1 (none)

Interest to the Knowledge Engineering and Knowledge Management Community
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=X= 5 excellent
== 4 good
== 3 fair
== 2 poor
== 1 very poor

Novelty
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== 5 excellent
=X= 4 good
== 3 fair
== 2 poor
== 1 very poor

Technical quality
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== 5 excellent
== 4 good
=X= 3 fair
== 2 poor
== 1 very poor

Evaluation
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== 5 excellent
== 4 good
=X= 3 fair
== 2 poor
== 1 not present

Clarity and presentation
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== 5 excellent
=X= 4 good
== 3 fair
== 2 poor
== 1 very poor

Review
Please provide your textual review here.

This paper introduces a set of metrics for lattices in Formal Concept Analysis as support for ontology design.
The paper raises many interesting issues, but it falls short in some respects.

The motivation for the evaluation procedures in Section 4.1 needs to be
improved. Why should the metrics have any impact on ontology design?
Does Algorithm 1 really change the way in which ontologies are designed?

The statement at the bottom of page 6 is puzzling:
"experts prefer the concepts that have many objects and
choose the objective metric NOO for evaluation."

Do the authors really mean
" suppose a set of experts prefer the concepts that have many objects and
choose the objective metric NOO for evaluation." ?

Otherwise, this is a strong claim that needs substantiation.

Section 4.2 is a list of heuristics, without any discussion or critical
analysis.

The central question of Section 5:

"Can the metrics support experts in making decisions on
changes and protecting important concepts from changes?"

is never really addressed.

There are similar difficulties in Section 6.
Consider the statement near the top of page12:
"When experts evaluate a concept, the metric values help them in sug-
gesting refinement and making decision on changes in the refinement process."

Is this statement a claim or a conclusion?

Overall, there should be more statistical analyses of the experimental results,
rather than the subjective evaluation displayed in statements such as
"From the experiment results, we observed that the metrics adapted from
ontology metrics are helpful in evaluating and refining the lattice"

Editorial Comments:
There are numerous grammatical errors, primarily caused by missing articles
and prepositions.

Review #2
Anonymous submitted on 25/Aug/2014
Suggestion:
[EKAW] conference only accept
Review Comment:

Overall evaluation
Select your choice from the options below and write its number below.

== 3 strong accept
== 2 accept
1 weak accept
== 0 borderline paper
== -1 weak reject
== -2 reject
== -3 strong reject

Reviewer's confidence
Select your choice from the options below and write its number below.

== 5 (expert)
== 4 (high)
3 (medium)
== 2 (low)
== 1 (none)

Interest to the Knowledge Engineering and Knowledge Management Community
Select your choice from the options below and write its number below.

== 5 excellent
4 good
== 3 fair
== 2 poor
== 1 very poor

Novelty
Select your choice from the options below and write its number below.

== 5 excellent
== 4 good
3 fair
== 2 poor
== 1 very poor

Technical quality
Select your choice from the options below and write its number below.
== 5 excellent
== 4 good
3 fair
== 2 poor
== 1 very poor

Evaluation
Select your choice from the options below and write its number below.
== 5 excellent
== 4 good
== 3 fair
2 poor
== 1 not present

Clarity and presentation
Select your choice from the options below and write its number below.
== 5 excellent
== 4 good
3 fair
== 2 poor
== 1 very poor

Review
Please provide your textual review here.

This paper proposes to assess several metrics on a lattice for helping experts build/refine an ontology.
The paper is interesting and relevant to EKAW.
The interest resides more in the assessment of existing metrics than in the development of new metrics, which is fine.
The application to a small set of triples extracted from the biomedical literature is interesting and somewhat original.

The main problem here is that the observations made about the metrics and the help they provide to experts amount more to anecdotal evidence of usefulness than to a real fledged evaluation. Moreover, the task used for the evaluation is not entirely specified, nor is the qualification of the experts.

Overall, this work seems preliminary, but the authors should be encouraged to pursue their investigation.

Moreover, this manuscript requires significant editing by a native speaker of English. The grammatical errors and improprieties, however, do not impede comprehension.

Minor comments
- SemRep is used in an application called SemanticMedline, that produces summaries of the relations extracted from PubMed articles. Although based on graphs, rather than lattices, this application also uses various graph-based metrics, some of which are close to your metrics (e.g., degree centrality). This would be worth discussing.
- There are other applications of FCA and lattices to biomedical ontologies, which seem relevant to this investigation. For example:
@inproceedings{DBLP:dblp_conf/semweb/ZhangB10,
author = {Guo-Qiang Zhang and
Olivier Bodenreider},
title = {Using SPARQL to Test for Lattices: Application to Quality Assurance in Biomedical Ontologies.},
booktitle = {International Semantic Web Conference (2)},
year = {2010},
pages = {273-288},
ee = {http://dx.doi.org/10.1007/978-3-642-17749-1_18},
crossref = {2010},
}
1: Jiang G, Chute CG. Auditing the semantic completeness of SNOMED CT using
formal concept analysis. J Am Med Inform Assoc. 2009 Jan-Feb;16(1):89-102. doi:
10.1197/jamia.M2541. Epub 2008 Oct 24. PubMed PMID: 18952949; PubMed Central
PMCID: PMC2605587.

Review #3
Anonymous submitted on 11/Sep/2014
Suggestion:
[EKAW] conference only accept
Review Comment:

Overall evaluation
Select your choice from the options below and write its number below.

== 3 strong accept
== 2 accept
== 1 weak accept
XX 0 borderline paper
== -1 weak reject
== -2 reject
== -3 strong reject

Reviewer's confidence
Select your choice from the options below and write its number below.

== 5 (expert)
== 4 (high)
XX 3 (medium)
== 2 (low)
== 1 (none)

Interest to the Knowledge Engineering and Knowledge Management Community
Select your choice from the options below and write its number below.

== 5 excellent
XX 4 good
== 3 fair
== 2 poor
== 1 very poor

Novelty
Select your choice from the options below and write its number below.

== 5 excellent
== 4 good
XX 3 fair
== 2 poor
== 1 very poor

Technical quality
Select your choice from the options below and write its number below.
== 5 excellent
== 4 good
XX 3 fair
== 2 poor
== 1 very poor

Evaluation
Select your choice from the options below and write its number below.
== 5 excellent
== 4 good
== 3 fair
XX 2 poor
== 1 not present

Clarity and presentation
Select your choice from the options below and write its number below.
== 5 excellent
XX 4 good
== 3 fair
== 2 poor
== 1 very poor

Review

This paper describes an approach to guiding users through the process of editing the concepts in an FCA lattice based on some quality metrics. The intent is to then convert the lattice into an ontology in a later stage.

Despite some recurring grammatical issues, the paper is very clearly written, well organized, and engaging. The problems that the paper attempts to address are stated clearly in the introduction, and the description of FCA is intuitive enough that the paper stands alone even for non-experts. For each metric used in the system, both a formal and intuitive definition is given, along with how it relates to the goal of evaluation and refinement of the FCA lattice, an example value based on a simple lattice, and references to any similar ontology-based metrics.

The paper is lacking in two main areas: there is no discussion of related work and the evaluation is limited. For the related work, I expected a discussion of at least interactive ontology building and/or validation, even if there is no directly related work on FCA lattices. The analysis given in Section 6.2 draws conclusions based on only a single dataset. Most of the results presented in this section are negative, in that the human users did not behave in accordance with the metrics in many cases. The authors speculate on the causes for this and revised their algorithm to compensate, but then the paper says that these changes produced better results, with no further detail or supporting data.

Some small questions:

What does "detailed and prototypical of their abstractions" mean with respect to the discussion of middle level concepts on page 5?

Why was DM normalized when none of the other metrics were?

What drove the decision to use r-b for the attributes rather than the alternative mentioned of r and r^-1?

A couple of minor grammatical things:

Instead of "the tasks evaluation and refinement" it would be better to say "the evaluation and refinement tasks" or just "the evaluation and refinement"

Instead of "loose" it should be either "loss" or "lose" for most of your purposes, e.g. "which will lead to loose the smallest number" should be "which will lead to the loss of the smallest number" or "which will lose the smallest number"

I think that "The greater DIT value is, the deeper the abstraction level of the concept is and the more concepts are inherited from this concept." should possibly be "the more concepts are inherited *by* this concept", since concepts further from the top concept have more superclasses rather than more subclasses.

Review #4
Anonymous submitted on 14/Sep/2014
Suggestion:
[EKAW] reject
Review Comment:

Overall evaluation
Select your choice from the options below and write its number below.

== 3 strong accept
== 2 accept
== 1 weak accept
X 0 borderline paper
== -1 weak reject
== -2 reject
== -3 strong reject

Reviewer's confidence
Select your choice from the options below and write its number below.

== 5 (expert)
== 4 (high)
X 3 (medium)
== 2 (low)
== 1 (none)

Interest to the Knowledge Engineering and Knowledge Management Community
Select your choice from the options below and write its number below.

== 5 excellent
X 4 good
== 3 fair
== 2 poor
== 1 very poor

Novelty
Select your choice from the options below and write its number below.

== 5 excellent
== 4 good
== 3 fair
X 2 poor
== 1 very poor

Technical quality
Select your choice from the options below and write its number below.
== 5 excellent
== 4 good
X 3 fair
== 2 poor
== 1 very poor

Evaluation
Select your choice from the options below and write its number below.
== 5 excellent
== 4 good
X 3 fair
== 2 poor
== 1 not present

Clarity and presentation
Select your choice from the options below and write its number below.
== 5 excellent
== 4 good
X 3 fair
== 2 poor
== 1 very poor

Review:

The paper entitled 'Introducing metrics in the lattice to build ontology' presents an approach that supports ontology engineers in deriving ontologies out of lattices. The topic as such is interesting and relevant for EKAW 2104.

The paper is clearly structured and the used figures and tables illustrate the presented ideas well. Unfortunately, even the updated version of the paper contain numerous grammatical errors and typos. They start with the title and continue all the way down to the references. Nonetheless, I would rate this paper as readable.

I have two major concerns that prevent me from giving the paper a higher rating.

First, the contribution and novelty are very limited. In fact, the paper largely relies on existing metrics and the only real contribution of the paper is the way they are applied to support ontology engineers or domain experts. This part, however, is rather naive and does not go beyond Algorithm 1 (which is just a top-down iteration of the lattice) and two different variations: bottom-up and middle-out. Unfortunately, the real problem in engineering ontologies and deriving ontologies from data or lattices is _not_ the order in which potential concepts are displayed to domain experts and ontology engineers. Additionally, the difficult problems of naming concepts, the fact that extracting ontologies from text turned out not to be very effective, etc are not addressed. From what I understand, the only really novel part is the impact index.

Second, the evaluation is rather descriptive/anecdotal and the lessons learned (i.e., the discussion section) are limited. For instance, it is well known that NOC and CI will not perform well. Think of continents as an example in comparison to Sand; or of Monotypic taxa in evolutionary biology. Finally, it is not clearly demonstrated how and whether the proposed approach supports domain experts 'in the task evaluation and refinement'. Ideally, the paper would have focused on this part and explain it in more detail.

Summing up, while the topic is relevant for EKAW, the paper does not add much in terms of novel methods, novel applications, or lessons learned.