Bringing phytopathology onto the reasoned Semantic Web: the Plant-Pathogen Interactions Ontology (PPIO)

Tracking #: 628-1838

Alejandro Rodriguez Iglesias

Responsible editor: 
Guest Editors Semantics for Biodiversity

Submission type: 
Ontology Description
Interactions between plants and plant-pathogenic bacteria have both scientific and economic importance, and are particularly relevant in the domain of biodiversity. While semantically-oriented resources exist that describe certain aspects of plant phenotypes, biodiversity, and plant disease, few are designed specifically to be used together with rich semantic reasoning, and none are specifically aimed at describing the interplay between plants and the organisms that infect them. We present here the Plant-Pathogen Interactions Ontology (PPIO), whose axiomatic models allow the integration of, and inference over, plant- pathogen interaction datasets in a semi- or fully-automated manner.
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Solicited Reviews:
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Review #1
By Ramona Walls submitted on 30/Jun/2014
Review Comment:

This manuscript describes initial development of the Plant-Pathogen Interactions Ontology (PPIO). The introduction is well written and clearly lays out the need for an ontology to cover plant-pathogen interactions. Furthermore, the manuscript contains many commendable ideas of how to develop such an ontology, such as using logical definitions (equivalence axioms) to classify instance data and importing existing classes from existing ontologies. Where it falls short is in the actually execution. As described in more detail below, there are many areas where improvement is needed in the PPIO before it is ready for publication.

Comments on specific sections of the manuscript:

Design principles and high-level overview of classes:
The “disease triangle” is a reasonable framework for modeling plant-pathogen interactions. I think a figure that links the conceptual model to the ontological model would be useful, especially for justifying how the creation of two ontology classes (Environmental parameter and Organism) represent the three concepts in the triangle.

Organism and use of taxonomy classes:
The organism class should be imported from the Common Anatomy Reference Ontology (CARO), rather than creating a new PPIO class. Likewise, PPIO:plant should be imported from NCBI-taxon (Viridiplantae). NCBI hierarchy is imported, but generally not used in the ontology. The manuscript says that the subclasses of PPIO:Organism are linked to NCBI classes, but there are no links in the ontology.

Logical definitions:
The definition of PPIO:host plant includes both “Plant and susceptible to some plant pathogen” as well as “Plant and expresses phenotype some Susceptibility phenotype”. These seem somewhat redundant. The definitions of ‘susceptible to’ and ‘Susceptibility phenotype’ should imply one another. As it is now, the authors have to maintain two separate hierarchies (one for relations and one for phenotypes), which makes it harder to maintain the ontology. Nonetheless, I laud the authors’ effort to use logical definitions to automatically classify data.

Phenotype classes:
There are multiple published examples of phenotype ontologies (e.g., Gkoutos et al. 2005; Köhler et al. 2013; Dahdul et al. 2010; Park et al. 2013), and the authors should review their design patterns and consider using some type of entity-quality model. While the entity-quality model is not the only valid way to model phenotypes, it does have a lot of merit and is widely used. Currently, logical definitions of phenotypes in the PPIO omit the entity, which can lead to incorrect inferences. For example, PPIO:Abnormal growth development phenotype is defined as equivalent to “modifies some cell growth development trait”. When the reasoner is run, it infers that PPIO:Necrotic lesion is equivalent to Abnormal growth development trait, but Necrotic lesion is a subclass of PPIO:Phenotypcic process, so this does not make sense.

Phenotypic process classes:
These terms are biological processes and should be developed in conjunction with the Gene Ontology, as subclasses of the GO:biological process class. The names for most of the classes here are ambiguous and seem to refer to material entities rather than processes. For example, “necrotic lesion” should refer to an actual lesion, which is a material entity, but this class instead refers to a process. A better name would be something like “lesion formation process”.

Trait classes:
There is no need for the class PPIO:Trait as a superclass of TO:plant trait. Instead, just replace PPIO:Trait with TO:plant trait. The manuscript says that the Trait class is axiomatically related to both the Phenotype and Phenotypic process classes within the PPIO, but in fact there are no axioms among those classes. What should be done is to add axioms linking specific PPIO phenotypics to specific subclasses of TO:plant trait.

How do you plan to integrate with Darwin Core? It is not clear what the relationship between PPIO and Darwin Core annotated data would be.

The link to the prototype data collection portal ( does not work.

The intention to automate ontology development is admirable and important, but without proper (human generated) knowledge model behind it, the PPIO cannot effectively organize plant disease data.

General comments about the ontology

No text definitions for most classes, only comments on some terms! Textual definitions are very important for human users and can act as check to insure that logical definitions are correct.

All of the logical definitions lack a subject and therefor are they are very broad and likely to lead to incorrect inference. For example, PPIO:Pathogen physiology trait is defined as PPIO:trait of some PPIO:Plant pathogen, where “trait of” is a property. Using an Aristotlean or genus-differentia definition (which is a more common practice in ontologies), this would be defined first as a subclass of trait: trait and trait_of some Plant pathogen. (Also, this definition is too broad, as it includes all traits of plant phathogens, not just physiological traits). Another example of incorrect inference due to poorly constructed logical definitions is that TO:tiller number is inferred to be a subclass of PPIO:Phenotypic process.

It is not clear why some of the TO traits show up as direct subclasses of “Thing” (e.g., internode color, leaf collar color) rather than in their appropriate place in the TO hierarchy.

All of the phenotype classes are defined logically using the “modifies” relation, but this relation is not defined, so it is hard to know what is actually meant by the definitions of phenotypes and phenotypic processes, but there are in fact no relations among PPIO:Trait, PPIO:Phenotype, and PPIO:Phenotypic process. What should be added is axioms linking specific phenotypes in PPIO to specific PO:trait subclasses. In fact, none of the relations are defined. However, they do specify domains and ranges, which is good.

What is the justification for modeling pathogens as individuals rather than classes?

Class names should not be capitalized.

The constructions of class URIs is good (use of numbers rather than term names).


Dahdul, Wasila M, James P Balhoff, Jeffrey Engeman, et al.
2010 Evolutionary Characters, Phenotypes and Ontologies: Curating Data from the Systematic Biology Literature. PloS One 5(5): e10708.

Gkoutos, Georgios V., E.C.J. Green, A.M. Mallon, J.M. Hancock, and D. Davidson
2005 Using Ontologies to Describe Mouse Phenotypes. Genome Biology 6(1): R8.

Köhler, Sebastian, Sandra C. Doelken, Christopher J. Mungall, et al.
2013 The Human Phenotype Ontology Project: Linking Molecular Biology and Disease through Phenotype Data. Nucleic Acids Research: gkt1026.

Park, Carissa A, Susan M Bello, Cynthia L Smith, et al.
2013 The Vertebrate Trait Ontology: A Controlled Vocabulary for the Annotation of Trait Data across Species. Journal of Biomedical Semantics 4(1): 13.

Review #2
By Birgitta Koenig-Ries submitted on 07/Oct/2014
Major Revision
Review Comment:

This manuscript was submitted as 'Ontology Description' and should be reviewed along the following dimensions: (1) Quality and relevance of the described ontology (convincing evidence must be provided). (2) Illustration, clarity and readability of the describing paper, which shall convey to the reader the key aspects of the described ontology.

The paper describes an interesting project that is certainly within the scope of the special issue. Unfortunately, the presentation remains somewhat cursory and does not provide enough details. Some of the more interesting aspects are barely scratched.
Thus, I would like to see this work in the journal, but not in its current form.

Some more detailed comments:

1. Title, Abstract, Introduction: fine. They provide a good motivation why the ontology is needed, what gap it fills and sketch the approach.

2. Modelling
Here, I was missing quite a bit of information.
For instance: Which ontology language do you use? Why?
For a paper claiming to describe an ontology, the details provided about the ontology are too few: I would have liked to see all the main classes AND their relationships. You mention that you relate things axiomatically, without further elaborating what that means.

For the reader, it might be easier, if you first described which information you are trying to capture in the ontology and then showed in some detail how this is modeled (preferably using some visual representation not a protege screenshot). Finally, you could show how this model translates to OWL (or whichever language you use).

3. Creation methodology
You write that pathogens are modeled as instances not classes and that this results in some problems. Then: Why don't you model them as classes? What are the advantages of your approach?

4. Discussion:
The discussion of related work is fine. Concerning the goal description I would have liked to get some information on how you intend to achieve this. How would you formalize the sample questions as queries to an ontology?

General: There are further open questions that I couldn't quite place in one of the sections. One important one is: how do you deal with changes in the ontology. If the automatic extraction process described in Sec. 3 delivers a changed outcome - what happens? What happens to things already annotated with this ontology? How do you keep track of changes?
How do you ensure sustainability of the ontology? Where is it available? Who ensures that it is maintained and remains available?
How agreed upon is your modeling in the community? Does the ontology reflect your view on plant-pathogen interactions or are you reasonably sure that most other scientists agree? How have you ensured this?

more formally, if there is just one subsection ( 2.1) omit that.