Plant Ontology Response to OBO Foundry Review

The Plant Ontology underwent a rigorous review in 2013 and was accepted as a full member of the OBO Foundry

Review document: Media:PO_Review_August_2013.pdf

OBO Foundry Principles

Domain of ontology: Plant anatomy, morphology and growth and development and their association to plant genomics data for all plants.

Our specific recommendations are contained in the report below. Thank you for participating in the OBO Foundry review process.

Summary of Review Findings

In general, we found that the Plant Ontology is a good ontology, largely following the principles as laid down by the Foundry. We have some specific recommendations for improvements but found no major significant shortfalls in the offering. The following table summarises the findings of this review on a per principle basis, and detailed discussion of each point follows.

#	Principle	Comments
1.	Open	Some improvement desirable
2.	Common format	Pass
3.	Foundry URIs	Pass
4.	Versioning	Pass
5.	Clearly delineated content	Some improvement desirable
6.	Textual definitions	Some improvement desirable
7.	Relations	Some improvement desirable
8.	Documentation	Pass
9.	Plurality of users	Pass
10.	Collaboration	Pass
11.	Single locus of authority	Pass
12.	Naming conventions	Pass
16.	Maintenance	Pass

PO Responses to OBO Foundry Review of Plant Ontology

Responses to the points requiring improvement shown in italics

Principle 1: The Ontology is Open

"Some improvement desirable"

"The self-review states that the PO is released under a Creative Commons license. However, it is not specified which Creative Commons license has been chosen. The ontology file does not contain a statement about the license or the policy for reuse of the ontology. However, the information is available on the website e.g. at http://plantontology.org/docs/otherdocs/principles_rationales.html: Plant Ontology by Plantontology.org is licensed under a Creative Commons Attribution-NoDerivs 3.0 United States License."

"We recommend that the exact license chosen be included in an additional ontology annotation in the ontology file."

"According to the OBO Foundry principle 1 documentation, this should make use of two annotations using the following properties:

• dc:license
• rdfs:comment

The license type goes in the dc:license field. The mode of attribution goes in the rdfs:comment field. "

"While 'Creative Commons 3.0 CC-by license' is recommended, this is not mandatory and therefore the chosen attribution-noderivs license is also compatible with the Open principle. However, we urge you to consider weakening the license to one that encourages sharing and reuse without constraint to further the adoption by the community and the value of the resource for the community." Reply: We chose the CC-BY-ND license, because in the past the derivatives (including changing the relationships and graph besides adding new terms) were created and it was difficult for us to track. Also by having ND clause, users are encouraged to go back to the source and request their suggested edits.

Done: The license info is at the bottom of every page of the browser, plus we created a License wiki page with the human-readable version of the file. The full text of the legal version of the license was also copied to a text file and saved in the Live Tag folder. We also added a note about the license as a comment in header.

Principle 2: Common Format

"Pass"

"The ontology is available in both OBO and OWL formats. It should be noted that the OBO form of the ontology contains semantics which are not yet available in the OWL form (i.e. the treat-xrefs-as-isa and treat-xrefs-as-genus-differentiae constructs). These are supported by the Oort release manager and can be instantiated in OWL versions of the ontology. See https://code.google.com/p/owltools/wiki/OortOptions

Reply: We can do this at the next release, as we use Oort to generate various different versions of the file anyway, or not depending on the effect. Should add a comment on the Release SOP Page if we are going to do so.

Principle 3: Foundry-style URIs

"Pass"

"The ontology uses numeric Foundry URIs."

Principle 4: Versioning

"Pass"

"The ontology uses date stamps for versioning. These are reflected in the OBO and OWL versions appropriately. We note that the PO version in OntoBee was not the same as their latest release described on their website and available from the OBO Foundry download page at the time of doing the review, however, this seemed to have been a problem with the OntoBee updating mechanism rather than with the PO itself."

Reply: This is not completely correct- we actually release the new versions of the PO on an approximately quarterly cycles. Those are numbered consecutively. Latest release was Version #20, July 2013.

Principle 5: Clearly Delineated Content

Some improvement desirable

"There are several sub-issues that are contained in this principle. - Firstly, the ontology needs to have a clearly delineated scope as expressed in a statement of scope. PO does have a clearly delineated scope, and this scope does not substantially duplicate the scope of any other OBO Library ontology. - Secondly, the ontology needs to have a clear upper level with root terms having definitions that indicate the content of the sub-ontologies included in the ontology. Here, we have some concerns as detailed below. - Thirdly, the ontology should not contain terminology that overlaps with other OBO ontologies except where content has been imported for reuse in specific contexts appropriate to the domain of the ontology. - Finally, the ontology should provide adequate coverage with respect to its stated domain so as to justify its use in applications. Concerns about the upper levels of the plant ontology:

"The definition of the root term ‘plant anatomical entity’ appears intended to be a plant specific subclass of the CARO term ‘anatomical entity’ and is defined as “An anatomical entity that is or was part of a plant.”

"The CARO class states that an anatomical entity is part of or located in an organism (or virus or viroid in the upcoming release of CARO), however here you include things that were once part of a plant. In OBI or ERO, such entities would be considered specimens or samples. Can you explain why this is needed? If it is justified, there is some cross-ontology coordination that should be performed."

Reply:

• CARO:0000000 anatomical entity: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.

• plant anatomical entity (PO:0025131): An anatomical entity that is or was part of a plant. Comment: Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces.

• specimen (obo:OBI_0100051): A material entity that has the specimen role. Note: definition is 'in specimen creation' objective which is defined as an objective to "obtain and store a material entity for potential use as an input during an investigation".

• sample from organism (obo:OBI_0000671): a material obtained from an organism in order to be a representative of the whole.

In the PO, we include anatomical entities that were part of a plant since many plant parts are no longer connected to the parent plant, for example grains or other fruits, wood, or leaves.

We could add a comment or Xref to refer to the OBI or ERO terms, but the problem with this is that the various plant parts are not representative of the whole plant nor are they always intended for input during an investigation. Also the OBI entities specimen and sample from an organism applies to the samples that were put together for isolating some features, in this case an RNA, DNA, protein etc. In our cases of annotation the whole body can be a specimen. Therefore, to keep the confusion of samples away and not mix it up with the OBI, we went to the intended path. On the other note. Is OBI funded and what’s the status of its maintenance and updates?

"There is a need to define the high-level distinction between plant structure vs. portion of plant substance better: currently ‘plant structure’ is defined as anatomical entity that is or was part of a plant; but substances are also (or were also) part of a plant. This is likely because these are intended to be subclasses of the CARO classes, that have more specific differentia, however, there is no mireot or subclass assertion to these classes other than in the comment field. Explicit use of the CARO classes will help differentiate these top-level nodes, and inclusion of their logical class definitions can help with error-checking."

Reply: Currently:

• plant structure (PO:0009011): An anatomical structure that is or was part of a plant, or was derived from a part of a plant.

Comment: 'Part' includes both proper parts and the whole plant. CARO:0000003 anatomical structure is defined as: Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome.

• portion of plant substance (PO:0025161): A portion of organism substance that is or was part of a plant.Comment: Refers to portion of organism substance (CARO:0000004) which is defined as: Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. For plants, the word "body" refers to a whole plant or part thereof. Can include substances like latex, xylem sap, phloem sap, resin, mucilage, oil, cuticle, cutin, sporopollenin.

The first is an “anatomical structure” while the second is a “portion of organism substance”. Since the PO is developed in OBOF, we added the comments to clarify that these are indeed referencing the CARO terms, which differentiate them. We also used the CARO ID as a DBXref.

The new version suggests that ‘portion of plant substance’ is a plant anatomical entity and is part of some other plant structure. e.g. Cuticular wax. (http://www.plantontology.org/amigo/go.cgi?action=dotty&view=details&search_constraint=terms&query=PO:0025386). This ontology graph is similar to the one we see for ‘cytoplasm’ in GO (http://amigo.geneontology.org/cgi-bin/amigo/browse.cgi?action=set-tree&term=GO:0005737).

"If you consider the above point on the definition of ‘anatomical entity’ referring to in vivo entities, you could consider moving ‘in vitro plant structure’ to be its own root outside anatomical entity, as it would technically be a derived structure and not part of or located within an organism (or are most of these simple plants cultured in vitro?). Efforts have been made recently in the CL and OBI to represent such things (e.g. “in environment” vs. “ex environment”, you could potentially leverage some of these design patterns and/or coordinate with them."

Reply: We disagree. Based on the CARO definition adopted by PO, it is still a plant structure that was once part of a plant. Unlike animals, we can regenerate the whole plant in-vitro as well from a single cell. Therefore we think it is placed in the appropriate location in the ontology graph.

"Other concerns from somewhat random sampling:"

"‘cultured plant embryo’ has two asserted superclasses. While asserted multiple inheritance is debatable in terms of ontology maintenance or ontological rigor (GO has a lot of this), in this case the example ensues because of a lack of logical class expression on this class. For example, this class could instead leverage a class restriction that states ‘plant embryo’ and is_specified_output of some in vitro plant culturing. In this way, you would infer the second parent, ‘in vitro plant structure’ (dependent on how you define things as per above). This would mean higher quality axioms, easier ontology maintenance, and interoperability with other ontologies such as OBI."

Reply: At the time of the revisions of this part of the ontology, when we set these up, there were no differentia we could use- tried to get PATO to add it, but had no success there. Class restrictions are available in OWL, but PO is developed in OBO.

For more info: see http://www.w3.org/TR/owl2-syntax/#Class_Expressions