This survey is now closed and is here for reference only.

Welcome to our survey on Ontology Reporting.
We* are attempting to understand what is useful to report when describing an ontology; usually in an academic paper. The aim is that when reading a paper both the reviewers and the final reader can understand the process by which an ontology was developed and understand the nature of the knowledge representation used within the ontology.

We’d like broad based community input into forming these reporting recommendations. We’d like comments on the importance of the aspects we propose, the wording of those recommendations or any things to report that we’ve missed. We need enough things to be reported about an ontology such that the ontology can be understood and explored, but not so much that the reporting will never happen. Nevertheless, all comments are welcome.

The survey is presented as a set of aspects which could be reported. We ask you to 'score' each aspect and leave an open answer for any further comments.
On average the survey has taken 7 minutes to complete.

Please do not forget to press submit on the last page so we receive your answers!

Many thanks for participating.
*Robert Stevens (robert.stevens@manchester.ac.uk), James Malone (james@factbio.com), Chris Mungall
Let's Do This Thing
 
We would like to collect some information about people that take part in this survey. We would like to be able to follow up any suggestions made as necessary; all data and responses will, of course, be kept confidential and not identified if used in any publication. We'd also like to know whether respondants are ontology developers, ontology users, paper readers, authors or reviewers (and possibly all). it is optional as to whether participants give this information.

Your name (optional):

 
Your email (optional):

 
Your involvement with bio-ontologies:


 
In your main job are you:


 
Please rate the following by considering "how important is it that this aspect is included in an ontology report?"

If you have further comments or think there is a missing aspect to report in the section please do add them. If you are unsure on any question you can skip it without answering.

 
The Basics
The ontology name

Please rate how important it is to you that this aspect is included in an ontology report. An ontology name would include the acronym and full name (e.g. GO, Gene Ontology)





 
The Basics
The ontology owner or group of people responsible.

This would be in the form of a named person or group and contact mechanism.





 
The Basics
The license under which it can be used.

This would include details on commercial and academic use, implications on use with data and derivatives.





 
The Basics
The URL of the current ontology location.

This could be the project homepage which includes a link to the latest ontology.





 
The Basics
The repository which includes current and previous versions of the ontology.

This includes specifically previous versions of the ontology and not just the 'latest'.





 
Any further comments on the Basics section.

Please add if anything is missing,
 
Motivation for the ontology.

Details on why an ontology is needed?







 
Motivation for the ontology.

Competition: If there is another ontology in the area, description on why the one being reported is needed instead/in addition.







 
Motivation for the ontology.

The target audience; who, what, where, when.







 
Any further comments on the Motivation section.

Please add if anything is missing.
 
Scope, requirement, community.

The scope and remit of the ontology.

What is the scope and requirements, how was it determined?





 
Scope, requirement, community.

The community that is being engaged and how it is being done.

This is applicable to an ontology that isn't solely a local application solution.





 
Scope, requirement, community.

Email list and issue tracking mechanism.

If I need to request a term or flag an error, how do I do it?





 
Any further comments on the Scope, Requirements, Community section.

Please add if anything is missing.
 
Knowledge Elicitation.

Detail on how the knowledge in the ontology was found, sorted, verified etc.






 
Knowledge Elicitation.

The 'raw data' location, if applicable.

This could be surveys, 20 question exercises, interviews, data files, etc.





 
Knowledge Elicitation.

The prioritisation of features. Which features were prioritised and how?

Was anything deliberately ruled out?





 
Any further comments on the Knowledge Elicitation section.

Please add if anything is missing.
 
Ontology Content.

The knowledge representation language used  and why.

e.g. OWL, OBO





 
Ontology Content.

The development environment used

e.g. Protege, OBO-Edit, PoolParty, TopBraid Composer





 
Ontology Content.

Number of classes, properties, axioms, etc.






 
Ontology Content.

Versions of external ontologies consumed in the ontology.






 
Ontology Content.

Naming conventions for ontology entities.

e.g. sentence case for labels, acronyms disallowed.





 
Ontology Content.

The entity identifier generation policy

e.g. how are URIs minted, do they resolve on the web





 
Ontology Content.

The entity metadata policy - was a selection of properties used to describe each class.

e.g. every class must have a label, a parent class, a textual definition





 
Ontology Content.

If an upper ontology used, which one is used and why. If not, why.






 
Ontology Content.

The relationships used in the ontology, which were used and why.

Were new relationships required? Why?





 
Ontology Content.

Axiom or statement patterns used in describing ontology classes.

If none were used, was the description ad hoc?





 
Any further comments on the Ontology Content section.

Please add if anything is missing.
 
Managing Change.

Sustainability plan.

Will the ontology live on? Will it be actively managed? Is it tied to a specific project? How will this happen?





 
Managing Change.

Deprecation strategy for ontology entities.

How are entities no longer required dealt with?





 
Managing Change.

The versioning policy of the ontology.

e.g. dated released, major and minor releases, working versus official releases.





 
Any further comments on the Managing Change section.

Please add if anything is missing.
 
Quality Assurance

Description of testing performed on the ontology.

Who tested the ontology, what was the method and outcome?





 
Quality Assurance

Evaluation of the ontology. Does the ontology accomplish the original requirements?






 
Quality Assurance

Examples of the ontology's usage.

Who is using it and how?





 
Any further comments on the Quality Assurance section.

Please add if anything is missing.
 
If you had to pick one thing that was most important when deciding on whether you would use an ontology, what would it be?

 
If you have any other comments you wish to include please do so in the box below. Alternatively you can email Robert Stevens (Robert Stevens robert.stevens@manchester.ac.uk) or James Malone (james@factbio.com)

Click submit below to complete the survey and send us your answers!

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