TraitBank: Practical semantics for organism attribute data

Tracking #: 1037-2248

Authors: 
Cynthia Sims Parr
Katja S Schulz
Jennifer Hammock
Nathan Wilson1
Patrick Leary1
Jeremy Rice
Robert J. Corrigan, Jr.

Responsible editor: 
Guest Editors Semantics for Biodiversity

Submission type: 
Tool/System Report
Abstract: 
Encyclopedia of Life (EOL) has developed a new repository for organism attribute (trait) data called TraitBank (http://eol.org/traitbank). TraitBank aggregates, manages and serves attribute data for organisms across the tree of life, including life history characteristics, habitats, distributions, ecological relationships and other data types. We describe how Trait-Bank ingests and manages these data in a way that leverages EOL’s existing infrastructure and semantic annotations to facili-tate reasoning across the TraitBank corpus and interoperability with other resources. We also discuss TraitBank’s impact on users and collaborators and the challenges and benefits of our lightweight, scalable approach to the integration of biodiversity data.
Full PDF Version: 
Tags: 
Reviewed

Decision/Status: 
Minor Revision

Solicited Reviews:
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Review #1
Anonymous submitted on 06/Apr/2015
Suggestion:
Accept
Review Comment:

This manuscript was submitted as 'Tools and Systems Report' and should be reviewed along the following dimensions: (1) Quality, importance, and impact of the described tool or system (convincing evidence must be provided). (2) Clarity, illustration, and readability of the describing paper, which shall convey to the reader both the capabilities and the limitations of the tool.

The revised version of this paper is more clearly articulated, more comprehensively referenced, and presents a broader and more analytical Discussion. The manuscript presents an important and measurable effort to "ontologize" a rich biodiversity data resources (EOL), and is worthy of publication in my view.

Review #2
By Jens Kattge submitted on 27/May/2015
Suggestion:
Accept
Review Comment:

This manuscript was submitted as 'Tools and Systems Report' and should be reviewed along the following dimensions: (1) Quality, importance, and impact of the described tool or system (convincing evidence must be provided). (2) Clarity, illustration, and readability of the describing paper, which shall convey to the reader both the capabilities and the limitations of the tool.

This is a well written and informative description of the Encyclopedia Of Life TraitBank. (1) No doubt EOL TraitBank will become a standard resource for organism attributes (traits) in biodiversity research and beyond, e.g. for application in schools. (2) The description is written clearly and informative, capabilities and limitations of the approach - which is more than just a tool - are well outlined.

Review #3
Anonymous submitted on 24/Jun/2015
Suggestion:
Accept
Review Comment:

This manuscript was submitted as 'Tools and Systems Report' and should be reviewed along the following dimensions: (1) Quality, importance, and impact of the described tool or system (convincing evidence must be provided). (2) Clarity, illustration, and readability of the describing paper, which shall convey to the reader both the capabilities and the limitations of the tool.

This revision is clearly written and much improved over the initial version. It does a more adequate job of presenting the potential broader impact of TraitBank. The lightweight semantic middleware approach taken in designing TraitBank is a good case study in how to build off of existing standards and ontologies while also integrating heterogeneous source material such as from natural language content. It represents a resource that has potential to be used by biodiversity researchers for a variety of tasks. The implementation section does a good job of documenting the community-driven governance process used to build and maintain TraitBank. I recommend accepting this paper for publication.

Given the lightweight, pragmatic approach taken in developing TraitBank, it is an excellent first step toward providing a general resource for biodiversity informatics (much as DBpedia has filled that role for concepts in Wikipedia). It provides a base for further research on improving the semantic depth of trait knowledge bases. As it stands many of the attributes described are compound properties that could be decomposed to allow richer reasoning. Improving the representation of geographic locations to be more than keywords is of high priority. This would allow for many interesting applications of spatial analysis of relationships between traits and species occurrences and other environmental features.

There are still occasional spelling mistakes throughout the document, so the authors should run through a spell checker, e.g.:

pg. 1: "accummulated"
section 3 para. 1: "futher", "implmeneted"
last para. section 3.5: "url" should be capitalized "URL"
3rd papa. section 4.1: "taxa,," (extra comma)


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