fdschneider
commented
6 years ago our reply, August 2018
flo schneider Jens Kattge • 10 days ago
Dear Jens and the TRY Steering Committee,
We very much appreciate receiving feedback on our preprint from you. Our intention of posting a pre-print of this paper was to prompt qualified criticism and engage a wider community of trait-based researchers before releasing an initial version (v1.0) of what could be considered a consensus standard vocabulary. In revising the manuscript and the trait-data standard, we are going to address these comments. Specifically, we will enhance clarity about our intentions and more broadly add a new section in which we discuss the advantages and disadvantages of a standard vocabulary for trait data.
We agree that, above all, trait-data should be published, regardless of format. Our proposal addresses the handling of a rapidly increasing number of trait datasheets that are published in non-standardised, open-access file-hosting services. The heterogeneity of their format makes re-using data from various sources very time consuming and – if this situation should remain unresolved – would inhibit large-scale synthesis research on organism traits. While for plant traits and few other taxa these issues have been largely resolved, thanks to the effort of curated databases such as TRY, data heterogeneity remains an impediment in all other organismic groups which lack such infrastructure. In our article we propose incentivising the use of data standards and ontologies in distributed publications, e.g. by providing an R-package, to enable these data to find their way into a semantic web and to be used in future analyses.
Concerning your specific comments: We, too, want to avoid building barriers and do not demand a specific data structure or set constraints over the number of data columns. We discuss two-dimensional data tables for providing trait co-variates/metadata (implicitly with a variable number of columns) simply because it is most common practice in standalone data publications. The use of our standard vocabulary does not preclude the use of additional, non-standard columns when publishing primary data, e.g. to keep the original data or to add further, unforeseen co-variates. But to support the preservation of these data, we will consider implementing explicit terms for user-defined/original values along with standardized values throughout the extensions (as we already do for the core terms).
We hope to maintain this open exchange and welcome any suggestions on improving compatibility with existing trait-data initiatives. We again want to stress that the current vocabulary is open to submissions of new and refinements of existing terms, to cover practices in specific research communities (e.g. plant-trait growth and measurement co-variates).
Best regards,
Florian D. Schneider, Malte Jochum, Gaëtane Le Provost, Andreas Ostrowski, Caterina Penone, David Fichtmüller, Anton Güntsch, Martin M. Gossner, Birgitta König-Ries, Pete Manning, Nadja K. Simons
Jens Kattge • July 2018 on biorxiv.org
I have read the preprint with great interest and discussed it with the Steering Committee of the TRY Plant Trait Database (www.try-db.org). We decided to provide a concerted comment, because we are concerned that this preprint has the potential to cause considerable confusion within the plant trait community.
We very much appreciate the proposed movement towards a more standardized representation of trait data in ecology. Especially we appreciate the two principles you suggest for trait measurements: (1) keeping the original information while adding standardized terms; and (2) using an agreed vocabulary, i.e. standardized trait definitions, whenever possible.
However, we are afraid that the organization of metadata in the two extensions for occurrence and measurement may lead to a loss of information and to data structures which may not be easily machine readable and hard to integrate into larger databases. We see two problems: (1) It seems that the principle of keeping original terms and data while adding standardized ones is not explicitly foreseen in the extensions: original data seem to be replaced by standardized ones. If there are mistakes in the standardization, original data cannot be reproduced. (2) The extensions are two-dimensional tables with metadata in columns. Plant trait data are often accompanied by a substantial number of metadata to characterize plant growth and measurement conditions. In these cases data providers would either have to fit their metadata to terms that exist in the standard but may not fit 100%, or skip part of the metadata, or add new columns to the tables. In the first two cases some of the original information would be modified or lost, which is a problem for data integrity. The last case would result in dataset-specific extensions with unsupervised, unstructured and potentially high number of columns. In combination with the organization of trait data along observations, we are afraid that the resulting datasets may not be easily machine-readable and thus would be difficult to integrate into larger databases.
An additional disadvantage of the proposed standard is that the original measurement tables need to be transformed into the standard structure. Even if an R tool provides support, this transformation is an additional barrier to making data publicly available. There is wide consensus that such barriers should be avoided.
In the context of plant trait data we strongly support the use of agreed vocabularies, but emphasize the importance of always providing the original terms and values for traits and metadata. According to our experience, common formats of plant trait datasets can easily be imported into an integrated database like TRY. We thus recommend publication of datasets without transformation to the suggested standard format.
In TRY however, we represent measurements of traits and metadata in a long-table format, always keeping the original values while adding standardized terms (see Kattge et al. 2011, Methods in Ecology and Evolution).
The preprint lacks a chapter ‘Discussion’, which would allow discussing advantages and disadvantages of the suggested ecological trait-data standard.
The Steering Committee of the TRY initiative
Jens Kattge Sandra Díaz Sandra Lavorel Colin Prentice Paul Leadley Gerhard Boenisch Christian Wirth