living spreadsheet on trait data #20
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Note for future, this might also help: |
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The R-package traits of Scott Chamberlain accesses the APIs of several trait database projects to pull data from those sources (We should discuss this R-package and its overlap with ours in the Methods paper). We should refer to those sources in our spreadsheet. The list of data sources can be found here: https://github.com/ropensci/traits |
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What we've listed in the Wiki: BWARS is the national society dedicated to studying and recording bees, wasps & ants (aculeate Hymenoptera) in Britain & Ireland. Budrys, E., Budriene., A. and Orlovskyte. S. 2014. Cavity-nesting wasps and bees database. A paper by Bartonova et al in Ecography has a data appendix on butterfly traits Plenty of answers to this question on researchgate about bird and butterfly traits AntProfiler collects trait data on ants. Only three contributors so far, database currently not accessible. GlobalAnt a new database on the geography of ant traits The DynaTrait project works on invertebrate traits in aquatic communities. The Edaphobase collects data on the distribution and ecology of soil invertebrates. The data can be accessed via the Edaphobase Portal. Traits seem to be mostly on niche preferences and reaction to anthropogenic stressors. Carabids.org has occurrence data and trait information on Carabid beetles. Traits include body size and dispersal for all species and other life-history traits for most species. Nadja: the traits for the carabid species within the Exploratories are mainly from this source araneae.org has a species list and occurrence data for all spiders in Europe. While it does not have a searchable trait database, body size and habitat preferences are given for most species. Nadja: some of our body size information is from this site The SCALES project has a trait database on reptiles which is maintained by Annegret Grimm. A list of plant trait databases can be found on the INNGE wiki. The Dispersal diaspore database collects data on seed dispersal. The Fine Root Ecology Database (FRED) collects root traits for plants or plant communities. It covers 316 root traits in 8 categories. |
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The Coral Trait Database: https://www.nature.com/articles/sdata201617#data-records Figshare-link: https://figshare.com/articles/Coral_Trait_Database_1_1_1/2067414 |
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found on ropensci/traits#73 Plant growth form data for > 49,000 on data dryad here: http://datadryad.org/resource/doi:10.5061/dryad.63q27. |
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Very valuable! Database by Morgan Ernest and group: Amniota (birds, mammals and reptiles) life-history traits database: http://onlinelibrary.wiley.com/doi/10.1890/15-0846R.1/abstract https://figshare.com/articles/Full_Archive/3563457 |
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Mammal Diet data: Kissling WD, Dalby L, Fløjgaard C, Lenoir J, Sandel B, Sandom C, Trøjelsgaard K, Svenning J-C (2014) Establishing macroecological trait datasets: digitalization, extrapolation, and validation of diet preferences in terrestrial mammals worldwide. Ecology and Evolution 4(14): 2913-2930. http://dx.doi.org/10.1002/ece3.1136 Dataset: http://datadryad.org/resource/doi:10.5061/dryad.6cd0v |
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PanTHERIA A global species-level data set of key life-history, ecological and geographical traits of all known extant and recently extinct mammals compiled from the literature. It also includes spatial databases of mammalian geographic ranges and global climatic and anthropogenic variables. |
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EltonTraits 1.0: Species-level foraging attributes of the world's birds and mammals global species-level compilation of these key attributes for all 9993 and 5400 extant bird and mammal species derived from key literature sources citation: Hamish Wilman, Jonathan Belmaker, Jennifer Simpson, Carolina de la Rosa, Marcelo M. Rivadeneira, and Walter Jetz. 2014. EltonTraits 1.0: Species-level foraging attributes of the world’s birds and mammals. Ecology 95:2027. |
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Do you want to put all these in the Google Spreadsheet or present it in a different form? And should we start transferring this in the spreadsheet now or wait? |
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Sure, those sources are all well suited for the Spreadsheet. If you find the time, you can start filling them in. But I will add the ones published as public domain (most figshare and data dryad sources) when I pull them for the R package. |
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Fire-related traits for plant species of the Mediterranean Basin. Ecology 90:1420 https://figshare.com/articles/Data_Paper_Data_Paper/3531092 citation: S. Paula, M. Arianoutsou, D. Kazanis, A. Tavsanoglu, F. Lloret, C. Buhk, F. Ojeda, B. Luna, J. M. Moreno, A. Rodrigo, J. M. Espelta, S. Palacio, B. Fernández-Santos,, P. M. Fernandes, and J. G. Pausas. 2009. Fire-related traits for plant species of the Mediterranean Basin. Ecology 90:1420. |
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Data retriever lists a wealth of biological data that we can copy. Plenty of trait data here: name: nematode-traits name: bird-size name: predator-prey-body-ratio name: predator-prey-size-marine name: mammal-metabolic-rate name: mammal-masses name: wood-density |
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Vertnet data including some traits are available from this site: http://vertnet.org/resources/datatoolscode.html The downloads are annual snapshots of a growing database. |
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Swen Renners bird trait dataset: Renner, S.C.; Hoesel, W. Ecological and Functional Traits in 99 Bird Species over a Large-Scale Gradient in Germany. Data 2017, 2, 12. |
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See also:
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The Kattge et al 2011 paper on the generic structure of plant trait databases has a list of existing plant trait databases. |
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Brun, Philipp; Payne, Mark R; Kiørboe, Thomas (2016): A trait database for marine copepods. PANGAEA, https://doi.org/10.1594/PANGAEA.862968, |
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After adding a few more, I wonder if the spreadsheet is actually the best method.. It is certainly the more elastic and easier for everyone to add a dataset but will people find/use it? Furthermore, how do we deal the overlap with other initiatives that use other solutions (e.g. https://ecologicaldata.org/home)? |
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I think the spreadsheet is positively informal and easy to handle. It collects datasets and is at the same time human readable. We could have a google form instead for new entries, but then we need to clean up messy entries before we publish them. We will point to the spreadsheet from the Manuscript and the website and advertise it on platforms like OpenTraits. It might become obsolete at some point, when other listings have better coverage. On the output side: Right now, I use the spreadsheet as an input to create our Appendix A of the manuscript (as a static copy). This can be repeated any time and published as a standalone list. Also, the spreadsheet could at some point be imported into ecologicaldata.org. Alternatively, with Rmarkdown it would be easy to build a website view around the spreadsheet that allows people to browse entries similar to ecologicaldata.org. |
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hehe ok, sounds all good, I'll continue to fill it then. And maybe we can think about doing a "traitdata.org" together with the OpenTraits initiative. Anyway, for the moment the spreadsheet is indeed the most easy tool. |
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More initiatives to include/cite (self-reminder):
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Caterinas suggestion on the table of existing trait databases:
If we think about publishing it as a general methods paper, a table collecting trait data might be a very good access point for a decentralised global analysis. Having a living document sounds the most practical approach, since we can only provide a glimpse on the traitdata existing in our reach. All the traitdatasets published along with a single paper will be difficult to find.
I just started a Google Spreadsheet. First step would be to enter all the databases from our wiki.
But this might also lead too far off. An internal whitepaper is primarily aiming for work within the exploratories and might not need this. If we publish it as a general methods paper, we might cut out all the Exploratories-specific stuff.
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