Project

Ecotaxonomy database

Goal: http://ecotaxonomy.org
Ecotaxonomy database is an open platform being developed to integrate ecological research with taxonomy and traits. The Ecotaxonomy is a repository for identification characters and ecological traits of species and morphospecies. Further, the Ecotaxonomy is a tool for data management in ecological projects. As a publicly available output, we provide pictorial catalogues and interactive identification keys for some taxa.

At the initiation moment, the Ecotaxonomy is connecting ecological and taxonomical work within the interdisciplinary research project EFForTS in Indonesia http://www.uni-goettingen.de/en/310995.html with focus on soil and arboreal arthropods. The database is linked to GBIF through it's taxonomic backbone thus is able to cover all described organisms and regions.

From 2019 on, the database is open for beta testing. You can approach us with e-mail (potapov.msu@gmail.com). In 2020 we're planning a public release.

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Project log

Anton Potapov
added a research item
Major research progress in ecology is being achieved through large-scale collaborations across people, groups and countries. In large-scale projects harmonization of data is tedious and time-consuming, but needs to be done reliably and rapidly. This is especially true if projects investigate under-explored organism groups such as tropical invertebrates. To link taxa to their role in ecosystems, functional traits of the taxa need to be considered. However, despite the urgent need for a common database for invertebrate traits, this is yet to be established. We developed an open web platform, Ecotaxonomy (ecotaxonomy.org), that allows traits, taxa, individuals and samples to be linked within research projects. Ecotaxonomy includes a virtual research environment, allowing project members to work jointly online on the data input, integration and retrieval. The taxonomic system of Ecotaxonomy is based on the Global Biodiversity Information Facility (gbif.org), but may be complemented by morphospecies, pictures, literature and other parameters. Any parameters can be customized inside the system and attached either to taxa, individuals, or environmental samples (Fig. 1). As public output, the system provides interactive identification keys and web catalogs of traits and taxa. Ecotaxonomy is implemented on GCore platform, that is being developed by Complex Cloud Solutions (http://ccs.msk.ru/en/). The GCore is based on Node.js, allowing for fast and efficient standardised programming. Thus, custom modules can be implemented in the future by external developers in the framework of the platform. Ecotaxonomy is now open for beta-testing. After a public release (presumably in 2020), our goal is to keep the system and the code open and ensure data interoperability via Darwin core standards. The initial stage of Ecotaxonomy development (2016-2023) is funded in the framework of a DFG-funded project (SFB 990). To ensure long-term sustainability, we are involving ecological laboratories around the world and ultimately seek to establish a permanent funding by governmental or non-governmental organisations. Using and developing Ecotaxonomy, and linking it to existing open repositories will greatly improve the efficiency and integration of research in trait-based ecology.
Anton Potapov
added an update
We are finally going more public! The first workshop on Ecotaxonomy will take place at our group in Goettingen in early December. All participant will create their own projects, taxonomic and trait collections and interactive 'Ecokeys' in the virtual research environment to explore strengths of the system. We cannot pay visits for external participants, but if you are very interested to join, send us a note.
More is to come in 2020.
You can explore our new web site (will be even more nice soon):
And especially new version of Ecokeys! You can cutomize the level of expertise and body part. And the key will suggest you the next most relevant characters to look at. The output now can be shown as only pictures, plates, or trait table:
 
Carlos Alberto Martínez-Muñoz
added an update
Ecotaxonomy Database allows the creation of a custom backbone taxonomy, drawn from GBIF backbone taxonomy (GBIF Secretariat, 2017). The general workflow is:
1) Identification of the collected specimens to the lowest taxonomic rank possible (family, genus).
2) Creation of a custom morphospecies based on the higher classification (e. g. ChiCry01, morphospecies 1 belonging to class Chilopoda, family Cryptopidae).
3) Entering the taxonomic characters and observed character states in EcoTaxonomy.
4) Retrieving a list of taxa from the published literature, reported to occur in Sumatra and at the same taxonomic rank of the recorded morphospecies (e. g. family Cryptopidae in Sumatra is represented by Cryptops doriae, C. ruficeps and C. modiglianii.
5) Scoring the same morphospecies' characters and character states for the known species.
6) Updating the internal backbone for all species and morphospecies (Fig. 1) and adding the characters and states to the higher taxonomic ranks sharing them (Fig. 2).
The result (Fig. 3) is that the morphospecies and the known species can be retrieved and visualized together, by means of the inherited characters and character states. The output list, pictures and characteristics inform ecologists and parataxonomists about a limited range of correct IDs. It also promotes engagement of professional taxonomists, which could retrieve the morphospecies from the system and identify them down to known species, by using the uploaded pictures and/or requesting material for examination. In several cases, it has turned out that the morphospecies represent species new to science!
Citation:
GBIF Secretariat (2017). GBIF Backbone Taxonomy. Checklist dataset https://doi.org/10.15468/39omei accessed via GBIF.org on 2019-09-14.
 
Anton Potapov
added an update
Following the announcement during the working session on the ISA10 in Paris, in the framework of the EUdaphobase COST action, we want to invite researchers to join a global synthesis study on the diversity and abundance of collembolan communities.
The primary idea is to compile published and unpublished data on abundance and species diversity (community data) of Collembola available from private archives of researchers around the globe. This is a huge effort, which is not possible to achieve alone, but it is possible if many people will contribute a piece.
If you find this initiative interesting, please, distribute this information among your colleagues who may be interested also. If you want to participate, please fill the form by August 31st, 2019. 
Link to the form: 
 
Anton Potapov
added a research item
Ecological roles of underexplored groups, such as tropical invertebrates, can be inferred from their functional traits, such as body mass, dispersal ability, reproductive mode and feeding habits. Despite a strong need, a common database for invertebrate traits is yet to be created. Traits are defined as a property of individual organisms, however many parameters are similar in groups of organisms, i.e., in species or even at higher taxonomic levels. Such parameters may be attributed to taxa instead of individuals. Linking both facilitates ecological and conservation studies based on taxa or phylogenetic units. Another problem hampering understanding of tropical ecosystems is the high proportion of undescribed species, particularly in soil communities. To estimate diversity, ecologists often have to operate with morphospecies instead of Linnean taxa. Morphospecies typically are defined independently in each project or even by each person, which does not allow consistent re-use. Ecotaxonomy database (ecotaxonomy.org), implemented as an open platform, addresses these issues (Fig. 1). The taxonomic system of Ecotaxonomy is based on the Global Biodiversity Information Facility (GBIF) taxonomic backbone (gbif.org), which is being complemented with traits, pictures, literature and other parameters. Both common and group-specific traits and characters can be customized in the system. Each morphospecies has to be defined by a common grid of identification characters, which is being developed in collaboration with group experts. Morphospecies then are incorporated into the existing GBIF taxonomic backbone and also inherit common characters and traits from the parental taxa. As an output the system provides open catalogs of traits and taxa, pictorial identification keys and trait matrixes. Further, by linking traits and taxa with individual-level and environmental data, Ecotaxonomy will be developed as a tool to push forward ecological research in underexplored groups and regions.
Anton Potapov
added an update
Good news! We are going to Leiden in October to present Ecotaxonomy on "Biodiversity_next" (https://biodiversitynext.org). Here is a brief publication:
 
Anton Potapov
added an update
We just visited a workshop for anatomy ontologies at the Alexander Koenig Museum in Bonn. The whole world of language, that is machine-readable, is essential for the future eScience. We were excited to learn about other Virtual Research Environments, pursuing the same goal as Ecotaxonomy. We have many strong sides, but also learned a lot. We will work to link all parameters in Ecotaxonomy to the ontologies.
 
Anton Potapov
added an update
It's finally turning to be more organised. Great initiative! I hope this will help to standardise traits across groups and biomes.
 
Anton Potapov
added a research item
1.Animals that have similar morphological traits are expected to share similar ecological niches. This statement applies to individual animals within a species and thus species often serve as the functional units in ecological studies. Species are further grouped into higher‐ranked taxonomic units based on their morphological similarity and thus are also expected to be ecologically similar. On the other hand, theory predicts that strong competition between closely related species may result in differentiation of ecological niches. Due to high diversity and limited taxonomic expertise, soil food webs are often resolved using supraspecific taxa such as families, orders or even classes as functional units. 2.Here we tested the trophic differentiation and consistency of supraspecific taxa across major lineages of temperate forest soil invertebrates: Annelida, Chelicerata, Myriapoda, Crustacea and Hexapoda. Published data on stable isotope compositions of carbon and nitrogen were used to infer basal resources and trophic level, and explore the relationship between taxonomic and trophic dissimilarity of local populations. 3.Genera and families had normal and unimodal distributions of isotopic niches, suggesting that supraspecific taxa are trophically consistent. The isotopic niche of local populations varied considerably resulting in large overlap of niches among species. Within the same genus, the effect of species identity on stable isotope composition of populations was not significant in 92% of cases. More than 50% of the variability in Δ15N values (trophic level) across lineages was explained by classes and orders, while the variability in Δ13C values (basal resources) was explained mostly by families and genera. The variability in stable isotope composition in Chelicerata and Hexapoda was explained by lower taxonomic ranks than in Myriapoda. 4.We compiled a comprehensive list of mean Δ13C and Δ15N values of invertebrate taxa from temperate forest soils allowing to refine soil food‐web models when measurements of trophic niches of local populations are not feasible. Supraspecific taxa are meaningful as trophic nodes in food‐web studies, but the consistency varies among taxa and the choice of taxonomic resolution depends on the research question; generally, identification of taxa should be more detailed in more diverse taxonomic groups. This article is protected by copyright. All rights reserved.
Anton Potapov
added an update
Rico Fardiansah is Indonesian student, who came in Museum of Hamburg to learn more about spiders. During a 6-months period, under a great supervision of Nadine Duperre and Danilo Harms he managed to finish and then publish 2 manuscripts, describing 7 new species of spiders! Amazing experience! Many morphospecies are yet to be described from our EFForTS project.
At the moment we are working to finalise our 'taxonomy module' which will allow reseachers from different projects and countries to develop consistent system of traits and identification characters within different taxonomic groups. The system is under tests now, but we already collaborating with some other laboratories. So if you are keen to contribute, please, just write me.
 
Anton Potapov
added a project reference
Anton Potapov
added an update
As one of the first steps, we're going to implement parameters from other databases in order to compile a 'comprehensive' list of traits across different groups and a list of various environmental factors.
Now establishing contacts with Edaphobase (https://portal.edaphobase.org) and BETSI (http://betsi.cesab.org). Looking forward future joint work!
 
Anton Potapov
added an update
We just finished our first introductory video for the GBIF Ebby Nielsen contest. In the video, a general overview of Ecotaxonomy modules and potential functions is presented.
 
Anton Potapov
added an update
The Ecotaxonomy database is now also on Facebook, if you prefer this way to be connected, you can subscribe to our group there:
We publish some photos and short news on Facebook. The major news will also appear here.
 
Anton Potapov
added a project goal
Ecotaxonomy database is an open platform being developed to integrate ecological research with taxonomy and traits. The Ecotaxonomy is a repository for identification characters and ecological traits of species and morphospecies. Further, the Ecotaxonomy is a tool for data management in ecological projects. As a publicly available output, we provide pictorial catalogues and interactive identification keys for some taxa.
At the initiation moment, the Ecotaxonomy is connecting ecological and taxonomical work within the interdisciplinary research project EFForTS in Indonesia http://www.uni-goettingen.de/en/310995.html with focus on soil and arboreal arthropods. The database is linked to GBIF through it's taxonomic backbone thus is able to cover all described organisms and regions.
From 2019 on, the database is open for beta testing. You can approach us with e-mail (potapov.msu@gmail.com). In 2020 we're planning a public release.