The aim of the (Taxonomic) Data Refinement Workflow is to provide a streamlined workflow environment for preparing observational and specimen data sets for use in scientific analysis on the Taverna platform. The workflow has been designed in a way that, accepts input data in a recognized format, but originating from various sources (e.g. services, local user data sets), includes a number of graphical user interfaces to view and interact with the data, the output of each part of the workflow is compatible with the input of each part, implying that the user is free to choose a specific sequence of actions, allows for the use of custom-built as well as third-party tools applications and tools. This workflow can be accessed through the BioVeL Portal here http://biovelportal.vliz.be/workflows?category_id=1 This workflow can be combined with the Ecological Niche Modelling Workflows. http://marine.lifewatch.eu/ecological-niche-modelling Developed by: Biodiversity Virtual e-Laboratory (BioVeL) (EU FP7 project) Technology or platform: The workflow has been developed to be run in the Taverna automated workflow environment.

The Ecological Niche Modelling Workflows offer an extensible framework for analyzing or predicting the impact of environmental changes on the distribution of biodiversity. Especially in combination with data aggregation workflows like the Taxonomic Data Refinement Workflow, the Ecological Niche Modelling workflows facilitate the analysis of species distribution patterns over large geo-temporal, taxonomic, and environmental scales. Examples for applications are studies of species adaptations to climate change, dynamic modeling of ecologically related species, identification of regions with accumulated risk for invasion, potential for restoration, or natural protected areas. Developed by: The Biodiversity Virtual e-Laboratoy (BioVeL) (EU FP7 project) Technology or platform: These workflows have been developed to be run in the Taverna automated workflow environment (https://incubator.apache.org/projects/taverna.html). In their current form, the workflow files (with the .t2flow extension) can be loaded and executed in the workbench variant of Taverna. They have been tested with Taverna Workbench version 2.4. These workflows can also be run in BioVeL Portal, a light weight user interface which allows browsing, reviewing and running Taverna Workflows without the need of installing any software.

iMarine is an open and collaborative initiative aimed at supporting the implementation of the Ecosystem Approach to Fisheries management and the conservation of living marine resources. The ultimate goal of iMarine is to contribute to sustainable environmental management with invaluable direct or indirect benefits to the future of our planet, from climate change mitigation and marine biodiversity loss containment to poverty alleviation and disaster risk reduction. iMarine provides an e-infrastructure that facilitates open access and the sharing of a multitude of data, collaborative analysis, processing and mining processing, as well as the publication and dissemination of newly generated knowledge. This is a complex process because it requires coordination with many actors and initiatives across different scientific and operational domains. It is also important to tackle data heterogeneity while relying on a multitude of resources and technologies, some of which are not yet ripe or powerful enough to meet the given requirements. Developed by: iMarine is co-funded by the European Commission, DG Connect Unit, under Framework Programme 7 and involves 13 international partners.

This service aims at running PEMA on all the sequences from the samples selected in Step 4 (ARMS Choose and Parameterize) of the ARMS workflow. It additionally requires a parameter file (a tsv file). The service can take some hours to run. It represents the Step 5.2 of the ARMS Workflow within the Internal Joint Initiative.

This service allows to choose which column of the MasterARMS file contains the specific data to process. Moreover, it permits to provide additional files or arguments as parameters. It represents the Step 4 of the ARMS Workflow within the Internal Joint Initiative.

This step of the ARMS IJI workflow does the following: - Input: the OTU tables from the previous step (running the omics pipeline), containing taxa (usually genus or species names) obtained from the databases used by the pipeline; - Check: using the WoRMS taxon match webservice to check for the WoRMS match to those taxa; - Output: the WoRMS match (yes or not) and, if matched, the scientific name and aphiaID. It represents the Step 7 of the ARMS Workflow within the Internal Joint Initiative.

This service aims to download the sequences files (fasq files) that have been choosen in Step 4 (ARMS Choose and Parameterize) in order to run PEMA. It represents the Step 5.1 of the ARMS Workflow within the Internal Joint Initiative.

This step of the ARMS IJI workflow does the following: - Input: the output from the previous step (running a taxon check on the input species names using the WoRMS taxon checker); - Input: geographical locations for the sample(s) that those species were found at; - Check: using the WRIMS taxon match webservice to check the known distribution of the species; - Output: information about whether the species are alien or native to the location they were found at. It represents the Step 8 of the ARMS Workflow within the Internal Joint Initiative.

This service aims to uploading a local file in the ARMS validation case. It represents the Step 2 of the ARMS Workflow within the Internal Joint Initiative.

This service aims at getting the ARMS collection file from the IMIS database. Since the URL of the ARMS file changes each time the file is updated, and this update is transmitted to the IMIS metadata record, it is necessary to always access the URL of the file from the field in the json format of the IMIS metadata record rather than via a fixed URL. This service represents the Step 1 of the ARMS Workflow within the Internal Joint Initiative.