LifeWatch-ERIC

The Alien Species Thesaurus

Biodiversity partitioning across nested spatial level.

There are many zoological, botanical, microbial, molecular and other types of collections spread in several academic and research establishments, such as zoological museums, botanical gardens, seed banks, etc. Many endemic terrestrial and marine species are included in these collections. Most of these collections have been digitised over the last years. This Service will make such collections available to the potential user from a single access point through the LifeWatchGreece site and will liaise them with similar collections from other EU countries.

BioMaS (Bioinformatic analysis of Metagenomic AmpliconS) is a pipeline develeped by IBBE in collaboration with INFN. The fundamental purpose of BioMaS is to equip the biomolecular researcher involved in taxonomic studies of environmental microbial communities with a comprehensive and user-friendly workflow including all the fundamental steps for the NGS amplicon-based metagenomic analysis, by guiding his path from raw sequences to final taxonomic identification. This version of BioMaS can be used for the analysis of Illumina MiSeq sequences from bacterial and fungal environments.

All the applications developed at the Instituto de Física de Cantabria (IFCA) using deep learning techniques.

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Data Services provide the users with tools in order to: a) publish their datasets and make them available to the community by providing information that allows a user to locate and access the resource and its curator/creator, b) import their datasets to the Lifewatch Greece Infrastructure and to GBIF or MedOBIS, c) perform biodiversity data and information quality improvement, and d) search about datasets of interest by providing an efficient way of querying semantic networks. The schema of the data that is provided by the users is mapped to the semantic model of the LWI and the data is transformed to LWI format before it is stored to the Infrastructure. The semantic model is based on CIDOC CRM (http://www.cidoc-crm.org/), CRM dig, CRM geo, CRM sci and MarineTLO (http://www.ics.forth.gr/isl/MarineTLO/).

Thesaurus on endemisms

Thesaurus on Fish morphological traits.

The online Services of the Genetics working group are focused on 16S Metagenomics, which involve specific 16S ribosomal marker gene amplification by PCR. The 16S analysis is the most common approach for biodiversity studies. The Service focuses on taxonomic analysis from data derived from 454 Roche as well as Illumina sequencing technologies and provides the relevant software to allow analysis for both sequencing technologies. Efficient noise removal for 454 data is accomplished using the AmpliconNoise (http://qiime.org/scripts/ampliconnoise.html) pipeline and the taxonomic assignment for both de-noised 454 and Illumina data is achieved via QIIME (http://qiime.org/index.html).

This Service acts as the taxonomic backbone of the infrastructure: a taxonomic identity code (ID) is assigned to all the taxa registered in the GTIS. All the information (e.g. systematic classification, taxonomic description, functional trait information, geographical distribution, registered material in the systematic collections of the Museums, etc.), which is relevant to a taxon can be assigned to its ID and through this to any other kind of information linked to that. The GTIS Service is directly based on those developed in Flanders Marine Institute (VLIZ), which have been developed in the course of several EU and international projects and initiatives, such as MarBEF (Marine Biodiversity and Ecosystem Functioning), PESI (Pan-European Species directories Infrastructure) and WoRMS (World Register of Marine Species).

Calculation of macrozoobenthic ISS index (Basset et al. 2012, Barbone et al. 2012). Given as input a dataset with macrozoobenthic individual observations (individuals occurence and body size), produce as output a list of ISS values per site. Weight values for species richness have been setted according to Basset et al. 2012, they can be modified from the script (lines 24-33).

Calculation of phytoplankton ISS index (Vadrucci et al. 2012). Given as input a dataset with phytoplankton individual observations (individuals occurrence and body size), produce as output a list of ISS values per site. Weight values for species richness and chlorophyll a values have been setted as Vadrucci et al. 2012, they can be modified from the script (lines 35-52).

Geo-referencing is one of the most problematic and troublesome steps in digitization of occurrence data. In museum samples, spatial references are typically provided as textual description of localities, an "informal" technique that requires appropriate processing in order to become a "formal" representation. The e-Biodiversity Research Institute LifeWatch-Italy is proposing an innovative approach for processing of geographic objects. This approach, which follows the GeoNames ontology, considers localities as "concepts", thus enabling: a) to loosen their connections with names and with static geographic representations and b) to explicitly insert them in the network of spatial and semantic relationships with other entities. It was decided to formalize the Italian place names taken from the IGM plates ("tavolette"), an authoritative source of place names of the Military Geographic Institute (Istituto Geografico Militare), according to these principles and in order to use these in the museum or biodiversity domain.

As a user or developer you can use the Marine Gazetteer webservices to feed your own application with the Marine Gazetteer standardized list of georeferenced marine place names and marine areas. In total 11 applications are available, for example getGazetteerRecordsByName, getGazetteerRecordsByType, getGazetteerRecordsByLatLong, getGazetteerNamesByMRGID