|Title||Description||Web Interface||END POINT availability||Details|
|Alien Species Thesaurus||
The Alien Species Thesaurus
Biodiversity partitioning across nested spatial level.
|BioMaS (Bioinformatic analysis of Metagenomic AmpliconS)||
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.
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
|Fish Traits Thesaurus||
Thesaurus on Fish morphological traits.
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).
|LW Toponyms IGM||
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.
MSA-PAD application is a multiple DNA sequence alignment framework designed to align conserved protein coding DNA sequences. The application accounts for either single or multiple protein domains coding sequences and uses this information in assembling its output. It is mainly useful for comparative genomics by the possibility to align genomes having different genic organization (i.e. bacterial genomes). It takes also into account and/or aligning genes’ exons, including those undergone intron loss or gain, respecting genomic organization. MSA-PAD has two different alignment modes: (i) genome and (ii) gene. The difference between the two modes resides in the organization of the final alignment.