LifeWatch-ERIC

The Alien Species Thesaurus

Biodiversity partitioning across nested spatial level.

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

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).

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.

Suite of logistic and quantile regression models for the analysis of taxa responses (both in terms of occurences and abundances) to environmental conditions.

Phytoplankton Size Distributions is a web service designed to support the investigation of size distributions patterns of phytoplankton communities. This web service provides a user-friendly workflow allowing to perform Modality (Hartigans' dip test), Normality or LogNormality (Anderson-Darling test, Cramer- von Mises) tests of Phytoplankton Biovolume (expressed as μm3) or Cell carbon content (expressed as pgC*cell-1) distributions. Criteria of data aggregation (i.e. spatial, temporal and EUNIS habitat type) can be selected from the users. The web service works on data resources shared on the LifeWatch Data Portal and harmonized according to the "LifeWatch Data Schema" (for more details, please see the dedicated training sections at http://training.servicecentrelifewatch.eu/course/view.php?id=5). It has been developed in the R environment (R Core Team 20017).

Phytoplankton Traits Computation is a web service designed to support traits-based studies of phytoplankton communities. The main purpose of this web service, based on R functions, is to provide a user-friendly workflow including all the fundamental steps for the computation of some phytoplankton traits, without using the command line. It allows to calculate morphological and demographic traits, such as hidden dimension, biovolume, surface area, surface-volume ratio, cell carbon content, density, carbon content and total biovolume (for more details about traits, please see http://thesauri.lifewatchitaly.eu/PhytoTraits/index.php). The web service works on data resources shared on the LifeWatch Data Portal and harmonized according to the "LifeWatch Data Schema" (for more details, please see the dedicated training sections at http://training.servicecentrelifewatch.eu/course/view.php?id=5). It is based on computations made in the R server (https://cran.r-project.org). WEB SERVICE SUBMISSION The Phytoplankton Traits Computation consists in two steps: 1. Selection of the input file from the knowledge bases stored in "My Knowledge" on the LifeWatch Data Portal. The knowledge bases are obtained by the "Data Advanced Search", using different filters, on one or more data resources for which you have requested the authorisation and for those you uploaded yourself (for more details, please see the dedicated training sections at http://training.servicecentrelifewatch.eu/course/view.php?id=5). To be processed by this web service, the input file must have some mandatory fields, such as scientific name, measurement remarks, length and width for "Simplified calculation", and scientific name, measurement remarks and linear dimensions (e.g. "a", "b", "c", etc.) for "Advanced calculation" (see the next step); 2. Selection of calculation modality and desired outputs: ➔ Calculation Type: - "Simplified" approximates the taxon specific-biovolumes calculation based on 2 linear dimensions only, length and width. "scientific name", "measurement remarks" (e.g vision of the organism, dimension more or less than 20 µm), "length" and "width" are the mandatory fields for this calculation type. - The "Advanced" modality allows a more accurate estimate of taxon-specific biovolume, but it requires more information. For each shape, at least 2 measured basic linear dimensions need to be provided from the user. The mandatory fields for this calculation type are "scientific name", "measurement remarks" (e.g vision of the organism, dimension more or less than 20 µm) and the measured linear dimensions according to the Phytobioimaging Atlas of Shapes and PhytoTraits thesaurus (for more details, please see http://phytoplankton.lifewatch.unisalento.it/en-us/products/AtlasOfShapes.aspx?ID_Tipo=0 and http://thesauri.lifewatchitaly.eu/PhytoTraits/index.php). ➔ Output Traits: allows the selection of one or more traits to be calculated and visualized in the final output data file. The user may select one or more output among hidden dimension, biovolume, surface area, surface-volume ratio, cell carbon content, density, carbon content and total biovolume. EXPECTED RESULTS The web service will return an output file in .csv format, including all input data and calculated records. RESULT RETRIEVAL An email, with a link pointing to the requested output, will be sent to your address.

Thesaurus on Phytoplancton Morphological Traits.

Evaluation of the estimated number of taxa for given sample size.