Cross-linking life science infrastructures for molecular and taxonomic data

Blue-Cloud, along with BiCIKL and AtlantECO projects, is organising on 7-9 March the "Cross-linking life science infrastructures for molecular and taxonomic data" worksop, at the European Bioinformatics Institute (EMBL-EBI), in Cambridge (United Kingdom).

Topics description & objectives

Topic 1 - Linking molecular data to biodiversity information systems - perspectives from participating infrastructures.

The objective is to present a quick overview of participating infrastructures and most importantly to highlight recent developments and interest in linking molecular data to biodiversity information systems. Suggested presentations,(15 min): Blue-Cloud (Stéphane), EBI-ENA (Joana), EBI-MGnify (Lorna), WoRMS (Leen), UniEuk (Javier), GBIF (Tobias?), OBIS (Pieter) and EMODnet/EurOBIS (Lynn?).

BiCIKL Round Table - Developing structured data formats and metadata standards for molecular ecology.

The objectives of the round table are to (1) discuss structured models for metagenomics and metabarcoding derived data submission, and (2) establish and reinforce collaborations in data standards and interoperability of molecular ecology data. Agenda

Topic 2 - Developing an operational “blue” partition of EBI’s life science data.

The objective is to present ENA’s recent work on defining a "blue partition" of its data, based on the geolocation and the taxonomy of samples, using shapefiles (IHO/EEZ, Longhurst and others) and WoRMS' environmental flags. We wish to discuss ways to improve the partition, and to extend its use across EBI resources in support to, and in collaboration with participating infrastructures.

Topic 3 - Developing a taxonomic/functional annotation pipeline for Eukaryotes at EBI.

The objective is to initiate the development at MGnify of a taxonomic/functional annotation pipeline that targets Eukaryotes, in collaboration with the existing P2R/EukRef pipeline developed by project UniEuk.

Topic 4 - Developing a programmatic flow of taxonomic/functional annotations from EBI to biodiversity information systems.

The objectives are to (1) progress on implementing the flow of taxonomic observations from MGnify to OBIS, in coordination with the API currently used by GBIF, and (2) discuss the flow of data from ENA to biodiversity information systems.

Topic 5 - Mapping taxonomic classifications of NCBI, WoRMS and UniEuk.

The objectives are to (1) discuss the methodology of mapping NCBI, WoRMS and UniEuk taxonomies,  and (2) propose a workflow to maintain and serve the mapping. The rationale is that EBI uses the NCBI taxonomy by default, so that (1) taxonomic annotations from EBI will provide NCBI:txids, and (2) WoRMS environmental flags need to be mapped to NCBI taxonomy.

Practical Information - Where we stay and how to get there

Holiday Inn Express in Whittlesford

From/To Stansted airport: There is a direct train (30 min) between the airport and Whittlesford Parkway train station

From/To London Kings Cross / St. Pancras: Several trains between Kings Cross & Cambridge, and from Cambridge you can take a taxi (30 mins) or train to Whittlesford Parkway (7 mins)

Genome Campus Shuttle schedule

We will use the 8h15 and 17h45 (or 18:15) shuttle

• from Whittlesford train station to Genome Campus (15 min ride) : 8:15, 8:45, 10:10, 10:40, 11:10
• from Genome Campus to Whittlesford train station (15 min ride) : 14:45, 16:15, 16:45, 17:45, 18:15, 20:10