The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic will be remembered as one of the defining events of the 21st century. The rapid global outbreak has had significant impacts on human society and is already responsible for millions of deaths. Understanding and tackling the impact of the virus has required a worldwide mobilisation and coordination of scientific research. The COVID-19 Data Portal (https://www.covid19dataportal.org/) was first released as part of the European COVID-19 Data Platform, on April 20th 2020 to facilitate rapid and open data sharing and analysis, to accelerate global SARS-CoV-2 and COVID-19 research. The COVID-19 Data Portal has fortnightly feature releases to continue to add new data types, search options, visualisations and improvements based on user feedback and research. The open datasets and intuitive suite of search, identification and download services, represent a truly FAIR (Findable, Accessible, Interoperable and Reusable) resource that enables researchers to easily identify and quickly obtain the key datasets needed for their COVID-19 research

The COMPARE Data Hubs

Data sharing enables research communities to exchange findings and build upon the knowledge that arises from their discoveries. Areas of public and animal health as well as food safety would benefit from rapid data sharing when it comes to emergencies. However, ethical, regulatory and institutional challenges, as well as lack of suitable platforms which provide an infrastructure for data sharing in structured formats, often lead to data not being shared or at most shared in form of supplementary materials in journal publications. Here, we describe an informatics platform that includes workflows for structured data storage, managing and pre-publication sharing of pathogen sequencing data and its analysis interpretations with relevant stakeholders

The ENA Source Attribute Helper: An API for improved biological source data

Metadata management for sequence data is essential for the accurate description of Earth’s biodiversity. Within metadata attributes, those that reference the biological sources of sequences and samples and allow linking to the specimen or sample of origin are fundamental for facilitating connections between molecular biology, taxonomy, systematic biology and biodiversity research, increasing the discoverability and usability of data by researchers worldwide.Sequence data is publicly archived at the International Nucleotide Sequence Database Collaboration (INSDC) that includes the National Centre for Biotechnology Information (NCBI), the DNA Data Bank of Japan (DDBJ) and the European Nucleotide Archive (ENA). Sequences stored at INSDC have associated a considerable range of metadata, including attributes related to its biological source, such as references to natural history collections or culture collections. But, these source attributes are not always submitted or may be incomplete, limiting the association of the sequence records to the original source material, hampering further data connections (e.g., biological data associated with the voucher or species distribution data). Therefore, we have developed the ENA Source Attribute Helper API, a tool that aims to assist users on the submission of accurate attributes referring to the biological source of samples and sequence data. This tool was developed within the scope of BiCIKL (Biodiversity Community Integrated Knowledge Library) (Penev et al. 2022), a Horizon 2020 project which targets building a wide, biodiversity related community for connecting data along the different axes of biodiversity research.The first version of the tool was designed to support correct annotation of the attributes that identify the source material from which the sample or sequence were obtained, namely /specimen_voucher, /culture_collection, and /biomaterial (INSDC 2021). These attributes follow a Darwin Core Triplet format (Wieczorek et al. 2012), composed of institution code, collection code and the specimen, culture, or material identifier, accordingly. Since the submission of the biological source attributes to the INSDC may be performed both when data is initially uploaded or on following updates using a variety of tools, we developed the API as an open source tool that is publicly accessible and may be used as a free-standing service. The API is built using Representational State Transfer (REST) API Architecture and it is designed to use the data available in the NCBI BioCollections (Sharma et al. 2018). NCBI Biocollections is a curated database of metadata for natural history collections, associated with records in INSDC, that includes the institution and collection codes. The API main functions include the querying of the metadata (the API presents both exact matches and similar matches) for the institutions and collections based on the user input, validation of institution and collection codes in the attribute strings provided by the user, and the construction of the attribute string based on the user-provided information. The API does not include the search or validation of the voucher specimen codes. The API is designed in a way that it can be extended easily for any future enhancements and initially expected to promote and support the submission and any subsequent curation of better structured and more richly described source data. We expect this tool to contribute to better connected biodiversity data and hence provide a stronger foundation to strengthen the value of natural history collections, taxonomic expertise, and biodiversity knowledge

Improving FAIRness of eDNA and Metabarcoding Data: Standards and tools for European Nucleotide Archive data deposition

The advancements in sequencing technologies have promoted the generation of molecular data for cataloguing and describing biodiversity. The analysis of environmental DNA (eDNA) through the application of metabarcoding techniques enables comprehensive descriptions of communities and their function, being fundamental for understanding and preserving biodiversity. Metabarcoding is becoming widely used and standard methods are being generated for a growing range of applications with high scalability. The generated data can be made available in its unprocessed form, as raw data (the sequenced reads) or as interpreted data, including sets of sequences derived after bioinformatics processing (Amplicon Sequence Variants (ASVs) or Operational Taxonomic Units (OTUs)) and occurrence tables (tables that describe the occurrences and abundances of species or OTUs/ASVs). However, for this data to be Findable, Accessible, Interoperable and Reusable (FAIR), and therefore fully available for meaningful interpretation, it needs to be deposited in public repositories together with enriched sample metadata, protocols and analysis workflows (ten Hoopen et al. 2017). Metabarcoding raw data and associated sample metadata is often stored and made available through the International Nucleotide Sequence Database Collaboration (INSDC) archives (Arita et al. 2020), of which the European Nucleotide Archive (ENA, Burgin et al. 2022) is its European database, but it is often deposited with minimal information, which hinders data reusability. Within the scope of the Horizon 2020 project, Biodiversity Community Integrated Knowledge Library (BiCIKL), which is building a community of interconnected data for biodiversity research (Penev et al. 2022), we are working towards improving the standards for molecular ecology data sharing, developing tools to facilitate data deposition and retrieval, and linking between data types. Here we will present the ENA data model, showcasing how metabarcoding data can be shared, while providing enriched metadata, and how this data is linked with existing data in other research infrastructures in the biodiversity domain, such as the Global Biodiversity Information Facility (GBIF), where data is deposited following the guidelines published in Abarenkov et al. (2023). We will also present the results of our recent discussions on standards for this data type and discuss future plans towards continuing to improve data sharing and interoperability for molecular ecology

Enabling Community Curation of Biological Source Annotations of Molecular Data Through PlutoF and the ELIXIR Contextual Data Clearinghouse

The advancements in sequencing technologies have greatly contributed to the documentation of Earth’s biodiversity. However, for exploring the full potential of molecular resources for biodiversity, there needs to be a good linkage between sequence data and its biological source, contributing to a network of connected data in the biodiversity research cycle. This requires a foundation of well-structured and accessible annotations in the molecular sequence repositories.The International Nucleotide Sequence Database Collaboration (INSDC), of which the European Nucleotide Archive (ENA) is its European node, holds a large amount of annotations associated with sequence data, relating to its biological source (e.g., specimens in natural history collections). However, for a number of records, these annotations may be incomplete (e.g., missing voucher information), ambiguous or even inaccurate.Therefore, we have implemented a workflow that allows third-party annotations to be attached to sequence and sample records using two existing services, the PlutoF platform and the ELIXIR Contextual Data ClearingHouse. This work was developed within the scope of the BiCIKL (Biodiversity Community Integrated Knowledge Library) project, which aims to establish open science practices in the biodiversity domain.PlutoF is an online data management platform that also provides computing services for biology-related research. PlutoF features allow registered users to enter their own data and access public data at INSDC. Users can enter and manage a range of data, as taxonomic classifications, occurrences, etc. This platform also includes a module that allows the addition of third-party annotations (on material source, taxonomic identification, etc.) linked to specimens or sequence records. This module was already in use by the UNITE community for annotation of INSDC rDNA Internal Transcribed Spacer sequence datasets (Abarenkov et al. 2021). These UNITE annotations are displayed in the National Centre for Biotechnology Information (NCBI) records through links to the PlutoF platform. However, there was the need for an automated solution that allowed third-party annotations to any sequence or sample record at INSDC. This was implemented through the operation of the ELIXIR Contextual Data ClearingHouse (hereafter as Clearinghouse). The Clearinghouse holds a simple RESTful Application Programming Interface (API) to support the submission of additions and improvements to current metadata attributes, such as information on material sources, on records publicly available in the ELIXIR data resources. The Clearinghouse enables the submission of these corrected metadata from databases (such as the PlutoF platform) to the primary data repositories.The workflow developed is shown in Fig. 1 and consists of the following steps: i) users annotate sequence metadata that is regularly downloaded from INSDC using NCBI’s E-utilities; ii) an annotation proposal is created and a verification notification is sent to an assigned reviewer; iii) the reviewer evaluates the annotation proposal and accepts it or rejects it with comments; iv) if the annotation proposal is accepted, the annotated fields that may be mapped to ENA fields are then pushed to the Clearinghouse using their RESTful API. The annotations when received at ENA are then reviewed before being displayed. This workflow is implemented through a web interface in PlutoF, which allows user-friendly and effortless reporting of corrections or additions to biological source metadata in sequence records.Overall, we expect this tool to contribute to the enrichment of metadata associated with sequence records, and therefore increase the links between the molecular and biodiversity resources, and enable sequencing data to deliver their full potential for biodiversity conservation

Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses

The COVID-19 pandemic has seen large-scale pathogen genomic sequencing efforts, becoming part of the toolbox for surveillance and epidemic research. This resulted in an unprecedented level of data sharing to open repositories, which has actively supported the identification of SARS-CoV-2 structure, molecular interactions, mutations and vari-ants, and facilitated vaccine development and drug reuse studies and design. The European COVID-19 Data Platform was launched to support this data sharing, and has resulted in the deposition of several million SARS-CoV-2 raw reads. In this paper we describe (1) open data sharing, (2) tools for submission, analysis, visualisation and data claiming (e.g. ORCiD), (3) the systematic analysis of these datasets, at scale via the SARS-CoV-2 Data Hubs as well as (4) lessons learnt. This paper describes a component of the Platform, the SARS-CoV-2 Data Hubs, which enable the extension and set up of infrastructure that we intend to use more widely in the future for pathogen surveillance and pandemic preparedness.</p

The COMPARE Data Hubs

Data sharing enables research communities to exchange findings and build upon the knowledge that arises from their discoveries. Areas of public and animal health as well as food safety would benefit from rapid data sharing when it comes to emergencies. However, ethical, regulatory and institutional challenges, as well as lack of suitable platforms which provide an infrastructure for data sharing in structured formats, often lead to data not being shared or at most shared in form of supplementary materials in journal publications. Here, we describe an informatics platform that includes workflows for structured data storage, managing and pre-publication sharing of pathogen sequencing data and its analysis interpretations with relevant stakeholders