LifeWatch – A European e-Science and observatory infrastructure supporting access and use of biodiversity and ecosystem data

There are many promising earth and biodiversity-monitoring projects underway across the globe, but they often operate in information islands, unable easily to share data with others. This is not convenient: It is a barrier to scientists collaborating on complex, cross-disciplinary projects which is an essential nature of biodiversity research. 

LifeWatch (www.lifewatch.eu) is an ESFRI (European Strategy Forum on Research Infrastructures) initiative which has just entered its construction phase. It is aiming at new ways of collaboration, in an open-access research environment to solve complex societal and scientific questions on biodiversity and ecosystems. It installs a range of new services and tools to help the researchers communicate, share data, create models, analyze results, manage projects and organize the community. The power of LifeWatch comes from linking all kinds of biodiversity related databases (e.g. collections, long-term monitoring data) to tools for analysis and modeling, opening entirely new avenues for research with the potential for new targeted data generation. At this level the interface with national data repositories becomes most important, as this opens the opportunity for users to gain advantage from data availability on the European level. LifeWatch will provide common methods to discover, access, and develop available and new data, analytical capabilities, and to catalog everything, to track citation and re-use of data, to annotate, and to keep the system secure. This includes computing tool-kits for researchers: for instance, an interoperable computing environment for statistical analysis, cutting-edge software to manage the workflow in scientific projects, and access to new or existing computing resources. The result: ‘e-laboratories’ or virtual labs, through which researchers distributed across countries, time zones and disciplines can collaborate. With emphasis on the open sharing of data and workflows (and associated provenance information) the infrastructure allows scientists to create e-laboratories across multiple organizations, controlling access where necessary

Ten outcomes to improve informatics interoperability in cyber/e-Infrastructures for biodiversity and ecological sciences : (through the use case of Essential Biodiversity Variables)

Data products for Essential Biodiversity Variables (EBV) must be (re-)producible and comparable for any geographic area, small or large, fine-grained or coarse; at temporal scale determined by need and/or the frequency of available observations; at a point in time in the past, present day or in the future; as appropriate, for any species, assemblage, ecosystem, biome, etc.; using data for that area/topic that may be held by any and across multiple research/data infrastructures; using harmonized, widely accepted protocols (workflows); capable of being executed in any infrastructure; by any (appropriate) person anywhere. To date, the GLOBIS-B project (www.globis-b.eu) established there are technical needs for: i) common dimensional structure, packaging and metadata descriptions of EBV data products; ii) consistent quality checking and assertion across data from different sources that contribute to EBVs; iii) EBV workflows with common representation that is independent of underlying computational infrastructure; and iv) use of standard mechanisms for recording provenance of EBV data products. However, too little is presently known about how the technical production of EBV data products will work in practice. Experimental implementation work is necessary, both to show what is technically feasible and useful, and to reveal what is really needed. We must, for example agree details of both the compact data/file structure for EBV data products, and programmatic interfaces to those data products. Experimental work must lead eventually to formal standardisation. Scientists, infrastructure providers, informaticians and GEO BON Working Groups must jointly address the specific problems of moving from limited, experimental, proof-of-concept type studies (such as the Atlas of Living Australia / Global Biodiversity Information Facility (GBIF) invasive species case study) to first trials producing and using real data products with real users. Beyond first trials, they must jointly move to more robust solutions that scale out and up, as well as providing the basis for the long-term support to GEO BON across a wide range of EBVs classes. Satisfying the EBV use case acts for generally improving informatics interoperability among diverse cyber / e-Infrastructures supporting biodiversity science and ecology. It is desirable to guide participating providers without restricting their autonomy to achieve what is needed in ways appropriate to their own business. We show ten specific outcomes we want to see achieved, with the mission being the ability to deploy and execute standard workflows for preparing, publishing and preserving fit-for-use EBV data products that are comparable with one another. Achieving such outcomes significantly improves the ability of infrastructure providers to support the EBV production process

Canonical Workflow Framework for Research (CWFR) - position paper - version 2 December 2020

With this paper we want to describe the motivation and basic ideas behind CWFR. Two working meetings were held to discuss the CWFR concept and to relate it with other work around “workflows” that has already been done. We intend to further develop this paper dependent on the growing insights based on the discussions and interactions we are planning to organise

‘openDS’ – progress on the new standard for digital specimens.

In a Biodiversity_Next 2019 symposium, a vision of Digital Specimens based on the concept of a Digital Object Architecture (Kahn and Wilensky 2006) (DOA) was discussed as a new layer between data infrastructure of natural science collections and user applications for processing and interacting with information about specimens and collections. This vision would enable the transformation of institutional curatorial practises into joint community curation of the scientific data by providing seamless global access to specimens and collections spanning multiple collection-holding institutions and sources. A DOA-based implementation (Lannom et al. 2020) also offers wider, more flexible, and ‘FAIR’ (Findable, Accessible, Interoperable, Reusable) access for varied research and policy uses: recognising curatorial work, annotating with latest taxonomic treatments, understanding variations, working with DNA sequences or chemical analyses, supporting regulatory processes for health, food, security, sustainability and environmental change, inventions/products critical to the bio-economy, and educational uses. To make this vision a reality, a specification is needed that describes what a Digital Specimen is, and how to technically implement it. This specification is named 'openDS' for open Digital Specimen. It needs to describe how machines and humans can act on a Digital Specimen and gain attribution for their work; how the data can be serialized and packaged; and it needs to describe the object model (the scientific content part and its structure). The object model should describe how to include the specimen data itself as well as all data derived from the specimen, which is in principle the same as what the Extended Specimen model aims to describe. This part will therefore be developed in close collaboration with people working on that model. After the Biodiversity_Next symposium, the idea of a standard for Digital Specimens has been further discussed and detailed in a MOBILISE Workshop in Warsaw, 2020, with stakeholders like the GBIF, iDigBio, CETAF and DiSSCo. The workshop examined the technical basis of the new specification, agreed on scope and structure of the new specification and laid groundwork for future activities in the Research Data Alliance (RDA), Biodiversity Information Standards (TDWG), and technical workshops. A working group in the DiSSCo Prepare project has begun on the technical specification of the ‘open Digital Specimen’ (openDS). This specification will provide the definition of what a Digital Specimen is, its logical structure and content, and the operations permitted on that. The group is also working on a document with frequently asked questions. Realising the vision of Digital Specimen on a global level requires openDS to become a new TDWG standard and to be aligned with the vision for Extended Specimens. A TDWG Birds-of-a-Feather working session in September 2020 discusses and plans this further. The object model will include concepts from ABCD 3.0 and EFG extension for geo-sciences, and also extend from bco:MaterialSample in the OBO Foundry’s Biological Collection Ontology (BCO), which is linked to Darwin Core and from iao:InformationContentEntity in OBO Foundry's Information Artifact Ontology (IAO). openDS will also make use of the RDA/TDWG attribution metadata recommendation and other RDA recommendations. A publication is in preparation that describes the relationship with RDA recommendations in more detail, which will also be presented in the TDWG symposium

Cardiff University’s Condor Pool: background, case studies, and fEC

Cardiff University’s Condor pool aims to cater for the high throughput computing needs of a wide range of users based in various schools across campus. The paper begins by discussing the background of Cardiff University’s Condor pool. The paper then presents a selection of case studies and outlines our strategy for Condorising applications using submit script generators. Finally the paper presents the findings of a fEC exercise and outlines our policy for attributing directly allocated costs to a particular research project

CReATIVE-B Deliverable D3.1: Comparison of technical basis of biodiversity e-infrastructures

Deliverable D3.1, prepared on the basis of available information at the time of writing, is the output of CReATIVE-B task T3.1, which aims to “Compare the technical basis of e-infrastructures for biodiversity research”. It provides a synopsis comparison of the technical approaches of the e-infrastructures analysed within the scope of the project and elaborates the interoperability analysis by defining it and making a quantitative comparison of the technical facts gathered thus far. It reflects as accurately as possible the technical findings, structured along dimensions of interoperability that match the functional areas and layers of the research infrastructures being analysed. Deliverable D3.1 aims at shedding light on existing similarities and differences between participating research infrastructures thus forming a solid information and knowledge basis for future interoperability guidelines developments in D3.2 and D3.3

An introduction to the Minimum Information about a Digital Specimen (MIDS) digitisation standard.

Digitisation is the process of converting analogue data about physical specimens to digital representation that includes electronic text, images and other forms. The term has been used diversely within the natural science collections community, and between different digitisation initiatives, the outputs can be quite different. Digitisation of individual specimens provides explicit and precise details about each object curated in a collection. This digitisation is based on diverse aims, the needs of specific projects and the specific practices and workflows in different institutions, so the digitised output has a wide range of uses. Capturing and presenting such data from future digitisation in standard formats is essential so that data can be more easily understood, compared, analysed and communicated via the Internet. By harmonising a framework that clarifies what is meant by different levels of digitisation (MIDS level), as well as the minimum information to be captured at each level, it becomes easier to consistently measure the extent of digitisation achieved over time and to set priorities for the remaining work. Similarly, ensuring that enough data are captured, curated and published is essential so they are useful for the widest possible range of future research, teaching and learning purposes. The Minimum Information about a Digital Specimen (MIDS) specification aims to address these problems. MIDS is a 'minimum specification', which means that the information specified as necessary at a each MIDS level is the minimum expected to be made digitally available following each major stage of digitisation. More is not precluded. From September 2020, MIDS specification work is now the work topic of an approved TDWG Task Group