Biodiversity Community Integrated Knowledge Library (BiCIKL)

Abstract

BiCIKL is an European Union Horizon 2020 project that will initiate and build a new European starting community of key research infrastructures, establishing open science practices in the domain of biodiversity through provision of access to data, associated tools and services at each separate stage of and along the entire research cycle. BiCIKL will provide new methods and workflows for an integrated access to harvesting, liberating, linking, accessing and re-using of subarticle-level data (specimens, material citations, samples, sequences, taxonomic names, taxonomic treatments, figures, tables) extracted from literature. BiCIKL will provide for the first time access and tools for seamless linking and usage tracking of data along the line: specimens > sequences > species > analytics > publications > biodiversity knowledge graph > re-use.

COVoc and COVTriage: novel resources to support literature triage

“…These questions emerged on the agenda of both SIB and ELIXIR and will require innovative responses at a global level with potential implications from leading publishers in the field. The BICIKL project, coordinated by Pensoft, could play a pioneering role with the development of a Biodiversity Knowledge Hub ( Penev et al , 2022 ), i.e. a one-stop entry point to search publications and data from all life sciences.…”

“…These collections are daily updated for the first two, punctually for the third. Additional collections regrouping supplementary data files from PMC as well as taxonomic treatments from Plazi ( Naderi et al, 2022 ; Penev et al, 2022 ) are planned.…”

Automating the Curation Process of Historical Literature on Marine Biodiversity Using Text Mining: The DECO Workflow

“…More effort is however needed, as exemplified by museum specimen collections and herbaria digitisation (Mora et al, 2011;Wheeler et al, 2012). The museum specimen collections and herbaria digitisation has 64 https://www.ghostscript.com/index.html 65 https://stedolan.github.io/jq/ 66 https://imagemagick.org/index.php 67 https://w w w.ncei.no aa.gov/pro duc ts/o ce an-climate-lab orator y/ global-oceanographic-data-archaeology-and-rescue 68 https://oceanspast.org 69 https://icoads.noaa.gov/reclaim/ multiple projects and infrastructures like Distributed System of Scientific Collections 70 (DiSSCo), Innovation and consolidation for large scale digitisation of natural heritage 71 (ICEDIG), Integrated Digitized Biocollections 72 (iDigBio) and Biodiversity Community Integrated Knowledge Library (BiCIKL) (Penev et al, 2022). Similar attention is required to rescue marine biodiversity data from historical documents that can contribute to a more complete global biodiversity synthesis (Heberling et al, 2021).…”

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

“…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.…”