Simon Chagnoux

Simon Chagnoux
Muséum National d'Histoire Naturelle · DSI

About

22
Publications
6,336
Reads
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264
Citations
Citations since 2016
20 Research Items
210 Citations
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Introduction
Skills and Expertise

Publications

Publications (22)
Article
Full-text available
In March 2019, the Muséum national d’histoire naturelle, Paris (MNHN) launched the datapoc.mnhn.fr project, funded by the French research infrastructures CollEX-Persée and E-recolnat. This proof of concept was imagined and is supported by a group of partners coming from different communities working at the Muséum (specimen collection curators, libr...
Article
Full-text available
The concept of building a network of relationships between entities, a knowledge graph, is one of the most effective methods to understand the relations between data. By organizing data, we facilitate the discovery of complex patterns not otherwise evident in the raw data. Each datum at the nodes of a knowledge graph needs a persistent identifier (...
Article
Full-text available
More and more herbaria are digitising their collections. Images of specimens are made available online to facilitate access to them and allow extraction of information from them. Transcription of the data written on specimens is critical for general discoverability and enables incorporation into large aggregated research datasets. Different methods...
Data
R script used to map data from FinBIF API to DwC
Data
Python script to upload the dataset to Zenodo
Data
Taxonomic coverage (interactive HTML file)
Poster
Full-text available
Natural History Collections allow tackling many questions in ecology and evolution, through the data provided by both the specimens themselves and the labels linked to the specimens, with rare advantages: data are real, spanned over time, checkable for accurate identifications, and the preserved physical objects make them not questionable. In parti...
Article
Full-text available
A simple, permanent and reliable specimen identifier system is needed to take the informatics of collections into a new era of interoperability. A system of identifiers based on HTTP URI (Uniform Resource Identifiers), endorsed by the Consortium of European Taxonomic Facilities (CETAF), has now been rolled out to 14 member organisations (Güntsch et...
Preprint
Full-text available
ICEDIG is a design study for the new research infrastructure Distributed System of Scientific Collections (DiSSCo), focusing on the issues around digitisation of the collections and making their data freely and openly available following the FAIR principles (data being Findable, Accessible, Interoperable, and Re-usable). As a design study, ICEDIG...
Article
Full-text available
The digitization of biocollections is a critical task with direct implications for the global community who use the data for research and education. Recent innovations to involve citizen scientists in digitization increase awareness of the value of biodiversity specimens; advance science, technology, engineering, and math literacy; and build sustai...
Article
Full-text available
While many programs are available to edit phylogenetic trees, associating pictures with branch tips in an efficient and automatic way is not an available option. Here, we present TreePics, a standalone software that uses a web browser to visualize phylogenetic trees in Newick format and that associates pictures (typically, pictures of the voucher s...
Article
Full-text available
With biodiversity research activities being increasingly shifted to the web, the need for a system of persistent and stable identifiers for physical collection objects becomes increasingly pressing. The Consortium of European Taxonomic Facilities agreed on a common system of HTTP-URI-based stable identifiers which is now rolled out to its member or...
Article
Full-text available
The new Franco-Brazilian website "Saint-Hilaire virtual herbarium" offers dynamic online consultation of all specimens and manuscripts of the naturalist Auguste de Saint-Hilaire, providing links between specimen images and associated textual data, including notes available in his field books. This tool aims at facilitating the work of taxonomy and...
Article
Full-text available
Because they house large biodiversity collections and are also research centres with sequencing facilities, natural history museums are well placed to develop DNA barcoding best practices. The main difficulty is generally the vouchering system: it must ensure that all data produced remain attached to the corresponding specimen, from the field to pu...

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Projects

Projects (2)
Project
ICEDIG – “Innovation and consolidation for large scale digitisation of natural heritage” - is an EU-funded project that aims at supporting the implementation phase of the new Research Infrastructure DiSSCo (“Distributed System of Scientific Collections”) by designing and addressing the technical, financial, policy and governance aspects necessary to operate such a large distributed initiative for natural sciences collections across Europe. more at www.icedig.eu