dataesr/scientific-paragraphs-categorization huggingface dataset:
Sonnerat serves as the core source for data delivered by other portals (e. g. , GBIF, e-ReColNat). As with all of the other shared collection databases at the MNHN, Sonnerat is a relational database and was developed under Oracle. The main tables constituting Sonnerat, with the header of the conlumns they contain and the relations between them are presented in a Unified Modeling Language (UML) diagram in Fig. 1. To manage the data and facilitate their dissemination over the web, a specific tool was developed under Java starting in 1997 by the Centre Informatique du Muséum. It was initially named JCIM (for Java [solution] of the Centre Informatique du Muséum) and later renamed JACIM in order to avoid internal confusion with the name of the Ichtyological collection database (GICIM). Updates and upgrades are performed internally by a dedicated team in the Direction des Services Informatiques.
Data are published online through the Data Portal of the MNHN  17. Additionally a Darwin Core archive (http://rs. tdwg. org/dwc/index. htm) is regularly generated and available on GBIF data portal (Data Citation 1). As for every collection database, the archive is generated using the Occurrence core. All field definitions (Darwin Core Terms) are available on the Darwin Core website (at: http://rs. tdwg. org/ dwc/terms/index. htm#occurrenceindex). The archive itself is constitute of 4 text files containing the structural information (the occurrence core, which here comes together with 3 extensions: multimedia, identifier and identification), an eml file containing the data themselves, and an xml file doing the link in between the source database (here Sonnerat) and the archive. Considering the sheer size of the collection at P, its digitisation has been a tremendous task and indeed this process is still ongoing to deal with the holdings that remain to be scanned (1% of the total; an estimated 10% of the collection remains to be databased).
The first databasing efforts were concentrated on the day to day activities of the herbarium, in particular recording specimens being sent on loan and new accessions related to studies conducted by MNHN researchers. Initially between 20,000 and 30,000 new entries were made per year, but since initiation of the mass digitisation of the collection carried out under the Renobota project starting in 2008, work on the database has changed radically and become a key tool for herbarium management, focusing mainly on updating and enriching the data and in particular adding collection information to those entries that have not yet been fully databased. Moreover, during the Renobota project only a single entry was made per specimen, even for those on which more than one distinct collection has been mounted (this is particularly true for the Cosson herbarium).
A Nikon D800 camera mounted on a Kaiser R1 copy stand system is currently being used to image all new specimens and for image updates. In order to increase the rate of databasing in addition to this routine herbarium work, systematic data entry efforts were developed from 2001 onwards, involving numerous skilled personnel (Supplementary File 1). Continental African Asteraceae, Malagasy Fabaceae-Caesalpinioideae and Papilionoideae, as well as specimens from Mayotte Island and the Union of the Comoros were treated during this process  15, 18, 19. The substantial dataset that is available today  17  (Data Citation 1) was also achieved through the MNHN's active involvement in several national and international databasing projects, each focusing on distinct aspects of data acquisition corresponding to different uses of the rich botanical collection housed at P.
Cyperaceae from tropical Asia and tropical Americas digitising project (2001-2003) Funding: Institut Klorane, MNHN Digitising for the Cyperaceae from tropical Asia and tropical Americas project focused on all Cyperaceae specimens from these regions. Over 8,000 specimens from Asia and 23,000 from America were treated over a three year period. Global biodiversity information facility project (2002-2004)   Funding: GBIF France The GBIF project was the first global databasing effort undertaken at P. It focused on tropical material of two families: over 34,000 specimens of Orchidaceae and 16,800 specimens of Solanaceae where databased, and a search for type specimens was implemented.
Millennium seed bank project (2004-2008) Funding: Royal Botanic Gardens, Kew This project, which focused on databasing specimens from Mali, Burkina Faso and Madagascar, was conducted in collaboration with the Kew Millennium seed bank. A total of 31,000 specimens from 120 families (45 for Madagascar and 75 for Burkina Faso and Mali) were fully databased, including post-facto calculated geolocation data. Funding: Andrew W. Mellon Foundation These three projects funded by the Mellon Foundation aimed at databasing and producing high-resolution (600 dpi) scans of all the type specimens held in herbaria throughout the world, including P. The first phase, the African Plant Initiative (API), which operated from 2004 to 2006, focused on the African type specimens. It was then followed by the Latin American Plant Initiative (LAPI), from 2007 to 2008, and finally the Global Plant Initiative (GPI) followed from 2009 to 2015, which sought to scan all types from throughout the world, with the exception of Europe.
These three projects resulted in the databasing and digitisation of 185,937 specimens (including 177,045 type specimens and 8,892 specimens of nomenclatural interest), amongst which 45,500 types were located for the first time in the collection, requiring verification. For most of these specimens, the digitisation process was done with Herbscan units, in which a scanner is mounted upside-down, which were provided by the Royal Botanic Gardens, Kew. For thick specimens as well as especially fragile material, high definition Leaf photographic equipment mounted on a motorized bench was used. A 300 dpi copy of each image is linked to the data on the MNHN server (Data Citation 1), while a 600 dpi image, together with the most important data, is duplicated on the Global Plants on JSTOR portal (materials contributed by the Muséum National d'Histoire Naturelle (P) available at: http://plants.
Herbier Lamarck project (2004) Funding: Centre national de la Recherche scientifique This project sought to digitise the totality of Jean-Baptiste Lamarck's herbarium, in its current composition, as part of a project portal dedicated to Lamarck's scientific legacy. All of the ca. 19,000 specimens were scanned after having been given an accession number, and are available on a dedicated portal (http://www. lamarck. cnrs. fr/herbier. php). When a record for an accession in the Lamarck herbarium also exists in Sonnerat, a link is automatically provided. The data from the Lamarck portal will be fully integrated into the P dataset in the near future (Data Citation 1).
Auguste de Saint-Hilaire virtual herbarium project (2009) Funding: Instituto de Botanica de São Paulo(IBt), Centro de Referência em Informação Ambiental (CRIA ), Fundação de Amparo à Pesquisa do Estado de São Paulo (Fapesp), Fundação Vitae, Institut des Herbiers Universitaires, CLF, Clermont-Ferrand This project, conducted remotely in Brazil, concentrates on digitising the herbarium material collected by Auguste de Saint-Hilaire (1779-1853) in Brazil from 1816 to 1822. Specimen data are presented in a dedicated portal under the form of a virtual herbarium, where the sheets are linked to the relevant pages of Saint-Hilaire's field notebooks. Data are harvested twice a day from Sonnerat by the virtual herbarium. To date P has contributed over 9,300 specimens, and the rate of data capture has increased significantly since 2012 mainly due to the databasing efforts of the Reflora project  20  (available at: http://hvsh.
Each sheet received a barcoded accession number label (if one had not previously been given) and was then scanned, with the exception of type specimens (stored in red folders, which had already been treated as part of the Global Plants Science projects; see above) and Vaillant specimens (stored in green folders and treated in part by the GPI team). Essential data were captured (accession number, geographic region and taxon name), which is the basic information necessary to link the virtual collection (i. e. , the scanned images) to the physical collection (the specimens). The resulting data and associated images were then uploaded into the Sonnerat database  12, 13. Over 5,000,000 specimens were digitised and for more than 90% of them, a new database entry was created in Sonnerat. The project resulted in a massive number of specimen entries, each associated with an image, but only limited collection label data were captured (Data Citation 1).
Les Herbonautes project (2012-present) Funding: MNHN, Fondation de la Maison de la Chimie, e-ReColNAt (ANR-11-INBS-0004), Muséum national d'histoire naturelle, Paris (MNHN) Les Herbonautes (http://lesherbonautes. mnhn. fr/) is an ongoing participatory science project aimed at transcribing the information written on herbarium labels through a dedicated web-based portal. Images are shown to registered web volunteers through thematic projects (called 'missions') designed by researchers curating collections and focusing on scientific research needs. The web volunteers (called 'herbonauts') transcribe, for each image, data on the collection locality, date, collector, collection number, identification, and geolocation, as requested. The data quality is cross-checked: in order to be validated, the same data must be captured independently by several different contributors.
Tests of data quality have shown comparable levels between data obtained using this method and professional standards. Since the opening of the website in December 2012, 37 missions have been launched, 35 of which have been completed. As of September 9, 2015, a total of 2,181 contributors have examined 119,956 specimens, providing 1,685,738 entries (i. e. , responses to a single question). After three years, the public's enthusiasm for databasing herbarium specimens remains high, although a certain seasonality can be seen: more contributions are made in winter than summer (Fig. 3 ). The initial version of the Les Herbonautes portal was developed as part of the Renobota project and a Version 2, developed through the e-ReColNat project, was released in January 2016. This new version allows for better follow up by both the project managers and the public.
Open Up! project (2013) Funding: Europeana grant for OpenUp! The OpenUp! project aims to provide images from natural history museum collections to the Europeana portal (http://www. europeana. eu/). The images, selected based on criteria for potential interest to the broad public, were chosen from among those generated during the Renobota project. In parallel, curation of the entire set of the taxonomic data in the Sonnerat database was performed (Data Citation 1). Data from 385,286 specimens of P were provided to the Europeana portal (available at: http://www. europeana. eu/).
Reflora project (2013-2016) Funding: Conseil National pour la Recherche (CNPq)-Vale The Reflora project aims to create a portal giving access to data from every botanical collection relating to the Brazilian flora. All of the ca. 300,000 images produced by the Renobota project from specimens collected in Brazil are being sent to the Herbarium Collection of the Rio de Janeiro Botanical Garden, where teams of botanists and students are databasing them. Data are then sent back to P for incorporation into Sonnerat (Data Citation 1). To date, some 130,000 images have been provided to Reflora and data derived from 30,000 of these have been added to the P dataset. The global data resulting from the Reflora project are available on a dedicated virtual herbarium (http://reflora. jbrj. gov. br/reflora/ herbarioVirtual/).
e-ReColNat project (2013-2019) Funding: PIA Agence Nationale de la Recherche-11-INBS-0004, Muséum national d'histoire naturelle. This project aims to facilitate online access to the biodiversity collections held in France. At P, it consists mainly of a quality control monitoring of the Sonnerat database, while also developing new accessibility tools. A platform (Explore, available at: https://explore. recolnat. org/), bringing together resources from most of the French natural history collections and allowing an advanced browsing and data enrichment process, is under development. Explore will allow enrichment of the databased specimens through participatory science projects, directly through the platform and through a dedicated version of Les Herbonautes. Additionally, using the structure created by e-ReColNat, a backlog of ca.
Additional databasing Most of the databasing efforts described above concerned the general herbarium collection at P. The standing-alone collections housed at MNHN (referred to as 'historical collections') were not part of the Renobota digitisation process. However, some were treated in part during various projects, as follows: -The Humboldt & Bonpland Herbarium was fully digitised and databased by the GPI team. 3525 entries are available in the P dataset. -The Lamarck herbarium was completely digitised during a dedicated project. Data remain to be uploaded to Sonnerat. To date, 4053 specimens are available in the P dataset. -The American specimens of the Jussieu herbarium, estimated to represent ca. 10% of the material in this collection, are being digitised and databased as part of the Reflora project; 13,500 specimens (including the American material and some other specimens) have so far been databased.
-Various specimens from other stand-alone collections were databased as part of the regular specimen loan procedure. The most significant of these are 543 specimens from the herbarium of Léon Mercurin (1898-1994), 230 from the Michaux herbarium, 133 from the Tournefort herbarium, 19 from Desfontaines Flora Atlantica herbarium, 18 from the herbarium of Elias Magloire Durand (1794-1873), and 6 from the Adanson herbarium. Data published through GBIF: http://collections. mnhn. fr/ipt/resource. do?r=mnhn-p (Data Citation 1).
Sonnerat database taxonomic coverage During the Renobota project, the organisation of the collections at P was modified to follow the linear family sequence based on the APG III classification  11. However, the placement of some specimens could not be updated at that time, and for various reasons, some collections are still filed under the same family as prior to the renovation, which followed the index developed by Théophile Durand (1855-1912) based on Bentham & Hooker's classification  22. The P herbarium includes all vascular plant orders. A recent comparison (as of 19 October 2015) with The Plant List v. 1. 1 (http://www. theplantlist. org/) showed that 34% of the accepted species names are represented by one or more specimens, and an analysis of the non-matching data indicated that this was due to errors both in the P dataset and The Plant List.
P dataset spatial coverage The collections at P, which are global in scope, have been divided into 12 sectors based on place of collection to facilitate curation, access and regional studies (Fig. 5 ). The distribution of the accessions among these sectors is heterogeneous (Table  2 ). The FRA sector, corresponding to metropolitan France, is one of the largest, with ca. 970,000 specimens. The two continents with the largest number of specimens, Europe and Africa, have each been sub-divided into distinct sectors. For Europe, this dates back to the donation of de Candolle's collection  8  and to the creation of the France herbarium, which has evolved into the FRA sector, separate from the EUR sector, which encompasses the rest of Europe. The European flora comprises the largest portion of the P herbarium, with 29% of the holdings, a situation shared with other natural history collections at the MNHN  23.
Somewhat later, Africa was also sub-divided based on biogeographic considerations into AFT (Tropical Africa), AFM (Madagascar and the Western Indian Ocean islands) and AFN (Northern Africa), which together represent ca. 25% of the collections at P. The taxonomic composition within each sector is indicated in Table  2. To date, 16% of the specimens included in Sonnerat are fully databased, resulting from a wide range of efforts (see detailed projects above). The percentages of specimens from which data are fully captured differ from one geographic sector to another (Table  2 ). All of the remaining specimens processed during the Renobota project are databased at least for family, genus and species names (when available), along with main geographical sector, but not for information related to the individual specimen (collector name, collection number, date, locality, etc.
). Europe, France and Northern Africa have a very low percentage of fully databased specimens. Similarly, the very low rate for cultivated material reflects the scientific focus of P botanists, which is primarily on wild plants. By the time the Reflora project is completed, data capture for specimens from Brazil should increase the rate for America significantly. Oceania is divided into two sub-sectors: CAL for New Caledonia and OCE for the rest of the region. The P herbarium contains at least 200,000 specimens from New Caledonia, but a technical issue makes it impossible to calculate the exact number, so the following numbers are provided for Oceania as a whole. The level of databasing for this sector is comparatively high since P botanists are working on the Polynesian  24, 25  and New Caledonian floras, which account for most of the material available.
The collections from Madagascar are among the most studied and actively curated at P, and have been since the early 20th century. As a result they are the most extensively databased (full data have been captured for 35%). Special efforts have been made on the collections from the circum-austral islands, which are relatively small in number (85% have been fully databased). Finally, the stand-alone (historical) collections were not treated as part of the Renobota imaging process so the only records are those resulting from projects that fully captured the associated data. As a consequence, the very low proportion for which data entry is not complete (0. 02%) corresponds to background error rates in databasing. Because of the heterogeneity in the proportion of fully databased specimens among geographic sectors, the distribution by country shown in Fig.
6a , which takes into consideration only these records, very likely does not reflect the true situation for the entire collection at P. For example, European and Northern African countries are under-represented while Madagascar and Brazil are over-represented. This map nevertheless provides important information on the geographical provenance of the specimens in the P herbarium. To facilitate interpreting this figure, we have calculated a factor of representativeness for each sector by dividing the average rate of full data capture per sector by the overall average for the collection as a whole: -Within Europe, metropolitan France is under-represented, as indicated by a factor of 0. 52, and the rest of Europe by a factor of 0. 38. However, excluding metropolitan France, the Mediterranean flora is better covered at P than northern Europe.
-Within Africa, Madagascar is over represented by a factor 2. 22, tropical continental Africa is close to the overall average with a factor 1. 03, and northern Africa is significantly under represented, with a factor 0. 37. Specimens from the former French colonies are well represented, but it is notable that South Africa, Ethiopia and Tanzania are as well. -For the Americas, the factor is 1. 12, indicating that this sector is over-represented among the records for which data have been fully captured. While there is no way to calculate the factor for Brazil, it will surely exceed the value for the sector as a whole given that several projects are focusing on its flora. The P herbarium is very rich in type specimens from throughout the world, a large proportion of which were systematically databased during the three Global Plants Projects.
By comparing the country of collection (as indicated by the country isocode in the fully databased portion of the herbarium) with the broad geographical sector assigned to the entire collection, an estimate can be made of the geographical error rate, including mismatches, invalid country codes, and unassigned sector codes (even though in principle each specimen must be assigned to a sector). However, because it is sometimes difficult to determine the country from which a specimen was collected, especially for older material, empty country codes were not considered as errors. We obtained a correct match for over 97% of the records.
In Paris this can be linked to decolonisation, but also to a decrease of funding for activities that generate material deposited in herbaria and to a societal perception of such collections as unimportant or unnecessary  23, 27, 28. The apparent renewal of interest since the 1990s, as suggested by the increase in growth at P, might be linked with the development of the database Sonnerat and the systematic databasing of new collections made by MNHN botanists, facilitating the production of specimen labels, which could this explain the apparent higher rate of collection during these years. The lower rate of databasing of specimens in the last decade is seen among many natural history collections database  23  and might be linked to the fact that significant numbers of specimens still being studied have not yet been incorporated into herbaria.
Databased samples collection and preservation methods Vascular plants collection (P) of the Muséum national d'histoire naturelle (MNHN-Paris), active databasing period: 1993-2015 (Data Citation 1). Specimen preservation methods. The collection consists in dry specimens mounted on herbarium sheets, dry wood samples, dry fruits and seed, samples preserved in alcohol, tissues and pollen mounted on microscope slides, tissue samples preserved in silica-gel. It is mostly composed of herbarium sheets, which are divided into a general systematic collection (5. 7 million specimens, 95% databased), ordered according to the APG III classification for the Angiosperms, and into several stand-alone collections of historical importance (estimated at 150,000 specimens, 14% databased), which are curated separately.
In addition to the herbarium, P also includes some complementary collections: -Histology (70,000 slides, not yet databased, 20,000 of which came from the collection of Philippe van Tieghem) -Palynology (45,000 slides, not yet databased, ca. 12,000 of which have vouchers in the P herbarium) -Specimens preserved in alcohol (estimated to comprise 15,000 specimens, 4% databased) -Wood collection (estimated at 14,000 specimens, 83% databased). An significative curation effort, including data management, is currently being made on this particular collection -Dry fruit and seed collection (estimated to include 28,000 specimens, 6% databased) -Samples preserved in silica-gel for molecular studies (ca. 7,300 samples, 100% databased) Sampling protocol. No single sampling protocol can be distinguished, the acquisition of the collection tremendously varies depending on the institute from which the sample is derived or the collector.
Acknowledgements The authors wish to pay their respects to two late colleagues,  Pr. Jean-Noël Labat , former curator of the herbarium, and  Sabine Comtet-Andriamanjatoarivo , a devoted technical staff member, neither of whom had the chance to see the completion of the herbarium renovated, even though they were important contributors to this project as well as to the P collection and dataset. A tribute also goes to the late Pr. Gérard Aymonin , the 'lost memory of the herbarium', and particularly of the French and historical collections at P. Thanks go as well to  Jessica Tressou  and  Ehoarn Bidault  for critically reading the manuscript,  Simon Chagnoux  and  Bérenger Dulac  for technical help with the database, and  Thierry Deroin  for kindly providing assistance regarding the collections under his charge.