dataesr/scientific-paragraphs-categorization huggingface dataset:
De novo sequence Assembly of the L. perenne Shoot Reference Transcriptome A de novo transcriptome analysis of L. perenne was carried out on leaves from plants subjected to a transfer experiment involving NOAE levels of chemical stressors and short periods of exposure. L. perenne seedlings were submitted to 3 conditions of short-term low-level xenobiotic exposure [glyphosate (G), tebuconazole (T), and a combination of the two (GT)] in comparison to control condition (C). Leaf cDNA libraries, corresponding to these 4 conditions, were prepared and sequenced using 454 mass sequencing. Before preprocessing, sequencing of cDNA libraries resulted in approximately 0. 7 Gbp of sequence data with a GC content of 54%. The genome size of L. perenne is estimated to be 2. 7 Gb  (Fiil et al. , 2011). Each quarter plate run was preprocessed, and the runs of each treatment were pooled, thus leading to  300,795, 249,254, 338,011, and 307 ,033 high-quality reads for, respectively, control, glyphosate, tebuconazole and glyphosate + tebuconazole treatments (Table  1 ).
The quality of the assembly was checked by comparing the resulting transcriptome to SRA data of L. perenne (43,049 sequences, E-MTAB-1556 in ArrayExpress,  Vigeland et al. , 2013). A tblastx analysis using an e < 10e-6 revealed that 45,962 sequences (13,782 contigs and 32,180 singletons) from the present transcriptome matched similar sequences from the deposited SRA data. The reference transcriptome was also compared to the complete mitochondrial (GenBank: JX999996. 1) and chloroplastic (NCBI Reference Sequence: NC_009950. 1) genomes of L. perenne using tblastx program. The mitochondrial genome contains genes corresponding to 14 tRNA, 3 rRNA and 34 proteins  (Islam et al. , 2013) , among which 27 genes matched with high identities (e < 10e-6) with unigenes from the present reference transcriptome.
Furthermore, 80 genes from the complete chloroplastic genome, which contains genes encoding 76 unique proteins, 30 tRNAs and four rRNAs  (Diekmann et al. , 2009) , were identical or very close (e < 10e-6) to the transcriptome unigenes. In order to validate further the assembled unigenes, sequencebased alignments were performed against the TAIR (Arabidopsis thaliana) database by using the tblastx algorithm  (Altschul et al. , 1997). According to tblastx data, 55. 44% (31,696 unigenes) of the matched sequences showed strong homology with TAIR data (e < 10e-50), and 84. 9% (48,550 unigenes) of the top hits exhibited lower but significant homology (e-value over 10e-6).
Functional Annotation of the L. perenne Shoot Reference Transcriptome Functional annotation of the reference transcriptome was undertaken using the Blast2GO tool and TAIR database. 9311 (16% of all unigenes) unigenes showed no blast hit in the TAIR (Arabidopsis thaliana) database. Among the unigenes yielding blast results, 204 (0. 32%) were not mapped and 1296 (2. 2%) mapped unigenes were not annotated, thus leading to 46,330 (81%) annotated unigenes. In many cases, multiple GO terms were assigned to the same unigene. GO terms were classified into functional groups according to biological process, molecular function, and cellular component classes. Distribution of the various GO terms identified for the L. perenne reference transcriptome is presented in Figure  1  for the major GO classes.
The subcellular localization of these processes and functions (Figure  1C ) showed the importance of gene products associated with intracellular organelles, chloroplasts (thylakoids, lightharvesting complexes), cytoplasm and ribosomal complexes. Functional distribution therefore demonstrated that this L. perenne reference transcriptome exhibited a good coverage of essential types of plant biological activities. The relative importance of various metabolic pathways was assessed from the assignment of unigene annotations in the KEGG database (Figure  2 ). Most of the predominant pathways were found to belong to carbon metabolism (Glyoxylate and dicarboxylate metabolism, Glycolysis/Gluconeogenesis, Starch and sucrose metabolism, Pentose phosphate pathway, Fructose and mannose metabolism, Amino sugar and nucleotide sugar metabolism, Pyruvate metabolism, TCA cycle, Galactose metabolism, Ascorbate, and aldarate metabolism) and to energy metabolism (Carbon fixation in photosynthetic organisms, Methane metabolism, Oxidative phosphorylation, Nitrogen metabolism, Photosynthesis).
This was the case for the CIPK9-annotated gene, which encodes a Calcineurin B-Like Protein (CBL)-interacting protein kinase highly conserved between monocot and dicot species (Supplemental Figure  1 ). This Serine/Threonine protein kinase annotated unigene, also known as sucrose non-fermenting (SNF)-related kinase family of serine/threonine kinase 3. 12 (SNRK3. 12), as well as a calcium sensing receptor-annotated transcript, were found to be DE (Table  3 ). DESeq showed a repression of CIPK9 by G and an induction by T and GT (Table  3 ). qRT-PCR analysis confirmed this repression by G (Figure  4 ). Transcripts related to protein phosphorylation and dephosphorylation were highly represented in the different datasets. The effects of xenobiotic stresses on highly conserved Serine/Threonine protein kinases (Supplemental Figure  1 ), such as comp7296_c0_seq6, annotated as a Serine/Threonine protein kinase, and a unigene comp2769_c0_seq1, annotated as a SNRK2 protein  (Kertesz et al.
Xenobiotic-Regulated RNA-Seq and qRT-PCR Markers Reveal Novel Potential Pathways of Chemical Stress Responses The present de novo RNA-Seq approach yielded a L. perenne xenobiotic-dependent genomic database (Figures  1, 2 ) that was coherent with recent transcriptomic analyses of L. perenne  (Farrell et al. , 2014; Duhoux et al. , 2015)  and that was very useful to explore relationships between metabolic changes, stress adjustments, regulation of metabolism genes and signaling pathways under conditions of xenobiotic stress. The experimental conditions of short-term exposure and low levels of xenobiotics led, in all of the cases (glyphosate, tebuconazole, GT mixture), to no observable adverse effects, especially on root growth, which is particularly xenobioticsensitive  (Serra et al. , 2013 (Serra et al.
ACKNOWLEDGMENTS We are grateful to  Dr Erwan Corre  from the  CNRS-UPMC ABIMS bioinformatics platform  ( Station biologique de Roscoff, France ) for providing help and support with bioinformatics analysis, the  ABGC technical core facility  ( UMR CNRS 6553 ,  University of Rennes 1, France ) for biochemical analyses and the  Biogenouest Environmental and Functional Genomics Platform core facility  ( UMS CNRS 3343 ,  Observatoire des Sciences de l'Univers de Rennes, France)  for transcriptome sequencing. We also wish to thank  Jean-Luc Foulon  ( UMR CNRS 6553 ,  University of Rennes 1, France ) for help with plant culture systems and  Sandra Rigaud  ( UMR CNRS 6553 ,  University of Rennes 1, France ) for administrative and accounting work. This work was supported by the  interdisciplinary program  " Ingénierie écologique " from the  Centre National de la Recherche Scientifique (CNRS, France)  and by the  Fondation pour la Recherche sur la Biodiversité (FRB, France).
Cis-element and transcription factor databases Systematic curation of cis-elements and their cognate transacting factors that define regulated transcription in eukaryotes is central to computational modelling of transcriptional networks  (Buchler et al. , 2003; Xie et al. , 2005; Mohanty et al. , 2012). Our recent survey of regulatory sequences of rice genes across the available public databases indicate that rice information has been steadily increasing given the level of global activity in rice functional genomics (Tables  2  and 3 ). During the last two decades, several data repositories have been developed to provide an annotated reference of cis-elements and their cognate trans-acting factors established from the results of wet-lab experiments. The first generation information repositories which include TRANSFAC, PLACE, PlantCARE and AGRIS served as initial foundation for large-scale computational prediction of the unifying regulatory features among co-expressed genes revealed by genome-wide transcriptome studies  (Wingender et al.
, 1996; Higo et al. , 1999; Lescot et al. , 2002; Davuluri et al. , 2003; Matys et al. , 2003). However, while TRANSFAC has been utilized for the analysis of rice data, its predictive power for novel plant-specific elements is quite limited. On the other hand, PLACE, PlantCARE and AGRIS have offered relatively higher resolutions for the analysis of rice data, given their stronger emphasis on monocot and dicot plants. More recent generations of cis-element databases like the Database of Arabidopsis Transcription Factors (DATF), have significantly improved the resolution of regulatory sequence prediction in rice genomic sequences given the broader emphasis on plant physiological processes  (Guo et al. , 2005; Gao et al. , 2006; Riaño-Pachón et al. , 2007; Shameer et al. , 2009; Perez-Rodriguez et al.
, 2010; Wang et al. , 2010; Zhang et al. , 2011). DRTF in particular holds information on more than 2,000 putative transcription factors and their computationally predicted target cis-elements anchored to the reference genome sequence of rice. Other more recent additions to available databases include the Plant Transcription Factor database (PlantTFDB), GRASSIUS and Osiris  (Guo et al. , 2008; Morris et al. , 2008; Yilmaz et al. , 2009; Zhang et al. , 2011). In summary, the number of public databases that curate information about regulatory sequences and transcription factors in plants has increased substantially over the last decade. The information contained in these resources are evolving constantly and their maximum utility for highresolution computational prediction of transcriptional networks in rice relies on systematic annotation based on experimentally validated data.
Conclusions and perspectives Applications of upstream sequence variation to genus-wide gene discovery, allele mining and network engineering The fundamental question about the architecture of rice promoters and the nature of their cognate regulator proteins remains very relevant in the era of comparative functional genomics. Our recent survey of the major public eukaryotic cis-element and transcription factor databases have indicated that sequences and annotation of cis-elements and their cognate transcriptional regulators in the reference rice genome are still far from being comprehensive to guide a systematic scrutiny of regulatory networks at a genome-wide and comparative scales. The 'finished' reference genome sequence of rice has been available to the community now for a decade, serving as nucleator for hypothesis-driven interrogation of gene function and evolution.
Acknowledgement This study was supported by a grant to BGDR from the  USDA-National Research Initiative  ( 2006-35604-1669 ) and base funding from the  Maine Agricultural and Forest Experiment Station  (Publication 3392). BM and DYL were supported by the  National Research Foundation of Singapore  ( NRF-CRP5-2009-03 ) and  Next-Generation BioGreen 21 Program  ( PJ009520 ),  Rural Development Administration, Republic of Korea. MRP was supported by  Korea Research Foundation Postdoctoral Fellowship  ( KRF-2006-352-F00002 ). SJY was supported by a grant from the  Regional Subgenebank Support Program of Rural Development Administration, Republic of Korea.
Acknowledgements The author wishes to acknowledge the hugely engaging and thoughtful contribution of the working group, who listened carefully and debated rigorously how the heritage science community could build a community and realise a most impactful future for heritage science research. The working group included  Agnes Brokerhof , Senior Scientist,  Cultural Heritage Agency of the Netherlands , the  Netherlands ;  Bertrand Lavédrine , Director of the  Centre de Recherche sur la Conservation des Collections, France ;  Webber Ndoro , Director of the  African World Heritage Fund, South Africa ;  Luca Pezzati , Senior researcher, and coordinator of the group  Beni Culturali  at the  National Institute for Optics of the National Research Council, Italy; Anupam Sah, Head of Art Conservation, Research and Training, CSMVS Museum Art Conservation Centre, Mumbai, India ; and  Min Seok Seo , Researcher of the  National Research Institute of Cultural Heritage, Korea.
Introduction The European Commission published the European Community Biodiversity Strategy, providing a framework for development of Community policies and instruments in order to comply with the Convention on Biological Diversity. This Strategy recognises the current incomplete state of knowledge at all levels concerning biodiversity, which is a constraint on the successful implementation of the Convention. Fauna Europaea contributes to this Strategy by supporting one of the main themes: to identify and catalogue the components of European biodiversity into a database in order to serve as a basic tool for science and conservation policies. With regard to biodiversity in Europe, both science and policies depend on a knowledge of its components. The assessment of biodiversity, monitoring changes, sustainable exploitation of biodiversity, and much legislative work depend upon a validated overview of taxonomic biodiversity.
Towards this end Fauna Europaea plays a major role, providing a web-based information infrastructure with an index of scientific names (including important synonyms) of all living European land and freshwater animals, their geographical distribution at country level and some additional useful information. In this sense, the Fauna Europaea database provides a unique reference for many user-groups such as scientists, governments, industries, conservation communities and educational programs. Fauna Europaea started in 2000 as an EC-FP5 four-years project, delivering its first release in  2004 (Jong et al. 2014)). After thirteen years of steady progress, in order to efficiently disseminate the Fauna Europaea results and to increase the acknowledgement of the Fauna Europaea contributors, novel e-Publishing tools have been applied to prepare data-papers of all major taxonomic groups.
For this purpose a special Biodiversity Data Journal Series has been compiled, called Contributions on Fauna Europaea. This work was initiated during the ViBRANT project and is further supported by the recently started E U BON project. This paper holds the first publication of the Fauna Europaea Gastrotricha data sector as a BDJ data paper. Within the EU BON project also further steps will be made to implement Fauna Europaea as a basic tool and standard reference for biodiversity research and to evaluate taxonomic expertise capacity in Europe. The Fauna Europaea data-papers will contribute to a quality assessement on biodiversity data by providing estimates on gaps in taxonomic information and knowledge.
General description Purpose: The Fauna Europaea is a database of the scientific names and distribution of all living, currently known European land and fresh-water animal species assembled by a large network of experts, using advanced electronic tools for data collations and validation routines. An extended description of the Fauna Europaea project can be found in  Jong et al. 2014). A summary is given in the sections below. The Gastrotricha are one of the 58 Fauna Europaea major taxonomic groups, and currently number 326 freshwater species worldwide, 224 of which reported from Europe. The data were acquired and checked by 5 specialists. No division of the taxa groups to be checked has been set among the specialists, thus all the specialists have to be considered responsible for the available data (Fig.
Addititional information: Gastrotricha The phylum Gastrotricha currently (May 2015) counts 813 species of free-living, microinvertebrates commonly present and actively moving on and into the sediments of aquatic ecosystems where they represent a significant component of meiofauna, with densities up to 364 ind/cm in marine sands and 168 ind/cm in freshwater sediments  (Nesteruk 1993 , Nesteruk 1996 , Todaro and Hummon 2008 ). FaEu data set Gastrotricha species per family: the updated number of species is reported in brackets. See Table  1  for family statistics. Gastrotricha have 'Aschelminthes' or 'pseudocoelomates' features such as a worm-like body, a complete intestine, and a primary body cavity even if almost vestigial  (Hyman 1951). Morphological and ultrastructural studies support a sister-group relationship of Gastrotricha with Cycloneuralia or with Ecdysozoa, whereas molecular analyses mainly carried out on the gene 18S rDNA have suggest to include the phylum into the Platyzoa, close to Gnathostomulida and acoelomate forms (for an overview of the major phylogenetic scenarios concerning Gastrotricha among the Bilateria as well as the internal relationships of the phylum, see  Balsamo et al.
European freshwater species The Fauna Europaea database (version 2. 4, January 2011) includes 215 species, 214 of which belong to the order Chaetonotida (4 families) and a single species incertae sedis is a member of the order Macrodasyida. Eight additional species of Chaetonotida have been described and another one has been recorded first for Europe after the release of the database, so that currently European freshwater species of Gastrotricha known so far add up to 224 overall (223 Chaetonotida + 1 Macrodasyida), that are considered in the present paper. A synthesis of European taxa is presented below. Family Chaetonotidae (Fig. 2 A-F ) Tenpin-like body, 84-770 µm in length. Two adhesive tubes forming the caudal 'furca'. Four cephalic ciliary tufts. Cuticle generally provided with ornamentations of various shape and size, in some cases smooth.
Personnel: The taxonomic framework of Fauna Europaea includes partner institutes, providing taxonomic expertise and information, and expert networks taking care about data collation. Every taxonomic group is covered by at least one Group Coordinator responsible for the supervision and integrated input of taxonomic and distributional data of a particular group. The Fauna Europaea checklist would not have reached its current level of completion without the input from several groups of specialists. The formal responsibility of collating and delivering the data of relevant families rested with a number of Taxonomic Specialists (see Table  1 ). For Gastrotricha the responsible Group Coordinator and Taxonomic specialist is Maria Balsamo, who is also Taxonomic Specialist, together with the other Associated Specialists listed in Table  2.
Data management. The data records could either be entered offline into a preformatted MS-Excel worksheet or directly into the Fauna Europaea transaction database using an online browser interface (Fig. 3 ). Data set. The Fauna Europaea basic data set consists of: accepted (sub)species names (including authorship), synonym names (including authorship), a taxonomic hierarchy/ classification, misapplied names (including misspellings and alternative taxonomic views), homonym annotations, expert details, European distribution (at country level), Global distribution (only for European species), taxonomic reference (optional), occurrence reference (optional). Sampling description: Fauna Europaea data have been assembled by principal taxonomic experts, based on their individual expertise, including literature sources, collection research, and field observations.
In total no less than 476 experts contributed taxonomic faunistic information for Fauna Europaea. The vast majority of the experts are from Europe (including EU non-member states). As a unique feature, Fauna Europaea funds were set aside for rewarding/compensating for the work of taxonomic specialists and group coordinators. To facilitate data transfer and data import, sophisticated on-line (web interfaces) and offline (spreadsheets) data-entry routines were built, integrated within an underlying central Fauna Europaea transaction database (see Fig. 3 ) This includes advanced batch data import routines and utilities to display and monitor the data processing within the system. In retrospect, it seems that the off-line submission of data was probably the best for bulk import during the project phase, while the on-line tool was preferred to enter modifications in later versions.
This system works well, but will be replaced after 2013. A first release of the Fauna Europaea index via the web-portal has been presented at 27 of September 2004, the most recent release (version 2. 6. 2) was launched at 29 August 2013. An overview of Fauna Europaea releases can be found here: http:// www. faunaeur. org/about_fauna_versions. php. Quality control: Fauna Europaea data are unique in a sense that they are fully expert based. Selecting leading experts for all groups assured the systematic reliability and consistency of the Fauna Europaea data. Furthermore, all Fauna Europaea data sets are intensively reviewed at regional and thematic validation meetings, at review sessions on taxonomic symposia (for some groups), by Fauna Europaea Focal Points (during the FaEu-NAS and PESI projects) and by various end-users sending annotations using the web form at the web-portal.
Additional validation on gaps and correct spelling was effected at the validation office in Paris. In general we expect to get taxonomic data for 99. 3% of the known European fauna after the initial release. The faunistic coverage is not quite as good, but is nevertheless 90-95% of the total fauna. For Gastrotricha the current taxonomic coverage is about 96% (see Table  1 ), and the distribution of faunistic data by country is quite heterogeneous, according to the nationality of researchers. Checks on technical and logical correctness of the data have been implemented in the data entry tools, including around 50 "Taxonomic Integrity Rules". This validation tool proved to be of huge value for both the experts and project management, and contributed significantly to preparation of a remarkably clean and consistent data set.
This thorough reviewing makes Fauna Europaea the most scrutinised data sets in its domain. The only other existing database specifically dedicated to freshwater species on a worldwide scale has been produced within FADA (Freshwater Animal Diversity Assessment Project), but it has not yet been published. A number of freshwater species th appear also in the WoRMS (World Register of Marine Species) taxonomic database of Gastrotricha, since some species have been occasionally reported from brackish waters. Step description: By evaluating team structure and life cycle procedures (data-entry, updating, etc. ), clear definitions of roles of users and user-groups, according to the taxonomic framework were established, including ownership and read and writes privileges, and their changes during the project life-cycle.
Geographic coverage Description: Species and subspecies distributions in Fauna Europaea are registered at least a country level, i. e. for political countries. For this purpose the FaEu geographical system basically follows the TDWG standards. The covered area includes the European mainland (Western Palearctic), plus the Macaronesian islands (excl. Cape Verde Islands), Cyprus, Franz Josef Land and Novaya Zemlya. Western Kazakhstan and the Caucasus are excluded (see Fig. 4 ). The focus is on species (or subspecies) of European animals of terrestrial and freshwater environments. Species in brackish waters, occupying the marine/freshwater or marine/ terrestrial transition zones, are generally excluded. The four species of Chaetonotida only known from brackish waters have been included in the database, in which their particular habitat has been specified.