dataesr/scientific-paragraphs-categorization huggingface dataset:
These 3D scenes provide geographical and bathymetric context that is crucial for the interpretation and assessment of tracer plumes near ocean margins or along ridges. The IDP2017 is the result of a truly international effort involving 326 researchers from 25 countries. This publication provides the critical reference for unpublished data, as well as for studies that make use of a large cross-section of data from the IDP2017. This article is part of a special issue entitled: Conway GEOTRACES -edited by Tim M. Conway, Tristan Horner, Yves Plancherel, and Aridane G. González.
The release of the IDP2014 was a big success and was widely covered by international news media as well as a broad range of scientific journals (e. g. ,  Morrison, 2014). The data product resulted from a significant effort to combine data from 15 cruises conducted by seven countries. The IDP2014 data cover the Atlantic, Arctic, Southern and Indian oceans and span the 2007 to 2012 period. There are data for 237 hydrographic parameters as well as trace elements and isotopes (TEIs) contributed by 133 scientists from 16 countries. Having such a large group of researchers collaborate on the project and submit high-quality data, sometimes unpublished, was a remarkable achievement. The IDP2014 is being used widely and has stimulated collaborative research that would not have been possible without such a large, aggregated dataset.
Since its release, users worldwide have downloaded the IDP2014 dataset 1410 times. Users of the data product are encouraged to cite the original papers written by the data originators, but the IDP contains significant unpublished data. The publications describing the IDPs thus provide the critical reference for unpublished data, as well as for studies that make use of a large cross-section of data from the IDP. The publication describing the IDP2014  (Mawji et al. , 2015)  has been cited 43 times, indicating that there is a significant number of scientific studies, such as large-scale modelling and basinscale to global TEI evaluations, that make use of large portions of the IDP2014 data and could not have been performed otherwise (e. g. ,  Abadie et al. , 2017; Chien et al. , 2016; Frants et al.
, 2016; Lerner et al. , 2016; Schlitzer, 2016). In particular, the aggregated dissolved iron datasets from IDP2014 facilitated the first rigorous intercomparison of dissolved iron cycling from 13 global ocean models  (Tagliabue et al. , 2016). Building on the success of the IDP2014 and following the long-term data product release plan, GEOTRACES released its second intermediate data product (IDP2017) at the Goldschmidt Conference 2017 in Paris. As with the previous product, IDP2017 consists of two parts: (1) the digital data compilation of TEIs as well as standard hydrographic parameters; and (2) the eGEOTRACES Electronic Atlas providing section plots and animated 3D scenes of the data. As described in detail below, the IDP2017 contains twice as much data compared to the previous IDP2014. For the first time, the IDP2017 contains significant amounts of biogeochemistry data as well as data for aerosols and rain.
Through the GEOTRACES programme, two additional intercalibration cruises were conducted for all the main TEIs and documented in a special issue of Limnology and Oceanography Methods in 2012 (Vol. 10 issue 6). Moreover, a cookbook detailing recommended sample collection methods was produced to support intercalibration (http://www. geotraces. org/images/Cookbook. pdf). This document was updated prior to IDP2017 with new intercalibration procedures for TEIs not included in the IDP2014. While the IDP2014 contained some data that were not quality controlled (identified as tier 2 data), IDP2017 is the first GEOTRACES intermediate data product in which all TEI data have passed the intercalibration procedures and been approved by the Standards and Intercalibration Committee (S&I Committee). This committee is currently a group of eight members approved by the GEOTRACES Scientific Steering Committee.
Its members cover a broad range of analytical expertise for the TEIs in IDP2017. In addition, there are element co-ordinators for each group of TEIs who can guide new investigators in developing sample collection and analytical methods (http://www. geotraces. org/sic/s-i-committee/elemental-coordinators). The intercalibration assessment of the TEI parameters for IDP2017 differed depending on several criteria. For example, the committee had to consider the maturity of the available analytical techniques for a given TEI, the type of TEI in GEOTRACES, the possibly transient nature of the signal, the nature of the data acquisition (e. g. , sensor vs. bottle), and the participation in other programmes (such as CLIVAR) that have their own intercalibration procedures. Irrespective of the quality criteria for individual TEIs, all data were expected to follow certain minimum standards, as shown in Fig.
IDP2017 digital data Creation of the IDP2017 was coordinated and overseen by the GEOTRACES Data Management Committee (DMC). Collation of the cruise data and linkage with extensive metadata was carried out at the GEOTRACES Data Assembly Centre (GDAC) located at the British Oceanographic Data Centre. GDAC received data submissions from four national data centres (Biological & Chemical Oceanography Data Management Office (BCO-DMO; https://www. bco-dmo. org/), Japan Oceanographic Data Centre (JODC; http://www. jodc. go. jp/jodcweb/), LEFE CYBER France (http://www. obs-vlfr. fr/proof/index2. php), NIOZ -Netherlands Data Centre (https://www. nioz. nl/en/research/researchdata)) or from GEOTRACES data originators directly. The lead author of this publication carried out the integration of the cruise data into global datasets.
The IDP2017 digital data package consists of three datasets: (1) discrete water sample data; (2) CTD sensor data; and, as a new dataset, (3) aerosol and rain data. The discrete sample and aerosol/rain datasets contain the GEOTRACES TEI data as well as data for a large suite of standard hydrographic data (discrete sample dataset only). The CTD sensor dataset contains high-resolution data from a variety of electronic sensors that are useful for TEI data interpretation and evaluation. The discrete sample datasets include data from 39 cruises conducted by 11 countries during the 7-year period from 2007 to 2014 (Table  1 ). Twenty-four of the 39 cruises are new in the IDP2017. The dataset covers the Arctic, Atlantic, Southern, Indian oceans and, the Pacific Ocean (Fig. 2 ). The best coverage and highest station density is found in the Atlantic, but the new data from the Pacific have already allowed accurate mapping of TEI distributions in parts of the South and North Pacific.
Nevertheless, compliant data and process studies fill gaps in the overall sampling scheme and provide invaluable data for the quantification of TEI sources and sinks as well as the study of the internal cycling of TEIs. Links to the cruise reports of all cruises in the IDP2017 are provided in Table  2. In total, the IDP2017 discrete sample dataset contains data for 1810 stations. Of these stations, 817 provide full-depth coverage of the water column. There are data for a total of 458 parameters, including (1) classical hydrographic parameters and tracers such as temperature, salinity, oxygen, nutrients, CFCs, SF 6 , Tritium, and He-3, (2) dissolved Table  1  List of cruises included in the GEOTRACES Intermediate Data Product 2017. Section suffixes denote individual parts of a section. A lower case "c" in the section name (as in GAc01) indicates compliant data while a lower case "pr" (as in GPpr01) indicates a process study.
g. , Hg, Pb), and tracers used as proxies to reconstruct the past (e. g. , Th-230, Pa-231, Nd isotopes). Data for the micronutrients are most abundant, with the total number of Fe measurements totalling 12,050; of these, 7690 are for dissolved Fe alone. There are 3768 data values for the radioactive isotope Th-234 and around 1800 values for Th-230 and Pa-231. The CTD sensor dataset contains temperature, salinity, oxygen, fluorescence, transmissometer, turbidity, and photosynthetically active radiation (PAR) data at 1827 stations at 1 m vertical resolution. The fluorescence and transmissometer data provide information on phytoplankton abundance and suspended particle concentrations and are thus important for the interpretation of TEI data. Where calibrated data were not available, raw values are provided.
Quality flags and error values are useful for data filtering and statistical data analysis. Quality flags are single character codes reflecting the quality of the respective data value. The IDP2017 uses the IODE quality flag set that is a standard flagging scheme for the exchange of oceanographic and marine meteorological data (www. iode. org/mg54_3). The IODE flagging scheme is generic and simple, only containing the five flags listed in Table  4. The IDP2017 is an "intermediate" product, and there is clearly a significant amount of further data to come from GEOTRACES cruises, Table  3  Number of measurements of selected GEOTRACES parameters in the discrete sample dataset of the IDP2017. Numbers in parentheses indicate the percentage of discrete samples that contain data for that parameter.
Parameter naming conventions The overall structure of the databases combined in IDP2017, including a single convention for naming all parameters (variables), was organised by a six-person Parameter Naming Committee (PNC) whose members interacted regularly with the Data Management Committee and with the Standards and Intercalibration Committee. With well over 400 parameters in IDP2017, and with the expectation that the number of parameters could eventually exceed 1000, a structure was sought that would allow users to search intuitively for data, using either tools incorporated into IDP2017 (see "Obtaining IDP2017 Data") or other search engines, utilising a common set of keywords or commands. The structure was designed to accommodate hydrographic and biogeochemical variables as well as TEIs, and to span a range of sampling environments, including seawater, aerosols and rain, while also anticipating the future addition of data from sea ice and sediments.
Metadata and publication references The IDP2017 digital datasets include the cruise reports of all the cruises (Table  2 ). These cruise reports provide detailed documentation of the ship operations, including descriptions of sampling procedures and gear as well as information on the laboratories and principal investigators involved. Access to the cruise reports is very easy. When using the ODV collection version of the IDP2017, a simple mouse click on the Cruise Report meta-variable opens the given cruise report and allows viewing in the web browser. In addition, the IDP2017 also contains, for every parameter and every cruise, a data info file containing information about data originators, sample preparation and analytical methods as well as links to original publications related to the data.
These info files are delivered with all IDP2017 output formats and can be viewed easily in the web browser. Access is particularly easy in ODV, where only one mouse click on the info symbol ⓘ is required to open the respective info file in the web browser and obtain detailed information about the data originator and the analytical methods for the clicked parameter and cruise. One more mouse click shows the references of the original publications associated with the given parameter and cruise. Fig. 4  shows an example publication list for parameter Fe_D_CONC_BOTTLE along GP16. Proper linkage of the originator and publication information with the actual data is an important feature of the IDP2017 that makes it easy for users to identify, contact, and acknowledge originators. The publication links in the IDP2017 info files refer to the reference database of original publications maintained at the GEOTRACES International Programme Office (IPO).
This reference database is dynamic and updated whenever new papers are published. Clicking on a reference link in the IDP2017 will always show the up-to-date publication list at the time of the click. Future requests of the publication list related to, for instance, Fe_D_CONC_BOTTLE along GP16 will, in addition to what is shown in Fig. 4 , also include new papers published since the Fig. 4  creation date of December 2017. This dynamic inclusion of papers published after the release of the data product was a required feature for the IDP2017, because many datasets were unpublished at the time of data submission. As a novelty for the IDP2017, the GEOTRACES IPO has made the publication database into a searchable on-line database available on the following GEOTRACES web page: http://www. geotraces.
org/library-88/scientific-publications/peer-reviewed-papers. This database is not limited to the IDP2017 as it also includes other publications that are relevant for GEOTRACES research along with Master and PhD dissertations. Three types of search functionalities are available: (1) Simple search: users can search publications by "author", "title" or "journal" entering the desired term into a search box, (2) Advanced search: by means of dropdown menus, users can select publications by "author", "title", "GEOTRACES cruise", "year" or "type of document", and. (3) Parameter search: allows users to access a list of publications by specific TEI. In addition users can also retrieve publications by group of parameters (e. g. , Aerosols, Dissolved TEIs, etc. ) or by predefined subgroups (e. g. , dissolved trace elements, etc.
Obtaining IDP2017 data The IDP2017 digital data are available in two forms: (1) as full package downloads, or, (2) as customised data subsets using a new online data extraction service. Both methods require users to register (or login if already registered) and agree to IDP2017 usage rules before being able to access and download IDP2017 digital data. The usage rules ask for proper citation of the relevant original papers associated with the particular data used, as well as citation of the IDP2017 data product itself (this paper). Users are also asked to describe the purpose of the IDP2017 data download. Full packages of the three IDP2017 datasets are available for download at https://www. bodc. ac. uk/geotraces/data/idp2017/. The data are provided in four formats: (1) ASCII text files suitable for usage in standard software, (2) Excel spreadsheet files for Microsoft Excel or similar software, (3) netCDF files suitable for access by models and netCDF readers, and (4) as ODV collections for use with the popular Ocean Data View software (https://odv.
awi. de). Users who only need data for a smaller subset of parameters and/or smaller geographical domain can use the new data subsetting and extraction service provided at https://webodv. awi. de/geotraces. After registration and login the user is guided through a three-step procedure. Step 1 allows for subsetting the set of stations to be downloaded by selecting one or more entries from the cruise list, zooming into a specific map domain and/or specifying one or more required parameters (variables). Only stations containing data for all the selected required parameters are included in the output dataset. Step 2 lets users customise the set of parameters (variables) to be included in the download file. This is done using a hierarchical tree of parameter groups and individual parameters. Users open/close parameter groups by clicking the +/-symbols.
Some browsers also allow download of the 3D movie file. All section and 3D animation pages contain groups of links near the bottom of the page. These include (a) links to other tracers along this section or in this scene, (b) other 3D scenes with this tracer, and (c) other sections with this tracer. These links greatly facilitate switching between and comparing of different tracers, sections, and 3D scenes. All section plots use the same window layout, and the different section plots perfectly match when switching between tracers. The links under category (c) allow easy transitions between section plots and 3D animations. Section and 3D scene pages also contain links to the original publications associated with the given tracer and section. Clicking on these links shows the current list of publications from the dynamically updated reference database maintained at the GEOTRACES IPO (see above).
Summary The new IDP2017 is a significant improvement over the earlier IDP2014 and roughly doubles the number of included cruises, stations, samples and parameters. The IDP2017 is a truly international product containing data from 326 researchers from 25 countries. The IDP2017 provides data for the Pacific Ocean, and the Mediterranean and Black seas, in addition to Atlantic, Arctic and Indian Oceans that were already represented in the previous data product. For the first time, the IDP2017 contains significant amounts of biogeochemistry data as well as TEI data for aerosols and rain. As before, users can obtain complete IDP2017 data sets as bulk downloads. Alternatively, there is now a customisable online data extraction service that allows data selections by domain, GEOTRACES sections, as well as parameters of interest.
The extractor delivers smaller, more manageable data packages. GEOTRACES invites and promotes use of the IDP2017 in the widest possible sense and envisages intensified collaboration within the marine geochemical community and beyond. Availability of large integrated and quality-controlled datasets, such as the IDP2017, enables a much wider range of studies than would be possible with individual single-cruise data alone. The new, updated eGEOTRACES electronic atlas now contains more than 590 section plots (compared to 330 in IDP2014) and more than 130 animated 3D scenes (95 in IDP2014). Section and 3D scene pages are interlinked, and switching between different GEOTRACES sections, ocean basins and parameters is achieved with simple mouse clicks. eGEOTRACES section and 3D scene pages are now connected to the GEOTRACES publication database, easily providing with a simple mouse click up-to-date reference lists to the original publications related to the displayed data.
This feature makes identification of data originators easy and encourages proper citation or initiation of collaborative research. The animated 3D scenes in the eGEOTRACES Atlas show large amounts of data in an intuitive way and with geographic and bathymetric context, thereby providing quick large-scale overviews of TEI distributions and helping the scientific interpretation of TEI data. In addition, these animations are also appealing to a wider target community, including scientists from other disciplines or policy makers, as well as interested members of the general public. GEOTRACES encourages wide usage of eGEOTRACES visuals for all purposes, including teaching and outreach. The IDP2017 is the second in a series of planned intermediate data products, with the next scheduled for release in 2021.
Acknowledgements We gratefully acknowledge financial support by the  Scientific Committee on Oceanic Research (SCOR)  through grants from the  U. S. National Science Foundation , including grants  OCE-0608600 ,  OCE-0938349 ,  OCE-1243377 , and  OCE-1546580. Financial support was also provided by the  UK Natural Environment Research Council (NERC) , the  Ministry of Earth Science of India , the  Centre National de Recherche Scientifique, l'Université Paul Sabatier de Toulouse , the  Observatoire Midi-Pyrénées Toulouse , the  Universitat Autònoma de Barcelona , the  Kiel Excellence Cluster The Future Ocean , the  Swedish Museum of Natural History, The University of Tokyo , The  University of British Columbia, The Royal Netherlands Institute for Sea Research , the  GEOMAR-Helmholtz Centre for Ocean Research Kiel , and the  Alfred Wegener Institute.
2 , Table  2  and Additional file 1: Table  S1 ). This is potentially of great utility for genome assembly. Similar observations have been made in a very recent comparison of different base-callers (https:// doi. org/10. 5281/zenodo. 1043611). As a gauge of the accuracy of Albacore read-calling, we compared a random subset of the longer reads with the WTSI N. brasiliensis reference genome. While overall there was generally a good equivalence, especially given the potential genetic difference between the two samples (see 'Methods'), there were numerous instances where reads were substantially longer than the matching sequence in the WTSI genome. Upon further examination, some of these were revealed to reflect the presence of very long stretches of complex tandem repeats (VeCTRs) that had been compacted in the WTSI genome (Fig.
brasiliensis strain (GLG et al. , unpublished) to correct the sequence of proteincoding genes, while not touching the genome assembly. Pilon  [28]  in combination with Bowtie2-based alignment, using the set of genome-guided Trinity transcript sequences, gave the best results as judged by the markedly improved BUSCO scores (with 88% complete), close to the score of 91% complete USCO genes for the de novo assembly from the same RNA-seq reads (Table  3 ). Our results indicate that the RNA-seq reads cover a substantial fraction of the transcriptome, and that the genome also has excellent coverage of most of the expressed N. brasiliensis genes. Within the assembled consensus sequence corresponding to expressed transcripts, about 1% of bases were locally corrected using the cDNA reads. The most frequent consensus errors   (10.
Although the resolution of repeats is greatly improved compared to the WTSI assembly, such sequences still present a challenge for assembly, as evidenced by the fact that the 5' end of this sequence corresponds to a contig end (tig00023164; coordinates on the left). The color code is as in Fig. 4. Very long stretch of a complex tandem repeat (VeCTR), Wellcome Trust Sanger Institute (WTSI) repeat regions. The continuing progress in base-calling and polishing methods promises to make short-readbased correction superfluous (see also https://doi. org/ 10. 5281/zenodo. 1043611). Since in the current study, the Trinity [genomeguided]-based approach using RNA-seq data gave a marginally higher complement of USCO genes, we used this gene set for further analyses. In addition to an elevated proportion of fragmented USCOs (see below), we also noted a high proportion of duplicated USCOs.
Inspection revealed that some of these were bona fide lineage-specific expansions. For example, the analysis uncovered three distinct loci encoding isoforms of fructose 1,6-bisphosphatase (PFAM: PF00316), as predicted also from the WTSI assembly. Pairs of USCOs were also found on homologous contigs. There were four such examples in the 12 heterozygous branch subgraphs alone; this presumably reflects haplotypic variants. While generating a complete high-quality annotation was beyond the scope of this study, we made use of expert knowledge regarding carbohydrate-active enzymes (CAZymes) to provide a complementary insight into the predicted genes compared to the WTSI set  [29]. Of the 62 different domain architectures among the 158 well-predicted CAZyme proteins from our assembly, only 36 were represented among the set of 96 such proteins in the WTSI reference proteome.
WGA methods can suffer from chimera formation and amplification bias. The proportion of WGA reads that mapped over 90% of their length to the WGA assembly was lower than that of WGA reads mapping to the final assembly (41. 9% vs. 53. 3%; Table  5 ), with a similar distribution of mapped read lengths, indicating that the WGA process did not produce significantly more chimeric reads than that for the unamplified DNA. Of note, any randomly combined chimeric sequences would be clipped by Canu's assembly process due to the absence of support for the chimeric structure. On the other hand, we did observe a higher than expected proportion of reads that mapped along close to 50% of their length to the target genome. Some of these reads may be template/complement read pairs that have been inappropriately combined by the software due to fast pore loading of the DNA fragments.