dataesr/scientific-paragraphs-categorization huggingface dataset:
Following the formation of national infrastructures for metabolomics, for example with the French infrastructure in Metabolomics and Fluxomics MetaboHUB and the Netherlands Metabolomics Centre Foundation (NMC), the COSMOS initiative  7  for the coordination of standards in metabolomics provided the first coordination action between all relevant efforts in metabolomics in Europe. Leading to the establishment of the worldwide metabolomeXchange network, COSMOS paved the way for PhenoMeNal. As a core organiser of the launch of the node for FAIR data  33  in metabolomics as part of the goFAIR initiative, the PhenoMeNal consortium made another necessary step to establish itself as an authority for metabolomics data ELIXIR Greece has included a computational metabolomics and protein interactomics Use Case, including the formation of standardized integrated metabolomic and proteomic databases and the evolvement of tools for combined metabolic and protein network analysis, in the strategic planning of its national infrastructure management and processing for the European Open Science Cloud (EOSC).
This is understandable from the perspective of Elixir and PhenoMeNal, but somewhat misrepresentative of the larger metabolomics community, which obviously hasn't yet matured to the stages of other (older) omics disciplines due to e. g. technical heterogeneity in platforms and difficulties in identification. On the other hand, these potentially different perspectives converge in the emphasis on metabolite identification. The manuscript is furthermore likely difficult to penetrate for those readers that may not be fully up to date on European and international efforts for streamlining bioinformatics infrastructures. A more thorough introduction would help lower that threshold.
What are the aims, objectives and functionalities of the use cases and how do they relate to the core challenges in the metabolomics community? Overlaps between use cases and challenges are addressed later in the article, but for something this important, this should have been addressed in the introduction. The challenges/bottlenecks in metabolomics have been expertly identified. However, these challenges are not exclusive to Elixir, but represents challenges to the entire metabolomics community. 2. "Genome-based metabolic reconstruction databases: These databases are built based on Correction: genome annotation, mostly of enzymes and their association to known reactions, and thus may not cover the entire metabolome since some have no enzymatic function associated" genes that are enzymes The section on current standards and techniques for multiOMICs integration is sketchy: "Currently, metabolomics data can be integratively visualised with transcriptomics data.
". There are several interesting and promising initiatives for data integration extending well beyond visual integration with transcriptomics as the authors are well aware. There is, however, a lack of validated tools. Especially for supervised data analysis of integrated data (data integration isn't limited to systems biology through pathway analysis, but is also highly relevant from a biostatistical point of view). But I also agree that there pathway analysis, but is also highly relevant from a biostatistical point of view). But I also agree that there is "a lack of integrated omic databases", although I believe that there are several crucial aspects of data integration that need to be addressed well before we go into database issues. The systems biology approach will furthermore not be advisable in an untargeted metabolomics setting: Where complementarity in biological information from the different omics layers may be utilised for predictive modelling of e.
7 and page 10 In page 6 the reference Pavlidis and Noble 2001 appears without any relevant number and is not mentioned in the references section Is the topic of the opinion article discussed accurately in the context of the current literature? Yes Are all factual statements correct and adequately supported by citations? Yes Are arguments sufficiently supported by evidence from the published literature? Yes Are the conclusions drawn balanced and justified on the basis of the presented arguments? Yes No competing interests were disclosed. Competing Interests: Referee Expertise: NMR based Metabolomics I have read this submission. I believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. 18 September 2017 Referee Report doi:10. 5256/f1000research.
the topic of the opinion article discussed accurately in the context of the current literature? Yes Are all factual statements correct and adequately supported by citations? Yes Are arguments sufficiently supported by evidence from the published literature? Yes Are the conclusions drawn balanced and justified on the basis of the presented arguments? Yes No competing interests were disclosed. Competing Interests: Referee Expertise: Integrative biology, metabolomics, metabolism, endocrinology, obesityI have read this submission. I believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. The benefits of publishing with F1000Research: Your article is published within days, with no editorial bias You can publish traditional articles, null/negative results, case reports, data notes and moreThe peer review process is transparent and collaborative Your article is indexed in PubMed after passing peer review Dedicated customer support at every stage For pre-submission enquiries, contact research@f1000.
7//www. cosmos-fp7. eu)7, coordinated data standards efforts amongst database providers, ontologists, software engineers and instrument vendors working towards open access data standardization and agreements. A Metabolomics Society Data Standards Task Group was subsequently established to foster and coordinate efforts in enabling efficient storage, compression, terminological annotation, exchange and verification of information within metabolomics datasets. However, no significant and coordinated effort has since been attempted on minimum reporting itself: there is now widespread agreement that the early work of the MSI needs to be taken up in a new initiative, linked with related activities such as the HUPO-PSI (http://www. psidev. info), and be 'completed'. Indeed, the lack of standardised and validated reporting in the field of metabolomics has now become a significant hindrance for data reuse and the translation of this technology into regulated areas of science.
For example, one conclusion from a European workshop on regulatory toxicology stated that "there are a number of R&D 1. Minimum information standards and early data capture 2. Global spectral databases 3. Tools and standards registries 4. Compound identifier mapping 5. Omics data integration 6. Metabolite identification These challenges are described in more detail in the following paragraphs. Identification of challenges Minimum information standards and early data capture In 2007 the Metabolomics Standards Initiative (MSI) 2,3 published a set of seminal papers with recommendations on minimal reporting standards for a number of aspects in metabolomics, summarized 6n 4. This work built on earlier efforts by the Standard Metabolic Reporting Structure initiative5and the Architecture for Metabolomics consortium (ArMet)6.
Although critical, the MSI work served only as a starting point. Since then, several initiatives have been set up to address elements of standardisation, particularly on data standards, building on the work of the MSI. The COS-MOS project (COordination Of Standards In MetabOlomicS, httpneeds, including a database to support metabolomics, standardisation, validation and reporting formats" (https://goo. gl/EiuTfM), and progress is now underway 8 (https://goo. gl/HapKhz). T e multiple task groups of the international Metabolomics Society have objectives to educate and reform reporting standards including the Metabolite identification and QA/QC task groups.
elixir-europe. org/use-cases). B. Metabolomics community would benefit most C. Can be exhaustively mapped onto the existing five ELIXIR Platforms. ELIXIR technical activities ELIXIR technical activities are performed by ELIXIR Nodes and supported by the Hub. The Nodes run bioinformatics resources and services focusing on national priorities and contributing to a harmonised strategy across Europe. At the national level, an ELIXIR Node consists of research institutes within a member country, building on their national strengths. At the European level, ELIXIR's activities are structured around Platforms and Use Cases, which bring Metabolomics activities are well represented within Europe and ELIXIR nodes. Following the establishment of national efforts such as the French MetaboHUB 31 and the Netherlands Metabolomic Centre, transnational efforts such as the FP7 coordination action COSMOS and the H2020 e-infrastructure PhenoMeNal followed.
The French Institute for Radiation Protection and Nuclear Safety (IRSN), with the support of the Ministry of Environment, compiled a database (BDFA) to define and characterize known potentially active faults of metropolitan France. The general structure of BDFA is presented in this paper. BDFA reports to date 136 faults and represents a first step toward the implementation of seismic source models that would be used for both deterministic and probabilistic seismic hazard calculations. A robustness index was introduced, highlighting that less than 15 % of the database is controlled by reasonably complete data sets. An example of transposing BDFA into a fault source model for PSHA (probabilistic seismic hazard analysis) calculation is presented for the Upper Rhine Graben (eastern France) and exploited in the companion paper (Chartier et al.
Introduction The practice acquired in nuclear regulation over the last decade as well as the feedback arisen from recent earthquake consequences on nuclear power plants (e. g. Kashiwazaki-Kariwa in 2007, Fukushima and North Anna in 2011)  have challenged the expertise of the IRSN (French Institute for Radiation Protection and Nuclear Safety). Hence, IRSN's research related to the geological aspects of seismic hazard analysis (SHA) has been focused on three principal axes: (1) updating national seismotectonic zoning pattern  (Baize et al. , 2013) , (2) performing and publishing collaborative studies on specific French active faults (see  Cushing et al. , 2008; Baize et al. , 2011; García-Moreno et al. , 2015; De La Taille et al. , 2015)  and (3) implementing the BDFA (from the French term Base de Données des Failles Actives which means active faults database), a database concerning the potentially active faults of metropolitan France.
These issues directly follow key aspects reported in the international recommendations for SHA in dedicated site evaluation guides (see  IAEA, 2010)  in which matters linked with both seismic motions and surface faulting are addressed and in the requirements of the the French deterministic fundamental safety rules  (RFS 2001 -01, ASN, 2001)  for the determination of ground motion at sites. The above-mentioned third axis started in 2009 and consists of the ongoing BDFA project  (Palumbo et al. , 2013). It represents a first step to supporting SHA calculation, which needs a collection of geological information in order to characterize seismic sources. This new database compiles available data on faults with post-Late Miocene activity evidence in metropolitan France, including geometrical properties, kinematics, slip rates, etc.
4 of this paper. 2 Rationale behind BDFA Despite its distance to active plate boundaries and relatively low to moderate seismotectonic activity (intraplate domain), both significant earthquakes (e. g. historical catalogue, SISFRANCE, 2016) and surface faulting (e. g. Sébrier et al. , 1997; Chardon et al. , 2005)  have occurred in metropolitan France during historical and pre-historical times. The starting point for building the BDFA relied on previous research, namely (1) the seismotectonic map released by  Grellet et al. (1993)  and the active fault database of southeastern France  (Terrier, 2004) , (2) the IRSN catalogue of faulting evidence affecting Quaternary deposits  (Baize et al. , 2002) , and (3) the French catalogue of neotectonic evidence (available online at www. neopal. net). This early work was based upon both a catalogue of published (scientific articles, PhD thesis, etc.
) and unpublished reports (technical reports, master thesis, etc. ) as well as an important interpretation phase performed by the authors themselves. BDFA aims to reflect the available data sets as much as possible, either for the establishment of fault mapping or for the description of the fault activity. Because various opinions may have been proposed by different authors at different times and at different scales, we compiled their interpretations/data in a specific form for each fault complementing the BDFA traces and tables. Our own choices of fault parameters and associated uncertainties are therefore tracked and referenced to the aforementioned form. These forms and the neotectonic and structural syntheses compiled at regional scales (i. e. Alps, Britany, Jura Mountains, etc. ) are written in French and are available upon request.
Discriminating whether a fault is considered active or not This task represents a key point of the database which is, however, not straightforward to determine, because of both scientific and regulatory issues. From a scientific point of view, when no sign of current activity is recorded along a fault (from seismicity and geodesy), which is often the case in intraplate domains, determining whether a fault is active or not is based upon the age of the youngest observed deformation, with particular attention to multiple movements occurring over the last thousands to hundreds of thousands of years. From a regulatory point of view, national and international definitions of when a fault should be considered active may differ when it comes to deciding on the temporal limits that should be taken into account.
S. NRC, 2017) which advises setting this limit to 35 kyr for faults that ruptured once at or near the surface or 0. 5 Myr for faults highlighting recurring earthquakes. At the metropolitan France scale, the orientation of the tectonic stress field has not experienced dramatic changes since the end of Miocene, with the persistence of the convergence between Africa and Eurasia. In parallel, the age of Plio-Quaternary sediments that may attest for deformation along faults are often absent or poorly constrained. In this context, we regarded the re-activation of past structures as possible and build the BDFA as a potentially active fault database, thus including the late Miocene to Quaternary structures as considered in a previous compilation by  Baize et al. (2013)  (Fig. 1 ). 3 The database structure and statistics The database structure (see the Supplement) was inspired by other databases developed in the world, such as the ones from the USA (QFAULT;  Haller et al.
, 2004) , New Zealand (NZAFD;  Langridge et al. , 2016) , Japan (Active Fault Database of Japan; AIST, 2016), Italy (ITHACA;  Michetti et al. , 2000)  and Iberia (QAFI;  García-Mayordomo et al. , 2012). The proposed map for metropolitan France is associated with a relational database describing the state of knowledge for each fault segment. This database is composed of several thematic tables (designed in Microsoft Excel spreadsheets) linked together with an identification key. The identification key for each fault described in BDFA (ID_Fault -IDF) corresponds to the one referenced in the French Geological survey (BRGM) fault database related to the 1 : 1 000 000 geological map. A new identification key gives a unique reference to each fault segment (ID_UNIQUE -UID). These two identification keys allow the following tables to be linked together: -The main table contains all gathered fault parameters with associated uncertainties when available (i.
e. map characteristics, geometry, neotectonics, ages and kinematics, calculation of a robustness index, editing notes and release date). -The index-ref and reference tables list the publications used to characterize the faults. -The index-evidence table includes all neotectonic evidence reported in the NEOPAL and IRSN databases  (respectively NEOPAL, 2009 and Baize et al. , 2002). -The index-seismic table reports the largest earthquakes, essentially events described in the historical archives (SISFRANCE) for which magnitude values are proposed by  Baumont and Scotti (2011). All fields are described in the BDFA table enclosed in the Supplement. Most of them are manually implemented, but we took advantage of GIS capabilities to implement cartographic parameters such as length, azimuth, tips coordinates.
It may also happen, in particular for long faults (e. g. the south Armorican shear zone is longer than 500 km), that only one or a few segments of a fault have been studied because of the occurrence of a particular local seismic crisis or the exposure of local neotectonic evidence. Consequently, precise mappings are often missing or not reliable due to coarse drawings. In this context, we complemented the available fault traces with a new mapping, including fault segmentation based on the following: -As defined earlier, the basic unit filled in the database is the fault segment (UID), grouped into a fault (IDF), forming a discontinuous trace at the surface. -In order to propose a surficial trace of the fault segments, we relied on the available map documents with a cartographic scaled approach.
Priority was given to large-scale geological maps from the French geological survey (1 : 50 000) and then, if not available, to lowerscale maps (1 : 250 000, 1 : 1 000 000). As a last resort, DEMs and derived slope maps, as well as air photos, were analysed to propose fault segment traces based on their topographic signature. Finally, each proposed fault segment trace goes along with a reliability index (TRA: reliable, uncertain, hidden, or suspect). This reliability index was also adopted to qualify all faults segments of the database. -Fault segments were archived into four typologies (major: M, parallel: P, oblique: OB and orthogonal: OX). This term was introduced to differentiate what is considered to be the main fault trace (major) from satellite or conjugate systems. This is especially useful for inherited faults in hard rocks (e.
Age of deformations and slip rates The age of the youngest deformed geological horizon will condition whether the causative fault/fault segment is considered in hazard calculations or not (French RFS 2001-01; IAEA, 2010; U. S. NRC, 2017). A second time, once a fault or a fault segment is considered, the associated slip rate will be the most influencing parameter in quantifying its seismogenic activity. Consequently, we designed the database to provide the necessary parameters to (1) assess the age of the last movement along a fault or fault segment, and (2) calculate slip rates or understand how they were derived. Concerning the age of the last movement, we defined the following parameters to be filled in the database for each fault segment: -The DCHR (deformed chronostratigraphic unit) field indicates the local terminology of the most recent chronostratigraphic unit involved in faulting.
-NWEU (north-west European chronostratigraphic stages) -because the terminology of Quaternary glaciations used over time in the French bibliography often refers to Alpine regional stages, we introduced a field referring to their corresponding north-western European stages. -UCHR (undeformed CHRonostratigraphic unit) indicates the local terminology of the oldest chronostratigraphic units not involved in the faulting. As mentioned previously, DCHR may cover a wide variety of terms. Concerning slip rates, we were rarely able to extract from the consulted references direct information concerning fault slip rates. Published slip rate values were controlled before integration into the database, when chronological and/or stratigraphical issues arose because of either ambiguous, vague, or even inconsistent information.
When reliable constraints in terms of chronology and amount of slip can be extracted from the consulted references (scientific papers, maps, etc. ), then we propose slip rates based on these observations. The following parameters are filled in the database: -NEOF (neotectonic offset). It informs the minimum and maximum offset values of the marker used to estimate slip rates and associated uncertainties. In general, it corresponds to the amount of slip registered by the youngest available dated and faulted marker. -OST (offset span time, in years). It reports the time span used to calculate slip rates. It could be either a single value or a bracket depending on the presence or absence of dated deformation markers. -AR (age used for rate). It mentions the name of the chronostratigraphic units constraining OST.
It may happen that OST does not correspond to DCHR because the amount of slip (i. e. NEOF) in the youngest affected sediments can not be quantified. In this case, longer-term slip rates may be derived from older stratigraphic/morphologic markers. Slip rate ranges are finally calculated by dividing NEOF with OST. When sufficient data are available, they may be decomposed in vertical slip rate (VSR) and/or horizontal slip rate (HSR). In Fig. 3 , we illustrate a theoretical case in which we reported the different fields informed in the database. This corresponds to an ideal case in which stratigraphic markers with absolute ages are available within the youngest deformed unit, which will allow for the recovery of a range of slip rates related to the most recent deformed horizon. A real example illustrating the use of long-term slip rates because of missing quantified tectonic offsets in the most recent formations is given for the Vuache fault and derived from the publication of  Baize et al.
(2011). The parameters introduced in the database for the 5317_2_M segment are reported in Table  1. Along this fault segment, faulted Quaternary deposits were observed in a quarry and dated at the end of Riss (≈ 139 kyr) through OSL (optically stimulated luminescence) techniques. Authors were unfortunately not able to quantify the deformation in these sediments. In order to define a long-term fault slip rate, they focused on a wellmarked morphological shift of 2 km of the Mandallaz anticline, related to the formation of the Jura Mountains, which started during the Miocene (between the onset of the Serravallian and the end of the Tortonian). Assuming a constant deformation rate since the Miocene, they estimated a 0. 15 to 0. 28 mm yr -1 slip rate that is reported in the database.
Robustness index The current version of the database includes 136 faults with a total of 581 fault segments. Among these 581 segments, 118 are reported as active during the Quaternary. We provide a robustness index (RI), estimated for each segment. This index aims to provide a ranking of the fault population in terms of reliability of their potential activity. RI (Eq. 1) follows the empirical expression modified from  Baize et al. (2012) : IR = TI + 0. 1 • TI + IAN + GI + 3HIST + 4INST + 2GDR , (1) where TI is the trace index (structural knowledge). It may be valued at 0 or 1, according to unknown or well-known tectonic structures, respectively (see field TRA in the BDFA tables). IAN is the age index (time of last recognized displacement). Having been derived from the NA field, it may be valued at 1, 2, or 3 for the Miocene, Pliocene, and Quaternary, respectively, and at 0 for undefined/presumably post-Paleogene.