dataesr/scientific-paragraphs-categorization huggingface dataset:
Here discovery implies the relatively easy possibility to uncover various materials that are somehow related. Finding meaning implies not simply uncovering new resources but also interpreting them, applying a deeper understanding to their value. When discovering, one does not simply see a new object but also comprehends it and can decide whether or not it will be of use in the context of her research. There was also a need to draw a distinction between the 'discovery' as the final end such as a paper or a dataset that has been discoveredthe 'object' of the discovery -and the definition of 'discovery' as the set of practices (e. g. existing explicit and implicit skills) and tools (e. g. search engines, recommender systems, multilingual tools), that used together allow a researcher to discover something-that is the process of discovery.
Participants were keen to have more control over what's important to them (for recommender systems and search algorithms). There was debate over the extent to which users should be guided or left free to make their own choices on discovery. The discoverability of relevant tools to analyse data and other software was mentioned as being problematic, GitHub is often used as a community resource, but this does not mean that the software is particularly discoverable. In another session, it was also noted that in some platforms or repositories, the researcher also has the opportunity to influence the discoverability of her work. This role is often overlooked but in many instances, it is the researcher who delivers the metadata, such as keywords, to the repository. While the average researcher will be the one with the academic expertise and best appointed to explain the value of a paper they have written, their knowledge of cataloguing systems might be limited.
It also allows for interoperability with different databases and data providers. However, since many providers apply different standards, ensuring a common workflow in relation to metadata may be a major difficulty for a discovery service aggregating resources from a number of places. Related to this, is the issue of stability of handles that might break or change. Finally, indexing, ranking and classification of resources should be at the centre of the process. With the current rate of knowledge production, it is difficult to keep track of existing research, even within one's niche; exploring important literature in a new field proves even more challenging. Filtering the results without narrowing down the discovery process too much is one of the main principles. While they should not be overwhelmed with the resources, users ought to be able to search in an open manner that would ensure that the process of finding what was not expected can also occur.
These observations are supported by the extensive user studies carried out in the TRIPLE project (see Table  1  for relevant quotes from participants). During the initial interviews with SSH researchers and other stakeholders, difficulty in getting an overview of the research field was a common theme, especially when the topic of research was new to the person trying to make sense of the information, or the topic was interdisciplinary. Although GS is often used as a starting point, it is usually backed up by searching via another method, such as a University library catalogue, Web of Science, Mendeley database, or a specific discipline database. This becomes even more difficult when the topic is interdisciplinary due to the siloed nature of publications and the way that traditional journal publications have become increasingly narrow in focus.
Researchers report the need to use many different information sources to try and gain this overview and to ensure that they are able to find all relevant publications or data. The complexity of a discovery process has been confirmed further in the TRIPLE research by having researchers 'map' their discovery journeys and the artefacts that they use for this. An example of a researcher's Discovery Journey is shown below in Figure  1. One of the reasons for the discoverability crisis is a lack of innovation in discovery systems. This would not be a problem if others could build on companies' search indices and databases, but this is usually prohibited. This is true for most commercial offerings, even though the business models differ. Elsevier (Scopus) and Clarivate (Web of Science) monetize their services primarily through license fees.
GoTriple: capturing the meaning of discovery platforms Acknowledging that there is not a one-size-fits-all solution for "discovering" in research, in this final section we introduce the TRIPLE project's effort to combine the technological and infrastructural developments of the past decade, to find a solution for meeting today's researchers' needs and desires-the GoTriple discovery service. Inter-language and inter-discipline coverage GoTriple provides two levels of semantic enrichments in the following nine languages: Croatian, English, French, German, Greek, Italian, Polish, Portuguese and Spanish. The first level relies on the twenty-seven SSH disciplines listed by the European project MORESS (Mapping Research Expertise in the European Social Sciences and Humanities). The twenty-seven discipline titles have been translated in eight languages and a thorough machine learning process made it possible to classify any GoTriple document according to these scientific fields.
The MORESS disciplines are also linked with major national controlled vocabularies (e. g. , English Library of Congress Subject Headings (LCSH), French RAMEAU or Spanish BNE). The second level relies on the GoTriple thesaurus. The thesaurus was elaborated from the SSH subset of the Frascati taxonomy for research. This subset allowed us to identify broad terms and their children in the LCSH. At the end of this process, the thesaurus gathered 2,565 concepts in English. After using both automated translation and human curation, the thesaurus now contains entries in nine languages, structured in SKOS (Simple Knowledge Organization System) and linked with Wikidata. The thesaurus is used to provide accurate and interlinked translations of the keywords collected by GoTriple in its harvesting process.
Thanks to these two levels of semantic enrichment, the GoTriple platform makes it possible to filter the search and to navigate its results, using either the SSH disciplines (which are broader and come from the MORESS categories), or the SSH topics (which are narrower and can be seen as the subject in a specific discipline) in nine languages. The nine languages were determined by the data and the linguistic skills available within the TRIPLE project, however, the work done has given the necessary expertise to add new languages to the platform in the future. Further monitoring and human expertise will create the possibility to enrich the thesaurus through time with new concepts. This could indeed become necessary to adapt to current events and societal trends (e. g. , global pandemic, COVID-19 or teleworking).
Systematic metadata retrieval GoTriple aims at referencing a wide range of scholarly resources coming from a high variety of sources in order to ensure biblio-diversity. The platform covers a diversity of disciplines and data types, such as scholarly articles and books, editorials, book reviews, grey literature, images, videos and datasets -all mostly in open access format. The harvesting process relies on a two-step strategy: collecting metadata through aggregators and supporting the data providers, so that they can make their metadata available for the aggregators. This strategy offers an inclusive set of scholarly outputs to the platform's users, and fosters the alignment of data management activities in the SSH area. GoTriple started collaborations with aggregators that are domain-specific (e.
Conclusion By design, the GoTriple platform is made with open source tools and can be adapted to different environments or disciplines as it can be enriched with other languages. This flexibility has opened several times the question of opening it for non-SSH domains. While the consortium has noticed an interest from others, our experience has shown that it is better to have dedicated tools for a specific community. This is why all the design and the components of the GoTriple platform have been thought to be reshaped for new perspectives and reused. Taking this into account, instead of having one GS platform, we could have linked discovery platforms in different languages and disciplines which can be interoperable to improve users' experience. There is a wish to see this platform as a first step in a more general process.
The article provides a cogent introduction to the GoTriple platform, with Google Scholar's limitations as the orienting foil. Limitations of GS around its indexing limitations (particularly around datasets and preprints), black box algorithm, and non-compliance with FAIR are used to set up a discussion of GoTriple, including the background of the TRIPLE project and the GoTriple design process. The core claim is that GoTriple provides an alternative approach, one that adheres to open data and open science principles, linguistic diversity, and transparency. An additional, if somewhat implicit, claim is that the design process, by consulting extensively with SSH academics, represents the expressed needs of the community in a way that commercial search engines like GS do not match. The paper includes an interesting discussion of the concept of "discovery" in a way that arguably extends the literature on this important, rarely defined, research practice.
The article is coherent and well-organized overall. The authors chose to structure their paper as a rejoinder of sorts to GS; as a result, the first half is devoted to documenting the limitations of GS. This is a defensible approach, mainly because of documented researcher reliance on GS for research discovery. GS is the 800-pound gorilla, so to speak, so framing the paper around its shortcomings works well to set up the GoTriple alternative. There are areas for improvement. More substantive issues are listed first, with lesser issues addressed second. There is a tension between discussing discovery across academia, on the one hand, and within SSH specifically, on the other. GS covers, or claims to cover, all research fields, while GoTriple is tailored to the SSH fields. This tension is partly resolved by the point, raised in the plain language summary especially, that SSH is especially poorly served by GS.
However, the bulk of the treatment of GS in the actual paper is not oriented to GS's SSH limitations in particular. The authors should elaborate on the plain language summary's points about SSH in particular in the "Why Google Scholar is not a complete discovery platform" section, to include issues like poor book-chapter indexing. More broadly, the SSH specificity of GoTriple should be more directly addressed; by design, it is not a "complete discovery platform" either. There is an opportunity, particularly in the conclusion, to discuss the need for non-SSH supplementation to GoTriple, perhaps on the GoTriple model of extensive discussion with working academics, etc.
○ A second area where the paper might better acknowledge GoTriple's particularity is in its European focus and origins. The paper notes this, but the European facet is in some tension with the "complete discovery platform" rhetoric. This is especially important because of the North-South inequality in scholarly communication more broadly. The relatively privileged geography, and still parochial scope in regional terms, should be acknowledged and openly grappled with. Is GoTriple's aim to be global in scope, within SSH? Is there openness to including non-European languages in its design? If not, this limitation should be acknowledged and addressed, perhaps with the claim that GoTriple's approach could be replicated elsewhere. The issue is that the paper's critique of GS rests, in part, on its Englishlanguage dominance; the less prominent critiques of Web of Science and Scopus make a similar point, if more so.
One major line of criticism of the latter, in particular, is that they favor the Global North, especially the North Atlantic inclusive of North American and Northern Europe, especially outside the German-language area. While GoTriple is certainly challenging some of that, in particular the hegemony of English, it is still a European project of the Global North. Any "complete discovery platform" will need to more proactively include research and researchers beyond the rich West. Perhaps GoTriple is designed with ○ this intent in mind, but in the current draft, there is little discussion of these global asymmetries. The paper places relatively little emphasis on the contrast between proprietary, for-profit services like GS, Scopus, etc. , on the one hand, and GoTriple, on the other. Much more attention might be paid to this crucial difference, which is not only about adherence to the latest open data standards or ongoing innovation, but instead to core principles of community-owned and -led scholarly infrastructure.
○ There is a discrepancy between the plain language summary and the paper itself. The summary makes a stronger case that GS excludes materials ("Some platforms tend to choose materials that are useful only to the majority"). The discussion contradicts this, saying that-yes, GS excludes datasets, book reviews-but noting evidence that it is quite comprehensive within its stated aims about published research. The issue raised in the critique-of-GS section along these lines-in addition to the data+preprint, etc, exclusions-is that the algorithm upranks cited and English-language results. But this is different than 'choosing material that is useful only to the majority'. I suspect the intended meaning here is that long-tail works are hard to discover -but exclusion isn't the right word.
Existing literature on GS and SSH specifically focus again on the comparison between GS and established citation databases. This literature shows that GS is more inclusive than the other services, at the price of less "Quality" in the material. In your comment there was a pointer to the fact that GS does not index book-chapters well (which of course are important publication items in SSH), however the literature does appear to say that GS is better at indexing e. g. chapters or dissertations if compared to databases. Nonetheless we added a paragraph pointing still to the limits of GS and arguing for the need of a specific and even more inclusive solution for SSH. This is now connected directly with the focus of GoTriple in codesigning together with the SSH community the solution, as well as on the much more encompassing idea of discovery focusing not only on publications but also on the discovery of people, projects etc.
1. About the "complete discovery platform": GoTriple aims for a global coverage of SSH scientific fields. "Complete" here is intended as in the complete discovery experience GoTriple offers in terms of openness, findability and coverage in comparison with GS 2. which limits users in their discovery process (silo effect, lack of reusability). Furthermore, the TRIPLE project is European-funded and thus naturally has a stronger focus on European data sources at the moment. But the inclusion of Spanish, Portuguese, Greek and Croatian among the 9 languages that were chosen reflects the objective to reach out to and include not only stakeholders from the rich west but also South-European and non-European research actors. We acknowledge that the sources included in the platform at the moment are more focused on Europe and the Global North, which mostly depends on our data providers and the data sources that we are using.
However, it is intended to extend the available data sources beyond the project duration to include sources from, e. g. , the Middle-and South Americas (Spanish, Portuguese). While European languages have been prioritised, the GoTriple platform is designed to enable the inclusion of non-European languages. For new languages to be added, a step-by-step process combined with an evaluation of the usage/demand for the additional language will be performed. GoTriple is presented as a complete discovery platform in terms of the experiences it provides: not only textual results, but also recommendations, visual results (graphs) or even crowdfunding to improve the discovery of SSH domain for citizens. It is complete also regarding the whole SSH disciplines it targets. However, by nature, it is not for all the scientific disciplines.
3. In addition, GoTriple is developed following open standards. GoTriple's data and source code are available under open licenses where possible. The advantage of this approach is that parts of the platform can easily be reused and that the system can easily be migrated. Proprietary lock-in effects are thus avoided. Making its enriched, high-quality data available means that not only GoTriple users will benefit from a better discovery experience, but that GoTriple will also play an important role in improving the data quality for SSH within the whole digital open science ecosystem. Indeed, the following paragraph has been added at the end of section 1: "In light of GS's limitations the TRIPLE project built a discovery platform, GoTriple, which aims to provide a service to discover SSH resources (data & publications, profiles of researchers and scientific projects) with a multilingual perspective.
Addressed. 10. Authors describe in particular the deficiencies and the limits of Google Scholar (GS), the biggest free platform used by researchers. Managing a solid theoretical framework, authors underline the problematic aspects of GS, addressing the limits of the affordances (e. g. the absence of research filters) as well as the lack of transparency of the service algorithms and how this makes GS "unlikely to be the exemplar of equality and transparency" (p. 4). To address this topic, the authors use accurately the literature that had previously analysed these platforms demonstrating a systematic job review of the state of the art. In the initial discussion about citation databases, the authors briefly mention the impact that platforms can have on minorities (p. 4, paragraph 4). We believe that further elaboration on this matter could benefit the article and make even more explicit how a well-structured bibliographic database could benefit the whole research environment.
Tools such as GS, Scopus and Web of Science provide long, unstructured lists of results with little context. These work well if you know what you are looking for. But for anyone diving into an unknown field, it can take weeks, even months, to identify the most important topics, publication venues and authors(Kraker et al. , 2021). This is far too long in a public health emergency. The result has been delays, duplicated work, and problems with identifying reliable findings(Ioannidis, 2020; OECD, 2020). This lack of tools to provide a quick overview of research results and evaluate them correctly, has created a crisis in discoverability itself(Kraker et al. ,  2021). The pandemic has highlighted this, but with three million research papers published each year(Johnson et al. ,  2020), and a growing diversity of other outputs such as datasets; discoverability has become a challenge in all disciplines(Kraker  et al.
For years a few large companies have dominated the market for academic search engines: GS; Microsoft's recently retired Academic (Microsoft, 2021); Clarivate's Web of Science, formerly owned by Thomson Reuters; and Elsevier's Scopus. But investment hasn't kept pace with the growth of scientific knowledge. What were once ground-breaking search engines have only been modestly updated, so that mainstream discovery systems are now of limited use(Kraker et al. , 2021). This would not be a problem if others could build on companies' search indices and databases, but this is usually prohibited (see for example Clarivate, n. d. ; Elsevier, n. d. ; Google, 2022; ResearchGate, 2020).
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Results Global population structure of Shigella. We assembled and sequenced a collection of 317 Shigella strains chosen on the basis of their representativeness of the known diversity of Shigella populations (i. e. , covering all serogroups and serotypes, and the different lineages or phylogroups of S. sonnei and S. flexneri). The genomic diversity of this "reference" dataset was further increased by adding another 81 publicly available Shigella genomes (these 81 genomes representing the "reference+" dataset). The 398 genomes studied were from strains belonging to the S. flexneri (n = 191), S. dysenteriae (n = 83), S. boydii (n = 80) and S. sonnei (n = 44) serogroups (Supplementary Table  4 ). We determined the wider phylogenetic context of these Shigella genomes by also analysing 95 E. coli genomes, including 27 EIEC from eight different EIEC genomic clusters and 68 (of the 72) strains from the ECOR collection, considered representative of the diversity of natural populations of E.
1  and Supplementary Fig. 1 ). Accordingly, by cgMLST, all 493 genomes belonged to the same HC2350 cluster (HC2350_1) defining the species Escherichia coli (Supplementary Data 1). As expected, all the Shigella and EIEC genomes contained the pathogenicity gene ipaH, whereas the ECOR genomes did not (Supplementary Fig. 2 ). A NINJA neighbour-joining (NJ) tree of core genomic allelic distances was generated with the dataset for the 493 Shigella and E. coli genomes (Fig. 1a ). The differential contribution of the reference and reference+ datasets to Shigella population diversity is shown in Supplementary Fig. 2. Visual examination of the colour-coded HC2000 tree revealed that the Shigella genomes were grouped into eight different HC2000 clusters (Fig. 1b ). Seven of these HC2000 clusters contained exclusively Shigella genomes.