Find research datasets worth reusing

opencc-by-4.0May 2019View details →

Data for "On the impact of Citizen Science-derived data quality on deep learning based classification in marine images"

This dataset contains all the annotations done by either citizen scientists or experts of the publication: "On the impact of Citizen Science-derived data quality on deep learning based classification in marine images" CSP.csv -> CS annotations of the Citizen Science Primer-experiment CSPExpert.csv -> Expert annotations of the Citizen Science Primer-experiment CSS.csv -> CS annotations of the Citizen Science Study CSSExpert.csv -> Expert annotations of the Citizen Science Study Visual exploration of the image data is possible in the BIIGLE 2.0 image annotation system at <a href="https://biigle.de/projects/139">https://biigle.de/projects/159</a> using the login <a href="mailto:cs@example.com">cs@example.com</a> and the password plosonecs.

opencc-by-4.0Jun 2019View details →

ScintPi: A low-cost, easy-to-build GPS ionospheric scintillation monitor for DASI studies of space weather, education, and citizen science initiatives

These data sets contain ionospheric scintillation (GPS L1) observations (S4 indices) collected by a ScintPi prototype during 2018 at a low magnetic latitude station (Presidente Prudente). ScintPi is a low-cost, easy-to-build GPS ionospheric scintillation monitor for DASI studies of space weather, education, and citizen science initiatives. The file named "ScintPi_PPR_S4_2018.mat" contains S4 values (s4mat) for 2018 as a function of universal time (utmat), day-of-year (doymat), GPS satellite identifier number (prnmat), GPS satellite elevation (elmat) and azimuth (azmat) angles. The file named "ScintPi_PPR_20180211.mat" contains example raw (10 Hz) measurements made by ScintPi on February 11, 2018. The file contains values of receiver's altitude, latitude and longitude (variables alt,lat, and lon), GPS satellite azimuth and elevation (variables el and az), GPS identifier number (prn), signal-to-noise ratio (snr), and day-of-year (doy).

Map of articles about "Teaching Open Science"

This description is part of the blog post "Systematic Literature Review of teaching Open Science" https://sozmethode.hypotheses.org/839 According to my opinion, we do not pay enough attention to teaching Open Science in higher education. Therefore, I designed a seminar to teach students the practices of Open Science by doing qualitative research.About this seminar, I wrote the article ”<a href="https://osf.io/preprints/socarxiv/b3zf7">Teaching Open Science and qualitative methods</a>“. For the article ”Teaching Open Science and qualitative methods“, I started to review the literature on ”Teaching Open Science“. The result of my literature review is that certain aspects of Open Science are used for teaching. However, Open Science with all its aspects (Open Access, Open Data, Open Methodology, Open Science Evaluation and Open Science Tools) is not an issue in publications about teaching. Based on this insight, I have started a systematic literature review. I realized quickly that I need help to analyse and interpret the articles and to evaluate my preliminary findings. Especially different disciplinary cultures of teaching different aspects of Open Science are challenging, as I myself, as a social scientist, do not have enough insight to be able to interpret the results correctly. Therefore, I would like to invite you to participate in this research project! I am now looking for people who would like to join a collaborative process to further explore and write the systematic literature review on “Teaching Open Science“. Because I want to turn this project into a Massive Open Online Paper (MOOP). According to the <a href="https://osf.io/preprints/socarxiv/b3zf7">10 rules of Tennant et al (2019) on MOOPs</a>, it is crucial to find a core group that is enthusiastic about the topic. Therefore, I am looking for people who are interested in creating the structure of the paper and writing the paper together with me. I am also looking for people who want to search for and review literature or evaluate the literature I have already found. Together with the interested persons I would then define, the rules for the project (cf. Tennant et al. 2019). So if you are interested to contribute to the further search for articles and / or to enhance the interpretation and writing of results, please get in touch. For everyone interested to contribute, the list of articles collected so far is freely accessible at Zotero: <a href="https://www.zotero.org/groups/2359061/teaching_open_science">https://www.zotero.org/groups/2359061/teaching_open_science</a>. The figure shown below provides a first overview of my ongoing work. I created the figure with the free software <a href="https://www.yworks.com/products/yed">yEd</a> and uploaded the file to zenodo, so everyone can download and work with it: To make transparent what I have done so far, I will first introduce what a systematic literature review is. Secondly, I describe the decisions I made to start with the systematic literature review. Third, I present the preliminary results. Systematic literature review – an Introduction Systematic literature reviews “are a method of mapping out areas of uncertainty, and identifying where little or no relevant research has been done.” (Petticrew/Roberts 2008: 2). Fink defines the systematic literature review as a “systemic, explicit, and reproducible method for identifying, evaluating, and synthesizing the existing body of completed and recorded work produced by researchers, scholars, and practitioners.” (Fink 2019: 6). The aim of a systematic literature reviews is to surpass the subjectivity of a researchers’ search for literature. However, there can never be an objective selection of articles. This is because the researcher has for example already made a preselection by deciding about search strings, for example “Teaching Open Science”. In this respect, transparency is the core criteria for a high-quality review.  In order to achieve high quality and transparency, Fink (2019: 6-7) proposes the following seven steps: <ol> <li>Selecting a research question.</li> <li>Selecting the bibliographic database.</li> <li>Choosing the search terms.</li> <li>Applying practical screening criteria.</li> <li>Applying methodological screening criteria.</li> <li>Doing the review.</li> <li>Synthesizing the results.</li> </ol> I have adapted these steps for the “Teaching Open Science” systematic literature review. In the following, I will present the decisions I have made. Systematic literature review – decisions I made <ol> <li>Research question: I am interested in the following research questions: How is Open Science taught in higher education? Is Open Science taught in its full range with all aspects like Open Access, Open Data, Open Methodology, Open Science Evaluation and Open Science Tools? Which aspects are taught? Are there disciplinary differences as to which aspects are taught and, if so, why are there such differences?</li> <li>Databases: I started my search at the <a href="https://doaj.org/">Directory of Open Science (DOAJ)</a>. “DOAJ is a community-curated online directory that indexes and provides access to high quality, open access, peer-reviewed journals.” (https://doaj.org/) Secondly, I used the <a href="http://base-search.net">Bielefeld Academic Search Engine (base)</a>. Base is operated by Bielefeld University Library and “one of the world’s most voluminous search engines especially for academic web resources” (base-search.net). Both platforms are non-commercial and focus on Open Access publications and thus differ from the commercial publication databases, such as Web of Science and Scopus. For this project, I deliberately decided against commercial providers and the restriction of search in indexed journals. Thus, because my explicit aim was to find articles that are open in the context of Open Science.</li> <li>Search terms: To identify articles about teaching Open Science I used the following search strings: “teaching open science” OR teaching “open science” OR teach &bdquo;open science“. The topic search looked for the search strings in title, abstract and keywords of articles. Since these are very narrow search terms, I decided to broaden the method. I searched in the reference lists of all articles that appear from this search for further relevant literature. Using Google Scholar I checked which other authors cited the articles in the sample. If the so checked articles met my methodological criteria, I included them in the sample and looked through the reference lists and citations at Google Scholar. This process has not yet been completed.</li> <li>Practical screening criteria: I have included English and German articles in the sample, as I speak these languages (articles in other languages are very welcome, if there are people who can interpret them!). In the sample only journal articles, articles in edited volumes, working papers and conference papers from proceedings were included. I checked whether the journals were predatory journals – such articles were not included. I did not include blogposts, books or articles from newspapers. I only included articles that fulltexts are accessible via my institution (University of Kassel). As a result, recently published articles at Elsevier could not be included because of the special situation in Germany regarding the Project DEAL (https://www.projekt-deal.de/about-deal/). For articles that are not freely accessible, I have checked whether there is an accessible version in a repository or whether preprint is available. If this was not the case, the article was not included. I started the analysis in May 2019.</li> <li>Methodological criteria: The method described above to check the reference lists has the problem of subjectivity. Therefore, I hope that other people will be interested in this project and evaluate my decisions. I have used the following criteria as the basis for my decisions: First, the articles must focus on teaching. For example, this means that articles must describe how a course was designed and carried out. Second, at least one aspect of Open Science has to be addressed. The aspects can be very diverse (FOSS, repositories, wiki, data management, etc.) but have to comply with the principles of openness. This means, for example, I included an article when it deals with the use of FOSS in class and addresses the aspects of openness of FOSS. I did not include articles when the authors describe the use of a particular free and open source software for teaching but did not address the principles of openness or re-use.</li> <li>Doing the review: Due to the methodical approach of going through the reference lists, it is possible to create a map of how the articles relate to each other. This results in thematic clusters and connections between clusters. The starting point for the map were four articles (Cook et al. 2018; Marsden, Thompson, and Plonsky 2017; Petras et al. 2015; Toelch and Ostwald 2018) that I found using the databases and criteria described above. I used yEd to generate the network. &bdquo;yEd is a powerful desktop application that can be used to quickly and effectively generate high-quality diagrams.” (<a href="https://www.yworks.com/products/yed">https://www.yworks.com/products/yed</a>) In the network, arrows show, which articles are cited in an article and which articles are cited by others as well. In addition, I made an initial rough classification of the content using colours. This classification is based on the contents mentioned in the articles’ title and abstract. This rough content classification requires a more exact, i.e., content-based subdivision and evaluation by others, who are experts in the respective fields/disciplines.</li> </ol>

Sub-sampled Fastq Files for ChIP-seq datasets from Click-Seq Science Paper (Science 2017, 10.1126/science.aal2066)

Data were downloaded from SRA. We then randomly sub-sampled 20% of the reads using seqtk_sample v 1.2 in galaxy (seed 4). This dataset is a support dataset for the <a href="https://www.embl.de/training/events/2019/EPI19-01/index.html">EMBL Course: Chromatin Signatures During Differentiation: Integrated Omics</a>

Sub-sampled Fastq Files from Click-Seq Science Paper (Science 2017, 10.1126/science.aal2066)

Data were downloaded from SRA. We then randomly sub-sampled 20% of the reads using seqtk_sample v 1.2 in galaxy (seed 4). This dataset is a support dataset for the <a href="https://www.embl.de/training/events/2019/EPI19-01/index.html">EMBL Course: Chromatin Signatures During Differentiation: Integrated Omics</a>

opencc-by-4.0Mar 2019View details →

Data for Medical Data Science Shortcourse

This is a .csv version of the World Bank Data on Health Nutrition and Population, cf. https://datacatalog.worldbank.org/dataset/health-nutrition-and-population-statistics and derived data sets for training purposes.

opencc-by-4.0Sep 2019View details →

Dataset - A Review on Blockchain Technology and Blockchain Projects Fostering Open Science

Dataset for publication (A Review on Blockchain Technology and Blockchain Projects Fostering Open Science) in "Frontiers in Blockchain" Journal: https://www.frontiersin.org/articles/10.3389/fbloc.2019.00016/.

Compilation of Moon internal structure models and seismic event locations presented in Garcia et al., Space Science Review, 2019 study

Compilation of of previously published internal structure model of the Moon in "named discontinuities" seismological format + 3 new models associated to the above mentioned study + previously published Moon quake location estimates by various authors. The study, the internal structure models and quake locations compilation were performed by the ISSI international research team on Moon Seismology and internal structure described here: http://www.issibern.ch/teams/internstructmoon/

opencc-by-4.0Nov 2019View details →

All Computer Science Papers @ arXiv.org -- A High-Quality Gold Standard for Citation-based Tasks

We propose a newly-created gold standard data set for citation-based tasks. This gold standard is based on all computer science papers in arXiv.org. Abstract. Analyzing and recommending citations with their specific citation contexts have recently received much attention due to the growing number of available publications. Although data sets such as CiteSeerX have been created for evaluating approaches for such tasks, those data sets exhibit striking defects. This is understandable if one considers that both information extraction and entity linking as well as entity resolution need to be performed. In this paper, we propose a new evaluation data set for citation-dependent tasks based on arXiv.org publications. Our data set is characterized by the fact that it exhibits almost zero noise in the extracted content and that all citations are linked to their correct publications. Besides the pure content, available on a sentence-basis, cited publications are annotated directly in the text via global identifiers. As far as possible, referenced publications are further linked to DBLP. Our data set consists of over 15M sentences and is freely available for research purposes. It can be used for training and testing citation-based tasks, such as recommending citations, determining the functions or importance of citations, and summarizing documents based on their citations.   More information can be found in our publication "<a href="http://www.lrec-conf.org/proceedings/lrec2018/pdf/283.pdf">A High-Quality Gold Standard for Citation-based Tasks</a>" (LREC'18). You can cite the data set as follows: <pre><code>@inproceedings{DBLP:conf/lrec/0001TJ18, author = {Michael F{\"{a}}rber and Alexander Thiemann and Adam Jatowt}, title = "{A High-Quality Gold Standard for Citation-based Tasks}", booktitle = "{Proceedings of the Eleventh International Conference on Language Resources and Evaluation}", series = "{LREC'18}", location = "{Miyazaki, Japan}", year = {2018}, url = {http://www.lrec-conf.org/proceedings/lrec2018/summaries/283.html} } </code></pre>

openother-openNov 2019View details →

CitSciDefinitions: Citizen Science Definitions

This is a public repository to host a community generated database of published definitions for citizen science, as described in the peer-reviewed literature, government publications and policies, etc.

opencc-by-4.0Nov 2019View details →

The ecosystem of technologies for social science research, data

This is the list of 417 software tools, packages, apps and platforms we have reviewed as part of SAGE Ocean. The dataset contains a number of features: name, pitch, type of tool, country, year, some papers, funders, founders, founding team etc. The latest version of this list will be available on github along with the metadata: <a href="https://github.com/danielagduca/SAGE_tools_social_science/tree/master/data">https://github.com/danielagduca/SAGE_tools_social_science/tree/master/data</a> The supporting white paper describing the tools is: Duca, D., & Metzler, K. (2019). *The ecosystem of technologies for social science research* (White paper). London, UK: Sage. doi: 10.4135/wp191101

opencc-by-4.0Dec 2019View details →

Figures 12-16. 12 in The types of Calyptratae (Diptera) preserved in the Museum fϋr Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science, Berlin, Germany, collected from Indian Sub continent

Figures 12-16. 12. Mydaea morose Stein Holotype and Original labels, 13(a&b). Pygophora tricincta Enderlein Type and Original labels, 14(a&b). Chrysomyia nigripes Aubertin Paratype and labels, 15(a,b&c). Lipoptena efovea Speiser Type and Original labels, 16(a&b). Gasterophilus elephantis Cobbold Paratype and labels.

opencc-by-4.0Dec 2019View details →

Figures 6b-11. 6b in The types of Calyptratae (Diptera) preserved in the Museum fϋr Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science, Berlin, Germany, collected from Indian Sub continent

Figures 6b-11. 6b.Dichaetomyia splendida (Stein) Holotype with labels 7 (a&b). Limnophora tinctipennis Stein Syntypes and labels, 8. Lispa mirabilis Stein Original type and Syntype labels, 9(a&b). Lispa sericipalpis Stein Holotype and Original labels, 10. Lispocephala tinctipennis (Stein) Original and Syntype labels, 11. Mydaea attenta Stein Holotype Original labels.

opencc-by-4.0Dec 2019View details →

Figures 1-6. 1. Coenosia angustifrons Stein Type with labels, 2a. Coenosia capitulate Stein Syntype, 2b. Original plus Syntype labels, 3 in The types of Calyptratae (Diptera) preserved in the Museum fϋr Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science, Berlin, Germany, collected from Indian Sub continent

Figures 1-6. 1. Coenosia angustifrons Stein Type with labels, 2a. Coenosia capitulate Stein Syntype, 2b. Original plus Syntype labels, 3(a&b). Coenosia ceylonica Enderlein Type and Paratype labels, 4. Coenosia indica Enderlein Original and Type labels, 5. Mydaea pallens Stein Original and Paralectotype labels, 6a. Dichaetomyia splendida (Stein) Holotype with labels.

opencc-by-4.0Dec 2008View details →

Text-fig. 4. A – Alasia sp., pollen ornamentation, compared with B – extant Quercus castaneifolia C.A. Mey (courtesy of Natalia Naryshkina, Institute of Biology and Soil Science, Vladivostok), with similar verrucate – scabrate elements. Scale bar 1 µm. in In Situ Pollen Of Alasia, A Supposed Staminate Inflorescence Of Trochodendroides Plant

Text-fig. 4. A – Alasia sp., pollen ornamentation, compared with B – extant Quercus castaneifolia C.A. Mey (courtesy of Natalia Naryshkina, Institute of Biology and Soil Science, Vladivostok), with similar verrucate – scabrate elements. Scale bar 1 µm.

Figure 5 in Effect of urban habitats on colony size of ants (Hymenoptera, Formicidae) In memory of Professor A. A. Zakharov (Russian Academy of Sciences, Moscow)

Figure 5. Colony size of species per different geographic area. A – Crematogaster subdentata; B – Lasius neglectus.

Figure 4 in Effect of urban habitats on colony size of ants (Hymenoptera, Formicidae) In memory of Professor A. A. Zakharov (Russian Academy of Sciences, Moscow)

Figure 4. Colony size of 9 species of ants in several habitats of the same geographic area (calculated according to (A. Zakharov, 1978, 2015). A – Lasius fuliginosus; B – Camponotus vagus; C – Lasius emarginatus; D – Lasius niger; E – Formica cinerea; F - Dolichoderus quadripunctatus; G – Lasius brunneus; H – Crematogaster subdentata; I – Lasius neglectus.

Figure 2 in Effect of urban habitats on colony size of ants (Hymenoptera, Formicidae) In memory of Professor A. A. Zakharov (Russian Academy of Sciences, Moscow)

Figure 2. Calculated curve of the size of the ant colony by the intensity of movement of foragers per 1 min along the trail (counting only in one direction, Zakharov, 1979; 2015). Within 14–140 - according to A. Zakharov (1979), from 184 to 307 - our data, with an additional calculation formula in this range of values.

Figure 3 in Effect of urban habitats on colony size of ants (Hymenoptera, Formicidae) In memory of Professor A. A. Zakharov (Russian Academy of Sciences, Moscow)

Figure 3. Colony size in 21 ant species, calculated by the formula of A. Zakharov (1979; 2015). Ukraine: A – Kyiv region, deciduous (Kd) and coniferous (Kp) forests, natural habitats; B – Kyiv, suburban habitats (Ks); C – Kyiv city, urban habitats; D – natural habitats in Crimea (C1 – mountain steppes, C2 – mountain meadows) and in the Carpathians (Carp, mountain meadows); Crimea, steppe areas, natural habitats (C_aet); suburban and urban habitats in Crimea (L_neg, C_sub); Crimea, oak-pistachio-juniper forests, natural habitats (P_tau; F_gag; C_sch); Russian Federation: E, F – Rostov-on-Don, suburban (L_neg_R2) and urban (L_neg_R1; C_sub_R1) habitats; Uzbekistan: G – natural (riparian forests, C_sub_tu) and urban (Tashkent city, everything else) habitats; Russian Federation: H – Ural, natural habitats (taiga). Ant species: L_pla – Lasius platythorax; Dol – Dolichoderus quadripunctatus; L_ful – Lasius fuliginosus; L_ema – Lasius emarginatus; L_bru – Lasius brunneus; F_ruf – Formica rufa; L_nig – Lasius niger; F_cin – Formica cinerea; C_vag – Camponotus vagus; C_aet – Camponotus aethiops; F_tru – Formica truncorum; F_pol – Formica polyctena; L_neg – Lasius neglectus; F_pra – Formica pratensis; P_tau – Plagiolepis tauricus; F_gag – Formica gagates; C_sch – Crematogaster schmidti; C_sub – Crematogaster subdentata; M_ber – Myrmica bergi; P_pal – Plagiolepis pallescens; F_aqu – Formica aquilonia.

Figure 1. D in Effect of urban habitats on colony size of ants (Hymenoptera, Formicidae) In memory of Professor A. A. Zakharov (Russian Academy of Sciences, Moscow)

Figure 1. D Locations of the study. Ukraine: 1 – Crimea (the Main ridge of the Mountainous Crimea and the South Coast, Saki region), 2 – Kyiv and Kyiv region, 3 – Carpathians; Uzbekistan: 4 – Tashkent city, tugai forests; Russian Federation: 5 – Ural, 6 – Rostov-on-Don city and region. Habitats. a – natural, b – suburban, c – urban.