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Annotated Dataset for Uncertainty Mining : Gold Standard
<p> </p> <h1>Description of the dataset</h1> <p>In order to study the expression of uncertainty in scientific articles, we have put together an interdisciplinary corpus of journals in the fields of Science, Technology and Medicine (STM) and the Humanities and Social Sciences (SHS). The selection of journals in our corpus is based on the Scimago Journal and Country Rank (SJR) classification, which is based on Scopus, the largest academic database available online. We have selected journals covering various disciplines, such as medicine, biochemistry, genetics and molecular biology, computer science, social sciences, environmental sciences, psychology, arts and humanities. For each discipline, we selected the five highest-ranked journals. In addition, we have included the journals PLoS ONE and Nature, both of which are interdisciplinary and highly ranked.</p> <p>Based on the corpus of articles from different disciplines described above, we created a set of annotated sentences as follows:</p> <ul> <li>593 were pre-selected automatically, by studying the occurrences of the lists of uncertainty indices proposed by Bongelli et al. (2019), Chen et al. (2018) and Hyland (1996).</li> <li>The remaining sentences were extracted from a subset of articles, consisting of two randomly selected articles per journal. These articles were examined by two human annotators to identify sentences containing uncertainty and to annotate them.</li> <li>600 sentences not expressing scientific uncertainty were manually identified and reviewed by two annotators<br><br></li> </ul> <p>The sentences were annotated by two independent annotators following the annotation guide proposed by Ningrum and Atanassova (2024). The annotators were trained on the basis of an annotation guide and previously annotated sentences in order to guarantee the consistency of the annotations. <br>Each sentence was annotated as expressing or not expressing uncertainty (<strong>Uncertainty</strong> and <strong>No Uncertainty)</strong>.<br>Sentences expressing uncertainty were then annotated along five dimensions: Reference , Nature, Context , Timeline and Expression. <br>The annotators reached an average agreement score of 0.414 according to Cohen's Kappa test, which shows the difficulty of the task of annotating scientific uncertainty.<br>Finally, conflicting annotations were resolved by a third independent annotator.</p> <p><br>Our final corpus thus consists of a total of 1 840 sentences from 496 articles in 21 English-language journals from 8 different disciplines.<br>The columns of the table are as follows:</p> <ol> <li><strong>journal</strong>: name of the journal from where the article originates</li> <li><strong>article_title</strong>: title of the article from where the sentence is extracted</li> <li><strong>publication_year</strong>: year of publication of the article</li> <li><strong>sentence_text</strong>: text of the sentence expressing or not expressing uncertainty</li> <li><strong>uncertainty</strong>: 1 if the sentence expresses uncertainty and 0 otherwise;</li> <li><strong>ref, nature, context, timeline, expression</strong>: annotations of the type of uncertainty according to the annotation framework proposed by Ningrum and Atanassova (2023). The annotation of each dimension in this dataset are in numeric format rather than textual. The mapping betwen textual and numeric labels is presented in the Table below.</li> </ol> <table> <tbody> <tr> <td>Dimension</td> <td>1</td> <td>2</td> <td>3</td> <td>4</td> <td>5</td> </tr> <tr> <td>Reference</td> <td>Author</td> <td>Former</td> <td>Both</td> <td> </td> <td> </td> </tr> <tr> <td>Nature</td> <td>Epistemic</td> <td>Aleatory</td> <td>Both</td> <td> </td> <td> </td> </tr> <tr> <td>Context</td> <td>Background</td> <td>Methods</td> <td>Res&Disc</td> <td>Conclusion</td> <td>Others</td> </tr> <tr> <td>Timeline</td> <td>Past</td> <td>Present</td> <td>Future</td> <td> </td> <td> </td> </tr> <tr> <td>Expression</td> <td>Quantified</td> <td>Unquantified</td> <td> </td> <td> </td> <td> </td> </tr> </tbody> </table> <p><br>This gold standard has been produced as part of the <a href="https://project-inscim.github.io/">ANR InSciM (Modelling Uncertainty in Science) project.</a> </p> <h1>References</h1> <p><br>Bongelli, R., Riccioni, I., Burro, R., & Zuczkowski, A. (2019). Writers’ uncertainty in scientific and popular biomedical articles. A comparative analysis of the British Medical Journal and Discover Magazine [Publisher: Public Library of Science]. PLoS ONE, 14 (9). <a href="https://doi.org/10.1371/journal.pone.0221933">https://doi.org/10.1371/journal.pone.0221933</a></p> <p>Chen, C., Song, M., & Heo, G. E. (2018). A scalable and adaptive method for finding semantically equivalent cue words of uncertainty. Journal of Informetrics, 12 (1), 158–180. <a href="https://doi.org/10.1016/j.joi.2017.12.004">https://doi.org/10.1016/j.joi.2017.12.004</a></p> <p><br>Hyland, K. E. (1996). Talking to the academy forms of hedging in science research articles [Publisher: SAGE Publications Inc.]. Written Communication, 13 (2), 251–281. <a href="https://doi.org/10.1177/0741088396013002004">https://doi.org/10.1177/0741088396013002004</a></p> <p>Ningrum, P. K., & Atanassova, I. (2023). Scientific Uncertainty: An Annotation Framework and Corpus Study in Different Disciplines. 19th International Conference of the International Society for Scientometrics and Informetrics (ISSI 2023). <a href="https://doi.org/10.5281/zenodo.8306035">https://doi.org/10.5281/zenodo.8306035</a></p> <p>Ningrum, P. K., & Atanassova, I. (2024). Annotation of scientific uncertainty using linguistic patterns. Scientometrics. <a href="https://doi.org/10.1007/s11192-024-05009-z">https://doi.org/10.1007/s11192-024-05009-z</a></p>
Fig. 21 in Solomon's Gold Mine: Description or redescription of 24 species of Caridina (Crustacea: Decapoda: Atyidae) freshwater shrimps from the Solomon Islands, including 11 new species
Fig. 21. Caridina poarae sp. nov. a. First pereiopod. b. Second pereiopod. c. Third pereiopod. d. Fifth pereiopod. e. Dactylus of third pereiopod. f. Dactylus of fifth pereiopod. g. Pre-anal carina. h. Uropodal diaeresis. i. Telson. j. Eggs. k. Cephalothorax. MNHN-IU-2018-2922 (a–k).
Fig. 18 in Solomon's Gold Mine: Description or redescription of 24 species of Caridina (Crustacea: Decapoda: Atyidae) freshwater shrimps from the Solomon Islands, including 11 new species
Fig. 18. Caridina piokerai sp. nov. a. First pereiopod. b. Second pereiopod. c. Third pereiopod. d. Fifth pereiopod. e. Dactylus of third pereiopod. f. Dactylus of fifth pereiopod. g. Pre-anal carina. h. Uropodal diaeresis. i. Telson. j. Eggs. k. Cephalothorax. MNHN-IU-2018-2900 (a–k).
Fig. 16 in Solomon's Gold Mine: Description or redescription of 24 species of Caridina (Crustacea: Decapoda: Atyidae) freshwater shrimps from the Solomon Islands, including 11 new species
Fig. 16. Caridina tupaia de Mazancourt, Marquet & Keith, 2019. Cephalothorax. MNHN-IU-2018 -2884.
Fig. 17 in Solomon's Gold Mine: Description or redescription of 24 species of Caridina (Crustacea: Decapoda: Atyidae) freshwater shrimps from the Solomon Islands, including 11 new species
Fig. 17. Caridina maeana sp. nov. a. First pereiopod. b. Second pereiopod. c. Third pereiopod. d. Fifth pereiopod. e. Dactylus of third pereiopod. f. Dactylus of fifth pereiopod. g. Pre-anal carina. h. Uropodal diaeresis. i. Telson. j. First male pleopod. k. Second male pleopod. l. Eggs. m. Cephalothorax. MNHN-IU-2018-2889: (a–i, m), MNHN-IU-2018-2891 (j–k) and MNHN-IU-2018-2895 (l).
Fig. 12. Caridina buehleri Roux, 1934. a. First pereiopod. b. Second pereiopod. c. Third pereiopod. d. Fifth pereiopod. e in Solomon's Gold Mine: Description or redescription of 24 species of Caridina (Crustacea: Decapoda: Atyidae) freshwater shrimps from the Solomon Islands, including 11 new species
Fig. 12. Caridina buehleri Roux, 1934. a. First pereiopod. b. Second pereiopod. c. Third pereiopod. d. Fifth pereiopod. e. Dactylus of third pereiopod. f. Dactylus of fifth pereiopod. g. Pre-anal carina. h. Uropodal diaeresis. i. Telson. j. Pre-anal carina. k. Eggs. l. Cephalothorax. MNHN-IU-2018-2845 (a–i, k), MNHN-IU-2015-20 (j) and MNHN-IU-2018-2846 (l).
Fig. 11 in Solomon's Gold Mine: Description or redescription of 24 species of Caridina (Crustacea: Decapoda: Atyidae) freshwater shrimps from the Solomon Islands, including 11 new species
Fig. 11. Caridina turipi sp. nov. a. First pereiopod. b. Second pereiopod. c. Third pereiopod. d. Fifth pereiopod. e. Dactylus of third pereiopod. f. Dactylus of fifth pereiopod. g. Pre-anal carina. h. Uropodal diaeresis. i. Telson. j. Eggs. k. Cephalothorax. MNHN-IU-2014-20883 (a–f, h, j–k), MNHN-IU-2014-20882 (g) and MNHN-IU-2014-20878 (i).
Fig. 10. Caridina typus H. Milne Edwards, 1837. a. First pereiopod. b. Second pereiopod. c. Third pereiopod. d. Fifth pereiopod. e in Solomon's Gold Mine: Description or redescription of 24 species of Caridina (Crustacea: Decapoda: Atyidae) freshwater shrimps from the Solomon Islands, including 11 new species
Fig. 10. Caridina typus H. Milne Edwards, 1837. a. First pereiopod. b. Second pereiopod. c. Third pereiopod. d. Fifth pereiopod. e. Dactylus of third pereiopod. f. Dactylus of fifth pereiopod. g. Preanal carina. h. Uropodal diaeresis. i. Telson. j. First male pleopod. k. Second male pleopod. l. Eggs. m. Cephalothorax. MNHN-IU-2018-2825 (a–c, e, h), MNHN-IU-2018-2842 (d, f), MNHN-IU-2018 -2826 (g, j–k), MNHN-IU-2018-2833 (i), MNHN-IU-2018-2832 (l) and MNHN-IU-2018-2824 (m).
Fig. 8. Caridina mertoni Roux, 1911. a. First pereiopod. b. Second pereiopod. c. Third pereiopod. d. Fifth pereiopod. e in Solomon's Gold Mine: Description or redescription of 24 species of Caridina (Crustacea: Decapoda: Atyidae) freshwater shrimps from the Solomon Islands, including 11 new species
Fig. 8. Caridina mertoni Roux, 1911. a. First pereiopod. b. Second pereiopod. c. Third pereiopod. d. Fifth pereiopod. e. Dactylus of third pereiopod. f. Dactylus of fifth pereiopod. g. Pre-anal carina. h. Uropodal diaeresis. i. Telson. j. First male pleopod. k. Second male pleopod. l. Eggs. m. Cephalothorax. n–o. Rostrum variations. MNHN-IU-2018-2817 (a–f, m), MNHN-IU-2018-2815 (h–i, l), MNHN-IU-2018-2816 (j–k), MNHN-IU-2017-2109 (n) and MNHN-IU-2018-2819 (g, o).
Fig. 3 in Solomon's Gold Mine: Description or redescription of 24 species of Caridina (Crustacea: Decapoda: Atyidae) freshwater shrimps from the Solomon Islands, including 11 new species
Fig. 3. Caridina barakoma sp. nov. a. First pereiopod. b. Second pereiopod. c. Third pereiopod. d. Fifth pereiopod. e. Dactylus of third pereiopod. f. Dactylus of fifth pereiopod. g. Pre-anal carina. h. Uropodal diaeresis. i. Telson. j. First male pleopod. k. Second male pleopod. l. Eggs. m. Cephalothorax. MNHN-IU-2014-20807 (a–i, l–m) and MNHN-IU-2014-20805 (j–k).
Fig. 6 in Solomon's Gold Mine: Description or redescription of 24 species of Caridina (Crustacea: Decapoda: Atyidae) freshwater shrimps from the Solomon Islands, including 11 new species
Fig. 6. Caridina choiseul sp. nov. a. First pereiopod. b. Second pereiopod. c. Third pereiopod. d. Fifth pereiopod. e. Dactylus of third pereiopod. f. Dactylus of fifth pereiopod. g. Pre-anal carina. h. Uropodal diaeresis. i. Telson. j. First male pleopod. k. Second male pleopod. l. Eggs. m–n. Rostrum variations. o. Cephalothorax. MNHN-IU-2014-20833 (a–g (top, with spine), h, l), MNHN-IU-2014-20836 (g (botom, without spine)), MNHN-IU-2014-20831 (i), MNHN-IU-2014-20829 (j–k), MNHN-IU-2014-20827 (m), MNHN-IU-2014-20837 (n) and MNHN-IU-2014-20826 (o).
Data for 'Formalizing Artisanal and Small-scale Gold Mining: a Grand Challenge of the Minamata Convention'
<p>Signatories to the Minamata Convention on Mercury with ‘more than insignificant’ artisanal and small-scale gold mining (ASGM) sectors are required to develop and implement National Action Plans (NAPs) to reform their ASGM sectors in line with Annexe C of the Convention. We compiled the budgets of available NAPs for reducing mercury emissions from ASGM sectors. As of 2021-12-31, these were available for 16 countries from: www.mercuryconvention.org/en/parties/national-action-plans. We used these data to estimate the approximate costs of expanding such approaches globally.</p>
Рис. 1. Карта-схема р. Амазар. Цифрами обозначены: I — места Αобычи россыпного зоΛота; II — участки иссΛеΑования в 2018–2019 гг.: 1 — реки Амазар и БоΛьшая Чичатка в районе пгт. Амазар, 2 — воΑохраниΛище, 3 — р. Крестовая, 4 — р. Амазар в нижнем течении Fig. 1. Schematic map of the Amazar River. Legend: I — placer gold mining areas; II — survey areas in 2018–2019: 1 — the Amazar and the Bolshaya Chichatka Rivers in the area of Amazar urban-type settlement, 2 — water storage reservoir, 3 — the Krestovaya River, 4 — the lower reaches of the Amazar River in Dynamics and current status of the Amazar River ichthyofauna after the construction of the PPM «Polyarnaya» hydroelectric complex
Рис. 1. Карта-схема р. Амазар. Цифрами обозначены: I — места Αобычи россыпного зоΛота; II — участки иссΛеΑования в 2018–2019 гг.: 1 — реки Амазар и БоΛьшая Чичатка в районе пгт. Амазар, 2 — воΑохраниΛище, 3 — р. Крестовая, 4 — р. Амазар в нижнем течении Fig. 1. Schematic map of the Amazar River. Legend: I — placer gold mining areas; II — survey areas in 2018–2019: 1 — the Amazar and the Bolshaya Chichatka Rivers in the area of Amazar urban-type settlement, 2 — water storage reservoir, 3 — the Krestovaya River, 4 — the lower reaches of the Amazar River
Linked collectors and determiners for: Solomon's Gold Mine: Description or redescription of 24 species of Caridina (Crustacea: Decapoda: Atyidae) freshwater shrimps from the Solomon Islands, including 11 new species.
Natural history specimen data linked to collectors and determiners held within, "Solomon's Gold Mine: Description or redescription of 24 species of Caridina (Crustacea: Decapoda: Atyidae) freshwater shrimps from the Solomon Islands, including 11 new species". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/5e1d0e63-c052-42fa-ba84-55f2166bfefd">https://bionomia.net/dataset/5e1d0e63-c052-42fa-ba84-55f2166bfefd</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/5e1d0e63-c052-42fa-ba84-55f2166bfefd">https://gbif.org/dataset/5e1d0e63-c052-42fa-ba84-55f2166bfefd</a>. Formatted as a Frictionless Data package.
Data from: Freshwater ecological quality assessment of the gold mining Mashcon watershed, Cajamarca - Peru
<p>These data were generated to investigate the aquatic community gradients across different types of anthropogenic impacts (reference, mining, rural and urban) and Andean environmental gradients (headwaters, midstream and downstream) in the Mashcon watershed. </p> <p>The macroinvertebrates' taxa abundance and abundance of traits modalities serve as biological values. The latter in combination with abiotic measurements of the freshwater habitats (i.e. physicochemical water quality and hydromorphology) constitute the ecological data.</p> <p>The values were obtained from river sediments (macroinvertebrates collection), water samples for laboratory analyses, field protocols and in-situ water quality measurements at 40 sites, wherein 6 were downstream of the gold mine's artificially recharged headwaters, 8 sites at near-pristine headwaters tributary streams, 14 sites at midstream rural areas and 12 sites at downstream urban areas (sample grouping information is shown in the Field_protocol.xlsx file).</p>
Data from: Limited biomass recovery from gold mining in Amazonian forests
<ol> <li>Gold mining has rapidly increased across the Amazon Basin in recent years, especially in the Guiana shield, where it is responsible for >90% of total deforestation. However, the ability of forests to recover from gold mining activities remains largely unquantified. </li> <li>Forest inventory plots were installed on recently abandoned mines in two major mining regions in Guyana, and re-censused 18 months later, to provide the first ground-based quantification of gold mining impacts on Amazon forest biomass recovery. </li> <li>We found that woody biomass recovery rates on abandoned mining pits and tailing ponds are amongst the lowest ever recorded for tropical forests, with close to no woody biomass recovery after 3-4 years. </li> <li>On the overburden sites (i.e. areas not mined but where excavated soil is deposited), however, aboveground biomass recovery rates (0.4 - 3.5 Mg ha<sup>-1</sup> yr<sup>-1</sup>) were within the range of those recorded in other secondary forests across the Neotropics following abandonment of pastures and agricultural lands. </li> <li>Our results suggest that forest recovery is more strongly limited by severe mining-induced depletion of soil nutrients, especially nitrogen, than by mercury contamination, due to slowing of growth in nutrient-stripped soils. </li> <li>We estimate that the slow recovery rates in mining pits and ponds currently reduce carbon sequestration across Amazonian secondary forests by ~21,000 t C yr<sup>-1</sup>, compared to the carbon that would have accumulated following more traditional land uses such as agriculture or pasture. </li> <li> <i>Synthesis and applications</i>. To achieve large-scale restoration targets, Guyana and other Amazonian countries will be challenged to remediate previously mined lands. The recovery process is highly dependent on nitrogen availability rather than mercury contamination, affecting woody biomass regrowth. The significant recovery in overburden zones indicates that one potential active remediation strategy to promote biomass recovery may be to back-fill mining pits and ponds with excavated soil. </li> </ol>
Data and code from: Investigating the Yanomami malaria outbreak: Gold mining and malaria
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Data from: Ecological resilience in a primate community affected by gold mining in Suriname
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Data from: Limited biomass recovery from gold mining in Amazonian forests
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Data from: Freshwater ecological quality assessment of the gold mining Mashcon watershed, Cajamarca - Peru
Open the record for dataset details and reuse information.
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