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The SISAL webApp: exploring the speleothem climate and environmental archives of the world

Published online by Cambridge University Press:  30 August 2023

István Gábor Hatvani Open the ORCID record for István Gábor Hatvani [Opens in a new window] ,
Zoltán Kern Open the ORCID record for Zoltán Kern [Opens in a new window] ,
Péter Tanos ,
Micah Wilhelm ,
Franziska A. Lechleitner Open the ORCID record for Franziska A. Lechleitner [Opens in a new window]  and
Nikita Kaushal Open the ORCID record for Nikita Kaushal [Opens in a new window]
István Gábor Hatvani
Affiliation:
Institute for Geological and Geochemical Research, Research Centre for Astronomy and Earth Sciences, ELKH, Budapest, Budaörsi út 45, H-1112, Hungary CSFK, MTA Centre of Excellence, Budapest, Konkoly Thege Miklós út 15-17., H-1121, Hungary
Zoltán Kern
Affiliation:
Institute for Geological and Geochemical Research, Research Centre for Astronomy and Earth Sciences, ELKH, Budapest, Budaörsi út 45, H-1112, Hungary CSFK, MTA Centre of Excellence, Budapest, Konkoly Thege Miklós út 15-17., H-1121, Hungary
Péter Tanos
Affiliation:
Department of Geology, Institute of Geography and Earth Sciences, ELTE, Budapest, Hungary
Micah Wilhelm
Affiliation:
Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
Franziska A. Lechleitner
Affiliation:
Department of Chemistry, Biochemistry and Pharmaceutical Sciences and Oeschger Centre for Climate Change Research, University of Bern, Switzerland
Nikita Kaushal*
Affiliation:
Exeter college, University of Oxford, United Kingdom
*
*Corresponding author: Nikita Kaushal; Email: [email protected]
Rights & Permissions [Opens in a new window]

Abstract

We present the ‘SISAL webApp’—a web-based tool to query the Speleothem Isotope Synthesis and AnaLysis (SISAL) database. The software provides an easy-to-use front-end interface to mine data from the SISAL database while providing the SQL code alongside as a learning tool. It allows for simple and increasingly complex querying of the SISAL database based on various data and metadata fields. The SISAL webApp version currently hosts SISALv2 of the database with 691 records from 294 sites, 512 of which have standardized chronologies. The SISAL webApp has sufficient flexibility to host future versions of the SISAL database, which may include allied speleothem information such as trace elements and cave-monitoring records. The SISAL webApp will increase accessibility to the SISAL database while also functioning as a learning tool for more advanced ways of querying paleoclimate databases. The SISAL webApp is available at http://geochem.hu/SISAL_webApp.

Keywords

SpeleothemsStable isotopesSQLDatabaseOnline application
Type
Thematic Set: Speleothem Paleoclimate
Information
Quaternary Research , Volume 118 , March 2024 , pp. 211 - 217
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Creative Commons
Creative Common License - CCCreative Common License - BY
This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0), which permits unrestricted re-use, distribution and reproduction, provided the original article is properly cited.
Copyright
Copyright © University of Washington. Published by Cambridge University Press, 2023

INTRODUCTION

Natural sedimentary archives are globally distributed and are valuable for local- to continental-scale assessment of past climate and environmental changes because they record the environmental conditions that prevailed during their formation (Williamson et al., Reference Williamson, Saros, Vincent and Smol2009; Birks et al., Reference Birks, Battarbee, Mackay and Oldfield2014). Speleothems are natural sedimentary archives formed of calcium carbonate and preserved in caves. Speleothems often have excellent age control (Fairchild and Baker, Reference Fairchild, Baker, Fairchild and Baker2012), are widely distributed in terrestrial regions around the world, and provide high-resolution records of past changes in climate and environment that are encoded mainly in carbon and oxygen isotopes (McDermott, Reference McDermott2004; Wong and Breecker, Reference Wong and Breecker2015) and trace elements (Fairchild and Treble, Reference Fairchild and Treble2009). SISAL (Speleothem Isotope Synthesis and AnaLysis) is a working group of the Past Global Changes (PAGES) project with the goal to provide a comprehensive compilation of speleothem records for climate reconstruction and model evaluation (Comas-Bru and Harrison, Reference Comas-Bru and Harrison2019).

The first version of the SISAL database, SISALv1 (Atsawawaranunt et al., Reference Atsawawaranunt, Comas-Bru, Amirnezhad Mozhdehi, Deininger, Harrison, Baker and Boyd2018), contained 381 speleothem records from 174 cave sites and was supported by publications on ways to use these data for data-model comparisons (Comas-Bru and Harrison, Reference Comas-Bru and Harrison2019) and regional interpretations of the isotopic records in the database (Kaushal et al., Reference Kaushal, Breitenbach, Lechleitner, Sinha, Tewari, Ahmad and Berkelhammer2018; Lechleitner et al., Reference Lechleitner, Amirnezhad-Mozhdehi, Columbu, Comas-Bru, Labuhn, Pérez-Mejías and Rehfeld2018; Braun et al., Reference Braun, Nehme, Pickering, Rogerson and Scroxton2019; Burstyn et al., Reference Burstyn, Martrat, Lopez, Iriarte, Jacobson, Lone and Deininger2019; Deininger et al., Reference Deininger, Ward, Novello and Cruz2019; Kern et al., Reference Kern, Demény, Perşoiu and Hatvani2019; Oster et al., Reference Oster, Warken, Sekhon, Arienzo and Lachniet2019). The last published version of the database, SISALv2, encompassed 691 speleothem records from 294 sites (Comas-Bru et al., Reference Comas-Bru, Rehfeld, Roesch, Amirnezhad-Mozhdehi, Harrison, Atsawawaranunt and Ahmad2020a) and provided additional standardized chronologies that are essential for better age control, which is required for analysis based on multiple speleothem records (Bühler et al., Reference Bühler, Axelsson, Lechleitner, Fohlmeister, LeGrande, Midhun, Sjolte, Werner, Yoshimura and Rehfeld2022). Regional and/or temporal subsets of the SISALv2 database provided essential data for evaluating environmental response to climate events in time (Kukla et al., Reference Kukla, Ahlström, Maezumi, Chevalier, Lu, Winnick and Chamberlain2021; Parker and Harrison, Reference Parker and Harrison2022), evolution of climate phenomena in a spatial domain (Parker et al., Reference Parker, Harrison, Comas-Bru, Kaushal, LeGrande and Werner2021; Gorenstein et al., Reference Gorenstein, Prado, Bianchini, Wainer, Griffiths, Pausata and Yokoyama2022), data-model comparisons (Bühler et al., Reference Bühler, Roesch, Kirschner, Sime, Holloway and Rehfeld2021, 2022), improved interpretations of speleothem data (Treble et al., Reference Treble, Baker, Abram, Hellstrom, Crawford, Gagan and Borsato2022), or improved assessment of the robustness of spectral analysis of unequally spaced sedimentary proxies with chronological uncertainty (Hatvani et al., Reference Hatvani, Tanos, Mudelsee and Kern2022). A third version of the database, SISALv3, is currently being compiled and will be made available to the public in 2023. The new database will also contain Mg/Ca, Sr/Ca, Ba/Ca, U/Ca, P/Ca, and Sr isotope records (Kaushal et al., Reference Kaushal, Wilhelm, Lechleitner, Braun, Rehfeld, Gabor Hatvani and Tanos2023). With this new version of the database, it will be possible to explore the global significance of trace-element signatures in speleothems systematically, and to refine climatic interpretations gained from the stable isotope records.

While the SISAL database is clearly useful for the climate community, additional applications and new scientific results can be achieved by effectively facilitating broader access to the database (Kaushal et al., Reference Kaushal, Comas-Bru, Lechleitner, Hatvani and Kern2021). At the moment, the SISAL database is hosted as an SQL file or multiple *.csv files that are linked together by identification numbers. These formats require the use of software such as MySQL, R, Python, or MATLAB to query the database. In addition, there has been a tremendous increase in the number of paleoclimate databases and in their use for research purposes over the last 10 years (Sundqvist et al., Reference Sundqvist, Kaufman, McKay, Balascio, Briner, Cwynar and Sejrup2014; PAGES2k Consortium, 2017; Konecky et al., Reference Konecky, McKay, Churakova, Comas-Bru, Dassié, DeLong and Falster2020; Kukla et al., Reference Kukla, Ahlström, Maezumi, Chevalier, Lu, Winnick and Chamberlain2021). Because researchers need to learn how to use such databases to address scientific questions at hand, and further how to appropriately query databases to get accurate datasets for analysis, we created the SISAL webApp in order to fill these knowledge gaps.

The paper aims to (1) describe the architecture of the SISAL webApp, (2) provide instructions on the logic by which databases can be mined for required data, and (3) provide accompanying SQL output code the user can build on the basic functionalities of the SISAL webApp by using a tool like MySQL to directly mine the database.

DESIGN

The SISAL webApp's architecture is based on the SISALv2 SQL database (Comas-Bru et al., Reference Comas-Bru, Atsawawaranunt and Harrison2020b). The SISAL Query Server, written in JavaScript using the node.js code library, is responsible for the database operations. The web interface accessible to users is served by the SISAL Query Client, which also is written in JavaScript and relies on the React.js code library. This architecture allows users to query the SISALv2 database using the most popular web browsers supporting ES5 methods (e.g., Google Chrome, Safari, Microsoft Edge, Mozilla Firefox) by specifying a few parameters. The graphical user interface created allows this without the user having to generate SQL code (Fig. 1). The SISALv2 database, the SISAL Query Server, and the SISAL Query Client are hosted on the severs of the Research Centre for Astronomy and Earth Sciences, Eötvös Loránd Research Network, Budapest, Hungary. We plan an update of the SISAL webApp to the SISALv3 database after its release.

Figure 1. Architecture of the SISAL webApp.

FEATURES

The SISAL webApp offers two types of querying. Basic querying, in which the SISALv2 database can be explored based on site name, geographical information, and/or temporal constrains. Basic querying provides the user with the metadata of the queried speleothem records, their sample data (δ 18O and δ 13C), and dating information, both the original author-generated chronology and seven SISAL-generated standardized chronologies (lin_interp_age, lin_reg_age, Bchron_age, Bacon_age, OxCal_age, copRa_age, StalAge_age) derived by different approaches for age–depth modeling (Amirnezhad-Mozhdehi and Comas-Bru, Reference Amirnezhad-Mozhdehi and Comas-Bru2019; Comas-Bru et al., Reference Comas-Bru, Harrison, Werner, Rehfeld, Scroxton and Veiga-Pires2019; Rehfeld et al., Reference Rehfeld, Roesch, Comas-Bru and Amirnezhad-Mozhdehi2020). The second type of querying supported by the SISAL webApp is the Advanced querying option through which database information can be extracted based on number of available radiometric ages and sample data resolution.

As an additional feature, the SISAL webApp provides SQL codes to help the user get a deeper insight into how the database is queried. It is our intention to make the webApp a steppingstone in the usage of the SISAL database and other databases like it.

Basic querying

Step 1: determining the basic spatiotemporal constraints

Basic querying provides the tool to extract SISAL database information based on the most fundamental filters. After providing an email address (recommended for query logging purposes) the user can choose to query based on the name of the cave site or within spatial (e.g., latitude and longitude limits) and/or within temporal constraints (interp_age). At least one of the following “Filter types” must be correctly filled out.

Filter type 1. Site name (site_name).

Filter type 2. Latitude and longitude (from–to; default is global coverage values from −90° to 90° and from −180° to 180°). In the first column, the southern and western boundaries should be provided for latitude and longitude, respectively. Latitude in degrees decimal (N: +; S: −) and longitude in degrees decimal (E: +; W: −). Other formats are not accepted, in which case the SISAL webApp will return no results. If asking for global coverage, only the metadata are made available through the SISAL webApp. A secure feature does not allow the user to overload the server, therefore download is limited to 30,000 rows.

Filter type 3. interp_age (interpolated age from younger–older) according to the original author-generated age model expressed in years BP, where BP refers to “before present,” (present = AD 1950). For details see Atsawawaranunt et al. (Reference Atsawawaranunt, Comas-Bru, Amirnezhad Mozhdehi, Deininger, Harrison, Baker and Boyd2018, table S9) and the SISAL repository at University of Reading.

This first querying step will return a list of speleothem records, their site and entity metadata fulfilling the query criteria provided. The sites with the queried entities are shown on a map (OpenStreetMap contributors, 2023); clicking on the markers shows information on site_name, site_id, geology, and rock_age.

In addition, the user can choose from querying (1) only non-composite records (tick ‘Non-Composite’ checkbox), (2) only composite records (tick ‘Composite’ check-box), or (3) both non-composite and composite records (tick both ‘Non-Composite’ and ‘Composite’ check-boxes). The default is set to only non-composite records.

Step 2: selection based on the metadata

All records fulfilling the criteria set in Step 1 can subsequently be selected by checking the box next to the doi column header. Alternatively, the user can specify a subset of data to be extracted, based on criteria specified in the metadata (e.g., mineralogy; Fig. 3).

Figure 2. Basic querying first step illustrating the query options. Only Filter type 2 is used determining the geographical constraints as Lat: −10° to 10° and Lon: −50° to 15°. Note that temporal constraints (Filter type 3) must be used if one aims to use the advanced query options later.

Figure 3. Basic querying output information and selection of SISAL chronology/chronologies. The example shows the output using the setting shown in Figure 2. The entity_name Abissal (entity_id = 79) and the entity_name RN4 (entity_id = 220) speleothem records are selected with the Bacon_age SISAL chronology.

The original author-generated chronology is a default output, and the user of the SISAL webApp has to choose at least one SISAL chronology to be extracted for the queried record(s) under the ‘Select chronos’ section (Fig. 3). The alternative age–depth models (SISAL chronologies with corresponding uncertainties) were provided by SISAL (Amirnezhad-Mozhdehi and Comas-Bru, Reference Amirnezhad-Mozhdehi and Comas-Bru2019; Rehfeld et al., Reference Rehfeld, Roesch, Comas-Bru and Amirnezhad-Mozhdehi2020) for records that are not composites (i.e., time series based on more than one speleothem record) and which are 230Th/U dated (see Comas-Bru et al., Reference Comas-Bru, Atsawawaranunt and Harrison2020b). All the SISAL chronologies can be selected with the ‘Select all’ checkbox, or in any combination, for example asking only for the Bacon_age SISAL chronology (Fig. 3).

Step 3: data extraction

By pressing the blue download buttons at the bottom of the page the user can download the (1) metadata of the selected records (called EntityList.xlsx), (2) their dating information (called DatingInfo.xlsx), and/or (3) selected chronologies and the sample data (called SampleData.xlsx) in three separate files. In addition, the SQL codes are provided in a worksheet called ‘SQL query’ in each output file to help the user get a deeper insight into how the database is queried.

The extracted sample data are trimmed according to the temporal constraints if applied in ‘Filter type 3 (interp_age)', but the complete dating information table is given for the selected record(s). Note that interp_age (original author-generated age model expressed in years BP, where BP refers to “before present” with the present being AD 1950) is provided by default in the fifth column of the output file SampleData.xlsx.

Advanced querying

Advanced querying provides tools to extract SISAL database information based on the number of available radiometric ages and sample data resolution. In descriptive words, this option would be suitable for a query like “extract all data from Asia, covering the last 2,000 years BP, where each record has at least two radiometric age measurements over the 2,000 year period, and the sampling interval for isotopes is less than ten years between successive samples.” This option is available after Basic filtering when a corresponding list of records are received and selected. Note that if no temporal constraint is applied in the Basic querying, the Advanced query will search within full temporal coverage of the selected records.

In advanced querying, two filters can be applied and combined: (1) minimum number of radiometric ages for the chosen record(s) regarding the whole available time interval, or shorter if a filter is applied in the Basic querying part: first step (note that ages excluded by the original authors to develop the age-depth models [i.e., where date_used = no in the database] are not considered); and (2) maximum allowed ‘age gap’ given as number of years in the original chronology (interp_age), or in another chosen sisal_chronology, considering the whole available time interval, or shorter if a filter is applied in the Basic querying part: first step (i.e., a large age gap means either the sample resolution is coarse and/or the estimated duration of any hiatus in the record exceeds the given maximum allowed ‘age gap’ in the queried interval).

In an example, the Middle Holocene (5500–6500 yr BP) was queried globally (Fig. 4A), which provided 178 records. When the ‘Advanced query filter 1’ was chosen and at least three radiometric ages were required (Fig. 4B) from each entity from within the Middle Holocene, the number of records decreased to 30, with 6065 lines of sample data altogether. This querying took 23 seconds for the server to finish. When the advanced constraints were made stricter with only a maximum of 100 years allowed between consecutive sample dates in interp_age (interpolated age based on original_chronology) to exclude the coarse resolution records (Fig. 4C), the number of obtained records dropped to 15, with the querying taking 24 seconds. When only ‘Advanced query filter 2’ is used (Fig. 4D) the output is 66 entities with 6332 lines of sample data in 25 seconds.

Figure 4. Advanced querying examples. Temporal constraints are applied in the basic querying (A). Advanced query filter 1 (B), filter 2 (C) and both advanced query filters (D) are applied with the copRa_age SISAL chronology chosen to accompany the sample data in the advanced query output.

In all cases the output table (called advancedRes.xlsx) consists of six worksheets: (1) reportInfo with the SQL code of the selection of the records (Step 2; Fig. 3); (2) entityAdvFiltered with the list of records meeting the advanced criteria provided; (3) datingAdvFiltered with the corresponding radiometric ages; (4) chronoAdvFiltered with the sample data and the chosen SISAL chronology (in this case copRa_age; Fig. 4B–D); (5) SQLsAdvFiltered with the SQL code of the advanced querying; and (6) ‘entity,’ ‘dating,’ ‘chrono,’ and ‘SQLs’ worksheets with the list of entities, radiometric ages, sample data, and SQL code, respectively, provided by the basic querying (Fig. 4A).

COMMON ERROR MESSAGES AND THEIR BACKGROUND/SOLUTION

Most common errors are associated with basic querying. If no field is completed, the SISAL webApp will return: “None of the query's filter parameters are specified correctly! Please specify the site_name and/or Lat-Lon coordinates and/or interp_age interval and try again!”.

In general, the user should pay attention to using the proper formatting of the spatial constraints and use decimal degree units, otherwise the SISAL webApp will return the message: “The coordinates are incorrect or some are missing! Please revise the coordinates, and try again! Default is global coverage from −90° to 90° and from −180° to 180°.”

Secondly, the temporal constraints should follow the instructions given in this paper and the user manual (http://geochem.hu/SISAL_webApp). If the interp_age is provided incorrectly, the following error message is given: “The interp_age interval is incorrect or incomplete! Please revise the beginning (younger) and end (older) of the interval, and try again!”.

Advanced querying does not work without the Basic querying part being used and at least one entity selected in Step 2; otherwise, the following error message is returned: “Download request denied! Please select at least one entity!”.

Please note, in case of large output tables (maximum 30,000 rows), querying may take up to minutes.

SOFTWARE AVAILABILITY, FUTURE UPDATES, AND TERMS OF USE

The SISAL webApp is available at the Research Centre for Astronomy and Earth Sciences (http://geochem.hu/SISAL_webApp), and has been tested to work in all major browsers (e.g., Google Chrome, Safari, Microsoft Edge, Mozilla Firefox). SISAL is continuing to expand the global database by including new records and extended sets of data and metadata information. The SISAL webApp is intended to be able to perform more advanced querying on the most updated version of the SISAL database.

Planned updates include (1) the option to allow the user to pick the annual laminated samples; (2) replacing the current map output with an interactive alternative, that would allow the selection of the area of interest, while showing the cave sites and records; and (3) making the SISAL webApp capable of providing information on the mean sample resolution and mean chronological uncertainty, providing input data for immediate verification of inherent constraints for spectral analyses (e.g., CUSP (https://geochem.hu/CUSP/); Hatvani et al., Reference Hatvani, Tanos, Mudelsee and Kern2022) of the considered speleothem record(s).

The PAGES-SISAL project is a community-lead effort. This dataset is licensed by the rights-holder(s) under a Creative Commons Attribution 4.0 International License: https://creativecommons.org/licenses/by/4.0/. In order to assure traceability, any presentation, report, or publication that uses the SISALv2 database should cite the dataset (https://doi.org/10.17864/1947.256) along with the following publications: Atsawawaranunt et al. (Reference Atsawawaranunt, Comas-Bru, Amirnezhad Mozhdehi, Deininger, Harrison, Baker and Boyd2018), Comas-Bru et al. (Reference Comas-Bru, Harrison, Werner, Rehfeld, Scroxton and Veiga-Pires2019), and Comas-Bru et al. (Reference Comas-Bru, Rehfeld, Roesch, Amirnezhad-Mozhdehi, Harrison, Atsawawaranunt and Ahmad2020a). If the SISAL webApp is used for data extraction from the SISAL database, it is required to cite the webApp itself (http://geochem.hu/SISAL_webApp) and this paper (Hatvani et al., 2023; doi: 10.1017/qua.2023.39).

If using individual sites, the literature citations for published work provided in the database also should be cited. Contact information of data contributors of unpublished data is also provided, and these data contributors should be contacted when unpublished records are used on an individual basis. In addition, users are advised to verify which queried reference reports the particular record downloaded, because for example, oxygen and carbon stable isotope records from the same stalagmite may be published in different papers.

Acknowledgments

This study was undertaken by SISAL (Speleothem Isotopes Synthesis and AnaLysis), a working group of the Past Global Changes (PAGES) project, which in turn receives support from the Swiss Academy of Sciences and the Chinese Academy of Sciences. The PAGES Data Stewardship Scholarship (DSS_108) also supported this work. We thank SISAL members who contributed their published data to the database and provided additional information when necessary. Authors also thank the IT team of the RCAES, namely Evelin Bányai for installing the app on servers. We are also grateful to the SISAL Phase 2 Steering Committee for help in debugging the app. This is contribution No. 85 of the 2ka Palæoclimatology Research Group. The first author dedicates this paper to the memory of his beloved grandmother, Marta Chiovini (1928–2023).

Author contributions

I.G.H conceived the idea and designed the app with P.T. P.T. developed the app with input from Z.K. and I.G.H. I.G.H. produced the figures. I.G.H and Z.K wrote the paper, with contributions from N.K., T.P., F.L., and M.W. All authors have read and agreed to the published version of the manuscript and helped in the debugging and final development of the app.

Footnotes

†

Authors have contributed equally to the work.

References

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Figure 0

Figure 1. Architecture of the SISAL webApp.

Figure 1

Figure 2. Basic querying first step illustrating the query options. Only Filter type 2 is used determining the geographical constraints as Lat: −10° to 10° and Lon: −50° to 15°. Note that temporal constraints (Filter type 3) must be used if one aims to use the advanced query options later.

Figure 2

Figure 3. Basic querying output information and selection of SISAL chronology/chronologies. The example shows the output using the setting shown in Figure 2. The entity_name Abissal (entity_id = 79) and the entity_name RN4 (entity_id = 220) speleothem records are selected with the Bacon_age SISAL chronology.

Figure 3

Figure 4. Advanced querying examples. Temporal constraints are applied in the basic querying (A). Advanced query filter 1 (B), filter 2 (C) and both advanced query filters (D) are applied with the copRa_age SISAL chronology chosen to accompany the sample data in the advanced query output.