Dendrochronologia 30 (2012) 209211

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Dendrochronologia
journal homepage: www.elsevier.de/dendro

Technical note

TRiDaBASE: A stand-alone database for storage, analysis and exchange of dendrochronological metadata
Esther Jansma a,b,c, , Rowin J. van Lanen c , Kit Sturgeon d , Steve Mohlke d , Peter W. Brewer e
a

Cultural Heritage Agency (Rijksdienst voor het Cultureel Erfgoed), P.O. Box 1600, 3800 BP Amersfoort, The Netherlands Faculty of Geosciences, Utrecht University, P.O. Box 80.115, 3508 TC Utrecht, The Netherlands Netherlands Centre for Dendrochronology RING, P.O. Box 1600, 3800 BP Amersfoort, The Netherlands d The Epison Group, 505 Hector Street, Ithaca, NY 14850, USA e The Malcolm and Carolyn Wiener Laboratory for Aegean and Near Eastern Dendrochronology, B-48 Goldwin Smith Hall, Cornell University, Ithaca, NY 14853, USA
b c

a r t i c l e

i n f o

a b s t r a c t
Dendrochronological data formats in general offer limited space for recording associated metadata. Such information is often recorded separately from the actual time series, and often only on paper. TRiDaBASE has been developed to improve metadata administration. It is a relational Microsoft Access database that allows users to register digital metadata according to TRiDaS, to generate TRiDaS XML for uploading to TRiDaS-based analytical systems and repositories, and to ingest TRiDaS XML created elsewhere for local querying and analyses. 2012 Istituto Italiano di Dendrocronologia. Published by Elsevier GmbH. All rights reserved.

Article history: Received 18 February 2011 Accepted 4 September 2011 Keywords: Dendrochronology Metadata TRiDaS controlled vocabularies data exchange

Introduction Dendrochronological research of wood from the cultural heritage traditionally was directed at establishing its absolute age and origin, and was focused on single locations, objects and structures. But nowadays the research focus is shifting towards larger-scale studies, in order to answer questions about the former (cultural) landscape, climate, economy and the wood-processing industry (e.g., Bntgen et al., 2011). This shift is possible because during the last decades the size of the data collections managed at tree-ring laboratories has drastically increased. To facilitate the new research directions, we need to combine or digitally link these collections. This is complicated because the manner in which dendrochronological metadata is recorded differs widely between laboratories. In addition many laboratories only keep paper administrations of their measurement series descriptive and interpretative metadata (Fig. 1). Against this background the current challenge is to develop and facilitate international standards for digital data and metadata registration, in this manner maximizing the digital exchangeability and potential digital linking of dendrochronological (meta)data

collections. To this end we recently developed the Tree-Ring Data Standard TRiDaS (Jansma et al., 2010). The primary resource for the sharing of data is currently the International Tree Ring Databank (ITRDB, Grissino-Mayer and Fritts, 1997). Although this is a great resource for the sharing of data, it stores very limited metadata and requires improvement to meet the needs of the community (Briffa and Cook, 2008). To take full advantage of the benets offered by TRiDaS, existing dendrochronology tools (such as the ITRDB) clearly need to be updated. However, a logical rst step is to produce a tool to enable researchers to collate the disparate sources of information describing their own data. We therefore present a new standalone database to fulll this requirement. The TRiDaSenabled database described here allows researchers to integrate research records including references to external les, to generate TRiDaS XML for uploading to TRiDaS-enabled analytical systems and repositories, and to ingest TRiDaS XML created elsewhere for local querying and analyses. TRiDaBASE is available from the Digital Collaboration Platform for Dendrochronology (see http://www.uu.nl/vkc/dendrochronology) and the TRiDaS website (http://tridas.org/software).

Corresponding author at: Cultural Heritage Agency (Rijksdienst voor het Cultureel Erfgoed), P.O. Box 1600, 3800 BP Amersfoort, The Netherlands. Tel.: +31 6 25 00 00 55. E-mail address: e.jansma@cultureelerfgoed.nl (E. Jansma).

Requirements of the TRiDaS database With respect to dendrochronological metadata the new database should full the following requirements:

1125-7865/$ see front matter 2012 Istituto Italiano di Dendrocronologia. Published by Elsevier GmbH. All rights reserved. doi:10.1016/j.dendro.2011.09.002

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store dates and times according to the ISO standard required by TRiDaS. Another challenge is the fact that Access offers limited options for form layout and only allows the use of bitmaps. This poses limitations to the design of the user interface. We had to use minimal form layout and illustrations in TRiDaBASE in order to optimize its performance. Structure of the database TRiDaBASE consists of two separate parts. The data le TRiDaS Data.mdb contains the data, controlled vocabularies and rules for enforcing relationships between data entities. The application, TRiDaBASE.mdb, contains the user interface forms, programming code and rules for converting the data to and from TRiDaS XML. Because of this dual structure, the application can be updated while the data section of the system remains untouched.
Fig. 1. Paper archive containing research metadata at the Netherlands Centre for Dendrochronology RING. Photo RING 2008.

The data model The content of TRiDaBASE is organized according to the eight TRiDaS information levels: Project, Object, Element, Sample, Radius, MeasurementSeries, DerivedSeries and Values. Using our growing experience with the data model, we developed TRiDaS from version 1.1 (Jansma et al., 2010) to version 1.2.2. TRiDaBASE is based on this latest version. The technical details of TRiDaS 1.0 through 1.2.2 are available online (see the TRiDaS website at http://www.tridas.org). Safety measures TRiDaBASE is designed to help safeguard the users dataset. It is a fully normalized database and uses automatically generated (non-human readable) unique identiers, in this manner insuring relational integrity.1 The database does not allow multiple occurrences of unique information. TRiDaBASE follows the requirements of TRiDaS, in this manner insuring compatibility with TRiDaScompliant applications and software. The system detects actions of users that drastically change either the content (e.g., by deleting projects) or the structure (e.g., by changing the TRiDaS-based relationships between elds). It then warns the user and asks for conrmation of the action. Manual data entry TRiDaBASE uses navigation screens in which content can be lled in manually (Fig. 2). Research projects are lled in hierarchically, starting at the top level (project information) and working down towards the lowest metadata level, which contains metadata belonging to the values level of TRiDaS. Once the user leaves a specic level, the content of this level is saved automatically. At this point the system validates new content against the requirements of TRiDaS. In case of invalid content the system gives a warning and will refuse to close the level in which the user has been working. This means that content at odds with the TRiDaS data model will not be saved. Import and export functionality TRiDaBASE has extensive functionality for ingesting and exporting TRiDaS XML project les. To import data, users specify a single

1. It should operate on stand-alone PCs utilizing an operating system that is commonly used and widely available in the whole of Europe, in this manner allowing as many researchers as possible to use the database when and wherever they want. 2. It should be designed for the long term and in such a manner that changes to the database structure do not affect the content of the database. 3. It should be structured according to the structural levels of TRiDaS, allowing scientists to store detailed descriptions of their research projects and results as well as references to associated les (e.g., measurement series, chronologies, photos and video). 4. It should safeguard content that is essential for the long-term identication of specic content, such as project and sample identiers. 5. It should allow the manual entry of content, validate manually entered content against the requirements of TRiDaS and warn users if content is not valid. 6. It should import TRiDaS XML produced by TRiDaS-enabled facilities and export user-dened selections into valid TRiDaS XML which can be uploaded to such facilities. 7. For metadata elds where TRiDaS requires the use of controlled vocabularies, it should force the use of these vocabularies; in addition it should offer users the opportunity to import and export locally developed controlled vocabularies. 8. It should enable users to query the content for metadata analyses. TRiDaBASE architecture Operating system and software TRiDaBASE is developed in Microsoft Access, because this functionality is commonly accepted and easily available to most Windows users. Creating advanced database functionality using Access is challenging due to the specics of the software. TRiDaBASE was developed in the USA for rst use in Europe and we encountered several problems arising from regional differences between time/date notation. Access uses the locale of the Windows operating system that it is running on to determine how to store time and date values. Date and time values entered on computers in different countries are therefore not directly comparable. Visual Basic for Applications code was required to force Access to consistently

Human readable identiers can also be used (e.g. local laboratory identiers).

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Discussion TRiDaBASE has been developed using Microsoft Access because this functionality is easily available and commonly known to Windows users. However, this feature also limits TRiDaBASE to Windows based computers, Microsoft Ofce functionality, and users with Microsoft Ofce licenses. In order for TRiDaBASE to reach its full potential, future versions of this application should be platform independent, license free, and easily accessible through the internet. Also, in its present form TRiDaBASE does not contain queries that allow for local analysis of its content. However, the database structure is open source and all users can add functionality locally. We expect that users may want to develop queries for producing, among others, overviews of wood species, object types and dates (and combinations thereof), and for automated project-based research reports. The Digital Collaboration Platform for Dendrochronology (http://www.uu.nl/vkc/dendrochronology), through which TRiDaBASE is distributed, is available as a platform for query exchange. Conclusion TRiDaBASE is a publicly available metadata-registration application designed especially for tree-ring research. It is a Microsoft Access database for digital metadata registration and for the exchange of metadata and controlled vocabularies using XML. TRiDaBASE meets all requirements of the TRiDaS data model and is exible enough to work with non-TRiDaS controlled vocabularies. It operates on stand-alone PCs and by means of strict safety measures protects its content. The structure of TRiDaBASE allows content to be queried. The structure of TRiDaBASE supports future adaptations to new versions of the TRiDaS data model. Acknowledgements The development of TRiDaBASE was funded by The Netherlands Organization for Scientic Research (NWO), section Humanities, as part of the medium investment project Digital Collaboratory for Cultural Dendrochronology (DCCD). TRiDaBASE was developed by the Epison Group (Ithaca, New York), who also supported the project nancially. References
Brewer, P., Murphy, D., Jansma, E., 2011. TRiCYCLE: a universal conversion tool for digital tree-ring data. Tree-Ring Research 67, 135144. Briffa, K., Cook, E., 2008. Tree rings proxy white paper: What are the sources of uncertainty in the tree-ring data: how can they be quantied and represented? In: Trieste 2008 Paleoclimate Uncertainties Workshop Final Report, NCDC, NOAA. Bntgen, U., Tegel, W., Nicolussi, K., McCormick, M., Frank, D., Trouet, V., Kaplan, J., Herzig, F., Heussner, K., Wanner, H., Luterbacher, J., Esper, J., 2011. 2500 years of european climate variability and human susceptibility. Science, doi:10.1126/science.1197175. Grissino-Mayer, H., Fritts, H., 1997. The international tree-ring data bank: an enhanced global database serving the global scientic community. The Holocene 7 (2), 235238. Jansma, E., Brewer, P., Zandhuis, I., 2010. TRiDaS 1.1: the tree-ring data standard. Dendrochronologia 28 (2), 99130.

Fig. 2. Screendump of TRiDaBASE; the left part shows the navigation panel, the right shows the form belonging to the project level of TRiDaBASE.

TRiDaS XML project le, and the content is then automatically placed in the relevant domains of the database. In combination with the TRiCYCLE universal dendro data conversion tool (Brewer et al., 2011), this functionality assists users to import and standardize existing metadata available in many dendro data formats. With data export the user denes the project that should be exported and the path and lename of the produced XML. TRiDaBASE then automatically converts the project content into valid TRiDaS XML. TRiDaBASE does not restrict import and export to dendrochronological content. It ingests and exports all relevant information, including project-related or even complete controlled vocabularies (if this is specied by the user). Controlled vocabularies If data sets are to be linked and made searchable across language boundaries, we need to start using standardized terminology for certain types of metadata. This is why TRiDaS prefers terms from (multi-lingual) controlled vocabularies and xed enumeration terms. Controlled vocabulary schemes are multi-lingual sets of predened terms in accepted thesauri. Enumeration terms are named values that (usually through identiers) behave as constants in language. TRiDaBASE enforces the use of TRiDaS controlled vocabularies and enumeration. TRiDaBASE also facilitates the use of non-TRiDaS vocabularies such as terminology developed in individual laboratories. These vocabularies can be placed in the vocabularies part of the system, after which users can make changes and add new terms. Because these vocabularies are not part of the TRiDaS data model they are not validated or enforced by TRiDaBASE. They can, however, be converted to TRiDaS XML, which enables researchers to exchange them. Creating queries TRiDaBASE allows users to create queries through the Microsoft Access query wizard, in design view, and using Structured Query Language (SQL).