More and more aspects of the research data life cycle involve some form of sharing – be it the protocols used to generate the data, the software to analyze it, metadata about the data, the data itself or other aspects of its life cycle, from ethical review to citizen science. This talk zooms in on some examples in different stages of different data life cycles and explores how the changing dynamics of data sharing interact with the dynamics of doing research more generally. The presentation will be given on the basis of https://github.com/Daniel-Mietchen/events/blob/master/3rd-BEXIS-2-User-and-Developer-Conference.md .
Nearly 10 years ago the first version of the Biodiversity Exploratories Information System (here BExIS1) was going online to act as data management platform and information system for the SPP 1374 “Biodiversitäts-Exploratorien” (BE). It was constantly developed over time and thereby many functionalities were strongly related to the design of the BE. The development of BEXIS2 was initiated due to make BExIS1 more generic, modular and extensible. To achieve this, several fundamental changes were made. Furthermore the development concentrates on the data-management functionalities. To make a successful switch to BEXIS2 inside the BE all existing functionalities of BExIS1 should be present. Even though the majority of BExIS1 functionalities are newly developed, there is still a lack of functionalities in BEXIS2. Some are related to basic functions and already in progress like a person/project management system, a dataset access request workflow, the integration of publication management, and a data quality management component. Other features are more specific and partly deeply BE related. This are features like species information extraction, Darwin core archive generation, data visualization, webGIS, and climate station data integration. Additionally the migration process involves transfer of data from one system to another. Here we will present the current state of migration.
Party package is not only managing all the entities as People, Projects, Organisations and etc., but also managing the relationships between them with specific rules. Furthermore, party package is able to connect to the other modules. Security module is now connected to it, storing extra information of each account.
Friederike Klan and Alsayed Algergawy
Within the Collaborative Research Centre AquaDiva we developed a semantic search component that provides access to both structured BExIS 2 datasets and to unstructured data in terms of scientific publications. A specifically tailored domain ontology provides the fundamental concepts for the description of observational research data and publications as relevant for the AquaDiva project. It is complemented by selected subsets of biomedical ontologies that define required domain-specific concepts. A data annotation scheme establishes the required link between the different data sources and the conceptual layer. On top of this, we implemented a prototype semantic search for the BExIS 2 system that allows for the integrated retrieval of heterogeneous data. In our presentation, we will demonstrate the capabilities of the search component and will explain the basic techniques behind it.
Jitendra Gaikwad (FSU Jena), Martin Hohmuth (FSU Jena), Bassem Bouaziz (Sfax, Tunisia), Birgitta König-Ries (FSU Jena)
In recent times, there has been tremendous advances in technologies for the creation of different kinds of multimedia data. Also, they have become more powerful and at the same time affordable. In the field of biodiversity science, multimedia data contained in various media formats such as images acquired from satellites, images-videos captured in camera traps and audios from acoustic monitoring is playing a crucial role in facilitating research agendas. However, the ability to efficiently store and effectively retrieve multimedia data lacks behind. Mainly, it is stored in file systems and access requires familiarity with the data and the storage structure. This hampers usage and in particular reuse of this data significantly and slows scientific progress. In the MAMUDS (Managing Multimedia Data for Science) project, we are developing a multimedia data management and content-based retrieval system geared towards biodiversity science, which will be integrated as a module into the open source research data management platform BEXIS 2. In this presentation we will demonstrate the workflows and protocols developed for integrating the multimedia data management system with BEXIS2.
Nearly 10 years ago the first version of the Biodiversity Exploratories Information System (here BExIS1) was going online to act as data management platform and information system for the SPP 1374 “Biodiversitäts-Exploratorien” (BE). It was constantly developed over time and thereby many functionalities were strongly related to the design of the BE. The development of BEXIS2 was initiated due to make BExIS1 more generic, modular and extensible. To achieve this, several fundamental changes were made. Furthermore the development concentrates on the data-management functionalities. To make a successful switch to BEXIS2 inside the BE all existing functionalities of BExIS1 should be present.Currently a couple of functionalities are already developed and will be presented. It involves fieldwork management related features like resource booking management, and the plot map management. Further features are related to event management, information/document sharing, land use intensity calculation, and dataset overview computation. The development followed the more generic, modular and extensible approach. Therefore these modules are adaptable to project specific needs and could be of interest for other BEXIS2 users.
BEXIS2 contains different types of data, e.g. dataset – metadata and primary data. But based on the data policy, such data may not be accessible to certain users. If those would like to get access, one option is to contact the administrator(s) and ask for permission. But that would be a cumbersome task for the administrator(s). Therefore, BEXIS2 offers a request management system to facilitate the data sharing among the users of the system.
There are numerous workflows where it is necessary to send notifications (email or sms). For example, the user forgot his/her password. In that case, there must be a way for the user to reset the password without contacting the administrator. Indeed, there are not only “security”-related workflows like that short example, but also more “data”-related scenarios, e.g. inform the owner of the dataset after a request was made. BEXIS2 provides a template-based notification system to cover most of such cases. Yet, it is only possible to send emails.
We replace our current authentication framework with a partial tailor-made implementation of ASP.NET Identity 3. So, we hope to improve the performance and stability of the system administration module. There are a lot of different authentication providers we can use now, e.g. Google, Facebook or ORCID. Additionally, we don’t have to code so much functions anymore, because the logic is already there – and we can rely on that.
The online access to the user manuals via the main application menu has been an important feature of BEXIS 2. While modifying modules or developing new ones, reflecting the changes in the user manuals is a must. These manuals are of HTML format, which can be edited directly but not in a straight forward manner. Instead, a more common and much easy way for creating the user manuals, including images, tables, etc., is the use of a word processor. We introduce a new converting tool that is able to read a user manual in DOCX format, convert it to HTML format and send it automatically into the expected place inside the software code.
VAT is a system for Visualizing, Analyzing and Transforming spatio-temporal data. It consists of a distributed back end for low-latency processing and a web front end that allows creating computational workflows in an exploratory fashion. Users have access to data sets from public repositories like GFBio and GBIF, and can also upload their own data. The results of workflows are visualized as map layers in the front-end. Lineage and citations are automatically tracked in the background and bundled together with the results for data export.
Ecology has become a very data intensive science. Data is made available via online platforms and research networks and data today is shared to an ever growing degree. New policies of funding agencies further support that by requiring the curation of data and its publication after the funding period. Fining data in a database is frequently supported by full text search on metadata. The limitations of a full text search renders the search very inefficient (e.g. lack support for synonyms, homonyms or spelling variants to augment the search keywords). Faceted navigation is another strategy which can assists the discovery of data and which can be combined with a full text search. The main challenge with a faceted navigation is the development of a suitable vocabulary which can be used to annotate the data efficiently. We developed a vocabulary supporting faceted navigation which has been specifically tailored to describe ecological data. We showcase the vocabulary and a web application which has been designed to help with the annotation process.
BEXIS is an open and modular platform for research data management. With the release of 2.11 we open its modular power to the public so that every interested institution or individual is able to develop and deploy its own modules on BEXIS. Modules can be shared and installed on running BEXIS instance. Their life cycle also can be easily managed. In this talk, we introduce the procedures to develop, bundle, and deploy a module.