Specimens form the falsifiable evidence used in plant systematics. Derivatives of specimens (including the specimen as the organism in the field) such as tissue and DNA samples play an increasing role in research. The EDIT Platform for Cybertaxonomy is a specialist's tool that allows to document and sustainably store all data that are used in the taxonomic work process, from field data to DNA sequences. The types of data stored can be very heterogeneous consisting of specimens, images, text data, primary data files, taxon assignments, etc. The EDIT Platform organizes the linking between such data by using a generic data model for representing the research process. Each step in the process is regarded as a derivation step and generates a derivative of the previous step. This could be a field unit having a specimen as its derivative or a specimen having a tissue sample as its derivative. Each derivation step also produces meta data storing who, when and how the derivation was done. The Platform's Common Data Model (CDM) and the applications build on the CDM library thus represent the first comprehensive implementation of the largely theoretical models developed in the late 1990ies (Berendsohn et al. 1999). In a pilot project research data about the genus Campanula (Kilian et al. 2015, FUB, BGBM 2012) was gathered and used to create a hierarchy of derivatives reaching from field data to DNA sequences. Additionally, the open source library for multiple sequence alignments LibrAlign (Stöver and Müller 2015) was used to integrate an alignment editor into the EDIT platform that allows to generate consensus sequences as derivatives of DNA sequences. The persistent storage of each link in the derivation process and the degree of detail on how the data and meta data are stored will speed up the research process, ease the reproducibility of research results and enhance sustainability of collections.
We present the model and implementation of a workflow that blazes a trail in systematic biology for the re-usability of character data (data on any kind of characters of pheno- and genotypes of organisms) and their additivity from specimen to taxon level. We take into account that any taxon characterization is based on a limited set of sampled individuals and characters, and that consequently any new individual and any new character may affect the recognition of biological entities and/or the subsequent delimitation and characterization of a taxon. Taxon concepts thus frequently change during the knowledge generation process in systematic biology. Structured character data are therefore not only needed for the knowledge generation process but also for easily adapting characterizations of taxa. We aim to facilitate the construction and reproducibility of taxon characterizations from structured character data of changing sample sets by establishing a stable and unambiguous association between each sampled individual and the data processed from it. Our workflow implementation uses the European Distributed Institute of Taxonomy Platform, a comprehensive taxonomic data management and publication environment to: (i) establish a reproducible connection between sampled individuals and all samples derived from them; (ii) stably link sample-based character data with the metadata of the respective samples; (iii) record and store structured specimen-based character data in formats allowing data exchange; (iv) reversibly assign sample metadata and character datasets to taxa in an editable classification and display them and (v) organize data exchange via standard exchange formats and enable the link between the character datasets and samples in research collections, ensuring high visibility and instant re-usability of the data. The workflow implemented will contribute to organizing the interface between phylogenetic analysis and revisionary taxonomic or monographic work. Database URL : http://campanula.e-taxonomy.net/
Several applications currently developed in our group and by our cooperators deal with multiple sequence alignments (MSA) or associated raw and meta data, and allow the user to view and edit it in a graphical user interface (GUI). Instead of implementing independent solutions for these different tasks, we decided to create a library containing powerful and reusable common GUI components. Since this library is open source (GNU GPL 3) it can be used and extended by other researchers, who are then able to focus on the core functionality of their applications, but can still provide a user-friendly GUI. Besides components allowing the displaying and editing of MSAs, several types of data (e.g. trace files, comments, statistical sequence information, positions of tandem repeats, hairpins or inversions) can be attached either to single sequences or to the alignment as a whole. All these data views implement a common interface that makes it easy for developers to create new custom views. Several components from our library (e.g. displaying different types of data) can be connected to each other in the application they are embedded in, so that the user can scroll through one of them while all others will automatically display the data associated with the current position. LibrAlign is fully interoperable with the BioJava API and all components are provided in a native Swing and a native SWT version (the two major GUI frameworks for Java), so that they can be integrated into any Java GUI application, including projects based on the Eclipse Rich Client Platform or Bioclipse. Several software projects based on LibrAlign are currently in development in- and outside our group. Among those are (i) the Taxonomic Editor of the EDIT platform which is extended to support sequence and alignment associated data for the Campanula portal of EDIT, (ii) a new version of the alignment editor PhyDE, (iii) AlignmentComparator (an application to visualize differences between alternative automatic and manual alignments, which we currently use in study investigating the influence of manual alignment corrections on phylogenetic studies), and (iv) HIR-Finder (an application which locates microstructural mutations like tandem repeats possibly associated with hairpins). LibrAlign download: http://bioinfweb.info/LibrAlign http://www2.ieb.uni-muenster.de/EvolBiodivPlants/en/Publications/ConferenceContribution?id=93978