Purpose of Morph·D·Base
The comparative approach takes in a central role in biological methodology and is fundamental to morphology. The essential prerequisite for its applicability is comparability and communicability of data. Unfortunately, morphology currently suffers from fundamental conceptual and methodological problems hat result from
- the lack of a commonly accepted, standardized, taxon-independent morphological terminology that is free of homology assumptions,
- the lack of a commonly accepted standardized and formalized method for describing morphological traits, and
- the lack of a rationale for the delimitation of morphological units.
We call this family of problems the Linguistic Problem of Morphology.
In order to establish comparability and communicability for morphological data, not only data production has to be made transparent and reproducibley by providing a detailed documentation of all the material, methods, and techniques applied (i.e. morphological metadata). It furthermore requires the development of a specialized and highly standardized and formalized method and language for conducting morphological descriptions (i.e. morphological data s. str.). This requires the standardization of both morphological data and metadata.
The need for standardization of data and metadata has been recognized throughout different disciplines in biology – except for morphology. The goal of our project and approach is to improve the quality of morphological data in two distinct ways:
- By providing with Morph·D·Base an online platform that takes in a central function as an integral tool for
- detailed documentation of all kinds of relevant metadata according to modern standards (e.g., Darwin Core), including information referring to specimens, taxonomy, literature, and general biology, together with the possibility to store and interlink various kinds of media material,
- managing and facilitating the generation of a combined morphological character matrix,
- enabling a convenient and manageable use of traditional glossaries in character matrices, and
- providing the possibility to differentially link all relevant metadata (i.e., specimens, literature, general biology, and media) to each matrix entry individually.
- By providing with MorphOntology a web ontology language (OWL) ontology that will, when implemented in Morph·D·Base, not only supply a taxon-independent and homology free morphological terminology, but also a formalized and standardized method of description. This new method of description will significantly increase comparability and communicability of morphological data and therewith solve the Linguistic Problem of Morphology.
History of Morph·D·Base
The basic idea for Morph·D·Base emerged during the PhD project of Lars Vogt (2000-2002 at the University of Bielefeld) in the context of the project "Methods of simultaneous weighting of molecular and morphological characters for phylogenetic analyses using Arenicolidae (Annelida) as example", which was funded by the German Research Foundation. The PhD project revealed conceptual and methodological deficiencies of morphological data in phylogenetics and a lack of transparency and reproducibility of morphological data production. Morph·D·Base started as the convinced belief in the requirement of a tool that would enable several morphologists to continuously work on a data matrix, which is directly linked to its underlying descriptions, while the descriptions at their turn are understood as the actual morphological data.
Between 2002 and 2003 the theoretical work and discussions with Wilko Ahlrichs, who reported from his experiences and problems with a growing and frequently changing data matrix for Rotatoria, resulted in the conviction that character matrices per se cannot surmount the problems of morphological characters. Instead, it is necessary to record and document morphological descriptions (i.e. morphological data) within a data base, just like DNA sequences in
Since in any morphological structure the same fundamental aspects can be differentiated and since they have the potential to separately change during evolution, they should be systematically distinguished in descriptions. Thus, morphological descriptions should be differentiated into biological and cognitive categories. These categories represent the basic descriptive dimensions of every morphological structure (compared to the two dimensions of nucleotide data: nucleotide type at a specific sequence position and its neighboring positions). Thus, already in 2003 the basic conception of Morph·D·Base existed.
In the process of preparing for a practical course at the Free University of Berlin (Morphological and molecular Character Analysis of Echinodermata), which was aimed at communicating the problems of morphological characters in phylogenetics and the difficulty of producing good (i.e. transparent and preferably reproducible) morphological descriptions, Lars Vogt and Peter Grobe discussed the idea of Morph·D·Base. Peter Grobe was immediately enthusiastic and suggested to program a real data base on the basis of these ideas. This data base was first used and tested during the practical course at the Free University of Berlin.
Part of the German Priority Program "Deep Metazoan Phylogeny"
In 2004 we suggested Morph·D·Base to provide the integrative tool for morphologists within the priority program "Deep Metazoan Phylogeny" of the German Research Foundation (DFG - SPP 1174) that was in the final stage of planning. In this priority program, Morph·D·Base provides the web platform not only for storing and documenting morphological data but also for collaborating, sharing information and discussing structures and their possible interpretations in terms of character and character state hypotheses. In October 2004 Lars Vogt handed in the proposal for the provision of a grant and in 2005 it got funded by the German Research Foundation.
In February 2006 we (Lars Vogt & Peter Grobe) organized a first workshop to present and give an introduction to the alpha version of Morph·D·Base. We received a lot of positive feedback and fair comments. We used the critics and particularly improved the interface and design with respect to handling and intuitive usability. Moreover, we complemented some of the features with additional input fields and implemented AJAX for some of the interface functions. Since February 2006, we were working hard on the final design of the web interface, the actual HTML programming and its connection to the data base. Finally, in September 2006 the first beta version went online. This beta version allows uploading of media files (bitmap and vector graphics, audio and movie files) and specimen entries. Furthermore, users can complement the ITIS taxonomy and nomenclature that was incorporated into Morph·D·Base by creating new taxon entries.
First Online Version
On October, 25th. 2006 we announced the first working online version of Morph·D·Base. It contains the working modules Specimen, Taxa, and Media as well as a Taxonomy browser.
Since optimization of the HTML interface of Morph·D·Base for various browser programs (e.g., Firefox, Microsoft Internet Explorer, Safari, Opera) consumes a lot of time, in which new modules could be developed and implemented, we decided for the first version of Morph·D·Base to optimize the interface only to the Mozilla Firefox browser. After we attended several conferences and symposia and gathered feedback from scientists all over the world, who criticized the limited accessibility of Morph·D·Base we realized that we had to make Morph·D·Base browser compatible.
Another complaint, which addresses a problem of many currently available biological online data bases, was that information that is actually interlinked (e.g., specimen information and images of the specimen) had to be uploaded in separate HTML pages (e.g., specimen information through a “Specimens” page and image files and their annotations through a “Media” page). When uploading data it would thus be very convenient to be able to switch back and forth between for example a specimen entry and a media entry and every change the user makes is immediately saved, which was not possible with the HTML interface of the first version. Thus, besides making Morph·D·Base browser compatible we also decided to improve our interface design.
Morph·D·Base Version 2
Morph·D·Base Version 2.0 also contains two new modules: 1) the possibility to reference various bits of information to an internal literature data base and 2) the possibility to generate a character matrix, in which each matrix entry can be linked to relevant specimen, media, literature, and taxon entries in Morph·D·Base.
|Development||Lars Vogt & Peter Grobe|
|Data base structure,
|Web design||Peter Grobe & Lars Vogt|
This website was prepared in the context of the Morph·D·Base project and funded by the German Research Foundation (DFG). The statements, finding, conclusions, and recommendations are those of the authors and users of Morph·D·Base and do not necessarily reflect the views of the German Research Foundation.
The Morph·D·Base web portal is hosted by the Zoological Research Museum Alexander Koenig
All accessible information on Morph·D·Base can be used for private, education, research or other non-commercial purposes for free, provided that the source and the copyright holder are cited. Any commercial use requires consent from the copyright holder. Contributors to Morph·D·Base agree to these terms.
Zoological Research Museum Alexander Koenig
- Leibniz-Institute for Animal Biodiversity -
Foundation under public law
53113 Bonn, Germany
Tel.: +49 (0)228 9122 255
Tax ID No.: DE308022782
Responsible Surveillance Authority
Ministerium für Kultur und Wissenschaft des Landes Nordrhein-Westfalen
Völklinger Str. 49, 40221 Düsseldorf
|German Research Foundation||Zoological Research Museum Alexander Koenig||University Bonn|
This data protection declaration clarifies the type, scope and purpose of the processing of personal data within the Morph·D·Base web portal. With regard to the terms used, such as "personal data" or their "processing", we refer you to the definitions in Art. 4 of the General Data Protection Regulation (DGPR).
Zoological Research Museum Alexander Koenig
Leibniz-Institute for Animal Biodiversity
Foundation under public law
You have the right to request a copy of all personal data stored about you and to request the deletion or correction of these data. The request can be send to the Biodiversity Informatics section of ZFMK (address see below) or via email to ZFMKdatacenter@leibniz-zfmk.de. Details on your rights to access, correct and delete your personal data are described in paragraphs 6, 7, 8, and 9 of this document.
1. Collection and processing of personal data
The Morph·D·Base portal serves as a data repository for morphological data in biological research. It provides researchers with online tools for managing their research data and for preparing, editing and cooperating on data publications. Therefore, the portal differentiates between registered users and portal visitors. Registered users are experts who can collect, edit and publish research data on biological specimens via the Morph·D·Base portal. Visitors are non-registered users who can access only the published research data without any registration. Different privacy protection policies apply to the groups of non-registered users and registered users (see paragraphs 2 and 3). The collection and processing of the research data is handled according to the rules and policies for research data management of the German Research Foundation (DFG). Privacy protection on research data is explained in paragraph 4.
2. Collected personal data of non-registered users
The following personal data are collected from non-registered visitors of the Morph·D·Base portal:
- IP-address, time stamp, browser-identification, requested pages within the Morph·D·Base portal.
These data are stored for 7 days to allow us to recognize and defend attacks on the Morph·D·Base portal servers. The IP addresses become anonymized after a period of 7 days to make identification of users impossible. The anonymized IP-addresses, time stamps, browser identifications and requested pages are stored for 6 months for statistic purposes to document project activity for our funding organization German Research Foundation (DFG).
In addition, the following data will be stored on the visitor's device:
- So called session cookies with a unique identifier.
Cookies are small data files that are created by the browser. The Morph·D·Base portal can access these files to get information on the user's current visit on the page. In the Morph·D·Base portal the cookies are used to control the user's access to the research data and for providing convenience functions. These session cookies are deleted when the user closes the web browser.
The setting of cookies can be prohibited by disallowing cookies via the browser preferences. Prohibiting cookies will disable the access to any of the published research data on the Morph·D·Base portal.
3. Collected personal data of registered users
Researchers interested in the repository and its tools can request a registration for the Morph·D·Base portal. The Morph·D·Base-team will register a requesting person as user when an adequate research interest is documented. A registered user will get the contact data of a Morph·D·Base-team member who will be available for questions on Morph·D·Base portal usage.
To review the required research interest and to get in contact with users when necessary (e.g. for informing them on software changes, new features) the following personal data are collected by the Morph·D·Base portal:
- Username, real name, and email address of the user.
- Affiliation in a research institute, a scientific society, or references of other experts
Registered users can voluntarily provide the following additional personal data:
- Phone number for direct contact with the Morph·D·Base-team in case of any questions or required support.
- Registered users can provide their website, academic title, and academic position.
These data are only collected in agreement with the respective user. Users are informed about data collection and asked to accept this private policy when they request a registration at the Morph·D·Base portal.
In addition to data collected for non-registered users the following data are collected when users are registered:
- Cookies with a unique identifier.
Cookies are small data files that are created by the browser. The Morph·D·Base portal can access these files to get information about the current visit of a user on the portal's pages. In the Morph·D·Base portal these cookies are used for managing access of users to their resources (access to research data, drafts and data publications, account management). The cookies are stored when the user logs into her / his account and become deleted when the user closes the web browser.
The setting of cookies can be prohibited by disallowing cookies via the browser preferences. Prohibiting cookies will disable the usability of the Morph·D·Base portal as registered user.
The Morph·D·Base portal is a collaborative online tool that allows researchers to edit and publish research data and associated documents in a cooperative manner. Therefore, users can share their research data and documents with other registered users who will then gain access to these data and documents. Users can delete all research data as long as they are not published (see paragraph 4). The publication is conducted by the users themselves.
4. Collection of personal data in the research data
The goal of the Morph·D·Base portal is to collect research data and information about morphology and occurrence of biological specimens. For quality assurance and re-usability of the research data it is important to have a complete documentation of data collection and applied research methods. Therefore, the research data stored and processed by the Morph·D·Base portal contain personal data like specimen collector names, sampling sites and their coordinates, and morphological and biological methods applied by researchers. In short, the data contain:
- Names of the researchers who take part in investigations and the description of specimens and their characters.
- Locality descriptions, coordinates and date of sampling locations, together with the names of collectors.
- Scientific analyses and applied methods, time and place of analyses and names of persons who conducted the analyses.
- Scientific assessments and evaluations on the provided research data.
These data are made publicly available under the condition that the collaborating experts (registered users) have given their permission. The decision on the publication of the data and associated documents can be done in a case-by-case manner and is controlled by the collaborating experts themselves. Published data will be made citable by registration of a Digital Object Identifier (DOI, https://www.doi.org) for each publication. Thus, deleting or changing published data is only possible, when legal or scientific reasons require a correction or revoke of the published data (copyright infringement, serious scientific errors). Published data and documents can only be revoked after consultation and in agreement with the Morph·D·Base-team. A deletion of data copied and stored by other services on the internet (e.g. archiving services, scientific portals) cannot be carried out.
According to the research data management policies (see: empfehlung_wiss_praxis_1310.pdf and: ua_inf_empfehlungen_200901.pdf) of the German Research Foundation (DFG) the collected research data with the contained personal data are stored for at least 10 years.
5. Sharing and disclosure of personal data to third parties
The collected research data will be published in order to fulfill the scientific goal of the Morph·D·Base-project and make the results available to researchers, scientific and administrative institutions and the interested public. The personal data of participating researchers can be anonymized on request before publication. The anonymization can be done after consultation of the Morph·D·Base-team. The request can be sent to the Biodiversity Informatics Department of the Zoological Research Museum Koenig (ZFMK) (see adress below).
6. Contact address to request deletion, correction, or accessing personal data and to revoke the agreement of personal data handling
For all requests on deletion, correction, access and agreement on personal data collected in the Morph·D·Base portal please contact:
Zoologisches Forschungsmuseum Alexander Koenig
Section for Biodiversity Informatics
7. Deletion or correction of personal data
Personal data will be deleted or corrected on request when they are not part of the research data uploaded by experts. Users can request the deletion or correction of their personal data by contacting a Morph·D·Base-team member or the Biodiversity Informatics section of ZFMK (see address above).
User authentication is required when requesting the deletion or correction of personal data. Deletion or correction of personal data contained in research data is only possible after negotiation and agreement of the Morph·D·Base-team, since the requirements and policies of the funding organization (DFG) must be taken into account.
8. Access to collected personal data
Collected personal data will be made available to the concerned person in machine-readable or human-readable form. Users can request information on their personal data and the data themselves by contacting the Biodiversity Informatics section of ZFMK (see address above). The request will be processed within a period of 4 weeks, if the requesting person can provide a valid authentication.
9. Revoke the agreement to collect personal data
Registered users can revoke their given agreement to the collection and handling of personal data by the Morph·D·Base portal. The collected data will then be deleted within 4 weeks. The person who wants to revoke his / her agreement will be asked for an authentication. The revoke-request can be sent to the Biodiversity Informatics section of the ZFMK (adress see above).
10. Right of appeal at the regulating authority
In accordance to article 13 of the GDPR users have the right of appeal at the regulating authority. The address is:
Landesbeauftragte für Datenschutz und Informationsfreiheit Nordrhein-Westfalen
Postfach 20 04 44
Public PGP-key: https://www.ldi.nrw.de/metanavi_Kontakt/key_ldi.asc
11. Contact data of the ZFMK data protection officer
The contact address of the data protection officer of the ZFMK is:
Zoologische Forschungsmuseum Alexander Koenig
Leibniz-Institut für Biodiversität der Tiere
Stiftung des öffentlichen Rechts