Overview of Morph·D·Base

Morph·D·Base has been developed to serve scientific research and education. It provides a platform for storing the detailed documentation of all material, methods, procedures, and concepts applied, together with the specific parameters, values, techniques, and instruments used during morphological data production. In other words, it's purpose is to provide a publicly available resource for recording and documenting morphological metadata. Moreover, it is also a repository for different types of media files that can be uploaded in order to serve as support and empirical substantiation of the results of morphological investigations.

Our long-term perspective with Morph·D·Base is to provide an instrument that will enable a highly formalized and standardized way of generating morphological descriptions using a morphological ontology that will be based on the web ontology language (OWL - http://www.w3.org/TR/owl-features/). This, however, represents a project that is still in development.

What can you do in Morph·D·Base?

You can upload information about the specimens you are studying (ID, identification & taxonomy, collection data, sampling data, museum IDs, sex, etc - all in accordance with the DarwinCore standard - http://rs.tdwg.org/dwc/), and link media files that already exist in Morph·D·Base to specimen entry. You can also upload different types of media files (bitmap and vector graphics as well as literature documents and 3D, audio, and movie files), which can be classified (e.g., table, drawing, SEM, CLSM, whole organism) and linked to an existing specimen or media entry.
The taxonomy and nomenclature in Morph·D·Base is based on the ITIS taxonomy (http://www.itis.gov). Since this taxonomy is not complete, you can create new taxon entries as well.

Scheme of the organisation of the different entry types (Specimen/Taxa, Media, Literature, and Matrix), and the organisation of the application and database layer in Morph·D·Base

Morph·D·Base also contains a literature data base for general referencing. You can generate phylogenetic character matrices in Morph·D·Base, and each entry of the matrix can be linked to relevant information within Morph·D·Base (specimens, media, literature, taxonomy). This way, character matrices can contain detailed information of all the materials, methods, and references used to support the respective primary homology statement in each entry of the matrix. Matrices in Morph·D·Base can be exported as Nexus files.Morph·D·Base furthermore enables easy co-operation of morphologists by the possibility of self-organization of users into particular groups. Groups allow to jointly edit yet unreleased entries in Morph·D·Base, including matrices.

How to use Morph·D·Base?

The web interface

The interface is organized into two parts: the header at the top, which contains the main navigation tool, and the content window, which displays all the information content of the data base.

The main navigation is situated in the header. The header is divided into two sections. To the right, with the lighter background, is the section that refers to user specific information, including messages and profile settings and general information about Morph·D·Base. The section at the top of the header contains the main navigation links to the actual data modules of Morph·D·Base. Rather than organizing the sitemap/navigation tree of Morph·D·Base according to the different data modules (taxon, specimen, general biology, media, literature, and matrix), which represents a very common way to organize an interface for a data base, we organized it according to whether one wants to browse released content, or edit and upload content. These two sections are accessibly by navigating using tabs at the top of the content window. As a consequence, one can upload new content or edit currently unreleased content and switch back and forth between for instance correcting and adding new annotations to an unreleased specimen entry, unreleased literature entries, and unreleased media entries by using the tabs within New/Edit Content.

As long as you are not logged in, you have access to the taxonomy tree and only to content of Morph·D·Base that has been fully released (i.e., only those entries that are accessible to all users).

The central content window of Morph·D·Base takes in most of the space of the interface. It is color-coded. Grey-blue indicates that you are currently looking for general information about Morph·D·Base, including help functions and user specific information. Dark blue indicates that you are currently in the "read-mode": you browse and search released data. Red, on the other hand, indicates that you are in the "write-mode": you upload new content to Morph·D·Base or edit existing but yet not released content.

Irrespective of what you are looking for, you can always switch back and forth between the various types of information or sections within one of these three modes by using the tabs at the top of the content window. All changes you have made are continuously saved to the data base, so that you can switch back and forth between the tabs and the tab you left will maintain its state.

Content of Morph·D·Base is accessible through either Browse Content or New/Edit Content, depending on whether the entry has been released and you possess the respective accession right or it is still editable and you possess the edit right. All accessible entries are usually depicted in an ordered list to the left of the content window, from which single entries can be selected in order to access their information content, which is then depicted to the right. The proportions that the two sections take in can be freely altered.

Uploading data

You can upload different types of data to Morph·D·Base. Uploading new content to Morph·D·Base is conducted via the New entry button in New/Edit Content section.

In Morph·D·Base, every user can decide to which group of users each entry shall be accessible. In this way, Morph·D·Base will allow users to share data exclusively with previously specified groups of researchers, therewith enabling virtual collaboration.

Citing Morph·D·Base and citing data from Morph·D·Base

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:

Name of the author (Year of release): MDB Accession Number; www.morphdbase.de.

Any commercial use requires consent from the copyright holder. Contributors to Morph·D·Base agree to these terms.

You would make us happy, if you would also include the following citation in all the publications where you have used the data base:

Grobe, P., and Vogt, L. 2009. Morph.D.Base 2.0: A public data base for morphological data, metadata, and phylogenetic matrices. http://www.morphdbase.de

Technical Overview

Morph·D·Base is freely accessible through a browser based GUI and HTML interface from the internet. Written using the Zope Application framework (Zope 2.10; http://zope2.zope.org), the web GUI is secure and easy to customize and/or extend. The system is based on the object-oriented programming language Python (http://www.python.org). AJAX components are used to provide an enhanced user experience on the selected components.
All metadata are stored in a relational database (MySQL 5.1; http://www.mysql.com). The Media files are stored using a HP Storage Array (http://www.hp.com) on the file system. Data and system are backed up on a daily basis.
To guarantee maximum performance with high security, the entire system is running on its own server and a backup server. The table below specifies further technical details.

 

Server 3 HP ProLiant Servers
Processors A total of 20 Cores are available
Storage 60 TB
Operating System Ubuntu Server

 

Morph·D·Base Manual

Interface Design

The interface is organized into two parts: the header at the top, which contains the main navigation tool, and the content window, which displays all the information content of the data base (Fig. 1).

Fig. 1: The welcome page of the web interface of Morph·D·Base. The main navigation is in the header at the top and a main display window below it. The status depicted is 'unregistered' with the login details already entered. Registered users can login through the login field, which is situated in the header. Unregistered guests can browse all fully released content of Morph·D·Base, but cannot upload new content.

The main navigation is situated in the header. The header is divided into two parts. The right part refers to user specific information, including messages and profile settings and general information about Morph·D·Base. The top part of the header contains the main navigation links to the actual data sections of Morph·D·Base. A login form is also located in the header, allowing login to registered users anytime during browsing.

Sitemap

  • Organizational
    • Home (using tabs)
      Start, Purpose of MDB, History of MDB, Imprint & Copyright
    • Help (using tabs)
      MDB Overview, Manual
    • My MDB (using tabs)
      My MDB, Profile, Change Password, Group Members
  • Content
    • Taxonomy
    • Browse Content (using tabs)
      Taxa, Specimens, Media, Literature
    • New/edit Content (using tabs)
      Taxa, Specimens, Media, Literature, Matrix [beta Version - access for testing on request]

The different data sections are accessible by navigating using the tabs at the top of the content window. Tabbed based browsing facilitates the switching between different sections. As a consequence, one can upload new content or edit currently unreleased content and switch back and forth between for instance correcting and adding new annotations to an unreleased specimen entry, unreleased literature entries, and unreleased media entries by using the tabs at the content window of New/Edit Content (Fig. 4).

As long as you are not logged in, you have only access to the taxonomy tree and only to content of Morph·D·Base that has been fully released (i.e., only those entries that are accessible to all users). Those links in the navigation area of the header that are not accessible (i.e. New/Edit Content, Ontology) are therefore labeled with dark text or are not present at all (i.e. My MDB) and lack the hyperlinks (Fig. 1).

Short information messages (i.e., tooltips) regarding the functionality of a button or the navigation links of the header appear dynamically on each page while hovering with the mouse over the respective section, like for instance the labels of input fields.

Fig. 2: The tooltip, a short info about the functionality of a button or a navigation link, appears dynamically on each page.

The content window of Morph·D·Base is situated in the middle of the interface. Depending on the color, you are in the "read-mode", in which you either look for general information about Morph·D·Base including help functions and user specific information (grey-blue; Fig 3, left) or browse and search data (dark blue; Fig. 3, middle), or you are in the "write-mode", in which you upload new content to Morph·D·Base or edit existing but yet not released content (red; Fig. 3, right).

Fig. 3: The color coding of the main display box: in grey (left) general information or user specific information, in dark blue (middle) biological data, and in red (right) the write-mode when uploading new content or editing previously unreleased content of Morph·D·Base..

After you have chosen whether to browse the content accessible to you, edit existing but yet unreleased entries to which you possess editing rights, or upload new content, you can switch back and forth between the various data sections of Morph·D·Base via the tabs (Fig. 4). This tabbed browsing maintains the state of each window you have visited, so that you can switch back and forth without having to navigate back to the point you left when switching. You could for instance go to New/Edit Content and select one of your editable media entries, start to edit its annotations, switch to the specimen module and select one of your editable specimen entries, editing its annotations, and then switch back to media and continue editing the media entry you previously selected, and the media page will be just the way you left it behind when switching to the specimen module. This use of tabs and saving every single change a user makes to the data base allows a more convenient handling of Morph·D·Base.

Fig. 4: Switching between different data modules of Morph·D·Base via tabs – in the case depicted, between different types of editable entries.

Content of Morph·D·Base is accessible through either Browse Content or New/Edit Content, depending on whether the entry has been released and you possess the respective accession right or it is still editable and you possess the edit right (for rights and groups see below). All accessible entries are usually depicted in an ordered list to the left of the content window, from which single entries can be selected in order to access their information content, which is then depicted in the right "edit" window. The proportions that the two windows take in can be freely altered (Fig. 5).

Fig. 5: Accessible entries are listed to the left. Selecting one entry from the list depicts its information content at the right side of the main display box. With the help of the i-button located the top right corner of each assigned entry, one can view the complete entry in a popup. The proportions between the listing frame and the information frame is customizable.

In order to allow easy access to various contents at different locations, shortcuts are available on various places. This allows the editing of unreleased assigned entries or the uploading of new entries in the assignment window (see below) without the need to navigate to the respective entry.

Uploading of new content to Morph·D·Base is conducted via the "New"-buttons in the edit and assign window of each section. Each entry type in Morph·D·Base has its own minimum information specified (depicted by "required entries" and indicated by a dark red background color), which necessarily has to be provided in order to be able to generate a new entry of this type in Morph·D·Base. Therefore, when generating a new entry, the necessary information must be provided (Fig. 6).

Fig. 6: Creating and uploading new content in Morph·D·Base ver. 2.2 is conducted via "Add new" buttons in each entry section (here: "Add new Taxon". The entry fields are reduced to the minimum required information needed to create the respective type of entry (Taxon, Specimen, Media or Literature).

Management Modules

Login System

In Morph·D·Base authors will enter the data base as 'users' who have to authenticate themselves via a login-system before they are able to upload new content. Guests that do not possess a user account have access to Morph·D·Base only in a 'read-only' mode, allowing access only to fully released content of Morph·D·Base. Only a user account allows the creation of new entries and join or create a group for cooperating with other users of Morph·D·Base (see below). One can apply for a user account via "Register". A user account is granted by request and requires a valid email address and evidence of respective scientific affiliation or intentions. Security of data transfer through the internet is provided by a secure socket layer (https) encrypted connection.

User Management

In Morph·D·Base all users have their own profile, in which they can provide information about for instance their research interests or of which taxa or methods they are experts. Within their profile they can also change their user password or manage the groups of users they created and administer (see next). In the profile users can also find links to all their different types of contributions to Morph·D·Base. Furthermore, Morph·D·Base possesses its own internal messaging system, which allows users to communicate with one another in private.

Group Management

One important function of Morph·D·Base is to establish the possibility to interchange results between different morphological projects. Within Morph·D·Base it is possible to create a group of users to which each member of the group can assign editing and viewing rights for their data entries (see below). There are two preset groups in Morph·D·Base: a) the group of all users of Morph·D·Base, to which every user is automatically a member and every other group a subgroup; b) the group of guests, whose members can only view fully released entries but cannot create own entries. Additional groups can easily be generated. For creating a new group one simply has to write an email to the administrators of Morph·D·Base including the name of the group and a list of users that shall receive member status to this group (during the funding phase, we will implement the possibility to create groups without having to contact the admins). The owner (i.e. creator and admin) of the group can decide whether the existence of the group is visible to all users of Morph·D·Base or only to the group members. Furthermore the group admin can add or delete users.

Accession Rights

For each entry in Morph·D·Base its author can assign distinct accession rights. Accession rights can be assigned to all groups of which the author possesses membership. Two different types of accession rights are distinguished: editing rights and viewing rights. As soon as a viewing right has been assigned to a group of users within Morph·D·Base, the respective entry is considered to be released. The entry receives a final, unique and quotable accession number, which is composed of the user name, the date of release, and a serial number. However, only fully released entries (i.e., entries released to all users of Morph·D·Base) can be cited. In order to indicate whether an entry to which a user possesses accession rights (either viewing or editing) is fully released, not fully released entries are marked in red in the listings in Browse Content and New/Edit Content. As soon as an entry has been released, it cannot be edited or deleted anymore. Editing rights on the other hand allow for collaborative work on the respective entry by all members of those groups to which the editing rights have been assigned. Members of such groups will be able to change information within the respective entry. However, only the author of the entry has the right to change the status of editing rights of the entry, release the entry to a group, or completely delete the entry (deleting an entry is only possible as long as it has not been released).

Copyright and Citation Policy of Morph·D·Base

The copyright of an entry remains with the author of the entry. The copyright holder is explicitly indicated for every data entry in Morph·D·Base. The following statement represents the general copyright and citation policy statement of Morph·D·Base:

"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:
Name of the author (Year of release): MDB Accession Number; www.morphdbase.de.
Any commercial use requires consent from the copyright holder."

All fully released content that is accessibly by all users and guests of Morph·D·Base falls under the creative commons copyright licensing (cc; http://creativecommons.org/licenses/by-nc-sa/3.0).