About MorphoBank

What is MorphoBank?

MorphoBank is a web application providing an online database and workspace for evolutionary research, specifically systematics (the science of determining the evolutionary relationships among species). One can think of MorphoBank as two databases in one: one that permits researchers to upload images and affiliate data with those images (labels, species names, etc.) and a second database that allows researchers to upload morphological data and affiliate it with phylogenetic matrices. In both cases, MorphoBank is project-based, meaning a team of researchers can create a project and share the images and associated data exclusively with each other. When a paper associated with the project is published, the research team can make their data permanently available for view on MorphoBank where it is now archived.

The phylogenetic matrix aspect of MorphoBank is designed to aid systematists working alone or in teams to build large phylogenetic trees using morphology (anatomy, histology, neurology, or any aspect of the phenotype) or a combination of morphology and molecular data. In contemporary systematic methods in which morphology is used to build trees of species, one starts by constructing a matrix made of characters and taxa. Characters are features of an organism that appear in different forms. Examples include "eyes: blue, green or brown" or wings: present or absent. To convert these to a form that fits in a matrix, one might translate these as follows, "eyes: state 1 (blue), state 2 (green), state 3 (brown)." Traditionally this has been done with desktop programs like MacClade, which record this information in what is called a nexus file (other formats have also been proposed). Until recently nexus files could not also keep a picture of the character state, something that is very useful for researchers actively making comparisons and for later researchers trying to understand the anatomical basis of some comparisons that might have been made decades ago.

MorphoBank allows researchers to upload and download their nexus files, and to edit them in the MorphoBank online workspace. It also allows researchers to upload images affiliated with each cell in a matrix, to zoom on these images, to label the images and to affiliate various kinds of metadata with an image (species, specimen number, etc.). Researchers can download images and can simultaneously collaborate on a matrix online.

Why is MorphoBank important?

We built MorphoBank for two main reasons.

1) Seeing the images that document the basis for a character state is enormously helpful to researchers during their research project. This is particularly important if their matrices are large (hundreds of taxa and thousands of characters). Before MorphoBank a researcher would have had to trust her memory as she made comparisons among hundreds of species. It seemed much more scientific to store an image of a character to refer to repeatedly while adding new data.

2) Too much information was being lost when morphologists produced phylogenetic trees. No archive existed for morphologists to store the images that backed up their character designations. This seemed wasteful and caused a lot of repeated work. The field of morphological systematics could subsequently not grow as fast (in terms of numbers of characters) as molecular systematics, the latter being well-databased in GenBank.

Why use MorphoBank?

Here are a few reasons:

1. You are working on a morphological matrix with a team of investigators.   Teams of investigators commonly collaborate on a single morphological matrix.  Because MorphoBank is a web application, a team can actually use the web to work on the same matrix.  All collaborators can see contributions from members of the team, and images associated with homology statements.  All information can be kept private to the team until the team chooses to make it public.
2. In conjunction with a paper, you wish to publish a morphological matrix that is easy for your readers to access, and which shows labeled images of your homology statements.  Morphological data collection increasingly requires visual documentation of homology.  Journals cannot always publish all images that support the research in a project.  The web also facilitates zooming and panning of images.
3. You are publishing a paper and wish to archive images associated with the research.  You do not need to be working with a matrix to use MorphoBank.  Because journals may not be willing to publish all images, it may be helpful to store these online, with associated information such as the repository and specimen number.

How do I cite MorphoBank?

O'Leary, M. A., and S. G. Kaufman.  2007.  MorphoBank 2.5: Web application for morphological phylogenetics and taxonomy. http://www.morphobank.org.

What is your image use policy? Who owns the images that are uploaded to MorphoBank?

MorphoBank does not own or assert any copyright on project data. Unless it is otherwise noted, copyright is assumed to reside with the person who uploaded that data. Simply uploading data to MorphoBank does not make it publicly accessible. An author must give pemission for the data to be 'published' or made 'live' on MorphoBank. However, once a project is published on MorphoBank (i.e., the project status is changed to 'published'), it becomes publicly accessible and the copyright status of the constituent data becomes a concern. In general, before uploading an image (or other data) to your project, make sure that one of the following applies:

1. You own the rights to the image (usually meaning that you created the image yourself).
2. You can prove that the copyright holder has licensed the image under a free license.
3. You can prove that the image is in the public domain.
4. You believe, and state, a fair use rationale for the specific use of the image that you intend.
5. You have obtained the required clearances from the copyright holder that specifically allow you to use the image on MorphoBank.

It is possible to keep specific images in a published project un-published. To hold back an image you must change the image's status from 'Publish when project is published' to 'never publish to project' in the media 'Basic Info' editing form.

Getting Started

How do I join?

There are two ways to join Morphobank: through invitation or signing up. To sign up send fill out the registration form with your contact information and a brief description of your project. After a brief review, a MorphoBank administrator will contact you with access information.  Invitations to join MorphoBank can also be given out by current MorphoBank members who are the "administrators" or creators of a particular Project and who wish to invite collaborators. Once a new person has joined, he or she is free to create new, separate projects.

We welcome and encourage students to join MorphoBank and use the software.  It is the policy of MorphoBank, however, to request that the student's advisor be made a member of any student project.

Can students use MorphoBank?

Yes.  However, students must also register their advisor as a MorphoBank project member in order to participate.

What kind of computer setup do I need to use MorphoBank?

MorphoBank should work with any recent web browser, including Internet Explorer versions 6 and 7, FireFox versions 1.5 and 2.0 and Safari 2.0 and 3.0 on all supported operating systems (Windows, Mac OS X and Linux/Unix). Certain MorphoBank features require the Adobe Flash browser plug-in: the high-resolution image viewer requires version 8 of Flash; the character editor requires version 9.

You can get the latest version of the Flash plug-in at http://www.adobe.com. If you have any problems with the image viewer or character editor loading you should try updating your Flash plug-in before contacting us for help.

What kind of data do I need to start my project?

MorphoBank supports two broad types of projects: those with matrices and images and those with images and associated metadata. You can start either project by simply uploading images, matrices or metadata. We recommend that a user upload all the taxonomic names, specimens and views affiliated with a given project as a good starting point. This makes the workflow easier.

For matrix-based projects, however, uploading an existing matrix as a Nexus format file will also upload all taxonomic names (as well as characters). A user then only has to add specimen names.

How do I change my password?

To change your password:

1) login you will see your name in the upper right corner, click on that
2) this will bring up a window that says "Edit Password..." at the bottom left, click on that.
3) the next screen allows you to change your password.

Do you have any suggestions for using MorphoBank most efficiently?

Yes.  There are sequences to entering data that may save time.  For example,images have to have identity - they should be affiliated with a specimen that is in a repository and which has a number and a taxon name.  Entering the identifying characteristics of the first is useful because often a researcher wants to enter mutiple images of the same specimen.

If you are not entering a matrix at the start:  it is a good idea to enter the names of taxa and specimens when you begin your project before you enter images.  Even if you occasionally need to go back and enter a new specimen number or a new taxon name, work flows faster if you enter as much of this  information as possible first.  Then you can use the bulk image upload feature (see "Adding many images at once") to add many images at once.  These images then exist in your workspace and can be affiliated with the taxon and specimen information that you have entered into the database.

If you are entering a matrix at the start: it is is a good idea to then immediately enter specimen numbers that go with the names of the taxa in your matrix. Then you can use the bulk image upload feature (see "Adding many images at once") to add many images at once.  These images then exist in your workspace and can be affiliated with the taxon and specimen information that you have entered into the database.

Managing Media

How do I add lots of media quickly?

In the top-right corner of each page is a 'file space' tab above your user name. Click on it and a new page will load, asking if you want to upload a file. The file space accepts any type of compressed file. The images will appear and, if clicked on, will allow you to add metadata. The file space is the same for all projects you are working on, so make sure you are in the correct project before adding metadata.

What media file formats are accepted?

MorphoBank accepts a variety image formats including JPEG, GIF, PNG, TIFF and Photoshop. Note that Photoshop files that use layer effects may not render properly on MorphoBank. For the most consistent results we recommend converting these files to TIFF format before uploading. All image files should be in RGB mode. Files in CMYK mode will probably not render properly.

You should upload image files at the highest resolution that makes sense for your project. MorphoBank will automatically create sized versions for use on the site as well as a full resolution version optimized for online viewing. The original uploaded file is retained and made available for download.

MorphoBank also accepts the following audio/video file formats: MPEG-4, QuickTime and WindowsMedia. The preferred video file format for upload to MorphoBank is MPEG-4 (with or without h.264 compression). Files in QuickTime and WindowsMedia format will usually work so long as the compression method used is supported by MorphoBank's video processor. In general, videos compressed with versions of WindowsMedia prior to version 10 will work, as will most QuickTime compression methods (some very old and rarely used methods like GIF compression are the notable exceptions). AVI file usually will note work and should be converted to MPEG-4 prior to upload. In general if your uploaded file is being rejected by MorphoBank it is recommended that you try re-encoding the file in the MPEG-4 format using one of the many video conversion tools available for Mac OS X, Windows and Linux.

Audio files may be uploaded to MorphoBank is MP3, AIFF or WAV format. Other formats, such as AAC, are not supported. If you need to convert or edit your audio files use a sound editing application such as Audacity (http://audacity.sourceforge.net/).

MorphoBank does not support the PowerPoint file format. If you need to use images from a PowerPoint presentation, you should export them from PowerPoint in a supported format such as JPEG and then upload those files.

Data access

Who can see my data?

Only those invited to the project and yourself may view your data until it is published. Upon publication it is accessible to anyone.

Who can edit my data?

Only those invited to the project and yourself may edit your data.

How long can I leave my data on MorphoBank?

You may leave your working data on MorphoBank for as long as you are actively working on your project. Published data may be left on MorphoBank indefinitely. We ask that once your project is completed you remove any unpublished data so that others may use the storage space.

How can I be sure my data is secure?

Another advantage of a web-based system like MorphoBank is that time-consuming maintenance tasks such as data backup can be centralized. MorphoBank runs on servers hosted by the State University of New York at Stony Brook. All data on the main MorphoBank server at the Stony Brook is backed up to tape, as well as to off-site mirror servers at the American Museum of Natural History.

Stony Brook servers are backed up nightly and serviced by a professional full-time staff of system administrators. Currently the Stony Brook backup system is scheduled to run nightly incremental backups.

If disaster should strike we should be able to recover virtually all lost data. For data recovery, the Morphobank system administrator will work with the Stony Brook system administrators to get the data loaded back in to the Morphobank Portal.

As an option we suggest you perform your own periodic back-ups using the project "backup" feature. This can be found in the "backup" tab under "project" and will provide you with a Zip-format archive containing all data from your project.

Note that there is currently no other program than MorphoBank that can fully reconstitute a downloaded backup. A downloaded backup to the desktop consists of separate nexus file and images, but on the desktop these are not possible to view linked to cells and labels. Thus we do not recommend deleting your work within MorphoBank if you do a manual download.

Can I allow an anonymous reviewer to access my matrix during review at a journal?

Yes.  On the bottom of the Project Information tab are instructions on how to do this.  Many journals like to provide reviewers access to matrix data so that they can check authors' results.  Please provide the editor with the login and password information from the Project Information tab.

Data Standards

Where can I see the MorphoBank database schema?

There schema is located here.

What information must I provide for a specimen?

At an absolute minimum you must provide the institution code and catalog number for the specimen. Both of these values should conform to the standards of the institution from which the specimen originates. If you are not sure of the formats for these values, contact the institution's collections manager. Typically, the institution code will be a 2-4 letter abbreviation of the institutional name (ex. AMNH = American Museum of Natural History, YPM = Yale Peabody Museum).

Whenever possible a collection code should be provided. As with the institutional code and catalog number, this should conform to institutional standards. Many, but not all, institutions use collection codes.

A taxonomic identification of the specimen should be provided for all specimens and is used by the matrix editor to retrieve relevant media, and by the media search/filtering system.

How can I record the information about my media, matrices or specimens that doesn't fit into the basic fields you provide?

The extended info tab provides a set of additional, optional fields for your use. Most of these fields are drawn from the Darwin Core. The Darwin Core (sometimes abbreviated as DwC) is a widely accepted standard designed to facilitate the exchange of information about the geographic occurrence of species and the existence of specimens in collections. More information is available at http://wiki.tdwg.org/twiki/bin/view/DarwinCore/WebHome.

If you need a field that is not present in the extended info field list, let us know at our Suggestion form. In most cases we will be able to add the field to the list for your use.

Matrix Editing

How can I control access to rows in a matrix?

To control access to specific rows (taxa) in a matrix double click on the taxon name in the matrix editor (you must be the project administrator to do this). You will see a window like this:

By default any row may be edited by any project member. If you wish to restrict access to the row to a single project memeber then select the user's name in the "user" drop-down menu.

If you wish to restrict access to a selected group of project members, then you must first set up a member group containing the selected users and then select it using the "group" drop-down menu.

To create a member group, first create the group using the "add new group name" link in the "member groups" tab. The "member groups" table is available under the "options" tab is your project, as shown below.

Once you have created the new member group, go to the "members" tab (also under the "options" tab in your project) and edit each member you wish to add to the group. In the member information form, there are checkboxes for each member group defined for your project. Check the boxes for the groups the member should belong to and save the record.

How do I know if I can edit a row in the matrix or not?

If you do not have access to a row a lock icon will appear next to the taxonomic name. Names with no lock are editable.

How do I add and/or reorder taxa in my matrix?

Click on the taxon list button:

You will see a window like this:

To add a taxon to your matrix simply drag the names from the list on the right (names in your project that are not in the matrix) to the list of the left (names that are in the matrix). To remove a taxon from your matrix drag it from the list on the left to the one on the right. NOTE: Once you remove a taxon all scoring and associated cell media are permanently removed!

To reorder taxa in your matrix simply drag-and-drop the taxa within the left-hand list.

Note that only taxonomic names that are part of your project are shown in the list. If you need to add a new name it must be done through the "taxa" tab in your project.

What's the difference between "member groups" and "project groups"?

Member groups are simply named groupings of project members. They're useful for controlling access to rows in matrices. With member groups you can assemble teams of project members and give them collective access to rows.

Project groups are groupings of projects. If you have several different projects and need to share data between them, project groups provide a mechanism by which to do so. Simply create a project group then add your projects to the group. Currently only bibliographic information is shared between grouped projects, but we are planning to expand this to include other data such as taxonomy, specimen data and media.

The matrix editor is not convenient for managing very large lists of characters. Are there any better tools available?

Yes, there are. The characters tab in your project is a versatile tool for character management, allowing you not only to view characters in a matrix or partition, but to:

• search for characters across all of the matrices in your project
• edit the name of a character without leaving the character list. To do so, simply click on the character's name. If you are allowed to edit it, the name will turn into an editable text entry area with "save" and "cancel" buttons.
• edit existing states and add new states to a character without leaving the character list. To edit a state, click on the name or number. If you are allowed to edit the state, the name or number will turn into an editable text entry area. To add a new state click on the "Add new state" link and enter the new state name. The number of the new state will be automatically set to the largest current state number plus 1.
• link media to a character or state. To do so, click on the "edit" button for the character while in the character list, then click on "media" from the menu on the left side of the screen. You may link a character and/or state to any media in your project. Simply enter some portion of the specimen number, taxonony or notes text into the search box and click on "search." A list of all matching media will be displayed. Click on the media you want, enter any notes, select a state (if applicable) and click on "save."
• move large blocks of characters around a matrix. To do so, click on the "show move character options" at the top of the characters tab. This option will only appear if you have access to edit the matrix in question. To move a block of characters, enter the number of the first and last characters a well as the number of the character before or after which you wish to move the block. The "Reset character order" is available should you wish to revert your matrix back to the character order that existed when it was imported or entered into MorphoBank.

Labels

How do the image labeling features work?

Label features permit explicit documentation and description of anatomical features and homolgies.

Activate the labels tool palette by selecting "labels" from the viewer tool bar

To activate the label menu click on the arrow button in the top right of the toolbar visible when viewing media. This causes the labels toolbar to appear. To add a label select the + option. This places a label on the image automatically. This label describes the character and character state scored in the matrix and can be edited.

Labels are edited in place

Publishing Your Data

What is the web address I can give others to access my project data?

Each MorphoBank project is issued a unique identifier beginning with the letter 'P' for project. This identifier is displayed next to your project title in the project list and on the project info tab in your project options. Once your project is published you may link to your project with a URL in the format

http://morphobank.org/permalink/?P44

where 'P44' is replaced with your project identifer. For unpublished projects, the only way to access data is by logging into MorphoBank.

In what ways can people access my published data?

Once published your data will be accessible in three ways:

1. As lists of published media and matrices linked to from a project summary page. These lists are similar to the matrix list and media browser in the MorphoBank editing interface, but without editing capabilities. The project summary can include an abstract, citation, links to the published article, and other relevant information.
2. In the MorphoBank search engine. Your media and matrices will be included in the results of searches on the MorphoBank.org site.
3. As folios. Folios are groupings of selected project media and matrices. Using the project folios tab, you can create as many named folios as you need. You may then select specific media and/or matrices to add to your folios using the folios tab within the media or matrices tabs. Once you have added items to your folio you can return to the project folios tab and change the order of the media and matrices, add annotations and preview the resulting folio.

Folios are published when the project is published and may be linked to using a URL in the format:

http://morphobank.org/permalink/?F20

where 'F20' is your folio identifier. Folio identifiers always begin with the letter 'F' and appear next to the folio name in the project folios tab. Your project must be published for folios to be accessible to the public.

Security

How can I be user my data is secure?

Another advantage of a web-based system like MorphoBank is that time-consuming maintenance tasks such as data backup are centralized. MorphoBank is run on servers hosted by the State University of New York at Stony Brook. All data on the main MorphoBank server at Stony Brook is backed up to tape, as well as to off-site mirror servers at the American Museum of Natural History in New York.

Stony Brook servers are backed up nightly and serviced by a professional full-time staff of system administrators. Currently the Stony Brook backup system is scheduled to run nightly incremental backups daily.

If disaster should strike we should be able to recover virtually all lost data. For data recovery, the Morphobank system administrator will work with the Stony Brook system administrators to get the data loaded back in to the Morphobank Portal as soon as possible, typically within 1 working day.

To provide yet another level of security, Morphobank provides you with the ability to perform your own periodic back-ups using the project 'backup' feature. Note that there is currently no other program than MorphoBank that can fully reconstitute a downloaded backup.

The downloadable backup utility can be found in both published and unpublished project areas. Just look for the 'options' tab for a given project, and open this page. Now click the 'data backup' tab, and you can create and download a Zip-format archive containing all data from your project to your local machine.

The downloaded backup will consist of a separate nexus file and images. On your local machine it will not be possible to view the data linked to cells and labels. Thus we do not recommend deleting your work within MorphoBank after a manual download, rather, this tool is to provide a backup that can be re-loaded into the MorphoBank web application in an emergency