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 phenotypes) or a combination of morphology and molecular data. In contemporary systematics when morphology is used to build trees of species, one starts by constructing a matrix made of characters and taxa (e.g., species). 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 landmark desktop programs like MacClade, which record this information in what is called a Nexus file (another popular format is called “TNT” format, MorphoBank supports both). Desktop programs have not been built to contain robust tools for manipulating pictures (e.g., media, 2D and 3D, movies) of the character state, something that is very useful for researchers actively making comparisons while they work. Media, especially if they have labels, are very useful 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 or TNT files, and to edit these in the MorphoBank online workspace. It also allows researchers to upload images, affiliate them with characters or 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 or matrices 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 homology - a character state or a cell score - 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 cell scores. This seemed wasteful and caused a lot of unnessecary repeated work. The field of morphological systematics has subsequently had trouble growing as fast (in terms of numbers of characters) as molecular systematics, the latter field being well-supported by powerful databases such as GenBank.
Why use MorphoBank?
Here are a few reasons:
- 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 in real time. All collaborators can see contributions from members of the team, and images associated with homology statements the second they are entered. Team members can argue in a shared, private workspace as they work through science problems. All information can be kept private to the team until the team chooses to make it public.
- 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. MorhoBank also enables zooming and panning of images.
- 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.
What does MorphoBank post live on its site?
MorphoBank permits the posting of peer-reviewed scientific research. Exceptions may be made ("MorphoBank Exclusives") at the discretion of the Executive Committee. These studies have typically been conducted under the supervision of research scientists. Use of MorphoBank for educational and popular initiatives is in the planning stages.
What is MorphoBank's policy on copyrighted media?
Media (e.g., 2D and 3D image, video) are placed on MorphoBank by content providers from the scientific community at large. These content providers also upload information on the copyright status of media and the restrictions governing the reuse of media. If you wish to reuse any media on MorphoBank you must also check the restrictions governing the media's reuse and adhere to those restrictions.MorphoBank encourages open sharing of media and places no copyright claim on site content. Content providers must choose a license from those offered at Creative Commons.Reuse of media from MorphoBank that does not comply with the Creative Commons license applied to those media requires new permission from the original copyright holder.MorphoBank would prefer for content providers to choose CC0 or CC-BY reuse policies because they (and only they) are Open Data licenses. Please be aware that choosing an NC (non-commercial usage only) license may prevent your data submission from being used on open-content only websites such as Wikipedia.
How to cite MorphoBank and permalinks for your data
O'Leary, M. A., and S. G. Kaufman. 2012. MorphoBank 3.0: Web application for morphological phylogenetics and taxonomy. http://www.morphobank.org.
Each MorphoBank project is issued a unique identifier beginning with the letter 'P' for project. You will see this identifier displayed in many places throughout MorphoBank while editing your project. For example, your project number appears next to your project title in the My Projects project list and on the project overview page. Once your project is published you may link to your project with a URL in the formathttp://morphobank.org/permalink/?P44
where 'P44' is replaced with your project identifer. Yes, the question mark should precede your number in your permalink, so it would look like this for another project: http://morphobank.org/permalink/?P660. For unpublished projects, the only way to access data is by logging into MorphoBank projects to which you belong.
Folios are published when the project is published, unless the folio's status dropdown is set to 'never publish to project', 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.
What is your image reuse 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 (content provider) must release the data by 'publishing’ it or making it live to the public on MorphoBank. However, once a project is published on MorphoBank (i.e., the project status is changed to 'published'), it becomes publicly accessible and authors should be sure that they have respected copyright for media they have released. In general, before uploading an image (or other data) to your project, make sure that one of the following applies:
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 editing form.
- You own the rights to the image (usually meaning that you created the image yourself).
- You can prove that the copyright holder has licensed the image under a free license.
- You can prove that the image is in the public domain.
- You believe, and state, a fair use rationale for the specific use of the image that you intend.
- You have obtained the required clearances from the copyright holder that specifically allow you to use the image on MorphoBank.
Who we are
MorphoBank is a collaboration among many scientists who are using phenotypes to build phylogenetic trees (phylophenomics) or who are documenting phenotypes for other aspects of biological and paleontological research. The project has been supported primarily by the National Science Foundation. You can read more about the team here.
How do I join?
There are two ways to join Morphobank: through invitation or signing up. To sign up, fill out the registration form with your contact information and a brief description of your project. 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 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 to MorphoBank. Click on the "Profile" link in the upper right corner above the search box.
2) this will take you to a form where you can edit the information you submitted during the registration process, including your password. Enter your new password and click save.
What kind of computer setup do I need to use MorphoBank?
MorphoBank should work with any recent web browser, including Internet Explorer versions 8 and 9, FireFox versions 5.0 or better and Safari 5.0 or better on all supported operating systems (Windows, Mac OS X and Linux/Unix). For optimal performance of MorphoBank please use one of these three browsers: Internet Explorer, Firefox or Safari (and please make sure you keep them up to date!) Certain MorphoBank features require the Adobe Flash version 10 (or better) browser plug-in.
Do you have any suggestions for using MorphoBank most efficiently?
Yes. There are sequences to entering data that may save time. For example, images need to have identity - they should be affiliated with a specimen that is in a repository and which has a repository number and a taxon name. Entering that information about the specimen first is useful because often a researcher wants to enter multiple 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 first enter as much of this information as possible. Then you can use the batch media 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 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 media 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.
I’d like to put my data in but I feel too busy to get started – can anyone help me?
Yes, we would be happy to help new members of the scientific community get started with the site. Please email email@example.com and describe what you want to do. Very likely we can help make your archiving or new project very painless.
Can I copy a project to use for my own research?
Yes, logged in users can request to duplicate an unpublished project they are a member of or any published project. To place the request click the "Request Project Duplication" link on the project overview page of the project you would like to duplicate. Users will be contacted by MorphoBank once the duplication request has been fulfilled. When users edit various parts of the duplicate project the changes do not have any effect on the master project.While MorphoBank aims to meet the needs of all users, storage is finite and some projects with media are quite large. We, therefore, ask that researchers consider best practices prior to submitting a request for duplication.
How do I add lots of media quickly?
There is an "Add media batch" button at the top of your project's media list. Following this link takes you to a form where you can upload an archived file of media and enter metadata that apply to all media in the batch. This will allow you not only to batch upload, but also to batch catalog a group of media.To prepare your media files (images, video, sound, etc.) for upload, you must convert the batch of files to a single archive file. MorphoBank will accept archives in either Zip or Tar format. Tar archives may be optionally compressed with Gzip or BZip2. To create Zip archives on Windows, you must use a program like WinZip. On Mac OS X, simply control-click on the folder containing the images and select "Create archive" from the pop-up menu.Your archive must contain files in MorphoBank's accepted media formats. (For detailed information on what media file formats are accepted see the next FAQ item, What media file formats are accepted?.) Other formats will be ignored. You may group files in nested folders - they need not be in a single folder.Your archive must be no greater than 2000MB in size. Archives exceeding this size will not process (please just break them down).
What media file formats are accepted?
MorphoBank accepts a variety of image formats including JPEG, GIF, PNG, TIFF and Photoshop. Note that Photoshop files that use layer effects may not render properly on MorphoBank. For consistent results we recommend converting these files to TIFF format before uploading. All image files should be in RGB mode. Files in CMYK mode may 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 will be retained and can be made available for download. MorphoBank also accepts the following video file formats: MPEG-4, QuickTime and WindowsMedia. The preferred video file format for upload to MorphoBank is MPEG-4. 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 WindowsMedia will work, as will most QuickTime compression methods (some very old and rarely used methods like GIF compression are the notable exceptions). AVI files usually will not 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 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 in MP3, AAC, AIFF or WAV format. Other formats 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 upload images from a PowerPoint presentation, you should export them from PowerPoint in a supported format such as JPEG and then upload those files.
You can upload your files in PLY, STL, ZIP, TIFF and DCM, file formats, as well as any acceptable video format if you are adding CT data to your project.
What are Folios?
Folios are groupings of selected project media. First create a new Foilio, then you may select specific media to add to your folios by clicking the "Edit folio media" link in your list of folios or by using the "Folio options" tool on the Media page. This tool allows you to add multiple media to a folio directly from media search results. Once you have added items to your folio you can return to the folios tab to change the order of the media and preview the resulting folio.
Folios are published when the project is published, unless the folio's status dropdown is set to "never publish to project", and may be linked to using a URL in the format:http://morphobank.org/permalink/?F20
where 'F20' is your folio identifier (and yes, the “?” is always a part of the permalink). 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.
Using the project Folios tab, you can create as many named folios as you need.
Can I upload CT data to my project?
You may upload a CT stack, comprised of hundreds or thousands of individual images, to Morphobank as a single ZIP-format archive. Your ZIP file should include only images with no extraneous files or sub-directories. All images in the stack should be TIFF or DICOM format and must be numbered sequentially. Any file with a missing number will be skipped during upload, resulting in an error or inaccurate 3D image. Please remember that ZIP-format stack uploads should be used for CT data only and not as a batch upload method for individual specimen images.
You may also upload media derived from CT data to Morphobank, including 3D surfaces in PLY and STL format and pre-rendered 3D animations in QuickTime, MPEG-4 and WindowsMedia formats.
To upload a CT scan or derived media, go to the Media tab of your project. Click on the button titled "Add new 2D/3D media file"
When a PLY or STL 3D surface is uploaded, the icon below will be shown in place of a thumbnail wherever the file appears in your project.
Who can see my data?
If your data are ‘unpublished’ only those invited to the project may view your data. Upon publication anyone can see it.
Who can edit my data?
Only those invited to the project and yourself may edit your data. You may design your project such that different members have different levels of access (for example, some may enter media but not score cells)
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 are archived permanently. We ask that once your project is complete you remove any unpublished data so that others may use the storage space.
Can I allow an anonymous reviewer to access my matrix during review at a journal?
Yes. Many journals like to provide reviewers access to matrix data so they can check authors' results. Project Administrators can enable an anonymous reviewer login for their project in the Project Info form accessed through the "Edit project info" link on the Project Overview page. Once enabled, reviewers can login by entering the project number in the email address field and the reviewer login password entered by the Project Administrator in the Project Info form. Don’t forget – you have to tell editors and reviewers your project number and reviewer password when you invite them to review your project.
Where can I see the MorphoBank database schema?
The 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 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 of your project 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 member, 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. Project Administrators can create Member Groups by following the "Edit Member Groups" link in the right column of the project overview page. Then you can select the Member Group using the "Member Group" drop-down menu in the screen above.
Once the Project Administrator has created the new Member Group, they can add project members to the group by following the "Manage members" link on the project overview page. 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.
How do the image labeling features work?
How to use the image viewer
Use the mouse to click and drag across the image. You can use the mousewheel or trackpad to zoom in or out of the image. The
-buttons and zoom slider bar at the top of viewer may also be used. The viewer displays the image at full resolution, loading detail as you zoom. The more you zoom the more detail will be visible.
You may annotate the image with text notes. Each annotation is associated with a point or rectangular area of the image. To create an annotation, select the line (point) or rectangle tool from the tool bar, then click on the location you wish to annotate. For point annotations a line will appear connecting the location with a text box. You may drag both the point of the line and the text box to adjust position. Click on the text box to add text. For rectangular annotations a rectangle will appear. Drag on the edges at the highlighted locations to resize the rectangle. Drag the rectangle on its interior to reposition it. You may also drag the text box into position. Click on the text box to add text. All changes to annotations are saved automatically as you work.
When this tool is selected clicking and dragging on the image will pan across it.
When this tool is selected clicking on the image will add rectangular labeled regions at a location. You can resize the region by clicking and dragging on the drag points. Click and drag on the center of the region to relocate the region.
When this tool is selected clicking on the image will add labels to associated with point locations. The area around the point location will be highlighted with a light transparent red circle. Click and drag within the circle to move the label.
You can see an overview of the entire image, with the currently visible area highlighted by clicking on this tool. Clicking on a point in the overview will pan the magnified image to that location.
You can use this button to prevent accidental movement or deletion of labels while navigating the image. When locked it will not be possible to move, editing, create or delete labels on the image. You can still use the zoom and pan tools when the labels are locked.
You can zoom out to fit the entire image, centered, in the viewer window by clicking on this tool.
Single-key shortcuts are available for common actions. Pressing the key is equivalent to the corresponding mouse action.
spaceto activate image panning
rto select the rectangle label tool
pto activate the point label tool
nto toggle visibility of the image overview
hto return the image to the centered, zoomed out 'home' position
cto toggle visibility of viewer controls
TABto hide controls and labels
]to zoom in in small increments
[to zoom out in small increments
?to pan the image in small increments
dto delete the selected annotation
lto lock and unlock annotations
Publishing Your Data
What is the web address or permalink I can give others to access my project data?
Each MorphoBank project is issued a unique identifier beginning with the letter 'P' for project. You will see this identifier displayed in many places throughout MorphoBank while editing your project. For example, your project number appears next to your project title in the My Projects project list and on the project overview page. Once your project is published you may link to your project with a URL in the formathttp://morphobank.org/permalink/?P44where 'P44' is replaced with your project identifer. Yes, the question mark should precede your number in your permalink, so it would look like this for another project: http://morphobank.org/permalink/?P660. For unpublished projects, the only way to access data is by logging into MorphoBank projects to which you belong.
In what ways can people access my published data?
Once published, your project will be included in the Browse Projects section of morphobank.org. Following the "View project" link will take site users to your project overview page which can include an abstract, citation, exemplar media, links to the published article, and other relevant information. There is also side navigation linking to your project's published matrices, media, views for media, specimens, taxa, folios, bibliography and documents. The data in these sections are presented similarly to the MorphoBank editing interface, but without editing capabilities.Your project's data will also be included in the results of searches on the MorphoBank.org site.
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 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.For optimal security we suggest you perform your own periodic back-ups using the project "download" feature. This can be found on the right side of the project overview page (the summary page displayed when you first select a project) and will provide you with a Zip-format archive containing all matrices and media from your project.Note that a project download is not a full backup in that it can not be reloaded into MorphoBank to reconstitute a project. The download consists of separate NEXUS files and images. Media, characters, taxa and scoring are all retained, but labels and links between matrix characters and cells to media will not be retained due to limitations in the NEXUS file format. Thus we do not recommend deleting your work within MorphoBank unless you are absolutely sure you no longer need your project.