1. What is MorphoBank?

Scientists around the world, including taxonomic experts studying everything from insects to viruses and dinosaurs to plants, work every day to add to our knowledge of biodiversity through scholarly research released in peer-reviewed publications. MorphoBank, developed and supported by funding from the U.S. National Science Foundation as well as institutional members, is a digital archive of those data, facilitating open sharing of observations published by today's scientists.

Specifically, MorphoBank assists scientists building the Tree of Life - the genealogy of all living and extinct species. In this endeavor scientists must collect data on all heritable features - both genotypes (e.g., DNA sequences) and phenotypes (e.g., anatomy, behavior, physiology).  MorphoBank is part of the new and growing cyberinfrastructure for phenotypes to house, save and share information on anatomy, physiology, behavior and other features of species. The genomic part of this work is archived at the National Center for Biotechnology Information.

Estimates suggest there may be 5-100 million living species on Earth, and hundreds of thousands of fossil species. Only a very small proportion of this diversity has been discovered and named, much less anatomically described, figured, and studied.  Capturing such knowledge of species impacts many areas of our lives from medicine and drug discovery, to agriculture, to understanding the current and past biodiversity of our planet.

2. How does MorphoBank help with building the Tree of Life?

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 (e.g., species names, anatomical descriptions) and a second database that allows researchers to upload morphological (phenomic) data and affiliate it with what are called 'phylogenetic matrices'.  Phylogenetic matrices are spreadsheets that have species in rows and obserations about those species in columns.  In both cases, MorphoBank is project-based, meaning a team of researchers can create a MorphoBank project within which they initially share images, matrices 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 public 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 (spreadsheet) made of characters (traits) and taxa (e.g., species or more inclusive taxa such as genera or families). Characters are features or traits of an organism that appear in different forms. Two types of characters are supported in Morphobank: discrete and continuous. Discrete are most widely used historically and describe a character as a finite number of character states. Examples include "eyes: blue, green or brown" or wings: present or absent. Continuous characters use a quantity, or range of quantities, to describe a feature. Examples include "pH: 6.7" or "temperature range: 40C - 65C". An example of discrete characters and character states is as follows, "eyes: state 1 (blue), state 2 (green), state 3 (brown)." For continuous characters a single specific quantity or a pair of quantities defining a range must be specified.  The practice of assembling lots of character observations on a set of species is called character scoring.

Traditionally character scoring has been done with in desktop programs like MacClade, Mesquite or Winclada, which record this information in formats called either Nexus files or TNT files (MorphoBank supports both). Desktop programs have not, however, been built to contain robust tools for manipulating images (e.g., media, 2D and 3D, movies) of character states, 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.  Additionally, desktop programs do not permit collaboration on a single matrix in real time as MorphoBank does, a feature that is extremely useful for collaborative teams.

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.

3. Why is MorphoBank important?

We built MorphoBank for two main reasons.

1) Too much information was being lost when morphologists produced an article with a new phylogenetic tree. No archive existed for morphologists to store the images and matrices that backed up their cell scores.  Images and matrices need to be readily available in both human- and computer-readable formats for the science of morphological systematics to be repeatable.  Publishing a matrix on MorphoBank in conjunction with a peer-reviewed article, now considered a best practice, guarantees that the anatomical descriptions of a character and its character states are easily accessible for other researchers to repeat and build on results. 

2) Seeing images that document the basis for homology in 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.

4. What type of content does MorphoBank make available on its site?

MorphoBank permits the posting of the data supporting peer-reviewed scientific research - i.e., phylogenetic matrices derived from morphology or phenotypes, 2D and 3D images, sound, and documents that further explain the research such as tree files.

5. What is MorphoBank's policy on copyrighted media?

MorphoBank does not own the cooyright of the media it hosts. Media (e.g., 2D and 3D images, 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.  MorphoBank encourages open sharing of media but leaves the decision to content providers as to which Creative Commons license suits their research needs.

MorphoBank encourages content providers to choose CC0 or CC-BY reuse policies because 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. 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.

6. 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 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.

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. MorphoBank is the only software package that offers this feature.  Moreover, MorphoBank also 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 archive these important images online with associated information such as the repository and specimen number.

7. How to cite MorphoBank and permalinks for your data

When you use MorphoBank please cite the software:

O'Leary, M. A., and S. G. Kaufman. 2012. MorphoBank 3.0: Web application for morphological phylogenetics and taxonomy. http://www.morphobank.org.

You may also be interested in citing the conceptual paper describing the the database and tool:

O'Leary, M. A., and S. Kaufman. 2011. MorphoBank: phylophenomics in the 'cloud'. Cladistics. 27:1-9.

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 format

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:

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.

8. 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 (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:

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 editing form.

9. 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 was developed at Stony Brook University between 1990-2021, after which it moved to the nonprofit scientific database hub Phoenix Bioinformatics. You can read more about the team here.

10. What does it cost to use MorphoBank?