Frequently Asked Questions


The vision for BIOSPEX was established at iDigBio's 2012 Public Participation in Digitization of Biodiversity Specimens Workshop. That group recognized a need for a resource to (1) lower barriers to creation and management of online public participation projects for this domain, (2) make data flow more easily among relevant actors (e.g., specimen data management systems, crowdsourcing platforms, web services) then back to the collections curating the physical specimens with provenance information, (3) build capacity for recruiting and engaging with public participants, and (4) enable co-created citizen projects (i.e., those in which citizen scientists participated throughout the research process, including choice of research focus). Those are the four principal goals of the BIOSPEX project.

Biodiversity specimen digitization is creation of digital content describing a biodiversity specimen (e.g., a butterfly on a pin, a fish in a jar, a fossil in a box, a plant on paper). The most common steps taken in digitization involve digital imaging of the specimen and associated labels, databasing of the specimen (i.e., transcribing label data into relevant database fields), and georeferencing the specimen's collection location. Only a small fraction of the world's ca. 3 billion biodiversity specimens have been digitized in some way. An excellent overview of the value of digitization is iDigBio's Why Digitization Matters video.

BIOSPEX is designed to be useful to the stakeholders of biodiversity specimen digitization. We anticipate that this will most commonly be the biodiversity specimen curators at universities and museums and those using the digital data (e.g., professional researchers and citizen scientists), but it could also be STEM educators who are using citizen science in the classroom and others. We are especially interested in supporting citizen scientists (e.g., amateur enthusiast groups, citizen's environmental monitoring groups) in the creation and management of digitization projects that they will find to be useful and engaging. A good example of this is the WeDigFLPlants BIOSPEX project managed by the Florida Native Plant Society and their partners.

BIOSPEX stands for BIOdiversity SPecimen digitization EXpeditions. Expeditions are specimen sets that are circumscribed in a way to make them compelling for crowdsourcing by tapping into a research need, human interest, an educational objective, or something else. The term "expedition", as applied to the packages of digitization tasks, was first used by our friends at Atlas of Living Australia's DigiVol.

BIOSPEX produces public pages summarizing the projects that it supports and the progress of their expeditions, which is potentially interesting and useful to you. However, it is not a site where crowdsourcing occurs, nor is it meant to provide an exhaustive list of all citizen science projects for this domain. Great places to contribute to digitization of biodiversity specimens include Notes from Nature, Atlas of Living Australia's DigiVol, and the Smithsonian Institution Transcription Center. A great place to find a near-exhaustive list of citizen science projects to which you can contribute is SciStarter.

The first step is to Register. It’s free and easy to register. From there, you can create a Group and invite your collaborators to the Group. They will receive an email with a Group Invite Code that they can use when they register with BIOSPEX. Members of a Group work together to manage a digitization Project. The next steps are to create a Project, import specimen information to the Project, and circumscribe specimens as Expeditions. The next steps after Expedition creation will be determined by the Project's workflow.

A Group is composed of those users jointly managing one or more digitization Projects. A Project has one or more Expeditions. BIOSPEX mints a public page for each Project (e.g., WeDigFLPlants), and Projects are described in quite a bit more detail than Expeditions. In many cases these public Project pages might be the only place online to find information about a Project, and we are working to provide interesting dashboard components for Projects to show progress across Expeditions on that page. Each Project has a workflow that establishes the actors that will be involved in your Project's pipeline of data creation. Each Expedition inherits its Project's workflow.

We very much want to make BIOSPEX useful to those in this situation. We encourage you to begin by familiarizing yourself with resources provided by iDigBio and the Small Collections Network and developing a strategy for data management and sharing. The Small Collections Network maintains a Symbiota portal for North American small herbaria to use, which would permit those collections to create skeletal records as they digitally image specimens and export that data as a Darwin Core Archive for upload to BIOSPEX. Similar resources might exist for your taxonomic group, and we encourage you to contact the Small Collections Network and Libby Ellwood at BIOSPEX for help finding them.

We’re actively working to add a crowdsourcing platform for georeferencing to the available BIOSPEX Project workflows. As a big step in that direction we recently published a paper on this topic in the inaugural issue of Citizen Science: Theory and Practice. Stay tuned!

We are very interested in providing additional useful options to our users and would love to speak with you about it. Austin Mast would be the best person to contact about this.

Email us using the form located on the Contact page. 

There are currently two actors that can be engaged in a BIOSPEX Project workflow: the iDigInfo Optical Character Recognition (OCR) web service and Notes from Nature v2. Notes from Nature v1 has been retired as a workflow component. You may choose to use just one of those actors or OCR followed by Notes from Nature. If you know relatively little about the subjects of the images that you'd like to have transcribed at Notes from Nature, inserting the OCR step into the workflow will provide you with potentially helpful text recognized in the images. You can then filter your specimens by, e.g., a county name appearing in that text.

BIOSPEX ingests specimen and image information provided in the format of Darwin Core Archives. Darwin Core Archives (DwC-A) are a standard interchange format for the biodiversity informatics domain. They are produced as an export format by most biodiversity specimen data management systems (e.g., Symbiota) and specimen data aggregators (e.g., iDigBio). The Southeastern Regional Network of Expertise and Collections (SERNEC) provides an example. Over 100 SERNEC-associated herbaria are digitally imaging plant specimens and creating skeletal records for each specimen in SERNEC's Symbiota portal. A herbarium curator wishing to create a BIOSPEX Project targeting her herbarium's specimens would search the portal for records from her collection that have been associated with images. These she would export as a DwC-A from the SERNEC portal and upload the DwC-A to her Project at BIOSPEX. If she chose to involve the iDigInfo OCR web service in her Project's workflow, the OCR text strings would be available with the skeletal record data after a sufficient amount of time (e.g., about 30 minutes for 1000 specimens). The progress of the upload and the OCR can be followed in the BIOSPEX Processes pop-up window. A user could alternatively provide BIOSPEX with a URL at which the system can get a DwC-A or provide an iDigBio record set id. Additional instructions for these alternatives are provided on the relevant BIOSPEX page.

You may use whatever organizing principle you think will be compelling to volunteers when establishing Expeditions. A few obvious ways to circumscribe Expeditions use geography (e.g., specimens from a local state park), taxonomy (e.g., all monarch butterfly specimens), collection (e.g., specimens from Florida State University's Robert K. Godfrey Herbarium), collector (e.g., specimens collected by your great aunt Sophia, the famous naturalist), management category (e.g., invasive organisms), or some combination of these. As the community gains more experience with the circumscription of Expeditions it should be possible to establish best practice recommendations. For now, we encourage you to ask yourself "how can I make the digitization most appealing to volunteers?" as you weigh alternative ways to circumscribe specimens into Expeditions.

BIOSPEX currently limits Expeditions to 5000 Subjects. For most purposes, a Subject corresponds to a specimen if there is a single specimen in each image. We do this for two reasons. First, introduction of each Expedition to the world represents an opportunity to generate more buzz for your Project and the crowdsourcing platform that you are using, and it means more opportunities to celebrate Expedition completions. Second, it gives the crowdsourcing platforms a bit finer control over the timing of release of new Expeditions so as not to overwhelm volunteer communities. If you have 5200 Subjects that fit the criteria that you established for an Expedition, split them into two 2600-Subject Expeditions and append the Expedition titles with "I" and "II".

Once Subjects have been uploaded to a Project, Group members can explore the specimen set using a workbook-like interface that permits a user to sort columns, create filters, and view Subject images.

In our experience, there are several ways you can increase awareness of, and participation in, your Expedition. (1) Create an informative Project page on BIOSPEX; (2) Advertise at the go-to sites for learning about citizen science projects (e.g., scistarter.org); (3) Invite volunteers using your social media accounts (e.g., Twitter and Facebook) and relevant hashtags; and (4) Host a digitization party focused on your Expedition. For help planning the last, visit WeDigBio's Resources pages. An additional strategy can involve partnering with educators to bring the activity into the classroom.