Account Details

How do I become a contributor?

Visit How To Become A Contributor for details

How do I edit my account information (ex. email, name, organization, etc.)?

Log in and navigate to your Dashboard. Select "Profile" from the left most gray column. Click the blue "Edit Profile"button. 

Data Submission 

Instructions for data submission can be found on our page How to Create and Edit Media

What is the preferred deposit structure? May I deviate from the preferred structure?

To view the preferred deposit structure, visit our page Preferred Deposit Structures 

Why isn't my file being accepted for submission?

Most often, this occurs when the incorrect Media Type was selected at the very beginning of the submission. Each media type has its own list of accepted file formats. To remedy this discrepancy, you will need to start over and select the correct media type on the first step. If your media type is correct, the problem may be the file format is not on the list of accepted formats. In this case, simply convert the file into a format listed in the "Upload File" box. To view the complete list of accepted file formats by media type, visit Critical Formatting Details

How can I duplicate my media entry so I don’t have to type in the same metadata over and over?

We don’t have the feature on the site. We used to have it in the previous version of MorphoSource, but we found too many errors in which people forgot to update scan parameters when necessary. We know how tedious the data input can be, but the payoff is not having to come back years later to correct information no one realized was incorrect. A suggestion is to open a Word or Notepad document and write in your data. From there you simply copy and paste the information for the fields so you save typing time.

Where do I upload replacement files for my media?

Go to the media record of interest, click “edit” and then go to the “file upload” tab. Delete the current file and upload the new file. Media records with DOIs are an exception. File modification is NOT allowed for media records with a DOI. If you believe this file replacement is necessary for a record with a DOI, email admins at morphosource@duke.edu

What is an "Occurrence ID" and how is it different from a "specimen number" or "catalog number"?

Occurrence IDs are intended to be globally unique identifiers (alphanumeric strings) that statically refer to a single physical specimen or observation event.  In addition, the Occurrence ID for a given specimen or event should be permanent. In otherwords, the Occurence ID for a given specimen should not change from year to year... or EVER. Not even for addressing the tiniest cosmetic issue.  Think of a snowflake made of diamond - diamondflake, if you will - that is your occurence ID. It's unique like a snowflake, but "diamonds are forever."

ARK identifiers and DOIs are sometimes also used as Occurrence IDs. This is fine. ARKs and DOIs are not guaranteed to be unique probabilistically, but are minted by coordinated services that makes sure ids arent duplicated. Resolveable Occurence IDs are sometimes used as a link to a specimen record in a museum's web database. This is also fine (and sometimes handy) but not a requirement.  When specimens have Occurrence IDs that are permanent and globally unique, this can improve interoperability among databases that reference different kinds of data about the same specimens and informatic utility of specimen records aggregated from multiple museums.

It is very important to recognize that occurrence IDs are NOT the same thing as the catalogue numbers or accession numbers that museums typically assign to specimens in their collection.  The relatively short catalog numbers museums assign to distinguish specimens in their local collections may not even be unique from one division to the next. When museum catalog numbers are concatenated with a museum's “institution code” and a specific “collection code” those three pieces of information often come close to uniquely identifying a specimen when drawing from a multi-museum database. This combination of three fields is referred to as a “Darwin Core Triplet”).  Darwin Core Triplets are very comforting and helpful to some humans because of the information they encode about a specimen's source museum and division. In fact, this is why the Darwin Core Triplet is the most prominent information displayed for MorphoSource specimen records (and why MorphoSource administrators will get annoyed and hound you if you try to create specimen records lacking an institution code and catalog number).  However, Darwin Core Triplets are not a subsistute for Occurrence IDs in an informatic sense, mostly because museums change the different components in their Darwin Core Triplet fields in subtle ways from time to time.

When you create a new specimen record in MorphoSource, the Occurrence ID field should be filled in ONLY IF you are positive it is the official, museum-assigned occurrence ID. You should never put a catalog number in this field, or try to intuit or deduce the Occurrence ID from first principles.  Even though Occurrence IDs may sometimes contain the specimen's catalog number as part of its value, it should again be emphasized that they are not the same thing.

Keeping the Occurence ID field "clean" unless it is know exactly, is important because MorphoSource uses the Occurrence ID field to automatically link user-created specimen records with museum authored ones on a periodic basis when museums publish new records on iDigbio that weren't available at the time of specimen creation.  Therefore, if you enter something that is not the official Occurrence ID for your specimen, there is a small risk that it could (by random chance) be the Occurrence ID of another unrelated specimen at a different museum and cause the system to incorrectly replace your specimen with a different record.

How do I edit the specimen record I created?

First, make sure you are on the specimen record and not the media record. The URL for specimen records will read "https://www.morphosource.org/concern/biological_specimens/000######". To edit information for the specimen record, simply press "Edit" on the top right of the specimen record page. Navigate to the appropriate tab for the information you wish to edit (Organization, Taxonomy or Object Details).

Why can't I edit a specimen record I created?

Currently, you can edit any specimens you created post-launch of MS2.0 but not records imported from MS1.0 . We went through an arduous process of normalizing specimen information in the lead up to the launch of MS2.0. Therefore, all MS1.0 specimens that were migrated to MS2.0 can no longer be edited, except by admins.  We don’t allow manual editing of idigbio linked records – because we want those updates to come from idigbio, and since we put time into normalizing and regularizing all those existing records, we want people to email admins at morphosource@duke.edu if they think changes are necessary.

How do I link hand-made specimen records to existing iDigBio specimen records?

Go to the iDigbio portal (https://www.idigbio.org/portal/search) and find the record there. View the specimen record to verify it is correct. Copy the Occurrence ID on the iDigBio record and paste the ID into the Occurrence ID field on the MorphoSource record. You will need to press "edit" on the MorphoSource specimen record to access the Occurrence ID field. While you wont see an immediate change, it will add the necessary information (a valid occurrenceID) for us to automatically merge your record with the museum authored record the next time we update records from iDigbio.

I added someone as my Proxy Uploader, why can't they add media to my projects and teams?

Proxy Status and Project/Team membership are necessarily independent in the system. Thus you must Add your proxy user's account to whichever projects and teams you want them to add media to. A Depositor Role is appropriate here.

What is the difference between a Specimen/Object Record and a Media Record?

There needs to be only ONE Specimen/Object Record per Specimen/Object. This record is equivalent to a Specimen/Object search result from a museum database. Information like the museum collection, catalog number, institution code, locality, etc. will be available on here to add and edit. The purpose of having only ONE Specimen/Object Record is so that all of the media created from this one specimen/object is associated together under one record. That will allow users to see all available media for that one Specimen/Object.  You will know you are viewing a Specimen/Object Record if you see /concern/cultural_heritage_objects/ or /concern/biological_specimens/ in the URL for a Specimen/Object Record. Media Records will contain all of the metadata about that particular media. Voxel size, data creator, media type, device information etc. will be available on here to add and edit. You will know you are viewing a Media Record if you see /concern/media/ in the URL. You cannot edit Specimen/Object information from the Media Record and likewise, you cannot edit Media information from the Object Record. 

How do I change which Specimen/Object Record is used by a Media Record?

In some cases one may need to change which specimen is associated with a media record. To make such a change when the correct specimen record already exists in MorphoSource, (1) go to the media record show page with the incorrect specimen; (2) click on "edit" (if you do not see "edit" on the media page, you may not be logged in or may not have necessary User Role to edit the media.  In that case you can contact the data manager or uploader to discuss needed changes.); (3) go to the "Physical Object" tab and follow instructions on the page to search for, select, and save a different existing specimen.

If the correct specimen is NOT already in MorphoSource, you should contact the morphosource@duke.edu and explain the situation so we can advise.

File Contents

What files can I include in my .zip folders?

Please see  Critical Formatting Details and Modality Specific Instructions on which file types can/should be provided as .zips and also to see what should or should not be included.

Projects, Teams, and Organization Records

How do I set up an organization record for my specimens?

The list of institutions with organization records on MorphoSource can be found here. If the institution managing your specimen is not in our records, we will need to create a new organization record. The following information will need to be emailed to morphosource@duke.edu :

Parent Institution name: ?? (this is most often a university, museum, or institute)

Organization Name/Title: ?? (this is the “official name” of the facility/ department/ collection with the specimen)

Institution Code(s): ?? (most often the acronym of the parent institution name)

Collection Code(s): ?? (most often a letter or short code corresponding to the collection ex. mamm, herp)

Website: ?? (this the url of the official website for the organization)

Address: ?? (this the physical address of the organization)

Contact Name and email: ?? (this is the name and contact of whomever should be contacted by MorphoSource users for the organization)

iDigBio Recordset: ?? (the list of iDigBio Recordsets can be found here, if your organization does not report to iDigBio, fill in "Not Applicable")

How do I set up an organization record for my scanning facility?

The list of institutions with organizations records on MorphoSource can be found here. If the institution managing your device is not in our records, we will need to create an organization record. The following information will need to be emailed to morphosource@duke.edu :

Parent Institution name: ?? (this is most often a university, museum, or institute)

Organization Name/Title: ?? (this is the “official name” of the facility/ department/ collection managing the device)

Website: ?? (this the url of the official website for the organization)

Address: ?? (this the physical address of the organization)

Contact Name and email: ?? (this is the name and contact of whomever should be contacted by MorphoSource users for the organization)

Device Manufacturer: ??

Device Model: ??

Device Modality ?? (photogrammetry, structured light, CT/microCT, MRI, etc.)

Can I add a user without contributor status to my team or project?

Yes - if you add them with Viewer or Downloader status. No - if you try to add them as Manager, Editor, or Depositor

How do I edit my Team information?

Go to your team page and click on edit. On the edit page click on “details”. Add text into “description” field and then click “save changes” in the Actions drop down.

How do I add existing media to a Project?

On the media record you'd like to add to a Project, press Edit and scroll down to the 'Collections Media Belongs To' section. Use the search bar in this section to find and select the Project(s). If the project does not show up, confirm you are a member of the Project. It is also possible to add multiple media to a Project from the Media and Objects tab in your Dashboard. Checkmark the boxes of the media needing to be added to a Project then press the 'Add to Collection' button. Use the search bar in the popup to find and select to Project.

Publication Procedures

How do I get DOIs for my media?

MorphoSource administrators mint DOIs for users. Please email morphosource@duke.edu with a list of all the media you need DOIs for. If all the media is within a project, you can send us the title of the project along with the project ID and let us know all the media within the project require a DOI. A metadata quality check is part on the minting process, so be prepared to receive a list of edits necessary on your media records or specimen records. For a detailed list of requirements, visit DOI Persistent Identifiers for Media

How can journal reviewers see my media if it is private?

You can now anonymously share access to private media and private projects by generating temporary links if you have edit access to a media record or are a project manager. By sending the link URL to someone else, they can view the private media or project without logging into MorphoSource or while logged into a MorphoSource account that would otherwise not have access to those records. This is our new recommended solution for granting journal reviewers anonymous access to private media. To read more on this feature, visit New Feature: Media and Project Temporary Access Links

How do I change my media's publication status from Private to Public?

After logging in, click on the media record you would like to make public. Press the Edit button on the top right corner. Once the fields become editable, scroll down to the Ownership and Permission section to edit the Download Permission. Use the dropdown to select either Open Download or Restricted Download. If Restricted Download is selection, make sure the correct user is listed as the Download Reviewer so download requests can get approved. 

Data Usage

What if my download request hasn't been approved for weeks?

The Download Reviewer for the media will be listed beside "Download Reviewer". Clicking on the user's name will lead you to their profile which contains their email. You can then send them an email letting them know you've sent a download request, and it needs to be either approved (or denied) by logging onto MorphoSource. Download Reviewers receive an email from MorphoSource when another user requests to download their data. It is then up to that user to log in, and make the data available or not. Most users keep up with these download requests, but it may be that the emails got buried in their inbox. 

How do I figure out what the permitted uses of the data I downloaded?

Media records have an Ownership and Permissions section which lists the Contributor's selected Copyright and Licensing. You are able to click on the links next to "Copyright statement" and "Creative Commons license" in order to see the permitted uses under the selected Copyright and License. For questions regarding commercial use, the field "Permits commercial use" will either state it is permitted or not permitted.  If these fields have been left blank, it is appropriate to contact the listed media manager. Clicking on the data manager's name will lead you to their profile which contains their email.

Who do I contact for special permissions that appear prohibited by the standard ownership and permissions?

Ownership and Permissions for MorphoSource data are controlled by Data Managers listed on the media page.  Usually data managers are museum staff in charge of the physical specimen represented by the scan. You can find the Data Manager of your media of interest under the Ownership and Permissions section next to the "Data managed by" field. Clicking on the data manager's name will lead you to their profile which contains their email.

How do I get information on use of my data?

Currently usage data can be accessed from the public view of team and project pages you manage.

1. Login using an account that has a "manager" role for the team or project.
2. Go to the team's "public view" page.
3. Go to the upper right and expand the "export CSV" button.  You can choose from 3 different exports currently:

Available exports:

1. Media downloads = 1 row per download event.  The number of rows equals the total number of download events for all media in your project.  For each download, the media id is given as well as the download date, and user name and email of the downloader. The text of the download request and the “download intent” are also included.  You could use this to tally download rates over time for particular media, for the whole project, or for particular usage intents (eg “research”) etc.

2. Media download counts = 1 row per media. The number of rows equals the number of media in the project. For each media a count of the number of download events, the number of downloads by unique users, etc etc is given.  You could sort this by different categories to see which media are most used and in what ways.

3. Media requests = 1 row per request that was made for the media to be released (ie this is not downloads, just requests for access).  Fields included should be self explanatory at this point.