Terms

Visitor – Someone who explores MorphoSource, but does not register an account. Such individuals cannot download data. No association between the identity of these individuals and their activity on the site is collected. However, if they view specimen media, that information will be stored with the specimen (i.e., we count the number of views that media experience).

User – Someone who registers an account with MorphoSource. There are no restrictions on who can register and there are no fees. Users can download media files that have been published. Users can also download metadata summaries of media files on MorphoSource. MorphoSource stores all data on which users download which datasets and makes that information available to data authors upon request. This policy promotes ethical use of data downloaded from MorphoSource and is one way of documenting impact of data uploaded by data authors or associated with particular with institutions or scanning facilities.

Data author – This is another name (our preferred name) for ‘data contributor.’ In other words it is someone who has uploaded data or entered metadata to the MorphoSource database. If you load media files to MorphoSource, you are the data author for those files. If you enter a new facility, institution, specimen number, or bibliographic reference to the database you are the data author for those items as well. Being the data author of a record means that, among other things, you have editorial control of it. There are tools for transferring data authorship of media files or other items between account holders when there is mutual agreement. Data authors have the ability to modify and delete media records they create. They also have the ability to modify non-media items they have created (i.e., specimen, institution, facility, and bibliography records). However, they will only be able to delete these records if no specimens or media in any projects held by any data author refer to them. This emphasizes another point about data authorship – while all media files uploaded by the data author remain private and inaccessible by anyone except the data author and specified ‘project members’ other records (i.e., specimen, institution, facility, and bibliography) become immediately public. This is to ensure that data authors working on unpublished projects do not inadvertently produce multiple instances of the same specimen, institution, etc. in the database.

Media – Any file uploaded to or downloadable from MorphoSource, with exception of user-customized summary tables. Media can represent raw data or derivative data files which include various 2D and 3D data formats. All media files are associated with a specimen record.

Media group – A collection of media files for which only one represents a raw data file and other represent different versions of derivative data. For instance, a media group could include a zipped file of volumetric data from a microCT scan (the raw data), and any number of mesh files extracted from that volumetric file (the derivative data). Examples of files that should NOT be included in the example group include 2D photographs of the specimen of interest, volumetric data created by other microCT scanners, or mesh files generated by other scanning modalities. Another example of media group would be a zip file of 2D photographs (the raw data), and mesh files created from these photos via photogrammetry (the derivative data). In some cases the data author may not wish to post a raw data file, but will post several derivative files associated with it. In this case, the derivative files should still be included in a single media group, even though their raw data file is not included.

Raw data - Media files that represent the original data from the digitization process. Such datasets include tiff or dicom stacks from microCT data, the initial output of a laser or structured light scanner (prior to merging, surfacing, or smoothing any individual components). There is no requirement that data authors provide the raw data for their 3D data. However, we definitely encourage it in the case of microCT data. The utility of providing raw versions of laser scan or structured light scanning data is less clear. One type of data we are not strongly interested in hosting is microCT projection data. In our perspective projection data generally inflates the file size and complicates the logistics of hosting microCT datasets to a degree that far outweighs any potential benefits to users or data authors. However, data authors should use their discretion and if they deem this level of data necessary then that will be respected within reason. Raw data files should NEVER represent more than a single specimen. If a specimen is represented by multiple elements or fragments, it is acceptable for one raw data file to contain several, or all of these. However, it is also okay for each element of a multi-part specimen (e.g. a skeleton) to be represented by a distinct raw data file.

Derivative data – Media files that are in some way derived from a raw data file, and whose metadata include parameters of the raw data file. For instance, multiple .stl files or a .ply files (two different mesh file formats) may be derived from a volumetric microCT file. Derivative data can represent reconstructed versions of fragmented specimens (e.g., a bone was scanned in pieces, segmented, and the segmented mesh files were digitally re-assembled). However, reconstructions representing composites of more than one specimen or with significant amounts of digitally sculpted morphology are NOT appropriate.

Publishing – On MorphoSource, publishing refers to the act of the data author releasing media files from his/her private account to the public archive. The publishing process is currently reversible. Data authors can change publication settings as much as they desire. MorphoSource will eventually allow (but not require) DOI registration. Once media are published with a DOI, it cannot be unpublished. Data authors should obtain permission from all relevant parties before publishing files. If data authors cannot get permission to publish their files with open access by third parties with whom they have binding agreements, they can still ‘publish with restricted access’. This setting allows users to see that data exist and to request access from the data author or other parties that the data author designates.

Creative Commons Licensing – When entering metadata on media files, the data author should be aware of copyright issues surrounding their digital imagery. We recommend that data authors confirm with their collaborating scanning facilities and institutions who the copyright holder of the data is so that this is specified correctly. Many museums also have third party distribution statements that researchers must sign before being allowed to scan specimens. In most cases, it is appropriate to display the text of these third party agreement statements in the notes field of media group entry form. Once copyright holder is determined, the creative commons licensing settings must be correctly set. We recommend “Permission to use data on MorphoSource is granted by Copyright holder" for the Copyright Permission field and “Attribution-NonCommercial CC BY-NC reuse but noncommercial" for the Copyright License field. Please do not publish media until you have assigned the appropriate license and entered the Copyright Holder. Click here for more information on Creative Commons Licensing.

Institution – This refers to the institution at which a specimen is vouchered or housed. Usually the institutional acronym in the specimen number represents the ‘institution’ of the specimen. However, it is not appropriate to re-use the institution acronym in the ‘institution’ field. Data authors should find the formal title and address data on their specimen’s institution and enter them here.

Facility – This refers to ‘digitization facility’ and can be a university or museum, a university or museum department or center, a PI lab, a private sector company, etc. It refers to the facility that provides the infrastructure for creating the raw data media files. For microCT scans, the equipment is not portable so the physical facility is obvious. For portable digitization devices (including cameras) the facility is the lab of the PI or the department that owns the equipment. If the equipment belongs to a graduate student, either the advisor’s lab or the graduate student’s department should be used as the facility. If you are not sure how to reference a facility, it is best to contact individual’s representing it to acquire their preferred, formal name.