How to get a DOI for your Publication

A digital object identifier (DOI) is a persistent identifier assigned to uniquely identify a digital object. Creating and assigning a new DOI for things in Synapse, such as datasets, allows you to reference them elsewhere like in a publication or on an external website.

See an example dataset with a DOI here.

Create a Synapse dataset

When planning a manuscript based on data hosted in the ELITE Portal, contact the EL DMCC through the AD + EL Service Desk as early as possible in the process.

Use the Request type, “Request a DOI for Publication”

1. Complete the “Request a DOI for Publication” Service Desk form. Ensure you provide the following:

   1. The Synapse username(s) of all users who need edit permission to your Dataset (e.g., manuscript coauthors, collaborators, etc).

   2. Whether you have analysis files related to your manuscript* that are not already in the ELITE Portal and that you need to include in the Dataset.

The EL DMCC will create:

• An empty dataset in Synapse with edit permission for you and any requested collaborators

• If you have analysis files, a Synapse folder labeled YourLastname_YourFirstname in the “Manuscript-Related Analysis Files” section of the ELITE Portal Synapse project. Your directory will be private, and you will have edit/delete permission to it.

Upload and add files to your dataset

2. Upload any additional files and analysis outputs to your designated Synapse folder.

   1. You can upload with the Synapse web UI or in bulk with one of the programmatic clients.

   2. We recommend creating sub-folders within your designated folder for different projects, because you will use the same designated folder for any future manuscripts.

3. (Optional) Annotate your files to further describe them.

*Manuscript-Related Analysis Files that you upload will not be curated by the DMCC and can only be uploaded if they meet open-access governance criteria. These can include: 

• Any files that contain summary-level data such as differential expression results, summary statistics, model parameters or estimates, etc (must NOT contain individual-level data like individual identifiers, sequence data, gene counts, or clinical data)

• Code or processing scripts

• Other manuscript-related files like supplementary tables, protocols, images, diagrams, etc, that help contextualize your analysis and that do not contain any identifying or sensitive information

Once your files are uploaded, the EL DMCC will verify that they do not contain any sensitive data and make them public so they can be included in a Dataset.

4. Go to your new Dataset and add items. You can add any files that you have access to from anywhere in Synapse, and you can specify the exact version of those files you used in your analysis if a file has multiple versions. For ELITE Portal Datasets, you should add:

   1. All raw or processed data files used in the analysis

   2. The individual, biospecimen, and appropriate assay metadata files from all ELITE Portal studies with data in your Dataset.

   3. Any analysis, results, or additional files from your personal “Manuscript-Related Analysis” folder. 

Add wiki information

5. Go to "Dataset Tools" and then "Edit Dataset Wiki" to customize the wiki information for your dataset. Please include:

   1. Manuscript title

   2. Author list 

   3. Manuscript preprint URL or published URL

   4. The Synapse username for a “Dataset contact” – someone whom data users can contact if they have questions about your Dataset. Do this by typing ‘@’ and search for the name.

   5. Any relevant acknowledgement statements and/or publications that secondary data users should reference in further publications. Data acknowledgement statements can be found on the Study Details pages for each study in the ELITE Portal. 

   6. (Optional) Any other information you would like to include to help contextualize your dataset or analysis. See here for information on adding links, tables, images, and more to your wiki. 

6. Edit the Dataset schema to customize the visible columns displayed with the Dataset. You can add, remove, or re-order any columns you want. A good default is to select the “Add Existing Annotations” option, which will include all of the annotations that we apply to files in the ELITE Portal.

7. Once the wiki details and Dataset items are finalized, create a stable Dataset version.

   1. Provide an informative comment when you create a stable version – e.g., “Dataset for manuscript submission April 2022” or “Finalized analysis for Smith et al. 2022 publication”.

   2. If you need to make additional changes after you create a stable version, go back to the draft version, make changes, and create a new stable version with a new informative comment. 

Create a DOI

1. From your stable version, go to "Dataset Tools" --> "Create a DOI" and mint the DOI for the stable Dataset version. DOI metadata becomes public information, so make sure to enter manuscript relevant information. See this example.

2. Add the DOI to the following manuscript Data Availability statement and provide the complete statement with your manuscript submission:

   1. “<data, analysis output, tools (describe content)> are available via the ELITE Portal (https://eliteportal.synapse.org). The ELITE Portal is a platform for accessing data, analyses, and tools generated by the Exceptional Longevity projects funded by the National Institute on Aging (NIA) to enable open-science practices and accelerate translational learning. The data, analyses and tools are shared early in the research cycle without a publication embargo on secondary use. Data is available for general research use according to the following requirements for data access and data attribution (https://eliteportal.synapse.org/Data Access). For access to content described in this manuscript see: <dataset DOI>”