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User Guide — de.NBI Service Registration

What is this?

This is the de.NBI & ELIXIR-DE Service Registration system. Use it to register your bioinformatics service for inclusion in the de.NBI services catalogue.

Registering a New Service

  1. Go to /register/ and fill in the form. All fields marked (*) are required.

  2. Work through each section:

Section What you need
A — General Today's date, your name and affiliation
B — Service Data Service name, description, year, category, EDAM annotations, publications
C — Responsibilities Responsible PI(s), host institute, contact emails
D — Links Service website, terms of use, license, optional repository and registry links
E — KPIs Whether KPI monitoring is in place
F — Discoverability Keywords for search and citation tracking
G — Consent Data protection consent (required to submit)

  1. Click Submit Registration.

  2. You will receive a confirmation email at the address you provided as internal contact, acknowledging that your registration was received. Keep this email for your records — it contains your Submission ID.

  3. Save your API key immediately. On the confirmation page you will see a box containing your unique API key. This key:

  4. Is shown exactly once — it will not be emailed to you.
  5. Is required to edit your submission later.
  6. If lost, contact servicecoordination@denbi.de to have a new one issued.

Editing an Existing Submission

  1. Go to /update/.
  2. Paste your API key into the text field and click Retrieve My Registration.
  3. Your form will be pre-populated with all existing values.
  4. Make your changes and click Save Changes.
  5. Two emails are sent automatically:
  6. Administration office — notified of your changes with a summary of what was updated.
  7. You — a confirmation email is sent to your internal contact address listing exactly which fields changed (previous value → new value).

Note: If your submission was already approved and you edit it, the status will reset to "Submitted" for re-review.

Security notice

If you receive a "your registration has been updated" email that you did not initiate, contact the de.NBI administration office immediately. The email will include instructions at the bottom.

Field Help

Publications (PMIDs/DOIs)

Enter comma-separated PMIDs (PubMed IDs, digits only) or DOIs (starting with 10.):

12345678, 10.1016/0022-2836(70)90057-4, 98765432

PMIDs are required for ELIXIR impact assessment.

Institute / Affiliation (Section A)

The affiliation field is a searchable combobox. As you type, it filters a list of known institute names drawn from registered PIs and previous submissions. If your institute is not in the list, simply finish typing the full name and press Enter (or click Use "…" in the dropdown) — the value you typed is accepted as-is.

Service Categories

Click any category to select or deselect it. Multiple selections are supported — no modifier key needed. Selected categories appear as pills at the top of the field.

Toolbox

If your service is part of a de.NBI toolbox, select Yes and enter the toolbox name. If you select "Associated partner" as a PI, you must provide their name and affiliation.

EDAM Ontology Annotations (Section B)

EDAM is a community ontology for bioinformatics. Annotating your service makes it discoverable in bio.tools, the ELIXIR Tools & Data Services Registry, and other platforms. These fields are optional but strongly recommended.

EDAM Topics describe the scientific domain of your service. Examples:

  • Proteomics
  • Genomics
  • Structural biology
  • Metagenomics
  • Metabolomics

EDAM Operations describe what your service does computationally. Examples:

  • Sequence alignment
  • Protein structure prediction
  • Visualisation
  • Pathway analysis
  • Database search

How to use the field:

  1. Click the search box and start typing — e.g. "prote" will filter to all terms containing that string.
  2. Select a term from the dropdown. The term label and its EDAM accession (e.g. topic_0121) are shown.
  3. You can select up to 6 terms per field.
  4. To remove a term, click the × next to it.

Tip: If your tool is already registered in bio.tools, the form will offer to prefill EDAM terms from your bio.tools entry automatically — see bio.tools Prefill below.

bio.tools Prefill

If your service already has a bio.tools entry, enter the URL in the Link to bio.tools entry field (Section D) and move to the next field (press Tab).

The form will automatically look up your tool in bio.tools and, if found, show a banner:

Metadata found in bio.tools — Fields have been pre-filled from your bio.tools entry. Review and adjust before saving.

Click Apply prefill to populate the following fields from bio.tools data:

  • Service name (if currently empty)
  • Service description (if currently empty)
  • Website URL (if currently empty)
  • GitHub URL (if currently empty)
  • Publications (if currently empty)
  • License (if a matching license is available)
  • EDAM Topics (adds bio.tools annotations; does not remove your existing selections)
  • EDAM Operations (same)

Important: Prefilled data is a suggestion — always review and correct it before submitting. Your submission is authoritative; bio.tools is the source of the prefill only.

If the bio.tools lookup fails (tool not found, or bio.tools is temporarily unavailable), a warning banner is shown and you can fill in the fields manually.

URL fields

All URLs must use https://. Plain http:// URLs are not accepted.

Domain-specific URL fields enforce a prefix match in addition to the HTTPS requirement:

Field Required prefix
Website URL https:// (any domain)
Terms of use URL https:// (any domain)
GitHub repository https://github.com/
bio.tools entry https://bio.tools/
FAIRsharing entry https://fairsharing.org/
Other registry https:// (any domain)

FAIRsharing (https://fairsharing.org/) is a curated resource of data standards, policies, and databases. If your service or the data formats it uses are listed in FAIRsharing, linking here helps with discoverability and FAIR compliance metadata.

Logo Upload (Section B)

You can optionally upload a logo for your service. This field is not required.

Property Value
Accepted formats PNG, JPEG, SVG
Maximum size 10 MB
Required No

How to upload:

  1. In Section B, click the logo upload field
  2. Select a PNG, JPEG, or SVG file from your computer
  3. The logo is validated automatically on form submission

What happens to uploaded logos:

  • JPEG and PNG files are re-encoded to strip any embedded EXIF metadata
  • SVG files are sanitised to remove scripts, event handlers, and external links
  • The original filename is discarded — a unique identifier is assigned internally
  • The logo appears in the admin view and is accessible via the API (logo_url field)

To replace a logo, simply upload a new one when editing your submission. Previous logos are retained on disk but replaced for display purposes.

Outreach and Survey fields (Section F)

Field What it means
Outreach consent You agree to de.NBI potentially showcasing your service on social media or newsletters. You can withdraw this consent at any time by editing your submission.
Survey participation You are willing to be contacted for de.NBI user surveys (e.g. annual usage statistics). Defaults to Yes.

License

Select the license that governs how users may use your service. Select "Not applicable" for services without a software license (e.g. pure databases).

Submission Status Lifecycle

Your submission moves through these states:

Status Meaning
Draft Saved locally but not yet submitted. Draft submissions older than 30 days are automatically deleted.
Submitted Form submitted. The de.NBI administration office has been notified.
Under Review Actively being reviewed by the service coordination team.
Approved Your service has been accepted and will appear in the de.NBI services catalogue.
Rejected The submission was not accepted. You will receive an email explaining why. You may edit and resubmit.
Deprecated The service is no longer active. You can mark your own service as deprecated via the edit form (see below). Only the registry team can reverse this.

If you edit a submission that was already Approved, the status resets to Submitted and the administration office is notified to re-review your changes.

Deprecating Your Service

If your service is no longer active, you can mark it as deprecated directly from the edit form:

  1. Log in with your API key via the Update / Edit page (/update/).
  2. Scroll to the Danger Zone card in the right sidebar.
  3. Click Deprecate this service and confirm in the dialog.

The status will be set to Deprecated and the registry team will be notified. Only registry admins can reverse a deprecation — contact servicecoordination@denbi.de if you need to reactivate a deprecated service.

What happens after submission?

  1. The de.NBI Service Coordination Office reviews your submission.
  2. You will receive an email at your internal contact address when the status changes.
  3. If approved, your service will appear in the de.NBI services catalogue.
  4. You can update your submission at any time using your API key.
  5. Every time you edit your submission, you will receive a confirmation email listing exactly what changed — so you always have a record of your updates.

Lost Your API Key?

Contact the de.NBI administration office at servicecoordination@denbi.de. Include your service name and the email address you used as the internal contact. An administrator will verify your identity and issue a new key.

Questions?

Email the de.NBI Service Coordination Office: servicecoordination@denbi.de