User Guide¶

What is this?¶

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

Registering a New Service¶

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

The form features a sidebar on the right with: - Quick navigation links to jump between sections (A-G) - A progress bar showing required field completion percentage - Contact information for support

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, start year (if applicable)
F — Discoverability	Keywords for search, citation tracking, and survey participation
G — Consent	Data protection consent (required to submit)

Click Submit Registration.
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.
Save your API key immediately. On the confirmation page you will see a box containing your unique API key. This key:
Is shown exactly once — it will not be emailed to you.
Is required to edit your submission later.
If lost, contact servicecoordination@denbi.de to have a new one issued.

API Key Scope¶

Each submission gets a write-scope API key by default, which allows full editing of your service registration. The registry team can also issue read-scope keys upon request for external consumers (e.g., dashboards or automated systems) that only need to view data without making changes.

Editing an Existing Submission¶

Go to /update/.
Paste your API key into the text field and click Retrieve My Registration.
Your form will be pre-populated with all existing values.
Make your changes and click Save Changes.
Two emails are sent automatically:
Administration office — notified of your changes with a summary of what was updated.
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.

Browsing the Service Catalogue¶

When the Service Catalogue is enabled by the site administrators, a Service Catalogue link appears in the top navigation bar.

The catalogue at /catalogue/ lists all approved services and supports:

Search — type in the search box to find services by name, description, host institute, or keywords (debounced, no page reload)
Filter — use the sidebar to filter by category or service centre (multi-select, combined with AND across dimensions)
Sort — choose A→Z, Z→A, recently updated, or recently added
Group — group results by category, service centre, or responsible PI (accordion sections)
Pagination — results are paginated server-side; URL state is preserved so you can share or bookmark any view

Each service card shows the service name, description, category, service centre, and optional EDAM topic badges. Where available, icon badges link directly to the service's GitHub repository, bio.tools entry, FAIRsharing record, or other registry.

The catalogue is read-only and requires no login.

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:

Click the search box and start typing — e.g. "prote" will filter to all terms containing that string.
Select a term from the dropdown. The term label and its EDAM accession (e.g. topic_0121) are shown.
You can select up to 6 terms per field.
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:

In Section B, click the logo upload field
Select a PNG, JPEG, or SVG file from your computer
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.

Form Auto-Save / Draft¶

While filling out the form, your progress is automatically saved to your browser's local storage. If you navigate away or close the tab, you can return later and your partially completed form will still be there — a "Draft restored" banner appears at the top of the form when this happens. Click Clear draft in that banner to discard the saved values and start fresh.

This draft is a browser-side convenience only — it is not visible to the registry team and does not count as a submission until you click Submit.

A few things to know:

Submitting the form always clears the draft — you will not see a restored draft after a successful submission.
Drafts expire after 7 days of inactivity. If you return after more than 7 days without having submitted, the draft will be gone and the form will start blank.
Some fields are not saved to the draft: the consent checkbox (you must tick it deliberately every time), the CAPTCHA, and any uploaded logo file.
If a service has been modified by an administrator since you last visited the edit form, the old draft is automatically discarded. The form always shows the current registered values in that case.

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. You can select one or more standard licenses from the list (e.g. MIT, Apache-2.0).

If none of the standard licenses apply, use the License note field below to enter:

"Not applicable"
"None of the above"
"Proprietary"
Or a custom license name

Note: At least one of License(s) or License note must be provided.

Submission Status Lifecycle¶

Your submission moves through these states:

Status	Meaning
Draft	Saved locally in your browser but not yet submitted. The browser draft expires after 7 days of inactivity and is always cleared when you submit.
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. Deprecated services are hidden from public listings but retain their history.

If you edit an Approved submission, what happens depends on which fields you changed:

Fields that reset status to Submitted (any core service content — name, description, categories, responsible PIs, contact details, licenses, etc.): The status is reset to Submitted and the administration office is notified to re-review your changes. Your maturity tags are cleared and will be re-assigned after approval. You will receive a confirmation email with a summary of what changed and a note that re-review has been triggered.

Fields that preserve Approved status (supplementary/reference fields — logo, GitHub URL, bio.tools URL, FAIRsharing URL, EDAM topic, operation annotations, etc.): The status stays Approved and your maturity tags are preserved. You receive a confirmation email listing what changed, with no lifecycle notice.

When in doubt, check your confirmation email

Every edit sends you an email listing exactly what changed. If the email includes the notice "your service registration has been reset to Submitted", the re-review cycle has been triggered. If it does not, your service remains approved.

What happens after submission?¶

The de.NBI Service Coordination Office reviews your submission.
You will receive an email at your internal contact address when the status changes.
If approved, your service will appear in the de.NBI services catalogue.
You can update your submission at any time using your API key.
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.

Deprecating Your Service¶

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

Log in with your API key via the Update / Edit page (/update/).
Scroll to the Danger Zone card in the right sidebar.
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.

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