A general introduction to GBIFs technical documentation (GBIF techincal support hour for nodes)

The topic for the next Technical Support Hour for nodes is A general introduction to GBIFs technical documentation which will occur on the 3rd of April 2024 at 4pm CEST (UTC+2). Note that we are switching to summer time in Denmark and therefore the session has moved one hour ahead.

Last year the GBIF Secretariat released the first version of the technical documentation and work is ongoing to improve and enrich the documentation. We will give you an introduction to what information is already accessible.

We will be happy to answer any question relating or not to the topic. Please feel free to post questions in advance in this thread or write to helpdesk@gbif.org.


I signed up, maybe even twice :wink: but I can’t seem to find the meeting calendar invite with zoom link. Has it been sent out?

Thanks @IsabelC it looks like we had a bit of a technical issue here. You should have received something. Let us know if not.

Thanx Marie, I did not receive anything

YES - I got the confirmation email, thank you

1 Like

The video is available here: A general introduction to GBIFs technical documentation on Vimeo

Here is the transcript of the questions during the session.

Have you thought about linking to the guides and other “non-technical” documentation from the technical documentation website?
We will link to relevant material in individual relevant topics. We now have this open GitHub issue suggesting a section of the documentation for external resources.

Do you plan to maintain the GBIF data blog (https://data-blog.gbif.org/)?
Yes, we plan to maintain it. We aren’t planning to put documentation on the blog any more but it will still contain tutorials and output of analysis.

Is there a plan to list the mailing lists for technical topics on the Technical documentation website? I don’t know where to subscribe to be notified of changes in GBIF, for example when new filters are added on GBIF.
Thank you, I have logged the idea to have the mailing lists linked from the documentation here. When it comes to new additions on the GBIF website, you can consult the release notes here: Release notes but we don’t have any notification system.

Is it possible to include some of the technical documentation on a hosted portal? Ideally, it would be translated.
You are very welcome to use the information available on the technical documentation website how you see fit. However, keep in mind that if you copy paste information to your website, you will have to make sure it doesn’t go out of scope. It might make more sense to link directly to the technical documentation website to avoid having to constantly update the information when it changes.

How can we cite the technical documentation? Is there a DOI?
There is no DOI, you can cite it as a page from GBIF. See the citation guidelines: Citation guidelines

Should the technical documentation be translated?
Some parts of the technical documentation (like the API documentation) are auto-generated and won’t be translatable. It is technically feasible to translate the rest of the documentation (like the description of issues and flags), but that work needs to be balanced between overall user needs and the volunteers who provide this valuable service. The priority is to first mature the current documentation.

Is there any technical documentation of the system behind GBIF and what is behind the long term preservation of data?
There isn’t in the current technical documentation yet but I have logged this GitHub issue. This is currently available on GitHub.

[there are bits and pieces, currently at GBIF Infrastructure: Data processing and GBIF Infrastructure: Occurrence index on the data processing part, though they need revision and are somewhat hard to find]

In the IPT, for a given dataset, I would like to be able to include someone as a metadata author but I don’t want this person to be included in the auto-generated citations. What can I do?
The metadata author being included in the citation is by design, see also the following FAQs:

  • https://www.gbif.org/faq?question=where-does-the-dataset-citation-text-come-from-i-published-this-dataset-and

  • https://www.gbif.org/faq?question=how-is-the-dataset-citation-text-auto-generated

The logic being that the citation refers to the dataset, which makes the metadata author a relevant person to cite. You are welcome to cite the scientific publication describing how the data was collected in the dataset metadata.

I think the inclusion of the metadata author should be optional. Would that be possible? Otherwise, would it be possible to let authors themselves to decide how to create their citation.
I have logged this GitHub issue.

Does it matter if a name is in the Basic metadata or added as an Associated party with the role “metadata provider”?
The name will still be added to the citation.

If you select the auto-generated citation in the IPT, it isn’t the same as the auto-generated citation on GBIF.org . Could they be aligned?
The citations are as aligned as they can be in the newest IPT version, you can follow up on this GitHub issue.

[in general: the citation in the IPT cites the dataset as available at source, and therefore also allows both authored and auto-generated versions, while the ingested version available from GBIF.org has the auto-generated citation be default]

We were trying to get citations with the literature API but we haven’t managed to query the citations for several datasets in one API call. Could you help?
You can select multiple dataset keys in the literature API search function (documented here). See for example: https://api.gbif.org/v1/literature/search?gbifDatasetKey=2d4204c7-fd45-4104-8b26-5b05eb17e93a&gbifDatasetKey=4fa7b334-ce0d-4e88-aaae-2e0c138d049e.
Note that you can do the same in the web interface. For example: Resources.
You are also very welcome to use the export function to download the result of your search as a TSV file.

We can track download activities for occurrences and occurrence datasets. Is it possible for checklists as well?
Each occurrence download generated on GBIF.org of via the GBIF API is associated with a DOI and requires authentication. We are able to track a lot of information. This isn’t available for checklists. Right now, users can only access the checklist content via the Species API (which doesn’t generate downloads) or by getting the Darwin Core Archive at the source. This isn’t something that can allow us to keep track of the activities easily.
Note that users can download full or parts of checklists from https://www.checklistbank.org. I have logged the idea of tracking downloads from checklistbank here.
If you are interested in the topic of accessing and downloading species information. You might be interested in attending our next Data Use Club webinar in May: Data Use Club practical sessions: accessing and downloading species information

1 Like