General structure of metadata submission template
by Vera Bockhorn
Dear colleagues,
in our weekly coding group meeting some questions regarding the structure (not the content!) of the excel submission template came up and we decided that it would be beneficial if we could all agree on some rules regarding the structure of the template, as well as a nomenclature that defines how properties should be named.
You might wonder why this is important, but it would enable us (the coding group) to write more universal code and generally simplify things. Below, I outlined our current preferences regarding template structure and nomenclature. Of course, none of this is set in stone yet and should you diagree with anything or want to add something, we will discuss this at our next TA1/2 meeting. I will also write this into the overview document under "3.7.2 Submission Template – General Structure & Nomenclature", you can just add to it there.
1. Relational classes (i.e. "Study", "Subject", ...) are each a single sheet in the file. The sheet name would be in Camel-case (i.e. "Study", "ExperimentalProtocol", "LabSample")
2. The properties for each class are each a column in the corresponding sheet. Column names are in Snake-case (i.e. "access_type", "sample_type", "species")
3. All relational keys (primary and foreign) follow the same syntax: First the sheet name in lower case, then an underscore and then "ID", examples: "subject_ID", "labsample_ID"
Open question: Should the template contain additional information that will guide the user when filling the template? Additional information could be: A short description of the property, allowed values / types, can multiple values be entered (and if yes, how to separate them correctly), is the property required/recommended/optional?
Looking forward to any feedback on this!
Best,
Vera
6 days, 6 hours
BioMed Interoperability Workshop 2025
by Böhm, Sebastian
Dear all,
I hope you're doing fine.
Trying to organise the in-person meeting in Leipzig, I identified
three dates for a two-days Workshop before summer holidays.
The following link will bring you to the poll, in order to
Identify which date is most suitable:
https://nuudel.digitalcourage.de/bKtTyKHItNqJzszG<https://scanmail.trustwave.com/?c=4477&d=qobl521VMpBwkaHLcQuQQEgMP1qYwZEn...>
If none of them are suitable, you can vote for a later date,
which will then be at earliest in October.
Please vote until the end of next week: DEADLINE 4th of April
so that we don't miss our favourite free spot for the workshop!
For the case that you are planning to attend, please make sure to vote,
so that I do have oversight about the group size.
We can discuss at our next regular meeting on the 07th of May the result of the poll
and the content of the Workshop. The Workshop should be suitable for everyones needs,
so please make sure to bring forward your needs at the next Meeting in May.
Looking forward seeing you there.
Best wishes,
Sebastian
Dr. Sebastian Böhm
Institut für Immunologie
___________________________________________
Friedrich-Loeffler-Institut
Bundesforschungsinstitut für Tiergesundheit
Federal Research Institute for Animal Health
Südufer 10 | 17493 Greifswald - Insel Riems
Tel: +49 38351 7 1889/1602
https://www.fli.de/
¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯
Instagram<https://www.instagram.com/loeffler_news>
LinkedIn<https://www.linkedin.com/company/friedrich-loeffler-institut>
1 week
TA1/2 Thursday call
by Stervbo,Ulrik
Dear all,
Is a need for the call tomorrow? Are there any updates from the groups and tasks we need to discuss?
I only have this one update: For the all hands meeting in Berlin, there will be a longer separate session focused on simulating a data submission process from opening a webpage to data deposit to searching for data. There should be no more than two participants form each TA as to not dilute the other break out sessions.
Best,
Ulrik
----
Dr. rer. nat. Ulrik Stervbo
Center for Translational Medicine, Immunology, and Transplantation
Marien Hospital Herne – Universitätsklinikum der Ruhr-Universität Bochum
Hölkeskampring 40
44623 Herne
Germany
Immundiagnostik
Marien Hospital Herne – Universitätsklinikum der Ruhr-Universität Bochum
Düngelstr 33
44623 Herne
Germany
Tel: +49 234 509 590 54
www.marienhospital-herne.de/TranslationaleMedizin<http://www.marienhospital-herne.de/TranslationaleMedizin>
www.babel-lab.de<http://www.babel-lab.de>
_______________________________________________________________
Mitten in der St. Elisabeth Gruppe:
St. Anna Hospital Herne, Marien Hospital Herne – Universitätsklinikum der Ruhr-Universität Bochum,
Marien Hospital Witten, Rheumazentrum Ruhrgebiet, St. Marien Hospital Eickel,
Medizinische Reha für psychische Gesundheit, St. Elisabeth Stift Herne, Senioreneinrichtungen Widumer Höfe,
Gästehaus St. Elisabeth, Ambulante Pflege, MVZ Ärzte – Herne | Wanne | Witten,
Lukas Hospiz Herne, St. Elisabeth Hospiz Witten, Bildungszentrum Ruhr, Bildungswerk,
Campus der St. Elisabeth Gruppe, Kinder in der St. Elisabeth Gruppe
_______________________________________________________________
Aufsichtsratsvorsitzender: Dr. Hans Willmes
Geschäftsführung: Dr. Sabine Edlinger, Simone Lauer
Registergericht:
HRB 9735 Amtsgericht Bochum
St.-Nr.: 325/5894/2251
_______________________________________________________________
Wir bitten wegen der aktuellen Virenangriffe um folgende Beachtung:
Das Sicherheitskonzept der St. Elisabeth Gruppe erlaubt momentan keine Zustellung von .doc
(x) und .xls(x) Dateien! Schicken Sie Dokumente nur in Form von .pdf Dateien oder nehmen Sie
Kontakt auf, um andere Übertragungsmöglichkeiten abzusprechen.
1 week, 1 day
Prototype deadline
by Stervbo,Ulrik
Dear all,
Now that were are closing in on summer and delivering the NFDI4Immuno prototype, we should set an actual deadline for the delivery.
I recommend marking the prototype done just before people leave for their summer holidays. therefore:
Please let me know when you are leaving for the summer?
Best,
Ulrik
----
Dr. rer. nat. Ulrik Stervbo
Center for Translational Medicine, Immunology, and Transplantation
Marien Hospital Herne - Universitätsklinikum der Ruhr-Universität Bochum
Hölkeskampring 40
44623 Herne
Germany
Immundiagnostik
Marien Hospital Herne - Universitätsklinikum der Ruhr-Universität Bochum
Düngelstr 33
44623 Herne
Germany
Tel: +49 234 509 590 54
www.marienhospital-herne.de/TranslationaleMedizin<http://www.marienhospital-herne.de/TranslationaleMedizin>
www.babel-lab.de<http://www.babel-lab.de/>
_______________________________________________________________
Mitten in der St. Elisabeth Gruppe:
St. Anna Hospital Herne, Marien Hospital Herne - Universitätsklinikum der Ruhr-Universität Bochum,
Marien Hospital Witten, Rheumazentrum Ruhrgebiet, St. Marien Hospital Eickel,
Medizinische Reha für psychische Gesundheit, St. Elisabeth Stift Herne, Senioreneinrichtungen Widumer Höfe,
Gästehaus St. Elisabeth, Ambulante Pflege, MVZ Ärzte - Herne | Wanne | Witten,
Lukas Hospiz Herne, St. Elisabeth Hospiz Witten, Bildungszentrum Ruhr, Bildungswerk,
Campus der St. Elisabeth Gruppe, Kinder in der St. Elisabeth Gruppe
_______________________________________________________________
Aufsichtsratsvorsitzender: Dr. Hans Willmes
Geschäftsführung: Dr. Sabine Edlinger, Simone Lauer
Registergericht:
HRB 9735 Amtsgericht Bochum
St.-Nr.: 325/5894/2251
_______________________________________________________________
Wir bitten wegen der aktuellen Virenangriffe um folgende Beachtung:
Das Sicherheitskonzept der St. Elisabeth Gruppe erlaubt momentan keine Zustellung von .doc
(x) und .xls(x) Dateien! Schicken Sie Dokumente nur in Form von .pdf Dateien oder nehmen Sie
Kontakt auf, um andere Übertragungsmöglichkeiten abzusprechen.
1 week, 5 days
Notifications for Individual Documents – Changes & Comments
by Sebastian Ferrara
Hello,
Christian Busse showed us a good way to enable notifications for individual documents, i.e., when someone makes a change or writes a comment.
First, go to your Nextcloud profile and open Settings (Einstellungen).
[cid:image002.png@01DB9A82.C68A25D0]
Then, go to "Notifications or Benachrichtigungen" on the left side.
[cid:image008.png@01DB9A82.C68A25D0]
Then go to activity.
Depending on what you want to enable, check the box for Mail for one or more of the following options:
[cid:image009.png@01DB9A82.C68A25D0]
If you scroll down, you can set how often you receive a notification.
[cid:image011.png@01DB9A82.C68A25D0]
Finally, you need to select the desired document, click on the button with the person and the plus sign, add your email address under "Share," and then you should start receiving notifications.
But it has to be your real account without the letter sign.
If it doesn't work, feel free to contact me.
[cid:image013.png@01DB9A82.C68A25D0]
Have a nice weekend,
Sebastian Ferrara
1 week, 6 days
INFO: Friendly reminder about tomorrow's TA1/TA2 call
by Stervbo,Ulrik
Dear TA1/2 Members,
This is a friendly reminder about our joint TA1/TA2 call scheduled for tomorrow from 11:00 - 12:00 (11:58). You can join the call using the following link: https://conf.dfn.de/webapp/#/?conference=979176819. The PIN is 7570 (host pin: 7579).
Please review and add milestones to the _OverviewDoc.docx in Task Area 1 > Call minutes.
Updates/FYI/reminders which we will not cover at the call:
- Registration open for Zooming into the Community III: The biannual virtual meeting of the AIRR Community: https://www.antibodysociety.org/the-airr-community/meetings/zooming-in-to...
You can find the call minutes on the NFDI4Immuno NextCloud under Task Area 1 > Call minutes (https://nextcloud.nfdi4immuno.de/f/1608). The agenda for tomorrow's call is stored at the same location.
If you're unable to attend, please let me know. Regular joint TA1/TA2 calls are every Thursday 11:00 - 12:00.
Best,
Ulrik
----
Dr. rer. nat. Ulrik Stervbo
Center for Translational Medicine, Immunology, and Transplantation
Marien Hospital Herne - Universitätsklinikum der Ruhr-Universität Bochum
Hölkeskampring 40
44623 Herne
Germany
Immundiagnostik
Marien Hospital Herne - Universitätsklinikum der Ruhr-Universität Bochum
Düngelstr 33
44623 Herne
Germany
Tel: +49 234 509 590 54
www.marienhospital-herne.de/TranslationaleMedizin<http://www.marienhospital-herne.de/TranslationaleMedizin>
www.babel-lab.de<http://www.babel-lab.de/>
_______________________________________________________________
Mitten in der St. Elisabeth Gruppe:
St. Anna Hospital Herne, Marien Hospital Herne - Universitätsklinikum der Ruhr-Universität Bochum,
Marien Hospital Witten, Rheumazentrum Ruhrgebiet, St. Marien Hospital Eickel,
Medizinische Reha für psychische Gesundheit, St. Elisabeth Stift Herne, Senioreneinrichtungen Widumer Höfe,
Gästehaus St. Elisabeth, Ambulante Pflege, MVZ Ärzte - Herne | Wanne | Witten,
Lukas Hospiz Herne, St. Elisabeth Hospiz Witten, Bildungszentrum Ruhr, Bildungswerk,
Campus der St. Elisabeth Gruppe, Kinder in der St. Elisabeth Gruppe
_______________________________________________________________
Aufsichtsratsvorsitzender: Dr. Hans Willmes
Geschäftsführung: Dr. Sabine Edlinger, Simone Lauer
Registergericht:
HRB 9735 Amtsgericht Bochum
St.-Nr.: 325/5894/2251
_______________________________________________________________
Wir bitten wegen der aktuellen Virenangriffe um folgende Beachtung:
Das Sicherheitskonzept der St. Elisabeth Gruppe erlaubt momentan keine Zustellung von .doc
(x) und .xls(x) Dateien! Schicken Sie Dokumente nur in Form von .pdf Dateien oder nehmen Sie
Kontakt auf, um andere Übertragungsmöglichkeiten abzusprechen.
2 weeks, 1 day
NFDI4Chem work with DCAT-AP
by Stervbo,Ulrik
Dear all,
Philip Strömert from NFDI4Chem is working on linking 4Chem to DCAT-AP. If there is interest I will set up a call with him to hear about his experiences and work.
Please ping me back if you are interested.
Best,
Ulrik
----
Dr. rer. nat. Ulrik Stervbo
Center for Translational Medicine, Immunology, and Transplantation
Marien Hospital Herne - Universitätsklinikum der Ruhr-Universität Bochum
Hölkeskampring 40
44623 Herne
Germany
Immundiagnostik
Marien Hospital Herne - Universitätsklinikum der Ruhr-Universität Bochum
Düngelstr 33
44623 Herne
Germany
Tel: +49 234 509 590 54
www.marienhospital-herne.de/TranslationaleMedizin<http://www.marienhospital-herne.de/TranslationaleMedizin>
www.babel-lab.de<http://www.babel-lab.de/>
_______________________________________________________________
Mitten in der St. Elisabeth Gruppe:
St. Anna Hospital Herne, Marien Hospital Herne - Universitätsklinikum der Ruhr-Universität Bochum,
Marien Hospital Witten, Rheumazentrum Ruhrgebiet, St. Marien Hospital Eickel,
Medizinische Reha für psychische Gesundheit, St. Elisabeth Stift Herne, Senioreneinrichtungen Widumer Höfe,
Gästehaus St. Elisabeth, Ambulante Pflege, MVZ Ärzte - Herne | Wanne | Witten,
Lukas Hospiz Herne, St. Elisabeth Hospiz Witten, Bildungszentrum Ruhr, Bildungswerk,
Campus der St. Elisabeth Gruppe, Kinder in der St. Elisabeth Gruppe
_______________________________________________________________
Aufsichtsratsvorsitzender: Dr. Hans Willmes
Geschäftsführung: Dr. Sabine Edlinger, Simone Lauer
Registergericht:
HRB 9735 Amtsgericht Bochum
St.-Nr.: 325/5894/2251
_______________________________________________________________
Wir bitten wegen der aktuellen Virenangriffe um folgende Beachtung:
Das Sicherheitskonzept der St. Elisabeth Gruppe erlaubt momentan keine Zustellung von .doc
(x) und .xls(x) Dateien! Schicken Sie Dokumente nur in Form von .pdf Dateien oder nehmen Sie
Kontakt auf, um andere Übertragungsmöglichkeiten abzusprechen.
2 weeks, 3 days
BioMed Interoperability Meeting
by Böhm, Sebastian
Dear all,
I hope you're doing fine.
This Email is a kind reminder for our upcoming meeting on Wednesday 19.03.2025.
The Meeting will take place via Zoom.
Please find the meeting details here:
Thema: NFDI BioMed - Interoperability Meeting
Zeit: 19.März 2025 13:00 Amsterdam, Berlin, Rom, Stockholm, Wien
An Zoom-Meeting teilnehmen
https://eu01web.zoom.us/j/66526241159?pwd=YUdsRwnRHvrFXF43yrFSdeKgiB95QL.1
Meeting-ID: 665 2624 1159
Kenncode: 410231
Our Agenda up to now is as follows:
* Welcome 5 minutes
* Presentation of Metadata /-structure ~60 minutes
* Update on the in-person meeting 5 minutes
* Discussion of further proceeding 10 minutes
* Collection of Metadata that were presented
* Mapping of the Metadata to each other
* Poll for in-person meeting
* Wrapping up 5 minutes
The presenters of the Metadata of their consortia on Wednesday are:
NFDI4Immuno: Ulrik Stevbro
NFDI4Microbiota: Noriko Cassmann&Maja Magel
NFDI4BioImage: Susanne Kunis
GHGA: Anandhi Iyappan
NFDI4Health: TBC
Each Presentation should not exceed 15 minutes, best would be about 10 minutes so that we still
have some time for discussion in the end.
Thank you very much in advance to all the presenters and very much looking forward seeing you all on Wednesday.
Best wishes,
Sebastian
Dr. Sebastian Böhm
Institut für Immunologie
___________________________________________
Friedrich-Loeffler-Institut
Bundesforschungsinstitut für Tiergesundheit
Federal Research Institute for Animal Health
Südufer 10 | 17493 Greifswald - Insel Riems
Tel: +49 38351 7 1889/1602
https://www.fli.de/
¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯
Instagram<https://www.instagram.com/loeffler_news>
LinkedIn<https://www.linkedin.com/company/friedrich-loeffler-institut>
2 weeks, 3 days
WG: Bioschemas meeting happening today at 17:00
by Stervbo,Ulrik
Von: Garcia-Castro, Leyla Jael <ljgarcia(a)zbmed.de>
Gesendet: Montag, 17. März 2025 09:05
An: section-infra(a)lists.nfdi.de; section-edutrain(a)lists.nfdi.de; section-metadata(a)lists.nfdi.de
Betreff: [Section-metadata] Bioschemas meeting happening today at 17:00
Dear all,
This is a gentle reminder of our Bioschemas community call today at 17:00 CET.
Agenda and link to the meeting at https://docs.google.com/document/d/1kd5F97ogdiPNhLTnkei-RVR8TC8Ohpc5QSPX3...
Who: John Kunze
What: The YAMZ.net collaborative vocabulary builder
Consensus on terms and definitions is at the heart of every discipline, standard, ontology, working group, or pick list. Yet ways to reach consensus are often stuck in antiquated, dreadfully inefficient, design-by-committee methods that don't support broad-scale testing and feedback. As an alternative, YAMZ.net offers a crowdsourced system for building long-lived vocabularies. It does not compete with standards, but is a substrate of working draft terms to support standards and working groups. Created by founders of Dublin Core metadata, YAMZ allows anyone to use and comment on others' terms, add and edit their own terms, and rate others’ terms via reputation-based voting. YAMZ is a domain-agnostic repository of metadata and jargon terms that aims to become as useful and compelling to researchers as Stack Overflow has become to developers. The goal is to be a high-quality substrate of widely reviewed, well-tested candidate terms and definitions.
Kind regards,
-----
Dr. Leyla Jael Castro | ljgarcia(a)zbmed.de | [Das Bild wurde vom Absender entfernt.] @lj_garcia
Semantic Retrieval team leader (part of the Knowledge Management group)
ZB MED – Information Centre for Life Sciences | www.zbmed.de<https://www.zbmed.de/en/>
Gleueler Straße 60. 50931 Cologne. Germany
INFORMATION. KNOWLEDGE. LIFE.
_______________________________________________________________
Mitten in der St. Elisabeth Gruppe:
St. Anna Hospital Herne, Marien Hospital Herne – Universitätsklinikum der Ruhr-Universität Bochum,
Marien Hospital Witten, Rheumazentrum Ruhrgebiet, St. Marien Hospital Eickel,
Medizinische Reha für psychische Gesundheit, St. Elisabeth Stift Herne, Senioreneinrichtungen Widumer Höfe,
Gästehaus St. Elisabeth, Ambulante Pflege, MVZ Ärzte – Herne | Wanne | Witten,
Lukas Hospiz Herne, St. Elisabeth Hospiz Witten, Bildungszentrum Ruhr, Bildungswerk,
Campus der St. Elisabeth Gruppe, Kinder in der St. Elisabeth Gruppe
_______________________________________________________________
Aufsichtsratsvorsitzender: Dr. Hans Willmes
Geschäftsführung: Dr. Sabine Edlinger, Simone Lauer
Registergericht:
HRB 9735 Amtsgericht Bochum
St.-Nr.: 325/5894/2251
_______________________________________________________________
Wir bitten wegen der aktuellen Virenangriffe um folgende Beachtung:
Das Sicherheitskonzept der St. Elisabeth Gruppe erlaubt momentan keine Zustellung von .doc
(x) und .xls(x) Dateien! Schicken Sie Dokumente nur in Form von .pdf Dateien oder nehmen Sie
Kontakt auf, um andere Übertragungsmöglichkeiten abzusprechen.
2 weeks, 3 days
Overview of error list for schemapack
by Sebastian Ferrara
Hello,
I have uploaded the presentation and the overview table of the error messages from schemapack to GitHub (Error_Messages_Schemapack) and to nextcloud (3_Code development). I have also uploaded the YAML files with the different errors to GitHub (Error_Examples_Schemapack).
Best,
Sebastian Ferrara
3 weeks