Merge pull request #620 from NFDI4BIOIMAGE/git-bob-mod-ROPHWyZLrB

Add content from communities: nfdi4bioimage, gerbi, euro-bioimaging, neubias, bio-formats, globias, rdm4mic

resources/nfdi4bioimage.yml

@@ -9951,3 +9951,82 @@ resources:
   url:
   - https://zenodo.org/records/14675120
   - https://doi.org/10.5281/zenodo.14675120
+- authors:
+  - Fortmann-Grote, Carsten
+  - Meireles, Mariana
+  description: This Poster was presented at the 2025 All Hands Meeting of the NFDI4BIOIMAGE
+    Consortium. It presents the current state of data integration activities at the
+    MPI for Evolutionary Biology. Various data and metadata resources such as the
+    internal image data repository OMERO and the Electronic Lab Notebook System OpenBIS
+    are converted into a RDF Knowledge Graph utilizing a R2RML mapping scheme based
+    on the Ontop-VKG framework. The materialized Knowledge Graph is then served via
+    the QLever SPARQL endpoint and user interface. A graphical query editor (SPARNatural)
+    assists users with no SPARQL knowledge in constructing their queries by selecting
+    triple elements from dropdown menus and other widgets. We also present a
+    benchmark comparison of query response times on 10 selected SPARQL queries run
+    against three different endpoint/triplestore implementations. 
+  name: Integration of Bioimage and *Omics data resources
+  num_downloads: 29
+  publication_date: '2025-02-03'
+  submission_date: '2025-02-04T11:17:47.530124'
+  url:
+  - https://zenodo.org/records/14792534
+  - https://doi.org/10.5281/zenodo.14792534
+- authors:
+  - Kuttler, Fabien
+  - "Dornier, R\xE9my"
+  description: 'The provided dataset contains 2 wells, 4 fields of view, 4 channels,
+    no T but different number of Z according to the channel
+
+
+    Cy3 : 1 Z
+
+    DAPI : 16 Z
+
+    FITC : 1 Z
+
+    Brightfield : 1 Z
+
+
+    The mix 2D/3D is not correctly supported and the .xcde file cannot be read.
+
+    A discussion thread is already open on that topic.
+
+    Bio-Formats version : 8.0.1
+
+     '
+  license: cc-by-4.0
+  name: InCell datasets with mix of 2D and 3D failed to be read
+  num_downloads: 24
+  publication_date: '2025-01-31'
+  submission_date: '2025-02-04T11:18:35.656931'
+  url:
+  - https://zenodo.org/records/14777242
+  - https://doi.org/10.5281/zenodo.14777242
+- authors:
+  - Kuttler, Fabien
+  - "Dornier, R\xE9my"
+  description: 'Two dummy datasets are provided in this repository : 
+
+
+    Dataset_Ok : 96 wells, 9 fields of view per well, 4 different channels (DAPI,
+    Cy3, FITC, Brightfield), no Z, no T. The .xcde file of this dataset is correctly
+    read by BioFormats, as the dataset is recognized as a plate, and can be imported
+    on OMERO
+
+    Dataset_fail: 20 wells, 4 fields of view per well, 5 channels, with one duplicate
+    (DAPI, FITC, Cy3, Cy5 wix 4 , Cy5 wix 5), no Z, no T. The .xcde file of this dataset
+    is not correctly read by BioFormats and no images are imported on OMERO.
+
+
+    BioFormats version: 8.0.1
+
+    A discussion thread has been open on this topic.'
+  license: cc-by-4.0
+  name: Dataset from InCell 2200 microscope misread as a plate
+  num_downloads: 34
+  publication_date: '2025-01-30'
+  submission_date: '2025-02-04T11:18:36.941157'
+  url:
+  - https://zenodo.org/records/14769820
+  - https://doi.org/10.5281/zenodo.14769820