Add more Neo content types by UlrikeS91 · Pull Request #62 · openMetadataInitiative/openMINDS_instances

UlrikeS91 · 2024-05-06T11:11:42Z

This will replace openMetadataInitiative/openMINDS_core#299.

The comments are in relation to the original PR from @JuliaSprenger and the review comments from @lzehl and @apdavison:

“alphaomega0.jsonld”: changed to “application_vnd.alphaomega.v0-eng.jsonld”
- 0 changed to v0 as suggested by @apdavison
- “-eng” most likely stands for “engineering” since it is part of the company name and also of their homepage URL (Alpha Omega Engineering - https://www.alphaomega-eng.com/)
“axon.jsonld”: removed since @apdavision pointed out that this is a duplicate; @JuliaSprenger please use “moleculardevices.axon.jsonld” instead
“axona.jsonld”: changed to “application_vnd.axona.jsonld”
- no content change, just update to new convention
“biocam+hdf.jsonld”: changed to “application_vnd.biocam+hdf5.jsonld”
- updated “hdf” to “hdf5” in accordance with similar instances
- added file extension “.hdf5” in accordance with similar instances
- changes synonym in accordance with similar instances
“klustakwik.jsonld”: changed to “application_vnd.klustakwik.jsonld”
- no content change, just update to new convention
“maxwell.jsonld”: changed to “application_vnd.maxwell+hdf5.jsonld”
- updated “hdf” to “hdf5” in accordance with similar instances
- added file extension “.hdf5” in accordance with similar instances
- changes synonym in accordance with similar instances
existing “application_vnd.mearec.jsonld”: updated to “application_vnd.mearec+hdf5.jsonld”
- added file extension “.hdf5” in accordance with similar instances
- changes synonym in accordance with similar instances
"neo+pickle.jsonld": changed to "application_vnd.neuralensemble.neo+pickle.jsonld" (following suggestion of @apdavison)
- otherwise no content change, just update to new convention
existing "application_vnd.neuroscope.jsonld": update with more content from "neuroscope.jsonld"
existing "application_vnd.neuroshapeapi.jsonld": updated to "application_vnd.neuroshape.api.jsonld" (following suggestion of @apdavison)
"neurosharetypes.jsonld": changed to "application_vnd.neuroshape.types.jsonld"
"numpy.jsonld": changed to "application_vnd.numpy.array.jsonld"
- changed synonym
- added description (because it was super easy to find)
existing "application_vnd.openephys.jsonld": updated with more content from PR
"phy.jsonld": changed to "application_vnd.phy.jsonld"
existing "application_vnd.spike2.sonpy.son" split into 32 and 64 bit version in accordance with PR and @apdavison suggestion for the synonym
"spikegadgets.jsonld": changed to "application_vnd.spikegadgets.jsonld"
existing "application_vnd.spikeglx.system.jsonld": updated with more content from "spikeglx.jsonld"
existing "application_vnd.tdt.jsonld": updated with more content from "tdt.jsonld"

Open questions:

should "application_vnd.neuroshape.types.jsonld" exist? @apdavision raised this question ("Does Neuroshare have its own file format(s)? I thought it was just an API to read in some existing formats.")
should "application_vnd.phy.jsonld" exist? @apdavison raised the question "What is different in phy files compared to simple .npy?"; I found this: https://phy.readthedocs.io/en/latest/. Not sure if it helps.

Additionally added:

"application_vnd.numpy.multiarray.jsonld" since it was mentioned by @apdavison in relation to the array

…arec+hdf5.jsonld

…ion_vnd.spike2-32.sonpy.son.jsonld

UlrikeS91 · 2024-05-06T12:30:10Z

@JuliaSprenger is also very welcome to review this PR and give feedback. I hope that I migrated everything correctly.

lzehl

updated to new namespace

lzehl

I would also like to have a one sentence description for each. @apdavison I think we should discuss those in detail.

lzehl · 2025-06-24T08:28:33Z

+    ".lsx",
+    ".mpx"
+  ],
+  "name": "application/vnd.alphaomega.v0-eng",


Suggested change

"name": "application/vnd.alphaomega.v0-eng",

"name": "application/vnd.alphaomega-eng.v0",

if -eng belongs to the company name and v0 points to the version it should be this way around, no? @apdavison

lzehl · 2025-06-24T08:33:01Z

+  "synonym": [
+    "MaxOne HDF5",
+    "MaxTwo HDF5"
+  ]


this is a bit weird, MaxOne and MaxTwo are different MEA systems. If they are using the same file format the synonym of the file format should not be combined with the system name (unless this is what they officially do). I would suggest calling this MaxWell HDF5, or MaxWell Biosystems HDF5

lzehl · 2025-06-24T08:35:00Z

+  "dataType": null,
+  "description": null,
+  "displayLabel": null,
+  "fileExtension": null,


No extension? is this not a content type for files but for bundles?

lzehl · 2025-06-24T08:35:37Z

  "dataType": null,
  "description": null,
  "displayLabel": null,
  "fileExtension": null,


no extensions? is this for bundles not for files?

lzehl · 2025-06-24T08:39:50Z

+  "@id": "https://openminds.om-i.org/instances/contentTypes/application_vnd.numpy.multiarray",
+  "@type": "https://openminds.om-i.org/types/ContentType",
+  "dataType": null,
+  "description": "File format by numpy that provides storage of array data using gzip compression.",


Suggested change

"description": "File format by numpy that provides storage of array data using gzip compression.",

"description": "A compressed archive format used by NumPy to store a collection of individual NumPy arrays (.npy files) in a single zip archive file.",

lzehl · 2025-06-24T08:40:58Z

+  "fileExtension": [
+    ".npz"
+  ],
+  "name": "application/vnd.numpy.multiarray",


@apdavison should this be ?

Suggested change

"name": "application/vnd.numpy.multiarray",

"name": "application/vnd.numpy.multiarray+zip",

lzehl · 2025-06-24T08:41:45Z

  "description": null,
  "displayLabel": null,
-  "fileExtension": null,
+  "fileExtension": [


is this really one content type? or rather different ones?

lzehl · 2025-06-24T08:52:31Z

+  "fileExtension": [
+    ".smr"
+  ],
+  "name": "application/vnd.spike2-32.sonpy.son",


Suggested change

"name": "application/vnd.spike2-32.sonpy.son",

"name": "application/vnd.spike2.sonpy-binary32",

what was the .son for?

we need to define a convention of bitness for our content types

lzehl · 2025-06-24T08:53:12Z

+  "fileExtension": [
+    ".smrx"
+  ],
+  "name": "application/vnd.spike2-64.sonpy.son",


convention for bitness should be different I think (see spike2-32)

lzehl · 2025-06-24T15:01:53Z

@apdavison @UlrikeS91 it seems that all content types from this PR are already in openMINDS. Before we continue we should double check this.

ree-gupta

I added my comments for the two formats in the PR that I am familiar with.

ree-gupta · 2026-01-14T11:11:06Z

+    ".tsq",
+    ".tbk",
+    ".tev",
+    ".sev"


Suggested change

".tsq",

".tbk",

".tev",

".sev"

".tsq",

".tbk",

".Tbk",

".Tdx",

".tev",

".tnt",

".sev"

ree-gupta · 2026-01-14T11:21:08Z

  "displayLabel": null,
-  "fileExtension": null,
+  "fileExtension": [
+    ".bin",


Isn't .bin generic? should we be more specific using the stream names? that is,.ap.bin, .lf.bin and .nidq.bin? Unless the system allows user-defined stream name.

UlrikeS91 added 22 commits May 6, 2024 13:07

Add files via upload

2464693

Update and rename application_vnd.mearec.jsonld to application_vnd.me…

9d76b91

…arec+hdf5.jsonld

Create application_vnd.neuralensemble.neo+pickle.jsonld

6d5e491

Update application_vnd.alphaomega.v0-eng.jsonld

08ae5f4

Update application_vnd.neuralensemble.neo+pickle.jsonld

f5a1269

Update application_vnd.klustakwik.jsonld

2a901a1

Update application_vnd.axona.jsonld

cdea0ab

Create euroscope.jsonld

b868a8b

Update application_vnd.neuroscope.jsonld

62c096e

Delete instances/latest/contentTypes/euroscope.jsonld

abec208

Update application_vnd.neuroshareapi.jsonld

453caf0

Create application_vnd.neuroshare.types.jsonld

e6718ca

Create application_vnd.numpy.array.jsonld

48ef6e4

Create application_vnd.numpy.multiarray.jsonld

c41ac1d

Update application_vnd.openephys.jsonld

19942cc

Create application_vnd.phy.jsonld

3a3c793

Update and rename application_vnd.spike2.sonpy.son.jsonld to applicat…

f622412

…ion_vnd.spike2-32.sonpy.son.jsonld

Create application_vnd.spike2-64.sonpy.son.jsonld

30917be

Update application_vnd.spike2-64.sonpy.son.jsonld

d597961

Create application_vnd.spikegadgets.jsonld

4bd96ce

Update application_vnd.spikeglx.system.jsonld

432bf0b

Update application_vnd.tdt.jsonld

7e5c417

UlrikeS91 marked this pull request as ready for review May 6, 2024 12:28

UlrikeS91 requested review from apdavison and lzehl May 6, 2024 12:29

UlrikeS91 added the ContentType ContentType instances - addition of new or update of existing ones label May 8, 2024

lzehl self-assigned this Oct 14, 2024

lzehl added 2 commits October 17, 2024 13:03

Update application_vnd.alphaomega.v0-eng.jsonld

79ed0a4

Update application_vnd.axona.jsonld

1a87f02

lzehl added 17 commits October 17, 2024 13:05

Update application_vnd.biocam+hdf5.jsonld

21815ba

Update application_vnd.klustakwik.jsonld

f015b4c

Update application_vnd.maxwell+hdf5.jsonld

79da225

Update application_vnd.mearec+hdf5.jsonld

828f2c3

Update application_vnd.neuralensemble.neo+pickle.jsonld

98f43f3

Update application_vnd.neuroscope.jsonld

3fd95bd

Update application_vnd.neuroshare.types.jsonld

1319ed2

Update application_vnd.neuroshareapi.jsonld

e57ab16

Update application_vnd.numpy.array.jsonld

12796ef

Update application_vnd.numpy.multiarray.jsonld

a0949cf

Update application_vnd.openephys.jsonld

a25fd40

Update application_vnd.phy.jsonld

f11139b

Update application_vnd.spike2-32.sonpy.son.jsonld

778d385

Update application_vnd.spike2-64.sonpy.son.jsonld

962a4c8

Update application_vnd.spikegadgets.jsonld

0570472

Update application_vnd.spikeglx.system.jsonld

ff113c9

Update application_vnd.tdt.jsonld

4d4d33b

lzehl reviewed Oct 17, 2024

View reviewed changes

solving conflicts

7b8d809

lzehl requested changes Jun 24, 2025

View reviewed changes

Raphael-Gazzotti requested a review from ree-gupta August 4, 2025 13:18

ree-gupta reviewed Jan 14, 2026

View reviewed changes

	"name": "application/vnd.alphaomega.v0-eng",
	"name": "application/vnd.alphaomega-eng.v0",

	"description": "File format by numpy that provides storage of array data using gzip compression.",
	"description": "A compressed archive format used by NumPy to store a collection of individual NumPy arrays (.npy files) in a single zip archive file.",

	"name": "application/vnd.numpy.multiarray",
	"name": "application/vnd.numpy.multiarray+zip",

	"name": "application/vnd.spike2-32.sonpy.son",
	"name": "application/vnd.spike2.sonpy-binary32",

-    ".tsq",
-    ".tbk",
-    ".tev",
-    ".sev"
+    ".tsq",
+    ".tbk",
+    ".Tbk",
+    ".Tdx",
+    ".tev",
+    ".tnt",
+    ".sev"

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lzehl commented Jun 24, 2025

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UlrikeS91 commented May 6, 2024 •

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