We should add:

• Tissue sample
• Tissue sample collection
• Protocol
• Subject Group

@lzehl

See thread:
obophenotype/uberon#577

pressure injection; injection technique where pressure is used to inject a substance

request for new cell type: basket cell; inhibitory GABAergic interneurons of the brain, found throughout different regions of the cortex and cerebellum

To be consistent, we should follow the lowerCamelCase syntax for everything in JSON(-LD).

https://github.com/HumanBrainProject/openMINDS_controlledTerms/blob/2400e43e873fbfadd9f776fa69bc541a86144c8a/terminologies/phenotype/wild_type.jsonld#L2

@ingrre asked if we could add "confocal light-sheet microscopy" and I think that it would make sense to do so. @tgbugs I checked the method ontology but couldn't find it there. Would it make sense to add it?

Additionally, I'm kind of wondering where we draw the line for the microscopy related terms? Below is a list of all microscopy term that we added so far:

• Brightfield microscopy
• Confocal microscopy
• Dual View Inverted Selective Plane Illumination microscopy
• Electron microscopy
• Epifluorescent microscopy
• Fluorescence microscopy
• Focused Ion Beam Scanning Electron microscopy
• Light microscopy
• Light Sheet Fluorescence microscopy
• Microscopy
• Polarized Light microscopy
• Scanning Electron microscopy
• Serial Section Transmission Electron microscopy
• Transmission Electron microscopy
• Two-Photon Excitation Fluorescence microscopy
• Widefield Fluorescence microscopy
• Widefield microscopy

The easy one first: "microscopy" needs to be removed. This is a duplication since it exists as an experimental approach (which obviously makes most sense anyway).

Then, I think widefield fluorescence microscopy & epifluorescent microscopy might be synonym (see here: https://oni.bio/nanoimager/super-resolution-microscopy/epifluorescence-microscopy/).

So, in short, my questions are:

1. Add "confocal light-sheet microscopy" - yes or no?
2. Remove "microscopy" (actual not a question)
3. "widefield fluorescence microscopy" same as "epifluorescent microscopy" - yes or no?
4. If 3. is answers with no, rename "epifluorescent microscopy" to "epifluorescence microscopy" to be consistent with the other fluorescence techniques?

@lzehl feel free to comment as well :)

@tgbugs I'd like to add "cryosectioning" as technique. what do you think?
(@MaaikevS)

I would like to propose two suggestions for "Attributes" in "Subject state":

1. drug infusion (should represent recordings taken during the infusion of a drug).
2. drug treatment (should represent recordings taken while the drug has developed its final "stable" dose).

As discussed offline with @MaaikevS and @lzehl, we should add a new terminology called "subcellular entity" (http://uri.interlex.org/ilx_0111157).

This would include controlled terms such as:

• (a)symmetric synapse
• neurites
• nucleus
• mitochondrion
• etc.

@MaaikevS would you be able to take care of this?

FYI @tgbugs

based on the ontology discussion with @tgbugs we agreed to rename this controlled term and kick-out the GDPR sensitivity part.

@UlrikeS91 I think we could put the GDPR into the EthicsAssessment. You made that suggestion yesterday and I think you are right. It actually fits in there. We could change entries there to: ("not applicable", "EU compliant, sensitive", "EU compliant, non sensitive") or ("not applicable", "EU compliant, GDPR sensitive", "EU compliant, non sensitive")

What do you think?

Trying to use and populate the controlled terms for strains has been a challenge. Based on feedback/concerns from e.g. @Majpuc and following a discussion between @lzehl and me, we are lining strongly towards removing the strains from the controlled terms and instead make them a schema in the core repository (potentially with controlled instances that follow that schema).

I worked on a rough first draft for such a schema:

Some resource I found useful:
https://www.ncbi.nlm.nih.gov/books/NBK224550/
http://www.informatics.jax.org/mgihome/nomen/strains.shtml
https://www.nap.edu/labcode/search_lc_nodep.php

Any feedback is very welcome!
Maybe: @tgbugs, @lzehl, @Majpuc, who else?

Hello Lyuba and Ulrike,

I'm in the process of migrating a dataset in which visual stimuli have been applied, but the KGE only lists auditory stimulation and direct current as possible options for Stimulation approach / Stimulus type. Could you please add visual stimulation? For stimulus type, the authors describe "visual target stimulus (CS+) and distracter stimulus (CS−)" in their paper, if that makes sense to add.

All the best,
Eszter

As discussed and agreed, we'll move all controlled instances of openMINDS to one GitHub repository: openMINDS_instances.
This is a clearer separation between openMINDS repos that contain metadata models vs other openMINDS repos.

@tgbugs: could you add the IRI to the corresponding ontological term for each term (JSON_LD) in v1.0-terminologies, or let me know where I can best check for them? The latter might be more convenient for you because the v1.0-terminologies will be extended step-by-step. Thanks in advance!

Hi,

Could you please add the following two phenotypes to the controlled terms?

• low aggression
• high aggression
  These phenotypes are for a dataset with zebrafish and this is the most differentiating characteristic between two groups. It is also important for the research objective, so it would be great to visualise this at the level of the subjects

Many thanks,
Maaike

@lzehl @UlrikeS91 We briefly talked about the naming convention of cell types offline. The thought was that we should use "neuron" if it can only be a neuron, otherwise "cell". It looks like there were some inconsistencies introduced in the past. Would this be something to clean up now (before adding more)?

This is the list we have at the moment:

astrocyte
basket cell
cerebellar interneuron
cerebellum basket cell
cerebellum Golgi cell
cerebellum granule cell
cerebellum stellate neuron
cholecystokinin expressing cell
cholinergic interneuron
cholinergic neuron
cortical basket cell
cortical interneuron
D1 receptor expressing cell
dopaminergic neuron
fast spiking interneuron
glial cell
granule cell
hippocampus CA1 pyramidal neuron
interneuron
macroglial cell
microglial cell
motor neuron
neocortex layer 2/3 pyramidal neuron
neocortex layer 5 tufted pyramidal neuron
neostriatum cholinergic interneuron
neostriatum direct pathway spiny neuron
neostriatum indirect pathway spiny neuron
neuron
parvalbumin expressing cell
Purkinje cell
pyramidal cell
sensory neuron
somatostatin expressing cell
spinal interneuron
spiny neuron
stellate neuron
striatal interneuron
striatum medium spiny neuron
vascular endothelial cell
vascular smooth muscle cell
vasoactive-intestinal peptide expressing cell

I would say, the following ones are the most relevant. If you want to keep it the way it is, then I feel that any new cell types should also have the name "cell" instead of "neuron":

cholecystokinin expressing cell
D1 receptor expressing cell
parvalbumin expressing cell
somatostatin expressing cell
vasoactive-intestinal peptide expressing cell

When I went over what instances we would actually register for confidence I realized that in principle it's exactly what we describe in with the citeriaQualityType instances:

• processive: "you can redo the process that let me to my result"
• asserted: "I say so"

I'm really not sure if I want to introduce other terms for confidence levels like "sure", "very sure", "maybe" etc.
I like the simplicity but explanatory power of processive and asserted.

@UlrikeS91 & @tgbugs Could we just unit those into one property called "criteriaConfidence" or "confidenceOfCriteria" or something like this?

Should these terms be merged or should we keep them separate?

disease definition "a disorder of structure or function in a human, animal, or plant, especially one that produces specific symptoms or that affects a specific location and is not simply a direct result of physical injury."
-> "all" diseases as controlledTerms

pathology definition "the structural and functional deviation from the normal that constitute disease or characterize a particular disease"
-> general category, meaning "healthy", "diseased", "impaired", "abnormal" as controlledTerms

OR merged under a single term with: "healthy" + "all" diseases as controlledTerms

If they are kept separate: should we add them both to subject (state) as well as tissue sample (state)?
We also ask currently for "functionalImpairments" e.g. "thumb missing at left hand" for subjects in addition.
I wonder if that could be also merged in or just put under "generalRemarks" (free comment field for a subject to add peculiarities)

@UlrikeS91 @tgbugs what do you think?

Hi!

Based on the datasets that I have been working with, I would like to suggest that the following few things may need to be added. If they are already covered by an existing term, please let me know.

1. electroporation as technique
2. stereology as experimental approach
3. volume fraction estimation as technique (or I need to add a different technique and put this in a protocol/execution)
4. intracellular electrophysiology as technique
5. high-frequency electrical stimulation as technique (currently only single pulse electrical stimulation is available)

Since "biologicalSex" is a required property for subject(Group)s and tissueSample(Collection)s, I was wondering if we could introduce something along the lines of "unknown".

I know that we did not want to leave this as an option because it should be known, but there are still cases where this information maybe cannot be provided.

My bigger concern is for the cases where the sex in fact cannot be determined yet, basically most stages before birth (e.g. an embryo).

I can see a few options for solving this:

1. Make "biologicalSex" optional (not preferred because it's not differentiating between "forgotten to fill in" vs. "not knowing but should have" vs. "really not possible to determine yet")
2. Add "unknown" as a controlledTerm (disadvantage: "not knowing but should have" vs. "really not possible to determine yet" would be collected under one term)
3. Add "unknown" & "undeterminable" (or similar) as controlledTerms - unknown for "not knowing but should have" & undeterminable for "really not possible to determine yet"

@lzehl? Who else?

It would be good to have some additional tissue sample states, for example:

1. Fixated
2. Not fixated / "fresh"

@UlrikeS91 @lzehl Let me know your thoughts and I would be happy to add them if you agree!

Change to:

• rawData
• derivedData
• experimentalData
• simulatedData
• GDPRSensitiveData

Idea is to combine the different term to describe the content of the dataset. For example, human non-aggregated data would need the terms derivedData + experimentalData + GDPRSensitiveData.

How about these new TissueSampleAttributes (?):

• sliced
• untreated
• mounted
• fixated

And this new TissueSampleType (?):

• tissue slice series

And this new SubjectAttribute (?):

• comatose (OR unconscious)

Missing initial capital in _type value => ProductAccessibility in productAccessibility.schema.tpl.json

@tgbugs : would it make sense to register neuron types such as 'D1 expressing neurons' or would you rather register this separately (e.g., in a study target field) as "neuron" and "D1 receptor" ?

Hi,

Could you please add RNA sequencing as a new technique? At the moment only single-cell RNA sequencing exists and the Data Provider does not think this is a suitable technique for his dataset. He would like to have "normal" RNA sequencing on the card.

Many thanks,
Maaike

@tgbugs does this make sense?

I discussed again with @olinux :
For convenience / lowering mistakes / mainenance in using the right / typical digital identifier (and digital identifier schema) for a corresponding instance (e.g., a person, a dataset, a model, etc) it is better to split up the DigitalIdentifier Schema into distinct types (e.g., DOI, ORCID). This would make the need for a DigitalIdentifierSchema obsolete.

The current DigitalIdentifier schema would become a concept schema (without a type) and extended to (for now) the following distinct types:

• DOI
• ORCID
• GRID
• ISBN

All of them will differ in the type, but follow the same basic (DigitalIdentifier) schema with only two properties now:

• "identifier" (required, count: 1)
• "how to cite" (optional, count: 1)

@apdavison @UlrikeS91 @jagru20 @skoehnen @bweyers @Peyman-N @tgbugs
a) Would you be against this suggestion?
b) There might be more digital identifier types to add: please let me know which ones are missing for our typical purposes.

The types
https://openminds.ebrains.eu/controlledTerms/SoftwareFeatureCategory
and
https://openminds.ebrains.eu/controlledTerms/StudyTargetType
seem to be unused by both core and SANDS. Maybe they should be removed?

Would it be possible to add weighted gene co-expression network analysis as a technique?

Weighted gene co-expression network analysis (WGCNA) is a bioinformatics application for exploring the relationships between different gene sets (modules), or between gene sets and clinical features (Langfelder and Horvath, 2008).

@bweyers & @jagru20

I've realized that a number of data types are listed under software features (SoftwareFeature schema + instances).
For example:

• 3DGeometryDataTypes
• 3DVectorDataTypes
• timeSeriesDataTypes
  etc.

Could we separate those as actual data types (DataTypes schema + instances)?
These are not really a feature, correct? But rather the overall class of data types the software can handle/produces?
If this is true, should this be listed as separate property in SoftwareVersion or still under "softwareFeature" as second linked type (SoftwareFeature + DataType)?

@tgbugs : we would like to add the following instances. Would you agree?
(some of them might only not exist in our list, but you have them already)

"NEW" TECHNIQUES SUGGESTIONS:

1. calcium imaging
2. fiber photometry
3. pupillometry
4. electrooculography
5. video-oculography
6. eye-attached tracking
7. ultrasound imaging
8. virus transfection OR virus-mediated transfection
9. neuronal tracing
10. retrograde tracing
11. voltammetry
12. cryopreservation
13. cryofixation
14. manual sectioning (if tissue was cutted by hand with a knife to smaller pieces)

Could we add a schema for administration type with the following controlled instances?

• oral
• subcutaneous
• interperitoneal
• intravenous

Any thoughts?

I've just add them for the moment to give full examples of a complete jsonld, but for the IRIs they would fail the validation.

The following cell types are needed for the Model migration that are not in the KG.

The names don't have to match these exactly, I can do a mapping if there is an entry in Interlex/Scicrunch for the same cell type but with a slightly different name.

• Golgi cell
• L2/3 pyramidal cell
• L5 tufted pyramidal cell
• cerebellar granule cell
• cholinergic interneuron
• fast spiking interneuron
• hippocampus CA1 pyramidal cell
• medium spiny neuron
• medium spiny neuron (D1 type)
• medium spiny neuron (D2 type)

Modalities have InterLex ids
https://github.com/HumanBrainProject/openMINDS_controlledTerms/tree/v1/terminologies/modality
are in https://github.com/SciCrunch/NIF-Ontology/blob/master/ttl/generated/modality-ILX-mapping.ttl and
https://github.com/SciCrunch/NIF-Ontology/blob/methods/ttl/modality.ttl.

I am working on protocol executions etc and I am missing some important units.

I am listing the ones I came across (and that might be useful to add) below:

• % w/v
• mg/kg
• percent
• ug/ml
• um/ml
• ml/g
• mg/ml
• degrees celsius
• mM

@lzehl @UlrikeS91 There are many additional options of course, but please let me know if we can add (some of) these. Again, I am happy to make the instances if you can tell me which ones to add and how we should name them.

Thanks!

Add cell types:
stellate cell
parvalbumin cell
cholecystokinin cell
cholinergic neuron
dopaminergic neuron
spiny projection neuron
somatostatin expressing neuron
vasoactive-intestinal peptide expressing neuron

Add technique:
infrared differential interference contrast (IR-DIC) microscopy (see dataset "Electrophysiological recordings of striatal low threshold-spiking interneuron")
ABC staining (avidin-biotin complex kit to visualise biotin-containing substances in tissue (histochemistry)

Would it be possible to extend the number of instances for "DeviceType"?

For example with:

• microscope
• vibratome
• microtome

Hi,

There are a few controlled terms for techniques that I think need to be reassessed and perhaps 'cleaned up'.

1) Fixation / perfusion
Currently there are a number of techniques that only differ slightly in my opinion.

• fixation technique
• tissue fixation technique
• perfusion fixation technique
• intracardial perfusion technique
• perfusion technique

I would reduce this to "fixation technique" and "perfusion technique".

Perfusions are typically done intracardially (I would not know how else to do it), first a saline solution is perfused and then a fixative. You would never perfuse with just a fixative. "Perfusing with fixative only" does not work and you would be better off dumping the tissue in a fixative immediately.

2) contrast enhancement vs contrast enhancement technique
It is not clear what the difference is, so I would just keep one and not both.

3) meta-analytic modeling vs meta-analytic modelling
Same thing, just different spelling

4) patch clamp vs patch clamp technique
It is not clear what the difference is, so I would just keep one and not both.

There are probably a few more that I would probably suggest to have another look at, but they might be a bit more involved.

https://github.com/HumanBrainProject/openMINDS_controlledTerms/blob/817a76151134945158905ee1b71f409875a43d24/v1.0/terminology.schema.tpl.json#L3

Based on a discussion with @lzehl and @tgbugs, we would like to rename modalities to approach because it is more descriptive for what it actually is.

@lzehl, anything to add?

list from @tgbugs on sample_types:

1. 'whole organism' (this we don't need, because this is a subject in our case)
2. 'whole organ' (is already in instances)
3. 'fluid specimen' (suggestion: integrate as "body fluid" ? )
4. 'tissue' (not sure what is meant here; we would need somthing like "tissue block"; cf. discussion below)
5. 'nerve' (could be integrated as is)
6. 'slice' (is already integrated as "tissue slice")
7. 'section' (see discussion points below)
8. 'cryosection' (I would not integrate this; mixes extraction / fixation procedure with tissue sample type)
9. 'cell' (suggestion: integrate as "single cell" ? )
10. 'nucleus' (I would not integrate this for now)
11. 'nucleic acid' (I would not integrate this for now)
12. 'slide' (see discussion points below)
13. 'whole mount' (see discussion points below)
14. 'cell suspension' (could be integrated as is)
15. 'single cell suspension' (not sure what the difference is to 'cell')

In openMINDS we registered so far:

1. 'biopsy sample' (cf. the above, I would keep this one)
2. 'brain hemisphere' (I would keep this one or is there a more general term, e.g. 'organ hemisphere' we would prefer?)
3. 'cell culture' (we discussed to replaces this with 'cell line' ?)
4. 'tissue slice' (cf. the above, I would keep this one)
5. 'whole organ' (cf. the above, I would keep this one)

'slice' vs 'slide' vs 'section' vs 'whole mount' vs 'tissue block'

• 'slice': a tissue slice is for me just an unprocessed thin slice from a larger sample; does typically require specific sectioning / slicing devices
• 'slide': a tissue slide is for me a tissue slice mounted on a object plate for, e.g., microscopy (can but does not have to be fixated and stained)
• 'section': is for me a synonym for slice
• 'whole mount': searched for it and mostly found "entire organism or structure which can be studied under microscope without further slicing" [so for me that would mean 'tissue block' is to 'whole mount' what 'slice' is to 'slide']
• 'tissue block': a tissue block measures for me a few centimeters or more; does not necessarily require specific devices (but a knife / scalpel)

@UlrikeS91 what do you think?
@tgbugs your thoughts??

for all (schemas and terms)

I suggest to add

• endothelial cell
• mural cell

to the "origin" controlled terms for TissueSample and TissueSampleCollection.

There might be other non-neuronal / non-glial cells that we want to add as well (that I cannot think of atm).

Decided on during an external discussion with @tgbugs, Mathew (don't know his GitHub) and @lzehl: We will make some major changes to the controlledTerms schemas.
1. Change "OntologyIdentifier" to "PreferredOntologyIdentifier". The preferred ID (as stated on InterLex) will be used here.
2. Add a new property called "InterlexIdentifier". This will also be an ontology ID, but specifically only InterLex IDs.
3. Add another new property called "KnowledgeSpaceLink". This will link to the corresponding KS wiki page for each controlledTerm instance.

What should be shown/used in the Knowledge Graph Search is the the "KnowledgeSpaceLink" redirecting the user to the KS wiki page for the controlledTerm instance.
(FYI @olinux)

Example for an "UBERONParcellation":

[...]
"name": "thalamus",
[...]
"preferredOntologyIdentifier": "http://purl.obolibrary.org/obo/UBERON_0001897",
"interlexIdentifier": "http://uri.interlex.org/ilx_0111657",
"knowledgeSpaceLink": "https://knowledge-space.org/wiki/UBERON:0001897#thalamus",
[...] 

SoftwareFeatureCategory should be deleted because it was replaced by SoftwareFeature

@tgbugs Is this a synonym or something different?

@tgbugs & @UlrikeS91 I'm surprised that no one requested that yet... we postponed this for a while.
do you agree adding the schema and at least some instances?

[@UlrikeS91 did you prepare something for this already? I have the feeling you did... if so, feel free to forward, I can take over if you want]