EPHYS related updates - full overview

UlrikeS91 commented 2 years ago

Since @lzehl and I requested quite a few changes and specifically also across openMINDS repositories, we thought it would be best to have one tracking/overview document that summarizes the changes needs to schemas across all repositories and the changes needed for openMINDS_ephys v0. v0 is the compromise for @apdavison and @Peyman-N to start using the ephys extension, but will not be included in the official openMINDS v3.0.0 release. openMINDS_ephys v1 will require some larger updates to the existing schemas, but if we can land on something fast, it could be included in the openMINDS v3.0.0 release.

This overview is focused on the required changes for openMINDS_ephys v0.

EPHYS schemas

BrainSlicingActivity

in issue #7 PR #13 (needs revision)

[x] rename schema to "TissueSampleSlicing"
[x] extends "core/ExperimentalActivity" (see core schemas)
[x] change input links to "core/SubjectState" & "core/TissueSampleState"
[x] change output to "core/TissueSampleCollectionState" & "core/TissueSampleState"
[x] add device linking to "core/Device" & controlledTerms/DeviceType" (new)
[x] add oscillationAmplitude, sectioningSpeed and vibrationFrequency (see proposal in this specific comment)
[x] change slicingAngle to array (0 - 2 items allowed), linking to "core/NumiercalProperty" (as embeddedType)
[x] rename bathSolution to tissueBathSolution

Open questions for v0: (see question summary below) 1) tissueBathSolution value

Craniotomy

in issue #8 PR #14 (needs refinement)

[x] rename schema to "CranialWindowPreparation"
[x] extends "core/ExperimentalActivity" (see core schemas)
[x] remove windowType
[x] add reinforcementType linking to "controlledTerms/CranialWindowReinforcementType" (new)
[x] add constructionType linking to "controlledTerms/CranialWindowConstructionType" (new)
[x] add dimension linking to "SANDS/MathematicalShape" (new)
[x] remove anesthesia & fluorescenceLabelling (instead use proposed option 2 or 3 to capture information)

Culturing

in issue #9
PR #15 (needs refinement)

[x] rename schema to "TissueCulturePreparation"
[x] extends "core/ExperimentalActivity" (see core schemas)
[x] remove cultureAge
[x] rename cultureSolution to cultureMedium
[x] change input to link to all specimen states

Open questions for v0: (see question summary below) 1) culturingMedium value 2) cultureEnvironment (pH, temperature, osmotic pressure, etc.): not for v0?

ElectrodePlacementActivity

in issue #10
PR #16 (needs revision)

[x] rename schema to "ElectrodePlacement"
[x] extends "core/ExperimentalActivity" (see core schemas)
[x] remove anesthesia (instead use proposed option 2 or 3 to capture information)
[x] add TargetPosition (see proposal in this specific comment

Open questions for v0: (see question summary below) 1) @apdavison comment about "ephys/ElectrodeContact" carrying part of the proposed "SANDS/AnatomicalLocation" new) schema

PatchClampActivity

in issue #11
PR #17 (needs revision)

[x] rename schema to "CellPatchPreparation" (or "CellPatching" if preferred)
[x] extends "core/ExperimentalActivity" (see core schemas)
[x] rename bathSolution to tissueBathSolution (for consistency reasons, compare "TissueSampleSlicing")
[x] rename temerpature to solutionTemperature (to avoid confusion for invivo experiments)
[x] rename technique to variation
[x] add pipette linking to "ephys/Pipette"
[x] add otherDevice linking to ephys/Device

Open questions for v0: (see question summary below) 1) tissueBathSolution value

StimulationExperiment

in issue #12
PR #18 (draft)

???

CORE schemas

Activity schemas

in issue https://github.com/HumanBrainProject/openMINDS_core/issues/322 PR https://github.com/HumanBrainProject/openMINDS_core/pull/323

Activity

[x] rename parameterSet to customPropertySet

ExperimentalActivity (new)

[x] extends "core/Activity"
[x] move isPartOf, protocol and preparationDesign from "core/ProtocolExecution" here with adjustments in instructions

ProtocolExecution

[x] extends "core/ExperimantalActivity" (new schema)
[x] remove isPartOf, protocol and preparationDesign

ParameterSet

[x] rename schema to "customPropertySet"
[x] adjust all instructions according to the schema name change
[x] remove parameter
[x] add definedIn (linking to "core/File", "core/Configuration" (new schema) and "core/PropertyValueList" (new schema))

NumericalParameter

[x] rename schema to "NumericalProperty"

StringParameter

[x] rename schema to "StringProperty"

Configuration (new)

see proposal in this specific comment

PropertyValueList (new)

see proposal in this specific comment

CONTROLLED TERMS schemas

DeviceType (new) related to issue #7 e.g. vibratome, microtome, etc.

CranialWindowReinforcementType (new) related to issue #8 e.g. crystalline, glassCoverslip, grinLens, polymer, prism, etc.

CranialWindowConstructionType (new) related to issue #8 e.g. skull thinning, skull clearing, skull removal, etc.

SANDS schemas

**MathematicalShape (new)*** related to issue #8

see proposal in this specific comment

OPEN QUESTIONS

ChemicalSolution from #7, #9, #11

string should be avoided; out of experience, the recuration effort will be very time-consuming
chemicalSolution schema proposed by @lzehl in this specific comment
alternative simplified suggestion by me in this specific comment
things to also keep in mind:
- solution is a specific type of (chemical) mixture; if we want to introduce a simplified "allround" schema for v0, we should name it "ChemicalMixture" which would work in combination with my proposal (basically stating all components and their concentrations using numerical properties (formerly numerical parameters)
- potential addition could be a "CommonName" (or similar)
- use case for when "solution" won't work: CultureMedium (can be liquid, solid or semi-solid)
- use case for when a "CommonName" would be useful: nutrient agar (seems to have a rather stable composition but nobody would recognize it just by the components); 1x PBS (phosphate buffered saline, also pretty stable composition but nobody would recognize it just by the components)

TissueCulturePreparation/CultureEnvironment from #9

pH, temperature, osmotic pressure and such are important properties but not captured in schemas yet; postponed to v1?

ElectrodePlacement/TargetPosition from #10

@apdavison comment about "ephys/ElectrodeContact" carrying part of the proposed "SANDS/AnatomicalLocation" new) schema
proposed solution by me in this specific comment

UlrikeS91 commented 2 years ago

@lzehl, @Peyman-N and @apdavison this is probably not a complete list yet, but it's a good start to keep an overview ☺️

Peyman-N commented 2 years ago

@UlrikeS91 Thanks a lot for this comprehensive list :+1:, only thing it is missing is my two pull requests to SANDS (#179 and #178)

UlrikeS91 commented 2 years ago

@UlrikeS91 Thanks a lot for this comprehensive list 👍, only thing it is missing is my two pull requests to SANDS (#179 and #178)

Very true! Thanks for the update ☺️

openMetadataInitiative / openMINDS_ephys