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ExPaNDS-eu / ExPaNDS-experimental-techniques-ontology

EU Photon and Neutron Ontologies (task 3.2)
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Superclasses of obtain spatial map seem wrong #115

Closed hgoerzig closed 3 weeks ago

hgoerzig commented 5 months ago

obtain spatial map has two high level super classes: 'defined by purpose' 'defined by functional dependence'

This seems wrong. I have the idea it should only 'defined by purpose' . Also all subclasses of obtain spatial map have 'imaging' as superclass which is subclass of'defined by functional dependence'

spc93 commented 5 months ago

Yes I need to look at this.

spc93 commented 5 months ago

It looks like the problem is caused by 'imaging' being a subclass of 'defined by functional dependence' and equivalent to 'obtain spatial map'. Probably it should not be a subclass of 'defined by functional dependence' but only equivalent to 'obtain spatial map'. The error is in confusing the functional dependence of the measurement with the purpose (my error -sorry!). An image/spatial map could be obtained by a direct measurement of spatial dependence, but it could also be determined by transforming from reciprocal space, which has a different functional dependence (versus Q). We might also need to look at measurements involving the conjugate variables time and energy (e.g. definition of spectroscopy).

I think the immediate fix is to remove subclass of 'defined by functional dependence' from the definition of 'imaging'.

Any other thoughts?

spc93 commented 3 months ago

115

Problem: 'obtain spatial map' is a subclass of 'defined by functional dependence'. This is wrong because 'obtain spatial map' (equivalent to 'imaging') may be obtained via a different functional dependence, e.g. a measurement in reciprocal space. The problem is in the definition of 'imaging'.

Solution: remove 'defined by functional dependence' from the definition of imaging.

Current definition: subclass of: 'defined by functional dependence' equivalent to: obtain spatial map

Proposed new definition: equivalent to: obtain spatial map

Test results (current version):

Properties of PaNET.PaNET01106 (Label: imaging) in http://purl.org/pan-science/PaNET/PaNET.owl:

Superclasses (direct and given by equivalent classes):

PaNET.PaNET00004 defined by functional dependence PaNET.PaNET00005 defined by purpose

No. of direct_superclasses of PaNET.PaNET01106: 2

All superclasses:

PaNET.PaNET00001 photon and neutron technique PaNET.PaNET00004 defined by functional dependence PaNET.PaNET00005 defined by purpose PaNET.PaNET01106 imaging

No. of superclasses of PaNET.PaNET01106 (including self): 4

Subclasses (children):

PaNET.PaNET01068 obtain high resolution spatial map PaNET.PaNET01069 microscopy PaNET.PaNET01070 obtain ultrahigh resolution spatial map PaNET.PaNET01071 obtain 3D spatial map PaNET.PaNET01088 absorption contrast imaging PaNET.PaNET01096 fluorescence tomography PaNET.PaNET01105 holography PaNET.PaNET01106 imaging PaNET.PaNET01110 infrared microspectroscopy PaNET.PaNET01112 fluorescence imaging PaNET.PaNET01113 fluorescence microscopy (Alt. Labels: Micro XRF, microfluorescence) PaNET.PaNET01116 phase contrast imaging PaNET.PaNET01123 scanning transmission microscopy (Alt. Labels: STM) PaNET.PaNET01129 tomography PaNET.PaNET01136 diffraction imaging (Alt. Labels: topography) PaNET.PaNET01145 electron microscopy (Alt. Labels: EM) PaNET.PaNET01146 photoemission electron microscopy (Alt. Labels: PEEM, photoelectron emission microscopy) PaNET.PaNET01147 scanning probe imaging PaNET.PaNET01148 scanning probe microscopy (Alt. Labels: scanning microscopy) PaNET.PaNET01151 absorption tomography PaNET.PaNET01152 propagation phase contrast tomography PaNET.PaNET01153 ultrafast tomography PaNET.PaNET01154 nanotomography PaNET.PaNET01155 absorption and phase contrast nanotomography PaNET.PaNET01174 coherent diffraction imaging (Alt. Labels: CDI, coherent diffractive imaging) PaNET.PaNET01175 infrared nanospectroscopy imaging (Alt. Labels: nano infrared spectroscopy) PaNET.PaNET01176 UV circular dichroism imaging PaNET.PaNET01178 infrared microscopy (Alt. Labels: IR microscopy) PaNET.PaNET01179 optical microscopy PaNET.PaNET01180 x-ray microscopy PaNET.PaNET01206 microtomography PaNET.PaNET01207 x-ray tomography (Alt. Labels: CT scan) PaNET.PaNET01208 x-ray microtomography PaNET.PaNET01209 absorption microtomography (Alt. Labels: Absorption-based tomographic microscopy) PaNET.PaNET01210 propagation phase contrast microtomography PaNET.PaNET01211 ultrafast microtomography (Alt. Labels: Ultra-fast tomographic microscopy) PaNET.PaNET01212 ptychography PaNET.PaNET01213 ptychographic nanotomography PaNET.PaNET01219 scanning transmission x-ray microscopy (Alt. Labels: STXM) PaNET.PaNET01230 single-shot imaging PaNET.PaNET01248 neutron transmission radiography PaNET.PaNET01249 cold neutron imaging PaNET.PaNET01250 high-resolution neutron imaging
PaNET.PaNET01251 THz near field microscopy PaNET.PaNET01261 x-ray refraction imaging (Alt. Labels: x-ray refraction radiography) PaNET.PaNET01262 x-ray refraction tomography PaNET.PaNET01266 x-ray holography PaNET.PaNET01285 x-ray imaging PaNET.PaNET01286 micro small angle x-ray scattering tomography (Alt. Labels: micro SAXS tomography) PaNET.PaNET01287 micro grazing incidence small angle x-ray scattering tomography (Alt. Labels: micro GISAXS tomography) PaNET.PaNET01288 scanning x-ray fluorescence PaNET.PaNET01289 soft x-ray imaging PaNET.PaNET01290 x-ray diffraction imaging PaNET.PaNET01291 scanning angle resolved photoemission spectromicroscopy PaNET.PaNET01292 nano angle resolved photoemission spectroscopy (Alt. Labels: nano ARPES) PaNET.PaNET01293 scanning photoelectron microscopy PaNET.PaNET01294 x-ray photoemission electron microscopy PaNET.PaNET01295 x-ray scanning microscopy (Alt. Labels: scanning x-ray microscopy) PaNET.PaNET01313 magnetic x-ray tomography PaNET.PaNET01314 correlative light x-ray microscopy (Alt. Labels: CLXM) PaNET.PaNET01315 cryo x-ray microscopy PaNET.PaNET01318 atomic force microscopy (Alt. Labels: AFM) PaNET.PaNET01319 atomic force microscope infrared spectroscopy (Alt. Labels: AFM-IR) PaNET.PaNET01327 x-ray birefringence imaging (Alt. Labels: XBI)

No. of subclasses of PaNET.PaNET01106 (including self): 64

Test results (new version):

Properties of PaNET.PaNET01106 (Label: imaging) in /dls/science/users/spc93/tmp/PaNET.owl:

Superclasses (direct and given by equivalent classes):

PaNET.PaNET00005 defined by purpose

No. of direct_superclasses of PaNET.PaNET01106: 1

All superclasses:

PaNET.PaNET00001 photon and neutron technique PaNET.PaNET00005 defined by purpose PaNET.PaNET01106 imaging

No. of superclasses of PaNET.PaNET01106 (including self): 3

Subclasses (children):

PaNET.PaNET01068 obtain high resolution spatial map PaNET.PaNET01069 microscopy PaNET.PaNET01070 obtain ultrahigh resolution spatial map PaNET.PaNET01071 obtain 3D spatial map PaNET.PaNET01088 absorption contrast imaging PaNET.PaNET01096 fluorescence tomography PaNET.PaNET01105 holography PaNET.PaNET01106 imaging PaNET.PaNET01110 infrared microspectroscopy PaNET.PaNET01112 fluorescence imaging PaNET.PaNET01113 fluorescence microscopy (Alt. Labels: Micro XRF, microfluorescence) PaNET.PaNET01116 phase contrast imaging PaNET.PaNET01123 scanning transmission microscopy (Alt. Labels: STM) PaNET.PaNET01129 tomography PaNET.PaNET01136 diffraction imaging (Alt. Labels: topography) PaNET.PaNET01145 electron microscopy (Alt. Labels: EM) PaNET.PaNET01146 photoemission electron microscopy (Alt. Labels: PEEM, photoelectron emission microscopy) PaNET.PaNET01147 scanning probe imaging PaNET.PaNET01148 scanning probe microscopy (Alt. Labels: scanning microscopy) PaNET.PaNET01151 absorption tomography PaNET.PaNET01152 propagation phase contrast tomography PaNET.PaNET01153 ultrafast tomography PaNET.PaNET01154 nanotomography PaNET.PaNET01155 absorption and phase contrast nanotomography PaNET.PaNET01174 coherent diffraction imaging (Alt. Labels: CDI, coherent diffractive imaging) PaNET.PaNET01175 infrared nanospectroscopy imaging (Alt. Labels: nano infrared spectroscopy) PaNET.PaNET01176 UV circular dichroism imaging PaNET.PaNET01178 infrared microscopy (Alt. Labels: IR microscopy) PaNET.PaNET01179 optical microscopy PaNET.PaNET01180 x-ray microscopy PaNET.PaNET01206 microtomography PaNET.PaNET01207 x-ray tomography (Alt. Labels: CT scan) PaNET.PaNET01208 x-ray microtomography PaNET.PaNET01209 absorption microtomography (Alt. Labels: Absorption-based tomographic microscopy) PaNET.PaNET01210 propagation phase contrast microtomography PaNET.PaNET01211 ultrafast microtomography (Alt. Labels: Ultra-fast tomographic microscopy) PaNET.PaNET01212 ptychography PaNET.PaNET01213 ptychographic nanotomography PaNET.PaNET01219 scanning transmission x-ray microscopy (Alt. Labels: STXM) PaNET.PaNET01230 single-shot imaging PaNET.PaNET01248 neutron transmission radiography PaNET.PaNET01249 cold neutron imaging PaNET.PaNET01250 high-resolution neutron imaging
PaNET.PaNET01251 THz near field microscopy PaNET.PaNET01261 x-ray refraction imaging (Alt. Labels: x-ray refraction radiography) PaNET.PaNET01262 x-ray refraction tomography PaNET.PaNET01266 x-ray holography PaNET.PaNET01285 x-ray imaging PaNET.PaNET01286 micro small angle x-ray scattering tomography (Alt. Labels: micro SAXS tomography) PaNET.PaNET01287 micro grazing incidence small angle x-ray scattering tomography (Alt. Labels: micro GISAXS tomography) PaNET.PaNET01288 scanning x-ray fluorescence PaNET.PaNET01289 soft x-ray imaging PaNET.PaNET01290 x-ray diffraction imaging PaNET.PaNET01291 scanning angle resolved photoemission spectromicroscopy PaNET.PaNET01292 nano angle resolved photoemission spectroscopy (Alt. Labels: nano ARPES) PaNET.PaNET01293 scanning photoelectron microscopy PaNET.PaNET01294 x-ray photoemission electron microscopy PaNET.PaNET01295 x-ray scanning microscopy (Alt. Labels: scanning x-ray microscopy) PaNET.PaNET01313 magnetic x-ray tomography PaNET.PaNET01314 correlative light x-ray microscopy (Alt. Labels: CLXM) PaNET.PaNET01315 cryo x-ray microscopy PaNET.PaNET01318 atomic force microscopy (Alt. Labels: AFM) PaNET.PaNET01319 atomic force microscope infrared spectroscopy (Alt. Labels: AFM-IR) PaNET.PaNET01327 x-ray birefringence imaging (Alt. Labels: XBI)

No. of subclasses of PaNET.PaNET01106 (including self): 64