ExPaNDS-eu / ExPaNDS-experimental-techniques-ontology

EU Photon and Neutron Ontologies (task 3.2)
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hierarchical phase-contrast tomography equivalent? #90

Open servansod opened 11 months ago

servansod commented 11 months ago

Is this HiP-CT technique in use at the ESRF included in one of the existing terms? Like the PaNET01152 (propagation phase contrast tomography)?

Motivation: In the frame of LEAPS working group on data, I'm listing open data resources and would like to link to PaNET terms for technique-specific resources whenever relevant (guess whose idea it was). The Human organ Atlas is exclusively using HiP-CT data.

Ex of the source yaml:

- short-name: EMDB
  name: Electron Microscopy Data Bank 
  link: https://www.ebi.ac.uk/emdb/
  pic: https://www.ebi.ac.uk/em_static/images/emdb/EMBD_logo_2017_light_background.png
  description: EMDB (the Electron Microscopy Data Bank) is a public repository for electron cryo-microscopy maps and tomograms of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, sub-tomogram averaging, fibre diffraction and electron crystallography.
  api: https://www.ebi.ac.uk/emdb/api/
  technique: 
    - IRI: http://purl.org/pan-science/PaNET/PaNET01145
      name: electron microscopy

- short-name: SASDB
  name: Small Angle Scattering Biological Data Bank
  description: SASBDB is a curated repository of freely accessible and fully searchable SAS experimental data, which are deposited together with the relevant experimental conditions, sample details, instrument characteristic and derived models. The quality of deposited experimental data and the accuracy of models obtained from SAS and complementary techniques is assessed by the site developers.
  link: https://www.sasbdb.org/
  pic: https://www.sasbdb.org/media/sasbdb-logo.png
  api: https://www.sasbdb.org/rest-api/docs/
  technique: 
    - IRI: http://purl.org/pan-science/PaNET/PaNET01124
      name: small angle scattering

By the way, if you consider issue #83, that'd be super helpful to automate update.

spc93 commented 10 months ago

So this looks to me to be a subclass of 'propagation phase contrast tomography' (http://purl.org/pan-science/PaNET/PaNET01152) or 'propagation phase contrast microtomography' (http://purl.org/pan-science/PaNET/PaNET01210).

Is it the actual measurement that is hierarchical (rather than the data display)?

If so then we should maybe thing of a new term relating to multi-scale techniques?

If the hierarchy is really related to the technique, and it always involves tomography at the 'micro' scale then I would propose making this a subclass of 'propagation phase contrast microtomography' for now, possibly fleshing it out more later?

rduyme commented 8 months ago

note : mentioned as missing in mapping of ESRF instruments : https://docs.google.com/document/d/1rElzrnPDql9k2uixP2G0RUdgPOM7jh4zooXosuAT0Hg (BM18)