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Published 20 hours ago • verified publisher icon enanomapper

Several terms needed for ACEnano KI dev are missing from ENM ontology

Open UanaF opened this issue 6 years ago • 19 comments

For ACEnano Knowledge infrastructure we need the following terms which are not present in ENM ontology but they are present in the ontologies from which ENM ontology is composed. Could we add/link them? I am writing here also the link of the terms from the other ontologies, it might be useful.

  • [x] Raw data http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C142663
  • [ ] ~~Compound http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C43366~~
  • [x] Medium http://purl.bioontology.org/ontology/npo#NPO_1853
  • [x] Pore size http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C112332
  • [x] Speed http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C41146
  • [x] Temperature http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25206
  • [x] Suspension http://purl.bioontology.org/ontology/npo#NPO_532
  • [x] Extraction http://purl.obolibrary.org/obo/CHMO_0001577
  • [x] Filtration http://purl.obolibrary.org/obo/NCIT_C16583
  • [ ] Freeze-drying http://purl.obolibrary.org/obo/NCIT_C28150
  • [x] Freezing http://purl.obolibrary.org/obo/NCIT_C48160
  • [ ] Storage temperature http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101707
  • [x] Hydrophobicity http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C63813
  • [ ] Electrophoretic mobility http://purl.bioontology.org/ontology/npo#NPO_1315
  • [x] X-Ray photon spectroscopy http://purl.obolibrary.org/obo/CHMO_0000404
  • [ ] ~~pH http://purl.obolibrary.org/obo/UO_0000196~~
  • [x] DLS intrument http://purl.bioontology.org/ontology/npo#NPO_1766
  • [x] Cells http://purl.obolibrary.org/obo/NCIT_C12508
  • [x] Powder http://purl.obolibrary.org/obo/NCIT_C45302
  • [x] Laser induced breakdown detection http://purl.obolibrary.org/obo/CHMO_0000258
  • [x] Small-Angle X-ray Scattering http://purl.obolibrary.org/obo/CHMO_0000204

I have more terms which need annotation but first maybe it is better to see how we can do with these ones. Would be okay if I start to add them based on the adding terms enm tutorial?https://github.com/enanomapper/tutorials/tree/master/Added%20ontology%20terms. Please let me know/keep me updated on the process.

UanaF avatar Jul 02 '19 14:07 UanaF

Yes, most certainly okay and indeed very much appreciated to follow the tutorial and add some terms! I recommend making one pull request for each term, and start with one, so that I can give feedback.

egonw avatar Jul 07 '19 14:07 egonw

@UanaF, let me know if I can assist.

egonw avatar Jul 14 '19 09:07 egonw

Hi Egon,

Thank you for offering the help and sorry for my late reply! The tutorial is a v useful resource and I think I can manage; I will start these days to add the terms and notify you for a feedback. I had other urgent tasks lately but will soon finish them and start with ENM ontology terms.

/Oana

Trimis de pe iPhone‑ul meu

Pe 14 iul. 2019, la 12:11, Egon Willighagen [email protected] a scris:

@UanaF, let me know if I can assist.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

UanaF avatar Jul 14 '19 17:07 UanaF

Hi Egon,

I tried to add "raw data" (http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C142663) as a child of "data item" (http://purl.obolibrary.org/obo/IAO_0000027). I added in the "ncit.iris" the following: "+(http://purl.obolibrary.org/obo/IAO_0000027):http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C142663 raw data". If I use bioportal to see if the term was added to ENM classes; "raw data" is not there. The same with "suspension" (http://purl.bioontology.org/ontology/npo#NPO_532) in npo.iris. Do the terms need approve from you to be seen in ENM or I am doing something wrong?

UanaF avatar Jul 18 '19 17:07 UanaF

You added them to the development version of the ontology. You need to load that version to do such a check. BioPortal only had released versions.

egonw avatar Aug 30 '19 07:08 egonw

But raw data is also not in the development version. In fact, it is not in the NCIT OWL we start with.

egonw avatar Aug 30 '19 08:08 egonw

We were using a rather old version of NCIT: https://github.com/enanomapper/ontologies/commit/4c68e083750d47a731e3d43a9c0b08eb2baca0c7

egonw avatar Aug 30 '19 08:08 egonw

suspension from NPO is actually correctly included.

egonw avatar Aug 30 '19 08:08 egonw

@UanaF, for Compound use http://purl.obolibrary.org/obo/CHEBI_23367 which is already in ENM.

egonw avatar Aug 30 '19 10:08 egonw

For pH use http://purl.bioontology.org/ontology/npo#NPO_1814 instead. See also https://github.com/enanomapper/ontologies/commit/75c1b35a3774b54513341692d1e592bce3bff501

egonw avatar Aug 30 '19 10:08 egonw

Finally (for now), can you explain why you need Temperature for? There are various related terms, which may be the one to use.

egonw avatar Aug 30 '19 10:08 egonw

We need temperature for the Measurement protocol > Instrument Parameters; when u set the instrument; which should be an alternative to it?

Oana C. Florean,

Research Scientist,

Edelweiss Connect GmbH

On Fri, Aug 30, 2019 at 1:54 PM Egon Willighagen [email protected] wrote:

Finally (for now), can you explain why you need Temperature for? There are various related terms, which may be the one to use.

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UanaF avatar Aug 30 '19 12:08 UanaF

@UanaF, I would suggest http://purl.bioontology.org/ontology/npo#NPO_1806.

egonw avatar Aug 30 '19 12:08 egonw

Ah, good, thanks!

Oana C. Florean,

Research Scientist,

Edelweiss Connect GmbH

On Fri, Aug 30, 2019 at 3:37 PM Egon Willighagen [email protected] wrote:

@UanaF https://github.com/UanaF, I would suggest http://purl.bioontology.org/ontology/npo#NPO_1806 http://bioportal.bioontology.org/ontologies/ENM/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2Fnpo%23NPO_1806&jump_to_nav=true .

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UanaF avatar Aug 30 '19 12:08 UanaF

Can I have a link for this dev version?

Oana C. Florean,

Research Scientist,

Edelweiss Connect GmbH

On Fri, Aug 30, 2019 at 10:46 AM Egon Willighagen [email protected] wrote:

You added them to the development version of the ontology. You need to load that version to do such a check.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/enanomapper/ontologies/issues/170?email_source=notifications&email_token=AGBVIURJ5QWPMKKTLVTZGILQHDF55A5CNFSM4H44G6Z2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5Q3K7Q#issuecomment-526497150, or mute the thread https://github.com/notifications/unsubscribe-auth/AGBVIUXCAL6AIAZL2YPIZ33QHDF55ANCNFSM4H44G6ZQ .

UanaF avatar Aug 30 '19 12:08 UanaF

It's in https://github.com/enanomapper/ontologies/blob/master/README.md

egonw avatar Aug 30 '19 12:08 egonw

Continuation of the new terms needed to be added

Chemical Methods Ontology (CHMO):

Ion-selective electrode http://purl.obolibrary.org/obo/CHMO_0002393 Laser induced breakdown detection http://purl.obolibrary.org/obo/CHMO_0000258 Time of flight secondary ion mass spectrometry http://purl.obolibrary.org/obo/CHMO_0000565 Tip Enhanced Raman Scattering (nano-Raman) http://purl.obolibrary.org/obo/CHMO_0000678 Transmission electron microscopy with electron energy loss spectroscopy http://purl.obolibrary.org/obo/CHMO_0000373 Wide-Angle X-ray Scattering http://purl.obolibrary.org/obo/CHMO_0000207

NanoParticle Ontology (NPO):

DLS intrument http://purl.bioontology.org/ontology/npo#NPO_1766 Electrophoretic mobility http://purl.bioontology.org/ontology/npo#NPO_1315 Medium http://purl.bioontology.org/ontology/npo#NPO_1853 Phase http://purl.bioontology.org/ontology/npo#NPO_1610

National Cancer Institute Thesaurus (NCIT)

Amplitude http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C70831 Conductivity http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C134263 Matrix-Assisted Laser Desorption/Ionization http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C48040 Parameters http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C80474 Purity (resistivity) http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C62352

UanaF avatar Sep 03 '19 13:09 UanaF

Freeze-drying http://purl.obolibrary.org/obo/NCIT_C28150 --> Already in ENM?

image

https://bioportal.bioontology.org/ontologies/ENM/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2Fnpo%23NPO_1957&jump_to_nav=true

lwinckers avatar Dec 11 '19 14:12 lwinckers

Electrophoretic mobility http://purl.bioontology.org/ontology/npo#NPO_1315 --> see issue #184

lwinckers avatar Dec 11 '19 14:12 lwinckers