OBI / OBI Terms / #794 New Term Requests: assays

James A. Overton - 2016-01-25

assigned_to: James A. Overton
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James A. Overton - 2016-01-25

We discussed this issue on the OBI developer call, 2016-01-25. The terms seem fine but there's a question of how we should coordinate terms with CMO. I'm going to send this tracker item to Colin Batchelor so that we can discuss it with him.

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James A. Overton - 2016-01-27

I discussed this with Colin, and he has agreed that OBI can adopt these four terms from CHMO, keeping their IDs but taking over maintenance. I'm going to think through the implementation a little more before proceeding to add these terms to OBI.

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- Yu Lin - 2016-01-27
  
  That's great! James!
  
  Looking forward to learning how you will implement this: keep CHMO's ID and
  maintain in OBI.
  
  Thanks,
  Asiyah
  
  On Wed, Jan 27, 2016 at 8:42 AM, James A. Overton jamesaoverton@users.sf.net wrote:
  
  I discussed this with Colin, and he has agreed that OBI can adopt these
  four terms from CHMO, keeping their IDs but taking over maintenance. I'm
  going to think through the implementation a little more before proceeding
  to add these terms to OBI.
  
  [obi-terms:#794] http://sourceforge.net/p/obi/obi-terms/794/ New Term
  Requests: assays*
  
  Status: open
  Group: general
  Created: Wed Jan 20, 2016 09:18 PM UTC by Rob Nash
  Last Updated: Mon Jan 25, 2016 07:20 PM UTC
  Owner: James A. Overton
  
  Hi,
  
  I would like to request some new assay terms for use at the Saccharomyces
  Genome Database (SGD). These terms are actually already present within the
  CHMO (with some minor differences). The CHMO has a very nice collection of
  terms that are often absent in OBI, and vice versa. As a general comment it
  might be worth considering working with CHMO to enrich the nice collection
  of assay terms currently in OBI.
  
  editor preferred term: light microscopy
  alternative terms: optical microscopy
  textual definition: A type of microscopy where the specimen is illuminated
  with visible light and a system of lenses is used to produce an image
  definition source for the textual definition: Chemical Methods Ontology
  (CMO) of the Royal Society of Chemistry (
  http://www.rsc.org/publishing/journals/prospect/ontology.asp?id=CMO:0000102;
  
  http://www.ontobee.org/ontology/CHMO?iri=http://purl.obolibrary.org/obo/CHMO_0000102
  )
  term editor: Rob Nash
  
  Note: should be an instance of imaging assay (OBI: 0000185)
  
  editor preferred term: fluorescence microscopy
  alternative names: FM; fluorescence imaging; fluorescence microscopic
  imaging
  textual definition: A type of microscopy where the specimen can be made to
  fluoresce and emit energy as visible light by illuminating it with light of
  specific wavelengths.
  definition source for the textual definition: Chemical Methods Ontology
  (CMO) of the Royal Society of Chemistry (
  http://www.rsc.org/publishing/journals/prospect/ontology.asp?id=CMO:0000087;
  
  http://www.ontobee.org/ontology/CHMO?iri=http://purl.obolibrary.org/obo/CHMO_0000087
  )
  example of usage: ?
  term editor: Rob Nash
  
  Note: should be an instance of imaging assay (OBI: 0000185)
  
  editor preferred term: liquid chromatography-tandem mass spectrometry
  alternative terms: LC-MS/MS; liquid chromatography-tandem mass spectroscopy
  textual definition: A method where a sample mixture is first separated by
  liquid chromatography (LC) before being ionized and characterized by
  mass-to-charge ratio and relative abundance using two mass spectrometers in
  series and used for the qualitative as well as quantitative determinations
  of compounds.
  definition source for the textual definition: Chemical Methods Ontology
  (CMO) of the Royal Society of Chemistry (
  http://www.rsc.org/publishing/journals/prospect/ontology.asp?id=CMO:0000701;
  
  http://www.ontobee.org/ontology/CHMO?iri=http://purl.obolibrary.org/obo/CHMO_0000701
  )
  example of usage: ?
  term editor: Rob Nash
  
  Note: should be a instance of mass spectrometry analysis (OBI: 0200085)
  
  editor preferred term: confocal fluorescence microscopy
  alternative terms: scanning confocal fluorescence microscopy; fluorescence
  confocal microscopy; confocal fluorescence imaging
  textual definition: A type of microscopy where the specimen can be made to
  fluoresce and emit energy as visible light by illuminating it with light of
  specific wavelength over its surface and using a spatial pinhole to
  eliminate out-of-focus fluorescence.
  definition source for the textual definition: Chemical Methods Ontology
  (CMO) of the Royal Society of Chemistry (
  http://www.rsc.org/publishing/journals/prospect/ontology.asp?id=CMO:0000089;
  
  http://www.ontobee.org/ontology/CHMO?iri=http://purl.obolibrary.org/obo/CHMO_0000089
  )
  example of usage: ?
  term editor: Rob Nash
  
  Note: should be an instance of imaging assay (OBI: 0000185)
  
  Cheers,
  Rob
  
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  Related
  
  OBI Terms: ~~#794~~
  
  alternate
  
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Rob Nash - 2016-01-27

Thanks for pursuing this with Colin. Looking forward to the addition of these terms from CHMO to OBI.

Cheers,
Rob

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bjoernpeters - 2016-10-31

labels: --> assay
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Rob Nash - 2017-02-15

Hi,

Were these terms ever added? I cannot seem to see them in OBI.

Cheers,
Rob

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jzheng - 2017-02-16

Hi Rob,

We will discuss the trackers (794, and 823) you submitted on OBI dev call next Monday and try to make them available on next OBI release.

Thanks for sending term request.

Jie

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Rob Nash - 2017-02-16

Thanks so much Jie. I was preparing for a future project which is now just around the corner.

Cheers,
Rob

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jzheng - 2017-02-20

Hi Rob,

We discussed the tracker on 2017-02-20 OBI dev call. James will add the terms. They will show up in next OBI release. The new release should be out in few weeks.

Thanks for your patient.

Jie

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Rob Nash - 2017-02-21

Hi Jie,

Much appreciated!

Thanks,
Rob

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James A. Overton - 2017-02-22

Hi Rob,

I apologize for dropping the ball on this. The terms have been added to OBI in commit 4090. The will be in the next release, which we plan to make in the coming weeks.

Unfortunately, adopting these terms from CHMO into OBI was not as straightforward as I had hoped. Several changes were made:

change subClassOf parents to fit OBI

remove equivalence for CHMO_0000701

map annotation properties from oboInOwl to IAO

requested changes to labels for CHMO_0000102 and CHMO_0000089

requested minor change to definition for CHMO_0000087

CHMO has many good terms, but hasn't been updated since 2014. If we want to adopt more terms into OBI then we will need a better workflow.
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James A. Overton - 2017-02-22

status: open --> closed
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Rob Nash - 2017-02-22

Thanks James!

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