New Term Requests: assays

obi-bot commented 8 years ago

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

Reported by: rnash

Original Ticket: obi/obi-terms/794

obi-bot commented 8 years ago

assigned_to: James A. Overton

Original comment by: jamesaoverton

obi-bot commented 8 years ago

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.

Original comment by: jamesaoverton

obi-bot commented 8 years ago

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.

Original comment by: jamesaoverton

obi-bot commented 8 years ago

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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Original comment by: linyumichigan

obi-bot commented 8 years ago

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

Cheers, Rob

Original comment by: rnash

obi-bot commented 7 years ago

labels: --> assay

Original comment by: bpeters42

obi-bot commented 7 years ago

Hi,

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

Cheers, Rob

Original comment by: rnash

obi-bot commented 7 years ago

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

Original comment by: zhengj2007

obi-bot commented 7 years ago

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

Cheers, Rob

Original comment by: rnash

obi-bot commented 7 years ago

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

Original comment by: zhengj2007

obi-bot commented 7 years ago

Hi Jie,

Much appreciated!

Thanks, Rob

Original comment by: rnash

obi-bot commented 7 years ago

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.

Original comment by: jamesaoverton

obi-bot commented 7 years ago

status: open --> closed

Original comment by: jamesaoverton

obi-bot commented 7 years ago

Thanks James!

Original comment by: rnash

obi-ontology / obi

New Term Requests: assays #777

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.

Cheers, Rob