Relation for devices and the materials that the devices uses

[wdduncan]

Is there a relation that holds between a device, such as a hematology analyzer, and the specimen/sample that device uses to produce the result?
Prov has a used predicate, but that holds between an activity and the thing the activity used.

Could add a utilizes relation? E.g, hemotology-device#1 utilizes blood-sample#1

cc @cmungall @matentzn @balhoff @dosumis

[wdduncan]

P.S. I realize that this can be done with a complex pattern like

hemotology-device#1 has-disposition 
  [a disposition; realized in [a analysis-process; has-input blood-sample#1]]

But that seems like quite a lot to have to say.

[linikujp]

I think the device utilizes specimen is a shortcut relation. This is my use case:
a diagnostic testing device - is capable of - RT-PCR assay; and RT-PCR assay -has specified input - a specimen

[cmungall]

I think the property chain makes sense, but the name 'utilizes' seems more general

how about naming this "capable-of-has-specified-input"?

Note you won't be able to make this in RO without importing OBI which introduces modularity issues

what about capable-of-has-input?

[linikujp]

capable-of-has-input is not human or non-ontologist understandable. I would prefer other more user-friendly labels. Regarding applying this as a RO term, we may need to think about it. It seems like a diagnostic testing device specific term.

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On Mon, Sep 27, 2021 at 4:16 PM Chris Mungall ***@***.***> wrote: I think the property chain makes sense, but the name 'utilizes' seems more general how about naming this "capable-of-has-specified-input"? Note you won't be able to make this in RO without importing OBI which introduces modularity issues what about capable-of-has-input? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#497 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACCPEPMTEKUWP2PQMC4IO43UEDGKPANCNFSM5EK6EYYA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[wdduncan]

I agree with @linikujp. "capable-of-has-input" will not be an easily accessible term. We can, of course, define a property chain on the relation:

'capable of' o 'has input'

I'm fine with with label utilizes. Another option might be processed by.

[linikujp]

This situation may change. Some diagnostic testings do not have the capability of testing. The kit is to collect samples, and then sent to a laboratory where a sequencing machine or a RT-PCR device to run the RT-PCR test... Some home-use kit may have the capacity of running kinds of RT-PCR testing or antigen-antibody detecting tests... The solution of 'capable of' o 'has input' will work on testings that have a component of assays. Other diagnostic testing kits have to combine with certain off-site (of collection) equipment in a controlled lab environment. Thanks, Asiyah .

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On Mon, Oct 4, 2021 at 11:39 AM Bill Duncan ***@***.***> wrote: I agree with @linikujp <https://github.com/linikujp>. "capable-of-has-input" will not be an easily accessible term. We can, of course, define a property chain on the relation: 'capable of' o 'has input' I'm fine with with label utilizes. Another option might be processed by. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#497 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACCPEPKUZV5BMECCLP6KBPLUFHDE3ANCNFSM5EK6EYYA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[wdduncan]

The 'capable of' o 'has input' property chain does not need to be restricted to assays. It is restricted to cases in which a material entity is an input to a process.

The collection of specimens is an interesting case. There is come kind of specimen collection process going on. Not sure if you want to say that the device utilizes specimen, though.

[linikujp]

Yes, aware of the specimen collection process. The device *utilizes *specimen is important to capture in the diagnostic testing modeling use case.

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On Mon, Oct 4, 2021 at 1:03 PM Bill Duncan ***@***.***> wrote: The 'capable of' o 'has input' property chain does not need to be restricted to assays. It is restricted to cases in which a material entity is an input to a process. The collection of specimens is an interesting case. There is come kind of specimen collection process <http://www.ontobee.org/ontology/OBI?iri=http://purl.obolibrary.org/obo/OBI_0000659> going on. Not sure if you want to say that the device utilizes specimen, though. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#497 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACCPEPPZGJXWW5H4QVLN6ILUFHM7JANCNFSM5EK6EYYA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[wdduncan]

I think for cases in which there are outputs that are produced by the device, utilizes seems fine. For cases of storing samples, utilizes seems wrong. For example, a freezer utilizes freon to produce/output a cold environment. It seems to odd to say that the freezer utilizes the items stored inside of it. Located in or some relation like it, seems more appropriate.

[linikujp]

Bill, good thoughts! The whole diagnostic testing may need to include the specific RT-PCR machine as part of it. What machines should be paired with each diagnostic testing kit are specified in the EUA documents. So the *'utilizes'* may still work here. Plus, the collection kit includes sample collection, sample transportation, and sample storage if it is not a self-testing kit. Therefore,

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On Mon, Oct 4, 2021 at 1:22 PM Bill Duncan ***@***.***> wrote: I think for cases in which there are outputs that are produced by the device, utilizes seems fine. For cases of storing samples, utilizes seems wrong. For example, a freezer utilizes freon to produce/output a cold environment. It seems to odd to say that the freezer utilizes the items stored inside of it. Located in or some relation like it, seems more appropriate. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#497 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACCPEPL5CV7HUBTHOENL22TUFHPDVANCNFSM5EK6EYYA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[linikujp]

OBI call today (01/10/2022) discovered the conflict:
OBI has been using "utilizes" linking process to device long time ago, and we are using utilizes for device to material. The OBI accidentally obsoleted the "utilizes" relation and they are reviving this relation.
Both are short relations. @wdduncan we need to resolve the conflict. We may create a new relation specifically for device to material rather than fix the utilizes. And I could propose to OBI that utilizes will be the reverse relation of 'capable of' in our setting.

[linikujp]

obi-ontology/obi#1480

[linikujp]

@wdduncan Can we finalize the relation from device to specimen?

[wdduncan]

@linikujp Sorry, I am not following you. Are you suggesting a new label?

[linikujp]

utilizes is in conflict with OBI use. Please see previous discussion. Yes to your question. Shall we use another label?

[wdduncan]

Yes. I am aware of the other discussion. Right now, utilizes is still obsolete in OBI. So, there isn't a conflict. I made a number of label suggestions. What label do you prefer?

[linikujp]

I like "device utilizes material" this is very straight forward. It was endorsed by Bjoern as well.

[linikujp]

@wdduncan can we finalize with creating this relation in RO? After the creation, this ticket can be closed.
Thanks,
Asiyah

[wdduncan]

@linikujp Do you have an ORCID?

[linikujp]

Yes. It is 0000-0003-2620-0345

[wdduncan]

Thanks. I'll use your ORCID as the value in term editor. That seems to be preferred now.

[wdduncan]

@linikujp See this PR.

[linikujp]

Thank you! That's great. When will it be ready to use?

[wdduncan]

@linikujp Let's wait for the PR be approved.

[wdduncan]

@linikujp The relation device utilizes material has been added to ro-edit.owl. It will be in the next release.