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The Ontology for Biomedical Investigations
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NTR specimen collection device and subclasses #1194

Open ddooley opened 4 years ago

ddooley commented 4 years ago

GenEpiO had been relying on NCIT terminology for a variety of specimen collection devices, but with some NTR requests via new MIxS specification for food sample collection, and more from the COVID19 effort, we've got more NTR terms esp. in swab department, and it would be good to consolidate them all.

GenEpiO currently has a "specimen extraction device" branch below but we will deprecate that term in favour of OBI "specimen collection device"; and we would create replacement OBI terms for a number of the NCIT and GenEpiO ones. There is some vagueness about whether some of the terms are sample storage devices or devices used to obtain a sample before transport / storage. We probably want to distinguish that?

image

(not shown are GenEpiO drag swab and surface wipe, in GenEpiO draft)

As well new swabs required (from google MIxS Food Extension sheet)

sponge-stick foam spatula drag swab (actually in GenEpiO draft) surface wipe (actually in GenEpiO draft)

As well there are these kinds of sample in-line sample liquid sample pre-moistened swab liquid sample (discuss if this is a swab type or a sample type).

And finally, needed for our Hsiao Lab COVID19 effort, these collection devices or sample storage devices:

specimen collection device - synonym "collection container"

Blood Collection Tube (NCIT_C113122) Bronchoscope (NCIT_C17611) Collection Cup Fibrobronchoscope Brush Filter (having role of specimen collection device role I guess) Air filter (ditto) Microcapillary tube Micropipette Needle (already have OBI_0000436) Fine Needle Serum Collection Tube (NCIT_C113675) Sputum Collection Tube Suction Catheter Urine Collection Tube Virus Transport Medium (reference to mediums designed to promote longevity of viral sample).

I'll fetch definitions for all these so we can review one by one but any preliminary feedback?

d.

cstoeckert commented 4 years ago

Note that some device terms needed may already be in OBIB. (e.g. vacutainer, cryovial). Happy to coordinate on them.

cmrn-rhi commented 2 years ago

Just imported the OBI "specimen collection device" [OBI:0002814] to replace the GENEPIO version, but don't understand why the definition specifies "container" rather than "device" or "tool":

A container used to collect a specimen.

Subclasses include items like "Surface wipe" which I wouldn't consider a container.

Is there an assumption that all of the items have an accompanying container? And if so perhaps this assumption should be included as an "editor note" or "comment"?

And all that being said, with this definition shouldn't it also be a subclass (or other relation) of "specimen container" [OBI:0002088]?

cmrn-rhi commented 2 years ago

Because this issue exploded into many terms, we've separated these terms into smaller issues formatted into ROBOT tables after discussion at the OBI 2022-08-08 meeting. Any overlap in template appear in the same tab, but may still be separated out into smaller issue as we were requested to provide smaller batches.

Following terms covered in #1580

ontology ID label
OBI:0002801 protected specimen brush
OBI:0002825 fibrobronchoscope brush
OBI:0002826 bronchoscope
OBI:0002827 fine needle
OBI:0002830 catheter
OBI:0002831 suction catheter
OBI:0002833 plastic vial
OBI:0002834 glass vial
cmrn-rhi commented 2 years ago

Following terms covered in #1581

ontology ID label
OBI:0002838 labeled sterile leakproof specimen bag
OBI:0002839 cryogenic vial
OBI:0002840 vacutainer
OBI:0002841 PAXgene DNA vacutainer
OBI:0002842 PAXgene RNA vacutainer
OBI:0002843 specimen collection tube
OBI:0002844 gold-top serum separator tube
OBI:0002845 red-top tube
OBI:0002846 plastic red-top tube
OBI:0002847 glass red-top tube
OBI:0002848 pink-top tube (EDTA)
OBI:0002849 light green-top tube
OBI:0002850 dark green-top tube
OBI:0002851 grey-top tube
OBI:0002852 ? Dan will work on label to reflect process tube is designed to support.
OBI:0002853 royal blue-top tube
OBI:0002854 yellow-top tube
OBI:0002855 pearl white-top tube
OBI:0002856 specimen collection tube containing antimicrobial
OBI:0002857 tube containing growth media
  tube containing preservative
OBI:0002858 microcapillary tube
OBI:0002859 whole blood collection tube
OBI:0002860 serum collection tube
OBI:0002861 sputum collection tube
OBI:0002862 urine specimen container
cmrn-rhi commented 2 years ago

Following terms (among others) covered in #1582

ontology ID label
OBI:0002815 food production sample
OBI:0002836 liquid food production sample
OBI:0002837 in-process food production sample

Following terms covered in https://github.com/obi-ontology/obi/issues/1583

ontology ID label
OBI:0002866 virus transport medium

Following terms covered in https://github.com/obi-ontology/obi/issues/1584

ontology ID label
OBI:0003451 swab
OBI:0003452 wet wipe
OBI:0003453 personal protective gown
cmrn-rhi commented 2 years ago

Resolve the following issues should close this (#1194) one:

ddooley commented 1 year ago

About Rhiannon's comment - shall we change specimen collection device definition from "A container used to collect a specimen." to "A device used to collect a specimen." ?

bpeters42 commented 1 year ago

'device' is save, we should use that.

ddooley commented 1 year ago

I've put in a pull request https://github.com/obi-ontology/obi/pull/1674 to tweak definition.

cmungall commented 9 months ago

Roles are an ontological minefield - it's easy to end up with something that will confuse users (e.g. CHEBI)

I assume you will only place devices that are obligate specimen collectors under this term. So syringe, shovel (for soil samples) would not be placed here. But this will confuse average users when they browse the grouping class and don't see expected terms. Or you could go the CHEBI route and have the (currently unaxiomatized) SCD mean something loose like "can potentially be used for specimen collection). But then you confuse everyone by having too many terms there.

Either way I'd recommend if you do have a grouping to axiomatize it and have a strategy for automating placement according to clear rules.

But overall I'd recommend fewer groupings, fewer injections, less ontological commitment. Flat lists under device are fine (there can be other ways that allow users to get bags of terms for a particular use case than hierarchy, e.g. value sets). This will make it easier to import devices en masse from other sources such as wikidata. But if you do want groupings, then best to restrict to function than to bake in role of the material that is the target of the function.