Specimen terms request

[linikujp]

Below is a list of verbatims copied from the EUA documents with limited redundant check. Those terms include synonyms, alternative terms and acronyms. Please sort it out with correct hierarchies before adding into CIDO. (Originally requested to CIDO CIDO-ontology/cido#7 Per @bpeters42 request, I request the terms to be added into OBI.

Please note the difference between swab and specimen took using a swab. Swab is a device/tool, you may need to add a specimen for terms ending with swab.

anterior nasal swab
BAL fluid
BAL specimen
BALs
bronchial aspirates
bronchial washings
bronchial washings (BW)
bronchoalveolar lavage
bronchoalveolar lavages (BAL)/bronchial washings (BW)
lower respiratory specimens
lower respiratory tract aspirates
mid turbinate nasal swabs
midturbinate
mid-turbinate
mid-turbinate nasal swab
nasal
nasal aspirates
nasal swab
nasal wash
nasopharyngeal
nasopharyngeal (NP)
nasopharyngeal and oropharyngeal specimens
nasopharyngeal and oropharyngeal swab and bronchoalveolar lavage (BAL) specimen
nasopharyngeal aspirates
nasopharyngeal aspirates (NA)/nasal washings (NW)
nasopharyngeal awash/aspirate or nasal aspirates as well as sputum specimens
nasopharyngeal swab
nasopharyngeal swabs/wash
nasopharyngeal wash
nasopharyngeal wash/aspirates
NP/OP
oropharyngeal (OP)
oropharyngeal (throat) swab
oropharyngeal swabs/throat swabs
saliva specimens
sputum
throat (oropharyngeal) swab
tracheal aspirates
tracheal secretions
upper respiratory specimens
stool specimen
human serum or plasma (EDTA) specimen

[jamesaoverton]

Unfortunately, OBI does not have a team of funded curators to handle term requests. While the OBI community tries to make the submission process as easy as possible, we require the submitter to do the work of providing the term details according to our Term Submission Guidelines.

I suggest creating a submission template based on https://github.com/obi-ontology/obi/blob/master/src/ontology/templates/biobank-specimens.tsv

I noticed that at least some of these terms are already in OBI.

[linikujp]

Will work on that. Thanks!

[linikujp]

Hi, I compared existing OBI terms and my list.

1. The major terms that are lacking in OBI are:
   tracheal aspirate specimen, mid-turbinate nasal swab, nasal wash/aspirate specimen, lower respiratory tract aspirates, upper respiratory specimen, lower respiratory specimen, anterior nasal swab specimen
2. Other major issues will be to differentiate the wash and aspirates.
3. Hierarchical terms such as upper respiratory specimen and lower respiratory specimen.

Will continue studying those, and submit a final excel sheet for new terms submission.

[updated on 7/8/20 per CDC' COVID 19 tests mapping ]

[linikujp]

Dear everyone,

Can you recommend any existing relation linking a specimen to the anatomical part where the spwcimen is supposed to be collected?

Thanks,
Asiyah

[cstoeckert]

For the biobank-specimens template (https://github.com/obi-ontology/obi/blob/master/src/ontology/templates/biobank-specimens.tsv) we are using 'derives from' (see Gross Anatomical Part column).

[linikujp]

Appreciate your help, Chris!

…

On Mon, Jul 6, 2020, 9:34 AM cstoeckert ***@***.***> wrote: For the biobank-specimens template ( https://github.com/obi-ontology/obi/blob/master/src/ontology/templates/biobank-specimens.tsv) we are using 'derives from' (see Gross Anatomical Part column). — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub <#1176 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACCPEPLIGXGNFWVL4B6SKB3R2HHE5ANCNFSM4N2QJGQQ> .

[linikujp]

Please see attached.
OBI_new_term_submission_specimen_1176.xlsx

I also suggested a new process term "aspiration specimen collection" for specimen collection.

Please let me know your feedbacks and if you like to make some changes.

[linikujp]

@jamesaoverton Please let me know if these terms were added or not.

[jamesaoverton]

Discussed on the 2020-8-17 call. These look good at a quick glance -- we need someone to do a closer review and make a PR. We'd prefer UBERON over FMA. @jamesaoverton will do this or delegate it.

[linikujp]

Thanks! The FMA terms were used because equivalent UBERON terms were not available.

[jamesaoverton]

I assigned Apurva to work on this, and reserved the following IDs using the OBI Term ID Reservation sheet

ID	Label
OBI:0002778	tracheal aspirate specimen
OBI:0002779	mid-turbinate nasal swab specimen
OBI:0002780	nasal aspirate specimen
OBI:0002781	lower respiratory tract aspirate specimen
OBI:0002782	upper respiratory specimen
OBI:0002783	lower respiratory tract specimen
OBI:0002784	anterior nasal swab specimen
OBI:0002785	aspiration specimen collection

[jamesaoverton]

OBI does not import from FMA. We plan to use the following UBERON terms instead of the submitted FMA terms:

submitted	replacement
FMA_57459 Middle nasal concha	UBERON:0005921 middle nasal concha
FMA_45662 Lower respiratory tract	UBERON:0001558 lower respiratory tract
FMA_45661 Upper respiratory tract	UBERON:0001557 upper respiratory tract

[linikujp]

Thank you, James. UBERON is not species specific, right?
What is the solution for human specific anatomical terms?
Thanks,
Asiyah

[jamesaoverton]

OBI uses UBERON, which has XRefs pointing to all sorts of species-specific anatomy ontologies. I don't want to add an FMA dependency at this point.

We've revised some of the definitions to fit OBI patterns. Please take a look and let us know if there are any problems:

obi/src/ontology/templates/biobank-specimens.tsv

Lines 69 to 76 in 948a6e6

	OBI:0002746 induced sputum specimen A sputum specimen that is collected from an organism following its inhalation of a nebulized salt solution. PMC3297553 subclass sputum UBERON_0007311 John Judkins
	OBI:0002778 tracheal aspirate specimen tracheal wash specimen A specimen that is collected with a suctioning tube from the trachea. PMID:25338241 subclass trachea UBERON_0003126 Asiyah Yu Lin|ORCID:0000-0003-2620-0345
	OBI:0002779 mid-turbinate nasal swab specimen A specimen that is collected with a mid-turbinate nasal swab from the turbinate area of the nasal cavity. https://seattlechildrenslab.testcatalog.org/catalogs/185/files/11633 equivalent middle nasal concha UBERON_0005921 Asiyah Yu Lin|ORCID:0000-0003-2620-0345
	OBI:0002780 nasal aspirate specimen nasal wash specimen|nasopharyngeal aspirate A specimen that is collected with a suctioning tube from the nasal cavity. Asiyah Yu Lin|ORCID:0000-0003-2620-0345 equivalent nasal cavity UBERON_0001707 Asiyah Yu Lin|ORCID:0000-0003-2620-0345
	OBI:0002781 lower respiratory tract aspirate specimen lower respiratory tract wash specimen A specimen that is collected with a suctioning tube from the lower respiratory tract. Asiyah Yu Lin|ORCID:0000-0003-2620-0345 equivalent lower respiratory tract UBERON_0001558 Asiyah Yu Lin|ORCID:0000-0003-2620-0345
	OBI:0002782 upper respiratory specimen A specimen that is derived from the upper respiratory tract Asiyah Yu Lin|ORCID:0000-0003-2620-0345 equivalent upper respiratory tract UBERON_0001557 Asiyah Yu Lin|ORCID:0000-0003-2620-0345
	OBI:0002783 lower respiratory tract specimen A specimen that is derived from the lower respiratory tract. Asiyah Yu Lin|ORCID:0000-0003-2620-0345 equivalent lower respiratory tract UBERON_0001558 Asiyah Yu Lin|ORCID:0000-0003-2620-0345
	OBI:0002784 anterior nasal swab specimen A specimen that is derived from the anterior nasal wall Asiyah Yu Lin|ORCID:0000-0003-2620-0345 equivalent anterior nasal wall UBERON_3000016 Asiyah Yu Lin|ORCID:0000-0003-2620-0345

[linikujp]

@jamesaoverton I checked. It is fine with me. And thanks for the information about UBERON.

[jamesaoverton]

Closed by #1231