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 https://github.com/CIDO-ontology/cido/issues/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 notifications@github.com 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 https://github.com/obi-ontology/obi/issues/1176#issuecomment-654241142, 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:

https://github.com/obi-ontology/obi/blob/948a6e62c68965d8cd1304bb81794d730be2b5ca/src/ontology/templates/biobank-specimens.tsv#L69-L76

[linikujp]

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

[jamesaoverton]

Closed by #1231