reduce length of short name nose_mouth_teeth_throat_disord [MIXS:0000283]

[only1chunts]

Current term details

Term name -  nose/mouth/teeth/throat disorder
Term ID - MIXS:0000283
Structured comment name - nose_mouth_teeth_throat_disord
Definition - History of nose/mouth/teeth/throat disorders; can include multiple disorders

Suggested update(s)

Term name -  nose/mouth/teeth/throat disorder
Term ID - MIXS:0000283
Structured comment name - nosal_oral_disord
Definition - History of nose/mouth/teeth/throat disorders; can include multiple disorders

Additional context FYI - the “nose_mouth_teeth_throat_disord” MIXS:0000283 was supposed to have been fixed as part of #84 by changing it to “nose_oral_disord” but it doesn’t appear to have stuck!

[turbomam]

Thanks @only1chunts. Can you link your source for those term details? It would be nice to look at them in both the native LinkML format and this other format that you prefer.

[only1chunts]

I did not intend to give the impression of a "preferred format", the ticket is simply a human readable thing to get the issue recorded and addressed (by other humans :-) ). The current term details are as shown here https://genomicsstandardsconsortium.github.io/mixs/0000283/ The suggested ones are as shown above, i.e. the source is ticket #84

[only1chunts]

FYI the v6 excel spreadsheet from here lists BOTH MIXS:0000283 and MIXS:0000270 with the short name "nose_throat_disord", I'm not sure how that happened (maybe the spreadsheet was manually created for v6?), but the spreadsheet is definitely wrong.

[turbomam]

Thanks, that's helpful background.

Here are the relevant LinkML blocks. In case I haven't emphasized this enough recently: the code below represents my unilateral attempt to resolve these two terms, which slipped through un-discussed in the large v6.2.0 PR.

  nose_mouth_teeth_throat_disord:
    description: History of nose/mouth/teeth/throat disorders; can include multiple
      disorders. The terms should be chosen from the DO (Human Disease Ontology) at
      http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825),
      mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091),
      or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974)
    title: nose/mouth/teeth/throat disorder
    keywords:
      - disorder
    slot_uri: MIXS:0000283
    multivalued: true
    range: string
  nose_throat_disord:
    description: History of nose-throat disorders; can include multiple disorders,  The
      terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org,
      lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory
      tract disease (https://disease-ontology.org/?id=DOID:974)
    title: nose throat disorder
    keywords:
      - disorder
    slot_uri: MIXS:0000270
    multivalued: true
    range: string

[turbomam]

I trust you or others to change this modelling based on whatever documented or mental recollections you have.

I will say that those descriptions are far from ideal. If the multivalued attribute is set to true, then there's no need to repeat "can include multiple disorders" in the description. And all of the notes about where to find should be captures in comments, because they are not descriptive of what a nose_mouth_teeth_throat_disord or nose_throat_disord is. They're comments on how the values should be selected or fomatted.

Ideally we will capture that with dynamic enumerations in the future.

[only1chunts]

discussed at CIG call. both terms(IXS:0000270 & IXS:0000283) have been used in NCBI Bio Samples >1000 times. we should explore the usage before mkaing a decision.

[only1chunts]

@turbomam has looked at usage of those terms in NCBI biosamples see ticket #760

[only1chunts]

(Copied note from #760 added by @lschriml)

As noted in the Feb 13th CIG notes: (Lynn): review of term usage:

→ Review notes below, I would say that we can merge these two terms. New definition: History of nose,mouth, teeth, and/or throat disorders: can include multiple disorders.

→ and to add in the information for the source of the terms possible values, where appropriate: The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org/, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974), (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091).

MIXS:0000270 - In the human-associated package: –Structured Comment (short name): nose_throat_disord – Package Name (long name):lung/nose-throat disorder -definition: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org/, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974).

MIXS:0000283 - In the human oral package:

– Structured Comment (short name): nose_throat_disord – Package Name (long name): nose/mouth/teeth/throat disorder – definition: History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org/, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974).

[only1chunts]

From the discussions in CIG calls and the comments above are we proposing : 1 - to deprecate MIXS:0000283 AND 2 - Update MIXS:0000270 to

  nose_throat_disord:
    description: Report any history of nose, mouth, teeth and/or throat disorders in the subject. May include multiple disorders.
    title: nose throat disorder
    keywords:
      - disorder
    slot_uri: MIXS:0000270
    alias: nose_mouth_teeth_throat_disord
    comment:  The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974)
    multivalued: true
    range: string

e.g. add an alias for the deprecated term name, and add the comment to hold the description of what values to add.

[lschriml]

CIG discussed on March 26th, agreed to go ahead with the comment on Feb 14th. Lynn

[turbomam]

nose_mouth_teeth_throat_disord has more records and has been in use longer

---

nose_throat_disord has been used 1,215 times with last updated dates from 2017-05-11 to 2023-11-06

nose_throat_disord	count
missing	312
NO	290
no	249
NA	128
not collected	121
Healthy - History of Otitis Media	36
Otits Media - middle ear effusion	18
Healthy - no Otitis Media history	17
No data available	17
Otits Media with perforation	7
not applicable	5
n/a	4
Acute Otits Media	4
No	1
1	1
6	1
5	1
4	1
3	1
2	1

---

nose_mouth_teeth_throat_disord has been used 1737 with last updated dates from 2013-10-02 to 2023-01-26

nose_mouth_teeth_throat_disord	count
not applicable	698
none	168
not particular	156
cancer	136
dental caries	74
recurrent tonsillitis	60
orofacial cleft [DOID:0050567]	55
PRIMARY SJGRENS SYNDROME	40
apical_periodontitis	36
healthy	33
Mucositis grade 1	30
Mucositis grade 2	28
periodontitis	28
Oral manifestations absent	25
malocclusion	22
control	19
Oral manifestations present	17
Mucositis grade 3	12
act_eoe	12
inact_eoe	10
Teeth	8
Advanced form of periodontitis, non-smoker	8
cleft	7
mouth	5
maleocclusion	4
apical periodontitis	4
Subject_PO02	3
Subject_PO03	3
Subject_PO04	3
Subject_PO05	3
inci_eoe	3
Subject_PO01	3
Subject_PR04	3
Subject_PR05	3
Subject_PR06	3
Subject_PO06	3
Subject_PR01	3
Subject_PR02	3
Subject_PR03	3
oral squamous cell carcinoma, oral submucous fibrosis	1
ppi_ree	1
teeth	1