look through NCBI Biosample for usages of the nose, throat, teeth type terms

[turbomam]

regenerate BBOP's SQLite and repopulate our Postgres on SPIN? That take several hours but makes the usage easier for me. It can be shared publicly as the SQLite file, but there isn't any public Postgres endpoint yet.

[turbomam]

Build database according to https://github.com/turbomam/biosample-xmldb-sqldb

• high RAM and storage requirements
• takes ~ 24 hours

select
    distinct attribute_name,
    harmonized_name
from
    all_ncbi_attributes_long
where
    to_tsvector('english',
    attribute_name) 
    @@ phraseto_tsquery('english',
    'throat');

attribute_name	harmonized_name
covid_symptoms_sore_throat
nose mouth teeth throat disord	nose_mouth_teeth_throat_disord
nose_mouth_teeth_throat_disord	nose_mouth_teeth_throat_disord
nose_throat_disord	nose_throat_disord
Symptom: Sore throat
throat_bright

[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, 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).

[mslarae13]

Change to oral and add nose, throat, teeth to the description?

See Chris' comment on the the other issue https://github.com/GenomicsStandardsConsortium/mixs/issues/743#issuecomment-1944092447

[lschriml]

To be closed, see #743

[turbomam]

@lschriml I don't see the corresponding changes in the mixs.yaml file

[turbomam]

Sorry, I see that you were encouraging activity to resume on #743