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CIDO-ontology / cido

CIDO: Coronavirus Infectious Disease Ontology
https://obofoundry.org/ontology/cido.html
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Specimen terms request to be added into CIDO #7

Open linikujp opened 4 years ago

linikujp commented 4 years ago

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. Some specimen terms can be imported from OBI.

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

linikujp commented 4 years ago

Please pay attention to swab and specimen took using a swab. Swab is a device/tool, you may need to add a specimen for terms ending with swab.

bpeters42 commented 4 years ago

Specimens are a key class in OBI scope, and there seems to be nothing 'covid' specific about these terms. If there are things not in OBI that you need, can you please request them? And note that the LOINC terms you linked to are all going to be in OBI as well.

linikujp commented 4 years ago

Just requested these terms to OBI: https://github.com/obi-ontology/obi/issues/1176 per @bpeters42's request. When OBI add those terms, this issue will be closed.

bpeters42 commented 4 years ago

All the ones I checked are in OBI already? Did you take a look, and if so, what could you not find?

On Wed, Jun 10, 2020 at 8:57 AM Asiyah Yu Lin notifications@github.com wrote:

Just requested these terms to OBI: obi-ontology/obi#1176 https://github.com/obi-ontology/obi/issues/1176 per @bpeters42 https://github.com/bpeters42's request. When OBI add those terms, this issue will be closed.

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-- Bjoern Peters Professor La Jolla Institute for Allergy and Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters

linikujp commented 4 years ago

anterior nasal swab BAL fluid BAL specimen BALs bronchial aspirates bronchial washings bronchial washings (BW) bronchoalveolar lavage OBI 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 OBI 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 OBI nasopharyngeal swabs/wash nasopharyngeal wash nasopharyngeal wash/aspirates OBI NP/OP oropharyngeal (OP) oropharyngeal (throat) swab OBI oropharyngeal swabs/throat swabs saliva specimens OBI sputum OBI throat (oropharyngeal) swab tracheal aspirates tracheal secretions upper respiratory specimens stool specimen OBI human serum or plasma (EDTA) specimen OBI

More reference see https://github.com/CIDO-ontology/CIDO-Diagnosis/issues/1