How to find updated term

[ACharbonneau]

I'm mapping a bunch of data to DO, and I am having trouble with obsoleted terms. As an example, I'm trying to map ICD0 8220/3 (adenocarcinoma in adenomatous polyposis coli) to DO. In the OWL file, I see:

[Term]
id: DOID:8269
name: obsolete adenocarcinoma in adenomatous polyposis coli
synonym: "adenocarcinoma in adenomatous polyposis Coli" EXACT []
synonym: "adenocarcinoma in adenomatous polyposis coli (morphologic abnormality)" EXACT []
is_obsolete: true

But it doesn't indicate what it was changed to, and I can't find another DO term that seems similar. I've searched all the github issues and release notes, and I can't seem to find anyone discussing it, so I'm not sure why it was obsoleted either, which leaves me a little stuck. I'm not sure how to go about finding the correct mapping without any indication what was wrong with the original one or what it might have changed towards. Are there any resources for tracking down what the DO term is now?

Thanks

[lschriml]

Hello Amanda, thank you for this request.
Looking back at the history of how this term was handled.
I see that there has been some re-classifications and nomenclature changes
that impact this disease.
This is now; DOID:0080409.
I have added the ICDO code to this term.
In the past, adenocarcinoma in adenomatous polyposis coli, was updated to familial adenomatous polyposis, which has subsequently been subtyped.
The updates will be in our public release at the end of this month.
Cheers,
Lynn

[ACharbonneau]

Thank you!

[allenbaron]

@ACharbonneau if there are other diseases that you have had trouble finding, would you open an issue and list them for us. We'd like to help with others, if they exist as well.

[allenbaron]

For others who might come to this discussion with a similar problem. There are two ways to find a disease that replaces one that's been obsoleted:

1. On the obsolete disease term, look for an annotation using term replaced by (IAO:0100001). This will point to the disease that replaced this one.

In the OBO files, that is rendered as simply replaced_by.

[Term]
id: DOID:0050549
name: obsolete Saldino-Noonan syndrome
def: "A syndrome characterized by congenital heart defects, failure to thrive, short stature, cogni
tive dysfunction, pectus excavatum, coagulation defects and craniofacial defects and that has_mater
ial_basis_in the mutation in the Ras/mitogen activated protein kinase." [url:https://en.wikipedia.
org/wiki/Noonan_syndrome]
is_obsolete: true
replaced_by: DOID:0110087 <-----------

2. Search the active diseases in the ontology for the DOID of the obsolete disease using the oboInOwl:hasAlternativeId annotation. This is essentially the reverse of term replaced by and indicates all the diseases which this active disease has replaced.

In the OBO files, this is rendered as alt_id.

[Term]
id: DOID:8224
name: central breast papilloma
alt_id: DOID:8226 <------------------------
def: "A breast duct papilloma that is located_in a major duct." [url:https://radiopaedia.org/artic
les/intraductal-papilloma-of-breast, url:https://www.ncbi.nlm.nih.gov/pubmed/21310798]
subset: NCIthesaurus
synonym: "large duct breast papilloma" EXACT []
synonym: "solitary intraductal breast papilloma" EXACT []
xref: NCI:C36087
xref: UMLS_CUI:C1332896
is_a: DOID:1626 ! breast duct papilloma

Tip

Alternate ID annotations have been around longer than term replaced by annotation and are more likely to be complete. Whenever a term replaced by annotation is added to an obsolete disease term, the corresponding Alternate ID annotation is always added to the corresponding active disease term.

Important

Not all obsoleted diseases will have another disease that they are replaced by. If you find an obsoleted disease that you feel should be active, please open an issue and explain your request.

How to find replacing diseases with ontology browsers

disease-ontology.org

The browser at https://disease-ontology.org/do/ does not include obsolete diseases. This is by design: it makes identifying active diseases easier and prevents accidental use of obsoleted diseases and disease information, which is generally NOT updated after a disease is obsoleted.

It is, however, possible to find diseases that replace those which have been obsoleted using the Advanced Search. To accomplish this, select the Advanced Search (1), choose "Alternate ID" from the drop down (2), then type in the DOID of the obsoleted disease and click Go!.

EBI OLS4

The general ontology browser provided by EBI can display obsolete diseases if you must review them. To see these, select the "Show obsolete terms" and choose "All classes". This will make obsolete disease terms appear in the browser, but will NOT make them searchable in the search interface.

Note

All obsolete diseases are displayed at the top-level of the disease hierarchy alongside disease (DOID:4).

Tip

To search obsolete disease terms on OLS4, instead of scrolling endlessely, use the internet browsers find functionality.

[ACharbonneau]

This is incredibly helpful, thank you!