Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[MNT] Replace Cognitive Atlas with SNOMED CT as the vocab for assessments #255

Merged
merged 1 commit into from
Jan 7, 2025
Merged

[MNT] Replace Cognitive Atlas with SNOMED CT as the vocab for assessments #255

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
17 changes: 9 additions & 8 deletions docs/data_models/dictionaries.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -120,8 +120,7 @@ syntax for [json-ld](https://w3c.github.io/json-ld-syntax/#the-context):
"nb": "http://neurobagel.org/vocab/",
"ncit": "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#",
"nidm": "http://purl.org/nidash/nidm#",
"snomed": "http://purl.bioontology.org/ontology/SNOMEDCT/",
"cogatlas": "https://www.cognitiveatlas.org/task/id/"
"snomed": "http://purl.bioontology.org/ontology/SNOMEDCT/"
}
}
```
Expand Down Expand Up @@ -187,8 +186,8 @@ Term from the Neurobagel vocabulary.

### Diagnosis

Terms from the [SNOMED-CT ontology](https://browser.ihtsdotools.org/) for clinical diagnosis.
Terms from the National Cancer Institute Thesaurus for healthy control status.
Terms for clinical diagnosis are from the [SNOMED-CT ontology](https://browser.ihtsdotools.org/).
Terms for healthy control status are from the National Cancer Institute Thesaurus.

```json hl_lines="10-11 13 15-16 19-20"
{
Expand Down Expand Up @@ -307,6 +306,8 @@ Possible heuristics:

### Assessment tool

Terms are from the SNOMED-CT ontology.

For assessment tools like cognitive tests or rating scales,
Neurobagel encodes whether a subject has a value/score for _at least one_ item or subscale of the assessment.
Because assessment tools often have several subscales or items
Expand All @@ -330,8 +331,8 @@ when instances of missing values are present (see also section [Missing values](
"Label": "Assessment tool"
},
"IsPartOf": {
"TermURL": "cogatlas:tsk_4a57abb949ece",
"Label": "Unified Parkinson's Disease Rating Scale"
"TermURL": "snomed:342061000000106",
"Label": "Unified Parkinsons disease rating scale score"
}
}
},
Expand All @@ -343,8 +344,8 @@ when instances of missing values are present (see also section [Missing values](
"Label": "Assessment tool"
},
"IsPartOf": {
"TermURL": "cogatlas:tsk_4a57abb949ece",
"Label": "Unified Parkinson's Disease Rating Scale"
"TermURL": "snomed:342061000000106",
"Label": "Unified Parkinsons disease rating scale score"
},
"MissingValues": [""]
}
Expand Down
17 changes: 8 additions & 9 deletions docs/data_models/term_naming_standards.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

## Naming conventions
### Namespace prefixes
- Names should be all lowercase (e.g., `nidm`, `cogatlas`)
- Names should be all lowercase (e.g., `nidm`, `snomed`)

### Properties (graph "edges")
- Names should adhere to camelCase (uses capitalized words except for the first word/letter)
Expand All @@ -27,14 +27,13 @@ What this might look like in semantic triples:
In cases where we reuse a term for a class that comes from an existing controlled vocabulary, and that vocabulary follows a different naming convention (e.g., all lowercase), we should follow the existing naming convention.

## Currently used namespaces
| Prefix | IRI | Types of terms |
| ---------- | --------------------------------------------------- | ----------------------------------------- |
| `nb` | http://neurobagel.org/vocab/ | Neurobagel-"owned" properties and classes |
| `nbg` | http://neurobagel.org/graph/ | Neurobagel graph databases |
| `snomed` | http://purl.bioontology.org/ontology/SNOMEDCT/ | diagnosis and sex values |
| `ncit` | http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl# | group designation (e.g., healthy control) |
| `nidm` | http://purl.org/nidash/nidm# | imaging modalities |
| `cogatlas` | https://www.cognitiveatlas.org/task/id/ | cognitive assessments and tasks |
| Prefix | IRI | Types of terms |
| ----- | ----- | ----- |
| `nb` | http://neurobagel.org/vocab/ | Neurobagel-"owned" properties and classes |
| `snomed` | http://purl.bioontology.org/ontology/SNOMEDCT/ | diagnoses, sex, and assessments or instruments |
| `ncit` | http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl# | group designation (e.g., healthy control) |
| `nidm` | http://purl.org/nidash/nidm# | imaging modalities |
| `np` | https://github.com/nipoppy/pipeline-catalog/tree/main/processing/ | processing pipeline and derivative metadata |


## What if an `nb` term already exists in another controlled vocabulary?
Expand Down
2 changes: 1 addition & 1 deletion docs/overrides/home.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -199,7 +199,7 @@ <h2 class="text-3xl font-bold tracking-tight text-white sm:text-3xl">Annotate yo
<h2 class="text-3xl font-bold tracking-tight text-white sm:text-3xl">
Work with standardized terminologies
</h2>
<p class="mt-6 text-lg leading-8 text-gray-300">Reap the benefits of curated vocabularies (e.g., BIDS, SNOMED CT, and the Cognitive Atlas) and linked data, without the implementation expertise.</p>
<p class="mt-6 text-lg leading-8 text-gray-300">Reap the benefits of curated vocabularies (e.g., BIDS, SNOMED CT, and NIDM) and linked data, without the implementation expertise.</p>
<div class="mt-10 flex items-center justify-center gap-x-6 lg:justify-start">
<a href="/dictionaries" class="text-sm font-semibold leading-6 text-white">Learn more <span
aria-hidden="true">→</span></a>
Expand Down
Loading