From 6b0f3a0201223ae3b29591d6eae3d4ab9bb13f03 Mon Sep 17 00:00:00 2001 From: Alyssa Dai Date: Fri, 20 Dec 2024 14:01:33 -0500 Subject: [PATCH] remove or replace cogatlas with snomed for assessments --- docs/data_models/dictionaries.md | 17 +++++++++-------- docs/data_models/term_naming_standards.md | 17 ++++++++--------- docs/overrides/home.html | 2 +- 3 files changed, 18 insertions(+), 18 deletions(-) diff --git a/docs/data_models/dictionaries.md b/docs/data_models/dictionaries.md index cf0f745f..84e9bf9e 100644 --- a/docs/data_models/dictionaries.md +++ b/docs/data_models/dictionaries.md @@ -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/" } } ``` @@ -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" { @@ -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 @@ -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" } } }, @@ -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": [""] } diff --git a/docs/data_models/term_naming_standards.md b/docs/data_models/term_naming_standards.md index db579e83..c2588a35 100644 --- a/docs/data_models/term_naming_standards.md +++ b/docs/data_models/term_naming_standards.md @@ -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) @@ -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? diff --git a/docs/overrides/home.html b/docs/overrides/home.html index 64326ecc..dedd2181 100644 --- a/docs/overrides/home.html +++ b/docs/overrides/home.html @@ -199,7 +199,7 @@

Annotate yo

Work with standardized terminologies

-

Reap the benefits of curated vocabularies (e.g., BIDS, SNOMED CT, and the Cognitive Atlas) and linked data, without the implementation expertise.

+

Reap the benefits of curated vocabularies (e.g., BIDS, SNOMED CT, and NIDM) and linked data, without the implementation expertise.

Learn more