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2 | 1.2.1 | Design and implement integration with controlled vocabularies | 5
The deliverable is Code and documentation for controlled vocabulary support
- Research existing implementations of controlled vocabularies,
- Design and implement code to extend metadata fields to use controlled vocabularies,
- Test and document controlled vocabularies.
Three in particular have been discussed.
- Unified Medical Language System (UMLS)
- Center for Expanded Data Annotation and Retrieval (CEDAR)
- Medical Subject Headings (MeSH)
Initial Understanding
For the first year, we believe that the work was to implement controlled vocabularies.
Dataverse has support for controlled vocabularies. They can be locally stored or can be dynamically pulled via an API. This was implemented by the community.
We believe this initial work has been done by the community. So we may be able to argue that the first step to this which is the intial implementation of controlled vocabularies is completed.
Links:
Related Deliverables: 2 | 1.2.2 | Define use cases for DDI-CDI support | 5 2 | 2.2.1 | Design and implement support for DDI-CDI 2 | 2.2.2 | Define use cases for supporting biomedical metadata standards 2 | 3.2.1 | Design and implement biomedical metadata standards, and add funding related metadata 2 | 4.2.1 | Assess and improve metadata support
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This issue represents a deliverable funded by the NIH This deliverable supports the NIH Initiative to Improve Access to NIH-funded Data
Aim 2: Increase support for biomedical and cross-domain metadata standards and controlled vocabularies
One of the useful characteristics of the Dataverse open-source software is its extensive support for metadata standards and additional custom metadata.
The standards currently supported include:
- The Data Documentation Initiative (DDI),
- Dublin Core,
- DataCite, and
- Schema.org.
In particular, DDI makes a Dataverse repository interoperable even at the variable/attribute level since it supports variable descriptive and statistical metadata. This allows data exploration and analysis tools to integrate easily with the repository and discovery engines to find variable information.
In this project, we propose to
- expand DDI support to include the recently released DDI-Cross-Domain Integration (DDI-CDI) schema
- build on existing support for biomedical-related standards relevant to NIH-funded research cases, following the recommendations from https://fairsharing.org/
- expand descriptive and citation metadata to support funding information and related fields, and
- integrate with external services to enable the support of controlled vocabularies for any metadata field, based on standardized, widely used data dictionaries. The HMS Research Data Management group will participate in the development of these standards and vocabularies for biomedical datasets, working directly with research laboratories.
September Update: (1.2.1) A spike for discovery (Dataverse GitHub Issue #8681) is in progress to determine what changes need to be made to support biomedical vocabularies, including the UMLS, CEDAR, and MeSH vocabularies. Progress on this Aim continues to be stalled while the team focuses on the re-architecture project (1.7.1).
October Update: (1.2.1) We are moving past the intial spike. Progress on this Aim continues to be stalled while the team focuses on the re-architecture project (1.7.1).
Updating Description- Replacing this text
The deliverable is Code and documentation for controlled vocabulary support
- Research existing implementations of controlled vocabularies,
- Design and implement code to extend metadata fields to use controlled vocabularies,
- Test and document controlled vocabularies.
Three in particular have been discussed.
- Unified Medical Language System (UMLS)
- Center for Expanded Data Annotation and Retrieval (CEDAR)
- Medical Subject Headings (MeSH)
Initial Understanding
For the first year, we believe that the work was to implement controlled vocabularies.
Dataverse has support for controlled vocabularies. They can be locally stored or can be dynamically pulled via an API. This was implemented by the community.
We believe this initial work has been done by the community. So we may be able to argue that the first step to this which is the intial implementation of controlled vocabularies is completed.
Links:
Related Deliverables: 2 | 1.2.2 | Define use cases for DDI-CDI support | 5 2 | 2.2.1 | Design and implement support for DDI-CDI 2 | 2.2.2 | Define use cases for supporting biomedical metadata standards 2 | 3.2.1 | Design and implement biomedical metadata standards, and add funding related metadata 2 | 4.2.1 | Assess and improve metadata support
Cleaned things up. Moved the day-to-day notes to the sidecar issue.
- https://github.com/IQSS/dataverse/issues/9043