[Metadata Improvement]: Standardize Measurement Techniques

[gtsueng]

Issue Name

Standardize Measurement Techniques

Issue Description

Similar to what we've done for healthConditions, species, infectiousAgent, we need to standardize the ingested values for measurementTechnique. This may be considerably more difficult than the standardization of healthConditions for which there was a hierarchy of ontologies to use.

The ontologies

In the case of measurementTechnique, relevant terms can be found in specific branches from eight different ontologies:

• EDAM topics:
  • Children of: http://edamontology.org/topic_3361
• Measurement Method Ontology
  • Children of: http://purl.obolibrary.org/obo/MMO_0000000
• NCIT:
  • Children of: http://purl.obolibrary.org/obo/NCIT_C20368
  • Children of: http://purl.obolibrary.org/obo/NCIT_C16203
  • Children of: http://purl.obolibrary.org/obo/NCIT_C16847
• EFO:
  • Children of: http://www.ebi.ac.uk/efo/EFO_0002694
  • Children of: http://www.ebi.ac.uk/efo/EFO_0001426
  • And http://www.ebi.ac.uk/efo/EFO_0004778
• BAO:
  • Children of: http://www.bioassayontology.org/bao#BAO_0002753
  • Children of: http://www.bioassayontology.org/bao#BAO_0003112
• CHMO:
  • Children of: http://purl.obolibrary.org/obo/CHMO_0000000 (deprecated)
  • Children of: http://purl.obolibrary.org/obo/OBI_0000070
• OBI:
  • Children of: http://purl.obolibrary.org/obo/OBI_0000011
• SNOMED:
  • Children of: http://snomed.info/id/71388002

Potential approaches

• Create a "MyTechniques.info" API
  • Use NCBO BioPortal mappings to address concepts duplicated across multiple ontologies.
  • Use the MyTechniques.info API to standardize the ingested values of the measurementTechniques field
• Organize the ontologies based on topicCategory. Note- Aside from the Chemistry edge cases using CHMO and potential clinical studies using SNOMED, there will be plenty of overlap between all the other ontologies
  • Based on the topicCategory for each record, determine which set of ontologies to search, hierarchically search the relevant ontologies
  • Other: please suggest

Next steps

• [ ] Evaluate potential approaches and determine the best path forward for standardization
• [ ] Create a benchmark dataset for measurementTechniques (see related issue)
• [ ] Develop standardization approach and apply against benchmark to evaluate performance

Issue Discussion

The start of this activity has been discussed in multiple bi-weekly meetings in Q1 2024

Please select the type of metadata improvement

• [X] Standardization (normalizing free text to an ontology)
• [ ] Augmentation (adding values for metadata fields missing values)
• [ ] Clean up (addressing redundancy or messy metadata)
• [ ] Structure (changing the structuring of the metadata to support front end UI features)

Meta URL

No response

Related WBS task

https://github.com/NIAID-Data-Ecosystem/nde-roadmap/issues/13

For internal use only. Assignee, please select the status of this issue

• [ ] Not yet started
• [ ] In progress
• [ ] Blocked
• [ ] Will not address

Status Description

No response

Request status check list

• [ ] This metadata improvement has yet to be discussed between NIAID, Scripps, Leidos
• [ ] This metadata improvement does not need to be discussed between NIAID, Scripps, Leidos
• [X] This metadata improvement has been discussed/reported between NIAID, Scripps, Leidos
• [ ] This metadata improvement has been implemented locally to generate data for review
• [ ] This metadata improvement has been implemented on Dev
• [ ] This metadata improvement has been implemented on Dev and the results have been reviewed and approved for staging
• [ ] This metadata improvement has been implemented on Staging
• [ ] This page/documentation/change has been approved for Production
• [ ] This page/documentation/change has been implemented on Production

[gtsueng]

@DylanWelzel it looks like CHMO merged their terms with other ontologies and deprecated the CHMO-specific identifiers associated with those terms.

From CHMO, what we're interested in are the children of http://purl.obolibrary.org/obo/OBI_0000070 (formerly CHMO_0000000 CHMO_0001133)

It's possible to parse this from the owl file by recursively getting terms which are subclassOf OBI_0000070, but hopefully BioPortal will have an easier way

[gtsueng]

@DylanWelzel There seems to be significant overlap between SNOMEDCT and NCIT. Let's ensure that we have what we need from NCIT since SNOMEDCT and NCIT have different hierarchical structures.

To do:

• [x] For SNOMEDCT: Pull all children (and grandchildren etc) of: http://snomed.info/id/71388002 (Procedure)
• [x] Pull the mappings between NCIT and SNOMEDCT from NCBO Bioportal (there's an API, but you'll need to register for an account to use it)
• [x] Filter for NCIT terms that map to SNOMEDCT terms ONLY if they are within the Procedure branch
• [x] Identify least common head for NCIT terms as additional potential branches to include