Comments (7)
This one has to do with the names given to analysis activities. Are we able to name the workflow actions differently for metaG and metaT for clarity? The activities in question are "Metagenome assembly XXXXX_XXXXX" (should have a name like "Metatranscriptome assembly XXXXXX_XXXXX" for metaT) and "MetagenomeAnnotation activity for gold:GpXXXXXXX" (should have a name like "MetatranscriptomeAnnotation activity for gold:GpXXXXXXX" for metaT).
from nmdc-schema.
I'd like to get @scanon @emileyfadrosh input on this. The issue is that while we differentiate at the omics_processing level (DNA was sequenced or RNA was sequenced), the assembly and annotation are the same analysis workflow. At one point Emiley had suggested calling the analysis simply "Annotation" because both metaT and metaG use the same analysis workflow. I'd like Emiley to indicate how things should appear in the UI and Shane to weigh in on differentiating (if necessary) in the analysis workflow metadata.
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In an email thread @emileyfadrosh indicated these should be specified/named differently in the analytic workflows. This requires a change in the schema by @wdduncan and a change to the pipeline by @scanon. Then @jbeezley needs to change the ingest.
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@scanon and @wdduncan is this something that can be done in the next week or two or should it be moved to a future sprint?
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@scanon do you need a schema change for this?
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@scanon just to confirm, you need the class/type MetatranscriptomeAnnotationActivity
. Right?
In the schema file it will be metatranscriptome annotation activity
.
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We need to differentiate metagenome analysis from metagenome analysis in two places.
Currently there are nmdc:MetagenomeAnnotation and nmdc:MetagenomeAssembly
To the schema we need to add nmdc:MetatranscriptomeAnnotation and nmdc:MetatranscriptomeAssembly and @scanon would need to modify how the type is set in metadata to use these two new analysis types.
Change requested to the two metaT workflow metadata: microbiomedata/metaT#8
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Related Issues (20)
- All click options should use hyphens not underscores HOT 3
- provide guidance for creating, managing and mentioning names
- remove commenting as part of the schema deprecation strategy HOT 1
- berkeley-schema-fy24 must migrate string "type" to object types consisting of the instances' class' `class_uri` HOT 2
- usability suggestions & self-documentation for `migrator` target in `project.Makefile` HOT 8
- add validation step after `local/nmdc-sty-11-aygzgv51.yaml` target using get-study-related-records
- Use schema v7.8.0 for validating records in the Napa MongoDB? HOT 1
- Update nmdc_databast_tools extract-study to extract NMDC schema version
- need to regenerate documentation
- add automation to retrieval and validation of Neon study-related records
- Update makefile and test extractions and validation vs schema v8.0.0
- Add get data objects by description to NmdcApi client and add as option to nmdc_database_tools.extract_study
- just remove docs link to style guide
- makefile target for showing files that have changed and should be committed
- put get-study-related-records output into Jena TDB and run basic queries
- create minimal class `name` to `class_uri` lookup with SchemaView
- try local fuseki server for nmdc triples (as an alternative to GraphDB)
- some data retrieval, migration and validation code could be moved out of nmdc-schema HOT 3
- (NEW) Fix range of slot compound on SolutionComponent
- `nmdc:bsm-11-1gzgce32` does not validate against berkeley-schema-fy24 following `make-rdf` HOT 1
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