microbiomedata nmdc-schema issues

microbiomedata / nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

https://microbiomedata.github.io/nmdc-schema/

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issues

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Update identifiers.md

#1924 aclum closed 6 months ago
2
1914 metabolite identification

#1923 brynnz22 closed 6 months ago
0
Add sets to `Database` for the `MaterialProcess` subclasses

#1922 anastasiyaprymolenna closed 6 months ago
5
Bump idna from 3.6 to 3.7

#1921 dependabot[bot] closed 6 months ago
0
Create `ChromatographicSeparationConfiguration` class and modify existing `ChromatographicSeparation` to accommodate

#1920 kheal closed 5 months ago
5
Hyperlink class blocks in mermaid class diagram

#1919 sujaypatil96 closed 6 months ago
0
Refactor `has_calibration` to use a class

#1918 brynnz22 closed 6 months ago
5
Refactor `principal_investigator` slot on `Study`

#1917 brynnz22 opened 6 months ago
2
support slot for when document was added

#1916 aclum closed 6 months ago
12
Bump pymongo from 4.6.2 to 4.6.3

#1915 dependabot[bot] closed 6 months ago
0
Rename `has_metabolite_quantification` and associated class to `has_metabolite_identification`

#1914 kheal closed 6 months ago
5
Create `MassSpectrometryConfiguration` class and modify existing `MassSpectrometry` class to accommodate

#1913 brynnz22 closed 5 months ago
0
Add permissible values to `FileTypeEnum` and `DataCategoryEnum` to accomodate workflow configuration `DataObject`s

#1912 brynnz22 closed 6 months ago
3
Add `workflow_version` slot to `WorkflowExecution` classes

#1911 brynnz22 closed 6 months ago
1
Edit slot usages to accommodate multiple detection configurations for single `MassSpectrometry` instance

#1910 brynnz22 closed 6 months ago
0
Expand `StationaryPhaseEnum` to include values needed for GC-MS and LC-MS metab data

#1909 brynnz22 closed 6 months ago
1
Add `StorageProcess` class (a subclass of `MaterialProcessing` with slots like `substances_used` (already exists) and `contained_in` slot (already exists), `duration` (already exists), and `temperature` (already exists). With `input` and 'output`

#1908 brynnz22 closed 6 months ago
4
Add `sample_portion` to `SubsamplingProcess`

#1907 brynnz22 closed 6 months ago
1
Flush out `SubstanceRoleEnum`

#1906 brynnz22 closed 6 months ago
1
Metabolomics Schema Updates Meta Issue

#1905 brynnz22 closed 5 months ago
6
QuantityValue.slot_usage.has_numeric_value.range: Float -> Double

#1904 turbomam opened 7 months ago
3
Biosample.slot_usage.gold_biosample_identifiers.range: external_identifier -> uriorcurie

#1903 turbomam closed 7 months ago
0
Update `connect_napa_mongo.py` to output tsv with deleted record identifiers

#1902 mbthornton-lbl closed 6 months ago
0
fix inconsistent `slot_usages`

#1901 turbomam opened 7 months ago
1
remove redundant `slot_usage`s

#1900 turbomam closed 7 months ago
1
Resolve omics processing has output data object referential integrity exceptions

#1899 mbthornton-lbl closed 7 months ago
0
`slot_usage` parent issue

#1898 turbomam opened 7 months ago
2
Resolve referential integrity exceptions for `nmdc:sty-11-547rwq94` Metagenome Omics Processing records

#1897 mbthornton-lbl closed 4 months ago
3
update code to delete unconnected workflow activity and data objects to same logging format as Michael's deletion function

#1896 aclum closed 5 months ago
1
Update instrument model and vendor enumerations

#1895 brynnz22 closed 7 months ago
0
Resolve omics_processing has_output data_object referential integrity exceptions in study nmdc:sty-11-dcqce727

#1894 mbthornton-lbl closed 7 months ago
3
`linkml-sqldb dump` crashes in `berkeley-schema-fy24` because of multiple possible `Study.part_of` paths

#1893 turbomam opened 7 months ago
0
`Study.slot_usage.protocol_link` should not assert `multivalued: true`

#1892 turbomam opened 7 months ago
2
update UML class diagram relationship arrow types

#1891 sujaypatil96 closed 7 months ago
0
Automate `data_qc` scripts

#1890 mbthornton-lbl closed 5 months ago
1
ensure that the origin of all `assets/` files can be determined by Makefile or Python code in the repo or high-quality comments

#1889 turbomam opened 7 months ago
0
ensure that each src/schema YAML file can be re-generated in isoloation

#1887 turbomam opened 7 months ago
1
1885 determine schema imports graph

#1886 turbomam closed 7 months ago
0
determine schema imports graph

#1885 turbomam closed 7 months ago
1
MobilePhaseComponents instead of Solutions

#1884 turbomam closed 7 months ago
0
1865 Extract Re-IDed Napa DB to YAML, Validate and check referential integrity

#1883 mbthornton-lbl closed 7 months ago
1
simplify usage of Solution by DissolvingProcess in berkeley-schema-fy24

#1882 turbomam closed 7 months ago
0
DataPortal can be searched for `Pathway`s and `OntologyGroup`s... does that justify leaving them in nmdc-schema?

#1881 turbomam closed 2 months ago
9
Automate MongoDB Referential Integrity Queries

#1880 mbthornton-lbl opened 7 months ago
0
remove `ecosystem_diagram.md` from berkeley-schema-fy24

#1879 turbomam closed 5 months ago
3
merge diagram creation project.Makefile targets into berkeley-schema-fy24

#1878 turbomam closed 7 months ago
0
analyse build log from berkeley-schema-fy24

#1877 turbomam closed 7 months ago
2
Assess the usefulness of nmdc-schema (not MIxS) subsets

#1876 turbomam opened 7 months ago
3
Find elements whose names contain white-space

#1875 turbomam opened 7 months ago
2
Review types that aren't used in any slot

#1874 turbomam opened 7 months ago
1

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