microbiomedata/nmdc-schema issues and pull requests

#487 - `data_object_type ` values of "Metagenome Raw Reads" in mongodb

Issue - State: closed - Opened by turbomam almost 2 years ago - 4 comments

#486 - support for converting Mongodb collections from schema 3.2 compliance to 7.0

Issue - State: closed - Opened by turbomam almost 2 years ago

#481 - biosample_category_enum updates

Issue - State: open - Opened by turbomam almost 2 years ago - 4 comments
Labels: backlog

#473 - Study title vs name

Issue - State: closed - Opened by mslarae13 about 2 years ago - 9 comments
Labels: schema change

#470 - dump biosample, study and omics processing Mongo collections inot an NMDC "Database"

Issue - State: open - Opened by turbomam about 2 years ago - 3 comments

#468 - aggregate NMDC identifier documentation and resources

Issue - State: open - Opened by turbomam about 2 years ago - 10 comments
Labels: documentation, identifiers, style-guide

#467 - annotate biosample_category_enum's permissible values

Issue - State: open - Opened by turbomam about 2 years ago - 5 comments

#465 - categorical tags for biosamples

Issue - State: open - Opened by turbomam about 2 years ago - 3 comments

#461 - Need methods for making visualizations of NMDC data

Issue - State: open - Opened by turbomam about 2 years ago - 2 comments

#455 - continue developing sample preparation modeling and sample files

Issue - State: open - Opened by turbomam about 2 years ago
Labels: needs_details

#454 - Show interclass relationships in mermaid diagrams in addition to improved heirarchy

Issue - State: open - Opened by turbomam about 2 years ago - 2 comments
Labels: diagrams

#453 - Totally omit a class' mermaid diagram if there are more than n slots

Issue - State: closed - Opened by turbomam about 2 years ago - 5 comments
Labels: diagrams

#451 - prefix issues not resolved in https://github.com/microbiomedata/nmdc-schema/pull/447 yet

Issue - State: closed - Opened by turbomam about 2 years ago - 3 comments
Labels: style-guide

#440 - remove mermaid diagrams until they are more useful

Issue - State: closed - Opened by turbomam about 2 years ago - 2 comments
Labels: diagrams

#439 - Concrete identifiers action: intrinsic or linking externally

Issue - State: closed - Opened by turbomam about 2 years ago - 3 comments
Labels: identifiers

#422 - how to determine whether a class or slot appears in MongoDB?

Issue - State: closed - Opened by turbomam about 2 years ago
Labels: validation

#421 - audit our enumerations, especially the annotations on the enums and the permissible values

Issue - State: open - Opened by turbomam about 2 years ago - 1 comment

#421 - audit our enumerations, especially the annotations on the enums and the permissible values

Issue - State: open - Opened by turbomam about 2 years ago - 1 comment

#420 - mermaid diagram in README.md doesn't render in PyPI etc.

Issue - State: open - Opened by turbomam about 2 years ago - 1 comment
Labels: diagrams

#410 - add referential integrity checks on external id used by nmdc-schema instances

Issue - State: open - Opened by turbomam about 2 years ago - 2 comments
Labels: referential integrity

#410 - add referential integrity checks on external id used by nmdc-schema instances

Issue - State: open - Opened by turbomam about 2 years ago - 2 comments
Labels: referential integrity

#409 - create more subslots of alternative_identifiers

Issue - State: closed - Opened by turbomam about 2 years ago - 3 comments
Labels: identifiers, gold, EMSL

#407 - `title`'s `description` is GOLD centered

Issue - State: open - Opened by mslarae13 about 2 years ago - 2 comments
Labels: nmdc-schema-mixs-submission, gold

#407 - `title`'s `description` is GOLD centered

Issue - State: open - Opened by mslarae13 about 2 years ago - 2 comments
Labels: nmdc-schema-mixs-submission, gold

#403 - GOLD 'ecosystem' slots at study level

Issue - State: closed - Opened by mslarae13 about 2 years ago - 5 comments
Labels: schema change, gold

#402 - nesting or relating slots in schema

Issue - State: closed - Opened by mslarae13 about 2 years ago - 1 comment
Labels: schema change, identifiers, gold

#402 - nesting or relating slots in schema

Issue - State: closed - Opened by mslarae13 about 2 years ago - 1 comment
Labels: schema change, identifiers, gold

#385 - We should be using regular expressions when having discussions about validation patterns

Issue - State: closed - Opened by turbomam about 2 years ago - 1 comment

#380 - whiteboard modeling project/study relationships

Issue - State: closed - Opened by turbomam about 2 years ago - 6 comments
Labels: backlog

#354 - Users shouldn't need to enter the NCBI BioProject Title in the submission portal

Issue - State: closed - Opened by turbomam over 2 years ago - 1 comment
Labels: nmdc-schema-mixs-submission

#353 - obsolescence of identifiables terms

Issue - State: open - Opened by turbomam over 2 years ago - 1 comment

#344 - biosample class definitions are so large that YUML URIs are rejected

Issue - State: open - Opened by turbomam over 2 years ago - 4 comments
Labels: documentation, gold, diagrams, EMSL

#339 - NMDC documents should refer to NMDC schema terms by their names or their titles

Issue - State: open - Opened by turbomam over 2 years ago - 1 comment
Labels: documentation, nmdc-schema-mixs-submission, style-guide

#326 - map bioscales type sots to chebi etc

Issue - State: open - Opened by turbomam over 2 years ago - 2 comments
Labels: nmdc-schema-mixs-submission, type

#326 - map bioscales type sots to chebi etc

Issue - State: open - Opened by turbomam over 2 years ago - 2 comments
Labels: nmdc-schema-mixs-submission, type

#325 - be consistent with slot ranges

Issue - State: open - Opened by turbomam over 2 years ago - 2 comments
Labels: mixs-text-val-range, needs_details

#321 - Create `nmdc-schema` ecosystem/consumers diagram and add it to `README.md`

Issue - State: open - Opened by turbomam over 2 years ago - 4 comments
Labels: diagrams

#318 - Identify strategy to support missing fields in the Submission Portal

Issue - State: open - Opened by ssarrafan over 2 years ago - 3 comments
Labels: backlog, nmdc-schema-mixs-submission

#313 - How will repair of NMDC DataHarmonizer submissions be triggered?

Issue - State: closed - Opened by turbomam over 2 years ago - 2 comments
Labels: nmdc-schema-mixs-submission

#309 - What NMDC resources depend on the nmdc-schema?

Issue - State: open - Opened by turbomam over 2 years ago - 3 comments

#309 - What NMDC resources depend on the nmdc-schema?

Issue - State: open - Opened by turbomam over 2 years ago - 3 comments

#308 - move mixs legacy and new LinkML file to assets dir and regenerate

Issue - State: closed - Opened by turbomam over 2 years ago
Labels: nmdc-schema-mixs-submission

#304 - document has_calibration in metabolomics analysis activity

Issue - State: closed - Opened by cmungall over 2 years ago - 3 comments
Labels: EMSL

#301 - Multiple PIs

Issue - State: open - Opened by mslarae13 over 2 years ago - 6 comments

#299 - consequences of changing MIxS import

Issue - State: open - Opened by turbomam over 2 years ago - 4 comments
Labels: nmdc-schema-mixs-submission

#298 - MIxS 5 vs 6 difference patterns

Issue - State: closed - Opened by turbomam over 2 years ago
Labels: nmdc-schema-mixs-submission

#297 - add test case to check if unit is enforced on depth schema element

Pull Request - State: open - Opened by sujaypatil96 over 2 years ago - 17 comments
Labels: bug, help wanted, medium priority, unfinished

#293 - `omics type` vs `omics_type` slots

Issue - State: closed - Opened by turbomam over 2 years ago - 3 comments
Labels: type

#289 - display hints without gratuitous subclasses

Issue - State: open - Opened by turbomam over 2 years ago - 1 comment
Labels: hints

#286 - person value subclasses for the sake of display hints

Issue - State: open - Opened by turbomam over 2 years ago - 3 comments
Labels: nmdc-schema-mixs-submission, hints

#285 - First pass at export of nmdc schema to TSV for DOE sample interop project

Pull Request - State: closed - Opened by cmungall over 2 years ago - 3 comments

#276 - working on code to routinely perform set analysis on the slots

Issue - State: closed - Opened by ssarrafan over 2 years ago

#267 - add display hint annotations for study slots that appear on study submission portal

Issue - State: open - Opened by turbomam over 2 years ago - 6 comments
Labels: nmdc-schema-mixs-submission, hints

#253 - long term: retire perl code that routes MIxS terms into NMDC schema

Issue - State: closed - Opened by turbomam over 2 years ago - 4 comments
Labels: backlog, nmdc-schema-mixs-submission

#252 - short term: programmatically tag the origin of MIxS terms when imported into NMDC schema

Issue - State: open - Opened by turbomam over 2 years ago - 11 comments
Labels: backlog, nmdc-schema-mixs-submission

#251 - restrict range of omics type

Issue - State: closed - Opened by wdduncan over 2 years ago - 4 comments
Labels: closed_via_berkeley

#250 - remove stray omics_type slot

Issue - State: closed - Opened by wdduncan over 2 years ago - 2 comments
Labels: type

#197 - Repair MIXS environment annotations

Issue - State: closed - Opened by ssarrafan almost 3 years ago - 7 comments
Labels: backlog, nmdc-schema-mixs-submission

#191 - Include distinct packages in the schema

Issue - State: closed - Opened by cmungall almost 3 years ago - 3 comments
Labels: nmdc-schema-mixs-submission

#167 - Data Harmonizer - additional tasks

Issue - State: closed - Opened by ssarrafan about 3 years ago - 8 comments

#134 - group class for workflow execution activities

Issue - State: closed - Opened by wdduncan about 3 years ago - 8 comments
Labels: gold

#113 - Add NER routine for suggesting biome terms based on package + sample description for fao_soil_class or other mixs controlled field of relevance to NMDC

Issue - State: open - Opened by ssarrafan about 3 years ago - 14 comments
Labels: backlog, nmdc-schema-mixs-submission

GitHub / microbiomedata/nmdc-schema issues and pull requests