CHANGELOG.md

Change Log

Changes to the schema are documented in this file.

Current (updates before releasing)

Added

• N/A

Fixed

• N/A

Changed

• range for started at time and ended at time is datetime (#258)

Removed

• N/A

2.0.0

Added

• N/A

Fixed

• N/A

Changed

• made part of slot required for biosample (#249)

Removed

• N/A

2022.01.26rc1

Added

• add descriptions for various slots (#198)

Fixed

• removed double quotes surrounding MIxS descriptions

Changed

• N/A

Removed

• N/A

2022.01.18rc1

Added

• applied roles (multivalued) slot (#216)

Fixed

• N/A

Changed

• deprectated applied role slot (#216)

Removed

• N/A

2022.01.14rc1

Added

• descriptions, comments and a see_also for gold_path_fields (#231)
• Direct Infusion FT ICR-MS Raw Data file type enum (#236)

Fixed

• example IDs for GOLD biosamples and analysis projects (#233)

Changed

• the descriptions for external identifiers are now scalars, not list items (#228)

Removed

• N/A

2021.12.22rc1

Added

• N/A

Fixed

• updated deprecation warning to reference "get_nmdc_jsonschema_dict"
• added missing image files for gh pages (#218)

Changed

• N/A

Removed

• N/A

2021.12.21rc1

Added

• N/A

Fixed

• use inlined_as_list for the database sets (#219)

Changed

• N/A

Removed

• N/A

2021.11.22rc1

Added

• N/A

Fixed

• get_nmdc_jsonschema_dict not returning correct data (#214)
• typo in NMDC Schema description

Changed

• N/A

Removed

• N/A

2021.11.19rc3

Added

• N/A

Fixed

• N/A

Changed

• set python version in setup.py to >=3.7

Removed

• N/A

2021.11.19rc2

Added

• N/A

Fixed

• access to nmdc-data cli tool

Changed

• N/A

Removed

• N/A

2021.11.19rc1

Added

• new file type enums for analysis output files (#207)
• nmdc-data util for accessing package data files

Fixed

• update examples of values for data objects (#206)

Changed

• use ISO 8601 for schema version

Removed

• N/A

2021.11.15rc1

Added

• N/A

Fixed

• updated file enums for workflows (#182)

Changed

• N/A

Removed

• N/A

2021.10.20rc1

Added

• option to specify the database set when validating data (#184)
• study image slot (#123)
• declare database class as the root (i.e., tree_root: true)
• slots to hold minimum and maximum values (#80)

Fixed

• N/A

Changed

• N/A

Removed

• N/A

2021.10.13rc2

Added

• command line utility fetch-nmdc-schema for downloading the jsonschema

Fixed

• nmdc-version command line utility (#183)

Changed

• N/A

Removed

• N/A

2021.10.13rc1

Added

• N/A

Fixed

• N/A

Changed

• N/A

Removed

• regex patterns for has function slot on class function annotation (#178)

2021.10.12rc2

Added

• part of slot for workflow execution activity (#176)

Fixed

• N/A

Changed

• N/A

Removed

• N/A

2021.10.12rc1

Added

• N/A

Fixed

• descriptions are inherited in induced slots (#174)

Changed

• N/A

Removed

• N/A

2021.09.30rc3

Added

• N/A

Fixed

• N/A

Changed

• re-added part of constraint to slot_usage section of biosample (#163)

Removed

• N/A

2021.09.30rc2

Added

• N/A

Fixed

• N/A

Changed

• removed part of from slot_usage section of biosample (#163)

Removed

• N/A

2021.09.30rc1

Added

• part of to slot section of biosample (#163)

Fixed

• N/A

Changed

• N/A

Removed

• N/A

2021.09.28rc2

Added

• websites slot to person value

Fixed

• N/A

Changed

• has output is not required for omics processing

Removed

• N/A

2021.09.28rc1

Added

• relevant protocols and funding sources slots
• ess dive datasets slot
• amplicon slots to omics processing (#139)
• alternate emails slot

Fixed

• N/A

Changed

• email slot is single valued.

Removed

• N/A

2021.09.21rc1

Added

• CreditAssociation class and related slots. Abstracts the roles borne by people within a strudy.
• email slot in core.yaml. Motivation = people (person value) associated with studies, but not constrained to that domain (cf. #100).
  • email made multivalued and assigned schema.org URI
• slot type defined using designates_type: true
• name slot added to person value. Noted that has raw value could be deprecated in the future.
• All yaml files are included in the package data (#153)

Fixed

• added name and title to mixs.yaml (#126)

Changed

• Linkml version updated to 1.0.4
• alternate identifiers to alternative identifiers (#125)

Removed

• alternate identifiers slot (#125)

2021.07.01rc1

Added

• metatranscriptome activity class and metatranscriptome activity set

Fixed

• N/A

Changed

• N/A

Removed

• N/A

2021.06.24rc1

Added

• depth2 and subsurface_depth2 slots added to biosamples (cf. issue 80).

Fixed

• N/A

Changed

• N/A

Removed

• N/A

2021.06.23rc1

Added

• alternative identifiers slot added to biosamples (cf. issue 75).

Fixed

• N/A

Changed

• N/A

Removed

• N/A

2021.06.17rc1

Added

• profile image url to hold the url pointing an image of the investigator (cf. issue 19)
• description for orcid slot.

Fixed

• N/A

Changed

• principal investigator name to simply be principal investigator.

Removed

• N/A

2021.06.16rc1

Added

• title slot as attribute of nmdc:study (cf. issue 51)
• objective slot as attribute of nmdc:study (cf. issue 51)
• alternative titles slot as attribute of nmdc:study (cf. issue 51)
• alternative dscriptiions slot as attribute of nmdc:study (cf. issue 51)
• alternative names slot as attribute of nmdc:study (cf. issue 51)
• keywords slot as attribute of nmdc:study (cf. issue 51)
• websites slot as attribute of nmdc:study (cf. issue 51)
• publications slot as attribute of nmdc:study (cf. issue 51)
• skos prefix to core and mapping for alternative names to skos:altLabel
• samp_mat_process slot as attribute of nmdc:biosample (cf. issue 67)

Fixed

• N/A

Changed

• N/A

Removed

• N/A

2021.06.10rc1

Added

• abstract slot for use with study (cf. issue 60)

Fixed

• N/A

Changed

• N/A

Removed

• N/A

2021.06.01rc2

Added

• N/A

Fixed

• N/A

Changed

• part of, has input, has output slots are required for omics processing objects (cf. issue 50)
• name, description slots required for data object objects (cf. issue 50)
• git url, has input, has output, was informed by, execution resource, type slots required for workflow execution activity objects (cf. issue 50)

Removed

• N/A

2021.06.01rc1

Added

• N/A

Fixed

• N/A

Changed

• MIxS triad properties required for biosamples (cf. issue 45)
• started at time and ended at time properties required for workflow execution activities (cf. issue 44)

Removed

• N/A

2021.04.28rc1

Added

• New class: metatranscriptome assembly
• New class: metatranscriptome annotation activity

Fixed

• N/A

Changed

• Updated part of slot to biosample to relate biosamples to the studies for which they were collected.

Removed

• N/A

2021.04.22rc1

Added

• Example data to test validation

Fixed

• N/A

Changed

• Updated part of slot to biosample to relate biosamples to the studies for which they were collected.

Removed

• N/A

2021.04.16rc1

Added

• N/A

Fixed

• N/A

Changed

• Enhance command-line nmdc-version tool to get metamodel version.

Removed

• N/A

2021.04.15rc3

Added

• nmdc.yaml to package data files

Fixed

• N/A

Changed

• N/A

Removed

• N/A

2021.04.15rc2

Added

• nmdc-version command-line tool to find out the nmdc schema version

Fixed

• N/A

Changed

• N/A

Removed

• N/A

20210414

Added

• SSSOM mapping file for mapping GOLD to MIxS

Fixed

• N/A

Changed

• Update python-publish.yml

Removed

• N/A

2021.04.15rc1

Added

• Command-line json validation tool validate-nmdc-json

Fixed

• N/A

Changed

• N/A

Removed

• N/A

2021.04.14

Added

• N/A

Fixed

• N/A

Changed

• Update python-publish.yml

Removed

• N/A

2021.04.14rc2

Added

• SSSOM file to package

Fixed

• N/A

Changed

• N/A

Removed

• N/A

2021.04.14rc1

Added

• N/A

Fixed

• N/A

Changed

• Update python-publish.yml

Removed

• N/A