GenomicsStandardsConsortium/mixs issues and pull requests

#856 - Add codespell support (config, workflow to detect/not fix) and make it fix few typos

Pull Request - State: open - Opened by yarikoptic 26 days ago

#853 - Term mismatch ENA / NCBI / MIxS

Issue - State: open - Opened by jjkoehorst about 1 month ago - 1 comment

#852 - add `---` document separator to beginning of deprecated.yaml file

Pull Request - State: open - Opened by turbomam about 1 month ago

#851 - add document separator to beginning of `src/mixs/schema/deprecated.yaml`

Issue - State: open - Opened by turbomam about 1 month ago

#850 - add readme documentation & directory to releases

Pull Request - State: open - Opened by mslarae13 about 2 months ago

#849 - Replace string serialisation with enum for HostSex categories

Pull Request - State: open - Opened by jfy133 about 2 months ago - 1 comment

#848 - Add HostSex enum and remove string serialisation for host_sex

Pull Request - State: closed - Opened by jfy133 about 2 months ago - 2 comments

#847 - Add host-sex enum and remove string serialisation

Pull Request - State: closed - Opened by jfy133 about 2 months ago

#846 - Replace string seralisation of `host_sex` categories with enumeration

Pull Request - State: closed - Opened by jfy133 about 2 months ago

#845 - what are our options for diffing schema changes?

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

#844 - I don't think permissible value URIs are being adequately escaped (from gen-owl)

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

#843 - do we ever want a LinkML `setting` to allow any number (including 0) of any characters?

Issue - State: open - Opened by turbomam about 2 months ago

#842 - double check unit setting

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

#841 - use consistent naming for anchor and URL for term table/term list

Issue - State: open - Opened by turbomam about 2 months ago

#840 - some enums and complex patterns

Pull Request - State: open - Opened by turbomam about 2 months ago - 12 comments

#839 - start converting `string_serialization`s to enumerations

Issue - State: open - Opened by turbomam about 2 months ago - 6 comments

#838 - Human / Host / Animal sex (discussion)

Issue - State: open - Opened by jjkoehorst about 2 months ago - 7 comments
Labels: 3-CIG

#837 - with enum descriptions

Pull Request - State: open - Opened by turbomam about 2 months ago - 4 comments

#836 - Give enumerations boilerplate definitions for now

Issue - State: open - Opened by turbomam about 2 months ago - 4 comments

#835 - A table of release dates for each MIxS release should be prominently displayed on the MIxS repo landing page or a GSC web page

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

#834 - DO NOT MERGE: MIxSv6_release.xlsx vs mixs_v6.xlsx data, code and output

Pull Request - State: closed - Opened by turbomam 2 months ago - 2 comments

#833 - Organization of generated TSV files

Pull Request - State: closed - Opened by sujaypatil96 2 months ago - 1 comment

#832 - Distinguishing LinkML/NMDC tasks and MIxS specific tasks

Issue - State: open - Opened by lschriml 2 months ago - 2 comments
Labels: 3-CIG, 4-TWG

#831 - Add report of slots shared between two extensions in `src/scripts/extension_slot_diffrences.py`

Pull Request - State: open - Opened by turbomam 2 months ago - 1 comment

#830 - `chlorophyll` slot is not associated with the `Plant` `Extension`!?

Issue - State: open - Opened by turbomam 2 months ago - 2 comments
Labels: low priority

#829 - add intersction slots to `extension_slot_diffrences` report

Issue - State: open - Opened by turbomam 2 months ago - 5 comments
Labels: 4-TWG

#826 - add `soil_conductivity` slot descriptions

Pull Request - State: open - Opened by mslarae13 3 months ago - 5 comments

#825 - correct description of `size_frac_low` and `size_frac_up`

Pull Request - State: open - Opened by mslarae13 3 months ago - 2 comments
Labels: 1-TermUpdate

#824 - Identify the @genomicstandardsconsortium and determine what their contributions can be

Issue - State: closed - Opened by turbomam 3 months ago - 2 comments

#823 - work in progress: YAML linting and auto-formatting super-issue

Issue - State: open - Opened by turbomam 3 months ago - 3 comments

#822 - Fix `make gendoc` target

Pull Request - State: closed - Opened by sujaypatil96 3 months ago - 1 comment

#821 - Add document start to `src/mixs/schema/mixs.yaml`

Pull Request - State: closed - Opened by sujaypatil96 3 months ago - 2 comments

#820 - deprecate climate_environment

Pull Request - State: open - Opened by mslarae13 3 months ago
Labels: 1-TermUpdate

#819 - Add deprecation documentation to github docs

Issue - State: open - Opened by mslarae13 3 months ago - 1 comment
Labels: 3-CIG

#818 - make URL for deprecation.yaml id

Issue - State: open - Opened by mslarae13 3 months ago - 1 comment

#817 - Marker Sequences, not Marker Specimens

Pull Request - State: closed - Opened by turbomam 3 months ago

#816 - Bump certifi from 2024.6.2 to 2024.7.4

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago
Labels: dependencies

#815 - 16s master issue

Issue - State: open - Opened by turbomam 3 months ago

#814 - Some slots have non-standard names

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

#813 - Schema elements should have descriptions

Issue - State: open - Opened by turbomam 3 months ago - 4 comments

#812 - ChatGPT analysis of `src/scripts/*.py` & TSV representations of MIxS classes

Pull Request - State: open - Opened by turbomam 3 months ago - 10 comments

#811 - Create minimal per-class slot reporter; compare to exisiting LinkML, NMDC and MIxS scripts

Issue - State: open - Opened by turbomam 3 months ago - 6 comments

#810 - Add user-specific and developer-specific documentation (in GitHub README files, website)

Pull Request - State: open - Opened by sujaypatil96 3 months ago - 1 comment

#809 - eDNA development - gather issues here for updates to MIxS and related ontologies/vocabularies

Issue - State: open - Opened by lschriml 3 months ago - 6 comments
Labels: eDNA

#808 - Linting of LinkML YAML schema files

Pull Request - State: closed - Opened by sujaypatil96 3 months ago - 1 comment

#807 - Create list of documents supporting or clarifying MIxS

Issue - State: open - Opened by turbomam 3 months ago

#806 - `idna` update by dependabot failing on bioregistry import

Issue - State: open - Opened by turbomam 3 months ago

#805 - add deprecation protocol for GSC

Pull Request - State: closed - Opened by mslarae13 4 months ago - 7 comments

#804 - Add GSC Deprecation method

Issue - State: closed - Opened by mslarae13 4 months ago

#803 - Bump urllib3 from 2.2.1 to 2.2.2

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago
Labels: dependencies

#802 - update HACCP_term regex to required FOODON, add multivalue example

Pull Request - State: open - Opened by mslarae13 4 months ago - 6 comments
Labels: 1-TermUpdate

#801 - Updates to terms 16S recovered [MIXS:0000065] and 16S recovery software [MIXS:0000066]

Issue - State: open - Opened by only1chunts 4 months ago - 7 comments
Labels: 1-TermUpdate, 3-CIG, MIxSv7.0

#800 - Rock-MIxS environmental package

Issue - State: open - Opened by lschriml 4 months ago - 1 comment

#799 - Quality classifications question

Issue - State: open - Opened by ranitori 4 months ago

#798 - Bump requests from 2.31.0 to 2.32.0

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago
Labels: dependencies

#797 - Separate attribution from descriptions in extension documentation

Issue - State: open - Opened by cmungall 5 months ago - 11 comments
Labels: 4-TWG, documentation-external

#796 - NCBI to MIxS mapping, NMDC

Issue - State: open - Opened by lschriml 5 months ago

#795 - Web documentation contains a broken link to the MIXS release

Issue - State: open - Opened by aclum 5 months ago

#794 - Bump jinja2 from 3.1.3 to 3.1.4

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies

#793 - Bump tqdm from 4.66.2 to 4.66.3

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies

#792 - Make the landing page more user friendly

Issue - State: open - Opened by cmungall 5 months ago

#791 - Bump idna from 3.6 to 3.7

Pull Request - State: open - Opened by dependabot[bot] 6 months ago - 3 comments
Labels: dependencies

#790 - Fix wide line in schema description

Issue - State: open - Opened by sujaypatil96 6 months ago - 3 comments

#789 - 606 mixs editing workflow and policy

Pull Request - State: open - Opened by cmungall 6 months ago

#788 - Add schema description to `src/mixs/schema/mixs.yaml`

Pull Request - State: closed - Opened by sujaypatil96 6 months ago - 2 comments

#787 - Bump pillow from 10.2.0 to 10.3.0

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago
Labels: dependencies

#786 - Update mixs-templates/README.md

Pull Request - State: open - Opened by turbomam 6 months ago

#785 - Rename folders in `mixs-templates/`

Pull Request - State: closed - Opened by sujaypatil96 6 months ago

#784 - Reformat term list table to `Title (Name)`

Pull Request - State: closed - Opened by sujaypatil96 6 months ago - 2 comments

#783 - Replace `>` with `>-` in Extensions descriptions

Pull Request - State: closed - Opened by sujaypatil96 6 months ago

#782 - document the files in the `assets/` directory

Issue - State: open - Opened by turbomam 6 months ago - 1 comment

#781 - stay on top of the w3id PR about the gensc namespace redirection

Issue - State: closed - Opened by turbomam 6 months ago - 1 comment

#780 - Bump black from 23.12.1 to 24.3.0

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#779 - Discuss renaming of Food extensions

Issue - State: closed - Opened by only1chunts 7 months ago - 3 comments
Labels: 3-CIG

#778 - Add Applicable checklists and extensions section into MIxS docs

Pull Request - State: closed - Opened by sujaypatil96 7 months ago - 3 comments

#777 - Add a broken link detector action

Issue - State: open - Opened by turbomam 7 months ago

#776 - replace \u2019 RIGHT SINGLE QUOTATION MARK with \u0027. APOSTROPHE (') in descriptions etc

Issue - State: open - Opened by turbomam 7 months ago

#775 - add an assets/ directory or come up with another strategy for sharing derived artifacts

Issue - State: open - Opened by turbomam 7 months ago

#774 - Add applicable classes (checklists/extensions) back into docs

Pull Request - State: closed - Opened by sujaypatil96 7 months ago - 1 comment

#773 - How do different INSDC repos use different linkml slots to key MIxS terms?

Issue - State: closed - Opened by Woolly-at-EBI 7 months ago - 3 comments

#772 - agree a controlled vocabulary for the section field

Issue - State: open - Opened by only1chunts 7 months ago - 2 comments
Labels: 3-CIG, MIxSv7.0, medium priority

#771 - agree the definition of the section field

Issue - State: open - Opened by only1chunts 7 months ago - 1 comment
Labels: 3-CIG, MIxSv7.0, medium priority

#770 - MIMARKS checklist names incorrect in LinkML

Issue - State: open - Opened by only1chunts 8 months ago - 1 comment
Labels: documentation-external

#769 - add descriptions and other annotations to extensions

Pull Request - State: closed - Opened by turbomam 8 months ago - 2 comments

#768 - modifications to mainly the MISAGS checklist

Issue - State: open - Opened by Woolly-at-EBI almost 2 years ago
Labels: 1-TermUpdate, 3-CIG

#767 - extension dendrogram with code

Pull Request - State: closed - Opened by turbomam 8 months ago - 2 comments

#766 - create dendrogram of MIxS extensions, or some other all-vs-all distance metrics

Issue - State: closed - Opened by turbomam 8 months ago - 1 comment

#765 - Can the documentation pages be available via ID number and name URLs?

Issue - State: open - Opened by only1chunts 8 months ago
Labels: documentation-external, low priority

#764 - Add MIxS 6.0 Core and Packages excel docs to MIxS repo

Issue - State: open - Opened by lschriml 8 months ago

#763 - Should we still limit structured comment names to 20 characters?

Issue - State: closed - Opened by ramonawalls 8 months ago - 2 comments

#762 - Renaming folders in `mixs-templates/`

Pull Request - State: closed - Opened by sujaypatil96 8 months ago - 1 comment

#761 - for visualizations, `slot_usages` over object properties should indicate narrowest range

Issue - State: closed - Opened by turbomam 8 months ago - 1 comment

#760 - look through NCBI Biosample for usages of the nose, throat, teeth type terms

Issue - State: closed - Opened by turbomam 8 months ago - 6 comments

#759 - write python test for terms that have non-UTF-8 characters in their attributes

Issue - State: open - Opened by turbomam 8 months ago - 7 comments

#758 - FAIRsharing query: Updating your records with us

Issue - State: open - Opened by allysonlister 8 months ago - 7 comments
Labels: 3-CIG, outreach

#757 - Slot report for sharing in LLMs

Pull Request - State: closed - Opened by turbomam 9 months ago

#756 - try using Claude for detecting appropriate keywords for slots and redundancy/conflict detection

Issue - State: closed - Opened by turbomam 9 months ago

#755 - PR checks will fail on digit first or x-digit slot names

Pull Request - State: open - Opened by turbomam 9 months ago

#754 - test for slots whose names start with a digit or 'x' followed by a digit

Issue - State: open - Opened by turbomam 9 months ago

#753 - scripted removal of unhelpful `slot_usage`s; manually assert dense dict forms

Pull Request - State: closed - Opened by turbomam 9 months ago - 1 comment

GitHub / GenomicsStandardsConsortium/mixs issues and pull requests