misnomer in mixs documentation

[only1chunts]

On this page : https://genomicsstandardsconsortium.github.io/mixs/ the names of the MIMARKS checklists is incorrect:

MIMARKSSpecimen | Minimal Information about a Marker Specimen: specimen

MIMARKSSurvey | Minimal Information about a Marker Specimen: survey

These should be: MIMARKSSpecimen | Minimal Information about a Marker Sequence: specimen

MIMARKSSurvey | Minimal Information about a Marker Sequence: survey

See original publication.

[turbomam]

Thanks. I'll review with @sujaypatil96

The page you are referring to was generated from @cmungall's older LinkML transformation

I have a new transformation that will be ready for general review and feedback at Bangkok.

I guess we should still update what we have in front of the public now anyway.

[sujaypatil96]

Happy to make the necessary schema change to update the description for the MimarksC and MimarksS checklists. Will have a PR out for this soon.

[turbomam]

@sujaypatil96 I am solving this issue now

[turbomam]

Find 'Minimal Information about a Marker Specimen' in src/mixs/schema/mixs.yaml and replace with 'Minimal Information about a Marker Sequence'

[turbomam]

Two hits, corresponding to the ...specimen and ...survey variants

[turbomam]

git diff src/mixs/schema/mixs.yaml

diff --git a/src/mixs/schema/mixs.yaml b/src/mixs/schema/mixs.yaml
index 01fb71033..4ac3c6df0 100644
--- a/src/mixs/schema/mixs.yaml
+++ b/src/mixs/schema/mixs.yaml
@@ -15283,7 +15283,7 @@ classes:
         recommended: true
     class_uri: MIXS:0010011
   MimarksC:
-    description: 'Minimal Information about a Marker Specimen: specimen'
+    description: 'Minimal Information about a Marker Sequence: specimen'
     title: MIMARKS specimen
     comments:
     - for marker gene sequences from cultured or voucher-identifiable specimens
@@ -15384,7 +15384,7 @@ classes:
         recommended: true
     class_uri: MIXS:0010009
   MimarksS:
-    description: 'Minimal Information about a Marker Specimen: survey'
+    description: 'Minimal Information about a Marker Sequence: survey'
     title: MIMARKS survey
     comments:
     - for marker gene sequences obtained directly from the environment

[turbomam]

now running date; make clean all test; date locally, in addition to the GitHub action

• started at Tue Jul 9 10:58:03 AM EDT 2024
• finished at Tue Jul 9 11:50:27 AM EDT 2024

~ 53 minutes

---

The GitHub action, which should be very similar, only took 19 minutes!