Feedback from curators

Synthesis

Questions for Ike

1. How can a user or administrator delete a study / experiment / signature?
2. When editing an experiment, Preview shows the following message: "Some parts of the edit form did not reach the server; double-check that your edits are intact and try again." There doesn't seem to be any problem, should we just ignore the message?
3. From "Show Changes" for a study, experiment, or signature, would it be easy to add the usual save / show preview / show changes / cancel buttons here?

Year 1 Issues for Ike

In approximate priority order:

1. Add a button on each experiment that says "Duplicate this Experiment" or something like that and it would bring up a preloaded form with those values.
2. A way to manually mark a study, experiment, or signature as incomplete or incorrect, so that we can search for these and complete them.
3. Put a delimiter just above the "summary" box and submission buttons, maybe with text like "Ready to Save?". Or change "Summary" to "Summary of your edits" - anything to make it clear this is not part of the study/experiment/signature data.
4. Data export: a way to export all studies, experiments, and signatures as .tsv files for external analysis. Could be joined as a single file, or as three files, however is easy.
5. Re-import of current data - after this, we will freeze our current spreadsheet and switch over to using only bugsigdb.org for curation

Policy updates

1. clarify to leave irrelevant things blank (such as LDA score if not applicable)
2. when only one variable region was sequenced, leave the upper region blank
3. To be notified of future edits, to a study, select "Watch" - you will also be notified of any changes to its experiments or signatures.
4. You can save an unfinished experiment or signature at any time and return to it later to finish it.

Ludwig some points from my side

• Several things (Shaimaa Point 3, Fatima Point 1-3, Other Point 2) are just "policy updates" that reflect changes from curating with the new system as compared to our old habits with the curation sheet: ie use blank instead of NA / unknown; new coding of alpha diversity; ...
• Shaimaa Point 1 reflects the fact that we haven't filled the autocomplete / predefined fields comprehensively with pre-existing values / ontologies; this also links to https://github.com/waldronlab/BugSigDB/issues/1#issuecomment-604098173 on the nature of these fields and how these fields should behave when new entries are to be made (all drop down with an admin adding new values as needed, or all autocomplete with the option of users adding new values themselves, however with the danger of invalidity)
• Fatima Point 4 links to https://github.com/waldronlab/BugSigDB/issues/4#issuecomment-603448469:

Summary / Minor edit / Watch page: what is the purpose of these fields on the bottom of the edit form?

We can remove these if it is confusing. See: https://meta.wikimedia.org/wiki/Help:Edit_summary https://meta.wikimedia.org/wiki/Help:Minor_edit https://www.mediawiki.org/wiki/Help:Watching_pages

And I wonder whether we should indeed remove these fields or do we consider them beneficial?

• I guess Other Point 1 (tedious re-entry) is important that results partly from the re-structuring in the data model, not sure how to best address it though, maybe prefill when adding an experiment to a study with the values of an already existing experiment of the study? Maybe we could even allow to select the experiment for pre-filling the fields when adding a new experiment to a study that already has > 1 experiments @tosfos?

Raw feedback

Comments from Shaimaa Elsafoury:

1. I didn’t find Cesarean section in the condition section.
2. I also realized that statistical test section is a free form section which is not the case in our spreadsheet
3. in alpha diversity section, what should we choose if the study didn’t conduct one of the tests.
4. I also didn’t finish the data entry, but I saved my work in case something happened. However, I am not able to return back again to complete the data entry.

Comments from Fatima Zohra:

1. Wasn't sure what to do when LDA Score is irrelevant (tried putting N/A and this was invalid) - add a note to tooltip?
2. Wasn't sure what to do when there is only one variable region (add to tooltip, make upper and lower the same)
3. Wasn't sure the difference between blank and unknown under Alpha Diversity - tooltip
4. Thought "summary" belonged to Alpha Diversity, didn't realize it meant a summary of the edit. Multiple curators thought this meant some summary of the study or experiment.

Other feedback from discussion:

1. tedious having to re-enter all data for nearly identical experiments, e.g. host species is always the same. Would be convenient only having to enter common values only once, either on their own forms or by copying previous experiment
2. Were unclear that Alpha diversity "increased" / "decreased" meant in cases relative to controls
3. For an experiment page, click "Subjects" [Edit] - it sends you to Editing Template:Experiments (section) which is template code, but user wanted the form again
4. Not clear how to view and track the history of a study and its associated experiments and signatures

Comments from Lucille Mellor.

1. If a study sequenced 2 difference variable regions instead of a range, there does not appear to be a way to enter this (i.e. V1&V6 instead of V1-V6)
2. For the statistical analysis field, it would be helpful if there was a drop-down list available to view available options (there appears to be a controlled dictionary for this field but also free-text can be entered)
3. Is there a way to delete a study or experiment entry? For example, if you enter the wrong PMID in error, there does not appear to be a way to delete the study from the database (if you edit the erroneous PMID, the new study adds but the original study remains as well)
4. For the example you provided on the tongue microbiome, there is a summary of the experiments entered on the main study page, but I don't see a summary like this for my test studies unless I look at the Recent Changes tab. This summary is helpful for seeing what you've entered so far
5. I don't see an option to add signatures for the experiments. Is this functionality available yet?

Responses

Shaimaa "I also didn’t finish the data entry, but I saved my work in case something happened. However, I am not able to return back again to complete the data entry." - this was just the caching / purging issue, you shouldn't notice this issue any more.