HCR terms are duplicated but have 'hcr' in the slot name

[mslarae13]

Describe the bug
A clear and concise description of what the bug is.

Extensions should NOT have their own slots / terms for every metadata field. For example, when measuring temperature of the sample, you should use the term 'temp' .. not make an extension specific term like hcr_term .

And with the expansion if LinkML IF there is need to say "This is specific for this extension in this way" you use slot usage.

Expected behavior
A clear and concise description of what you expected to happen.

Slot usage should be implemented and slots should be evaluated if they're repeated.

[mslarae13]

not sure if this is a bug, but seemed right? Cuz it's not 1 slot specific.. I just referenced 1 slot.

[turbomam]

@mslarae13 I think you meant _temp, not _term in your initial comment

not make an extension specific term like hcr_temp .

[cmungall]

I agree in principle across all terms, but it needs to be clear whether a property refers to a sample or some aspect of the environment in which the sample was collected. These may not be the same.

However, this should not be done by prefixing with the extension or something specific like hcr, rather it should be consistent use of prefixes like sample_ and environmental_

[mslarae13]

Other slots to review for redundancy

samp_transport_cond vs samp_transport_temp

• Both of these have temp... 1 has temp + duration

• samp_transport_temp
  -- FoodAnimalAndAnimalFeed
  -- FoodFoodProductionFacility
  -- FoodHumanFoods

• samp_transport_cond
  -- HydrocarbonResourcesCores
  -- HydrocarbonResourcesFluidsSwabs

---

[only1chunts]

Other slots to review for redundancy

samp_transport_cond vs samp_transport_temp

Can we keep one ticket to one bug/suggested update, I think this ticket started out as remove duplicate 'HCR_temp' and replace with 'temp' in relevant extensions.
I believe thats a good call and should be done. I've added the CIG review label

[turbomam]

we can always make grouping issues, where the first comment contains a checklist like

• wake up
• drink favorite morning beverage
• solve world's problems

Then each of those items will have a bulls-eye like button to the right that converts it into an individual issue.

implementation:

- [ ] wake up
- [ ] drink favorite morning beverage
- [ ] solve world's problems

[lschriml]

Regarding the hcr_temp. The definition is: Original temperature of the hydrocarbon resource. Temperature: Temperature of the sample at the time of sampling These should not be combined.

…

On Thu, Oct 19, 2023 at 12:30 PM Mark A. Miller ***@***.***> wrote: we can always make grouping issues, where the *first comment* contains a checklist like - wake up - drink favorite morning beverage - solve world's problems Then each of those items will have a bulls-eye like button to the right that converts it into an individual issue. implementation: - [ ] wake up - [ ] drink favorite morning beverage - [ ] solve world's problems — Reply to this email directly, view it on GitHub <#664 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABBB4DLRBKOFFTNPEOE3MKLYAFITZAVCNFSM6AAAAAA6F2IEBCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONZRGMZTMNBVGM> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- Lynn M. Schriml, Ph.D. Associate Professor Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 670 W. Baltimore St., HSFIII, Room 3061 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 ***@***.***

[turbomam]

@lschriml thanks for the feedback on this particular issue. Can you please help address the more general issue raised by @cmungall above?

[turbomam]

In my humble opinion, worrying about backwards compatibility withhcr_temp may not be justified. It does not appear anywhere in LBL's July 2023 SQL dump of NCBI Biosmaple, as an attribute_name or a harmonized_name.

I think this is an equivalent search though the NCBI Biosample web interface, but I am not an expert on that: https://www.ncbi.nlm.nih.gov/biosample/?term=hcr_temp%5BAttribute%5D

Are there other databases that I should be looking in?

[lschriml]

To date, we have not included this type of prefix. Perhaps this could be noted in the sections ?? Sent from my iPhoneOn Oct 18, 2023, at 9:14 PM, Chris Mungall ***@***.***> wrote: I agree in principle across all terms, but it needs to be clear whether a property refers to a sample or some aspect of the environment in which the sample was collected. These may not be the same. However, this should not be done by prefixing with the extension or something specific like hcr, rather it should be consistent use of prefixes like sample_ and environmental_ —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[lschriml]

This term is for hydrocarbon sampling. Being used by the petroleum industry. May not be in public databases.Sent from my iPhoneOn Oct 19, 2023, at 1:21 PM, Mark A. Miller ***@***.***> wrote: In my humble opinion, worrying about backwards compatibility withhcr_temp may not be justified. It does not appear anywhere in LBL's July 2023 SQL dump of NCBI Biosmaple, as an attribute_name or a harmonized_name. I think this is an equivalent search though the NCBI Biosample web interface, but I am not an expert on that: https://www.ncbi.nlm.nih.gov/biosample/?term=hcr_temp%5BAttribute%5D Are there other databases that I should be looking in? —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: ***@***.***>

[turbomam]

@mslarae13 I forgot to say that I've created some tools that might simplify researching an issue like this. I haven't advertised them much because they're not totally ready for prime time.

1. download mixs_derived_class_term_schemasheet.tsv
2. open in a spreadsheet editor
3. remove schema-sheets specific rows 2-4
4. turn on your spreadsheet's auto-filtering mode
5. filter the keywords column (S) on the text "temperature"
6. you will get a report that should theoretically include all slots whose titles include the word temperature, or something synonymous

• air_temp
• air_temp_regm
• annual_temp
• avg_temp
• cons_food_stor_temp
• ferm_temp
• hcr_temp
• host_body_temp
• samp_store_temp
• samp_transport_temp
• season_temp
• soil_temp
• study_inc_temp
• surf_temp
• temp
• temp_out
• tvdss_of_hcr_temp
• water_temp_regm

One part of "not completely ready for prime time" is that I added the keywords with a text-mining/human curation approach. I have suggested that we should have a discussion about ongoing keyword maintenance.

[turbomam]

I think most or all of those slots should have a see_also to temp and a comment that explains how they are different from temp

And I think we should follow that pattern for all other clusters of similar slots.

[turbomam]

And I think they should all follow the same validation pattern in the absence of some traceable reason.