Determine if and how link_class_info will be used in the submission schema

[mslarae13]

slot link_class_info has no guidance or examples.

criteria for completion

• identify how the slot has been used (if at all) in the past, @turbomam provide a query of NCBI?
• Update nmdc.yaml (or mixs.yaml?) to add more context and examples
• update NMDC submission portal to match schema slot usage (Mike)

[mslarae13]

? Leave it out? Not really used... non-actionable DB field

[turbomam]

link_class_info values in the BBOP SQLite version of NCBI biosample_set.xml as of 2023-05-18

value	count	link notes
not collected	432
not applicable	415
NA	114
http://geointa.inta.gov.ar/visor/?p=model_suelos	108	This site can’t be reached;Check if there is a typo in geointa.inta.gov.ar.;DNS_PROBE_FINISHED_NXDOMAIN
http://doi.org/10.1002/jpln.200521814	71	Chernozem—Soil of the Year 2005
missing	65
http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups	64	Page not found
https://www.fao.org/3/i3794en/I3794en.pdf	60	World reference base for soil resources 2014
Chromic Haploxernt	48
na	19
doi:10.1016/j.fcr.2011.09.019	6	https://www.sciencedirect.com/science/article/abs/pii/S0378429011003340, "Evidence of improved water uptake from subsoil by spring wheat following lucerne in a temperate humid climate"
http://esdac.jrc.ec.europa.eu/resource-type/european-soil-database-maps	1	live

[turbomam]

Specification from https://github.com/GenomicsStandardsConsortium/mixs/blob/main/mixs/excel/mixs_v6.xlsx

Environmental package	agriculture	soil
Structured comment name	link_class_info	link_class_info
Package item	link to classification information	link to classification information
Definition	Link to digitized soil maps or other soil classification information	Link to digitized soil maps or other soil classification information
Expected value	PMID,DOI or url	PMID,DOI or url
Value syntax	{PMID|DOI|URL}	{PMID}|{DOI}|{URL}
Example
Requirement	X	X
Preferred unit
Occurrence	1	1
MIXS ID	MIXS:0000329	MIXS:0000329

[turbomam]

It seems like link_class_info might function like one of the many x_meth fields, which state how the value for slot x was determined. But I can't tell what slot link_class_info might provide context for.

As shown above, the number of biosamples that are annotated with an informative link_class_info is in the low hundreds, out of 35 million. (I am defining informative as something other than a synonym for "not available" or a live web link.)

@mslarae13 I propose that we omit this field from NMDC submission templates. A longer term action could be filing an issue at https://github.com/GenomicsStandardsConsortium/mixs/issues asking for documentation or examples of this term's use. I hope that that request wouldn't be construed as invitation for open-ended discussion about the subject. I suppose it could also be useful to be put in touch with the person who requested that term in the first place.

[turbomam]

link_class_info has not been used for any biosamples in the NMDC production MongoDB yet

db.getCollection("biosample_set").find( { link_class_info : { $exists : true } } );

0

[ssarrafan]

Adding to current sprint per Mark. Need feedback from @mslarae13

[mslarae13]

I propose that we omit this field from NMDC submission templates. A longer term action could be filing an issue at https://github.com/GenomicsStandardsConsortium/mixs/issues asking for documentation or examples of this term's use.

-- I agree with this @turbomam

[ssarrafan]

@turbomam can this be closed now that Montana has provided feedback?

[mslarae13]

@ssarrafan I don't think we can close it yet. Steps for resolution are remove from NMDC submission portal. & submit issue to GSC

[ssarrafan]

@ssarrafan I don't think we can close it yet. Steps for resolution are remove from NMDC submission portal. & submit issue to GSC

Ah ok. I thought this ticket was just to "determine if and how..."
I'll move to the next sprint

[mslarae13]

Chris Hunter suggest deprecating this term in GSC. Montana will put an issue into GSC.

@turbomam
Should we remove from NMDC now, or wait for GSC update?

[mslarae13]

GenomicsStandardsConsortium/mixs#590

[turbomam]

I'll remove it in 7.6.1

[mslarae13]

@turbomam did this get removed?

[mslarae13]

Currently manually managing. We do not ingest all MIxS slots, see https://github.com/microbiomedata/nmdc-schema/blob/main/assets/import_mixs_slots_regardless.tsv

MIxS that we pull into NMDC schema is 6.0 ..Should pull in 6.2, but some slot changes have been made (names, presence/absence)

• Will require migration
• How/ when with respect to berk? Does it affect postgres?
• There are some no impact changes. samp_collec_meth & device

[ssarrafan]

I'm moving this to the current sprint based on @mslarae13 last comment on 4/29.

[ssarrafan]

@turbomam @mslarae13 should this just be in the backlog? I can remove it from the sprint.

[ssarrafan]

Sprint over, removing from sprint.