Open mslarae13 opened 1 year ago
? Leave it out? Not really used... non-actionable DB field
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 |
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 |
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.
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
Adding to current sprint per Mark. Need feedback from @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
@turbomam can this be closed now that Montana has provided feedback?
@ssarrafan I don't think we can close it yet. Steps for resolution are remove from NMDC submission portal. & submit issue to GSC
@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
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?
I'll remove it in 7.6.1
@turbomam did this get removed?
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)
I'm moving this to the current sprint based on @mslarae13 last comment on 4/29.
@turbomam @mslarae13 should this just be in the backlog? I can remove it from the sprint.
Sprint over, removing from sprint.
slot link_class_info has no guidance or examples.
criteria for completion