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Inconsistency between data in GOLD and data from bioregistry #93

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sujaypatil96 opened this issue Jun 7, 2022 · 0 comments
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sujaypatil96 commented Jun 7, 2022

A cursory evaluation of a biosample record from GOLD and the same biosample record from bioregistry:

Case 1: GOLD

sample-annotator git:(spatil/pull-insdc-identifiers) ✗ curl  -u user_name:password  https://gold.jgi.doe.gov/rest/nmdc/biosamples\?biosampleGoldId\=Gb0239939

[{"biosampleGoldId":"Gb0239939","biosampleName":"Banana cropland soil microbial communities from Singapore - 
Seedorf71.JP2soil.20","ncbiTaxId":null,"ncbiTaxName":null,"sampleCollectionSite":"Banana cropland 
soil","geographicLocation":"Singapore","latitude":1.43492266,"longitude":103.7112946,"ecosystemPathId":4213,"ecosystem
":"Environmental","ecosystemCategory":"Terrestrial","ecosystemType":"Soil","ecosystemSubtype":"Unclassified","specific
cosystem":"Agricultural 
land","altitudeInMeters":null,"altitudeInMeters2":null,"dateCollected":null,"depthInMeters":null,"depthInMeters2":null,"descri
ption":"Banana cropland soil microbial communities from Singapore","hostDiseases":
[],"elevationInMeters":19,"elevationInMeters2":null,"geoLocation":"Singapore","habitat":"Banana cropland 
soil","hostGender":null,"hostName":null,"hostNcbiTaxid":null,"isoCountry":"Singapore","longhurst":null,"nitrateConcentration
":null,"oxygenConcentration":null,"ph":null,"pressure":null,"salinity":null,"salinityConcentration":null,"sampleBodySite":null,"s
ampleBodySubsite":null,"sampleCollectionTemperature":null,"subsurfaceDepthInMeters":null,"subsurfaceDepthInMeters2":n
ull,"visitNum":null,"mixsPackage":"Standard","envoBroadScale":{"id":"ENVO_01000245","label":"cropland 
biome"},"envoLocalScale":{"id":"ENVO_00000119","label":"planted forest"},"envoMedium":
{"id":"ENVO_02000059","label":"surface soil"},"modDate":"2022-04-08","addDate":"2019-09-03","contacts":
[{"name":"Janet Jansson","email":"[email protected]","jgiSsoId":"62","roles":["other"]},{"name":"Antonio David Paez 
Espino","email":"[email protected]","jgiSsoId":"8722","roles":["other"]},{"name":"Emily 
Graham","email":"[email protected])","jgiSsoId":"null","roles":["submitter"]},{"name":"Emily 
Graham","email":"[email protected]","jgiSsoId":"52018","roles":["other"]},{"name":"Ruonan 
Wu","email":"[email protected]","jgiSsoId":"59483","roles":["other"]},{"name":"Russell 
Neches","email":"[email protected]","jgiSsoId":"55080","roles":["other"]}]}]%                                                                                  

See that for biosampleGoldId="Gb0239939", we have sampleCollectionTemperature set to NULL.

Case 2: bioregistry

Follow this link to find the corresponding bioregistry record: https://www.ebi.ac.uk/biosamples/samples/SAMEA7724289

You'll see that there is temperature is set to 32 degree celsius.

What is the reason for this inconsistency between the same records in the two places? Is GOLD not up to date?

CC: @cmungall @emileyfadrosh

@sujaypatil96 sujaypatil96 added the bug Something isn't working label Jun 7, 2022
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