NMDC types as they appear in RDF artifact

[turbomam]

PREFIX nmdc: <https://w3id.org/nmdc/>
select distinct ?t (count(?s) as ?s_count) 
where {
    ?s nmdc:type ?t .
}
group by ?t
order by ?t

?t	?s_count
ControlledTermValue	15
ndmc:NomAnalysisActivity	50
nmdc:Biosample	658
nmdc:DataObject	25301
nmdc:GeolocationValue	35
nmdc:MAGsAnalysisActivity	761
nmdc:MetaProteomicAnalysis	52
nmdc:MetabolomicsAnalysisActivity	209
nmdc:MetagenomeAnnotation	377
nmdc:MetagenomeAnnotationActivity	425
nmdc:MetagenomeAssembly	1040
nmdc:MetatranscriptomeActivity	16
nmdc:MetatranscriptomeAnnotationActivity	16
nmdc:MetatranscriptomeAssembly	16
nmdc:NomAnalysisActivity	788
nmdc:OmicsProcessing	1927
nmdc:Study	8
nmdc:metaT	39

• why doesn't ControlledTermValue have a prefix
• why are they strings, not URIs?
• are all of those really NMDC schema classes?

[turbomam]

are all of those really NMDC schema classes?

• no such class as MAGsAnalysisActivity
  • should be MagsAnalysisActivity
• no such class as MetaProteomicAnalysis
  • should be MetaproteomicsAnalysisActivity
• no such class as MetagenomeAnnotation
  • should be MetagenomeAnnotationActivity
• no such class as metaT
  • should be MetatranscriptomeActivity

[turbomam]

why doesn't ControlledTermValue have a prefix

nmdc:68958f6a-5dd9-4cb7-8334-3ccbee159ad6 dcterms:description "Soil microbial communities from the East River watershed near Crested Butte, Colorado, United States" ;
    mixs:0000009 [ a nmdc:GeolocationValue ;
            wgs84:lat 38.92045766 ;
            wgs84:long -106.9484528 ;
            nmdc:has_raw_value "38.92045766 -106.9484528" ] ;
    mixs:0000010 [ a nmdc:TextValue ;
            nmdc:has_raw_value "USA: Colorado" ] ;
    mixs:0000011 [ a nmdc:TimestampValue ;
            nmdc:has_raw_value "2017-05-09" ] ;
    mixs:0000012 [ a ENVO:00000108 ;
            nmdc:has_raw_value "ENVO:00000108" ;
            nmdc:type "ControlledTermValue" ] ;
    mixs:0000013 [ a ENVO:00000292 ;
            nmdc:has_raw_value "ENVO:00000292" ;
            nmdc:type "ControlledTermValue" ] ;
    mixs:0000014 [ a ENVO:00005802 ;
            nmdc:has_raw_value "ENVO:00005802" ;
            nmdc:type "ControlledTermValue" ] ;
    mixs:0000018 [ a nmdc:QuantityValue ;
            nmdc:has_numeric_value 5e+00 ] ;
    mixs:0001107 "igsn:IEWFS000I" ;
    nmdc:community "microbial communities" ;
    nmdc:ecosystem "Environmental" ;
    nmdc:ecosystem_category "Terrestrial" ;
    nmdc:ecosystem_subtype "Unclassified" ;
    nmdc:ecosystem_type "Soil" ;
    nmdc:habitat "soil" ;
    nmdc:igsn_biosample_identifiers "igsn:IEWFS000I"^^xsd:anyURI ;
    nmdc:location "The East River watershed near Crested Butte, Colorado, USA" ;
    nmdc:name "Soil microbial communities from the East River watershed near Crested Butte, Colorado, United States - ER_145" ;
    nmdc:ncbi_taxonomy_name "soil metagenome" ;
    nmdc:sample_collection_site "soil" ;
    nmdc:sample_link "gold:Gs0135149" ;
    nmdc:specific_ecosystem "Unclassified" ;
    nmdc:type "nmdc:Biosample" .

but also

nmdc:776a2199-8708-43f3-99ed-97e14fc904af dcterms:description "Bulk soil microbial communities from the East River watershed near Crested Butte, Colorado, United States" ;
    mixs:0000009 [ a nmdc:GeolocationValue ;
            wgs84:lat 38.920405856 ;
            wgs84:long -106.948682649 ;
            nmdc:has_raw_value "38.920405856 -106.948682649" ] ;
    mixs:0000010 [ a nmdc:TextValue ;
            nmdc:has_raw_value "USA: Colorado" ] ;
    mixs:0000011 [ a nmdc:TimestampValue ;
            nmdc:has_raw_value "2017-06-08" ] ;
    mixs:0000012 [ a ENVO:00000108,
                nmdc:ControlledIdentifiedTermValue ;
            nmdc:has_raw_value "ENVO:00000108" ] ;
    mixs:0000013 [ a ENVO:00000292,
                nmdc:ControlledIdentifiedTermValue ;
            nmdc:has_raw_value "ENVO:00000292" ] ;
    mixs:0000014 [ a ENVO:00005802,
                nmdc:ControlledIdentifiedTermValue ;
            nmdc:has_raw_value "ENVO:00005802" ] ;
    mixs:0000018 [ a nmdc:QuantityValue ;
            nmdc:has_numeric_value 1.5e-01 ;
            nmdc:has_raw_value "0.15" ;
            nmdc:has_unit "meter" ] ;
    mixs:0001107 "ER_198" ;
    nmdc:add_date "2018-06-22" ;
    nmdc:community "microbial communities" ;
    nmdc:ecosystem "Environmental" ;
    nmdc:ecosystem_category "Terrestrial" ;
    nmdc:ecosystem_subtype "Meadow" ;
    nmdc:ecosystem_type "Soil" ;
    nmdc:gold_sample_identifiers "gold:Gb0191678"^^xsd:anyURI,
        "gold:Gb0192125"^^xsd:anyURI ;
    nmdc:habitat "bulk soil" ;
    nmdc:igsn_biosample_identifiers "igsn:IEWFS0015"^^xsd:anyURI ;
    nmdc:img_identifiers "img.taxon:3300042849" ;
    nmdc:insdc_biosample_identifiers "biosample:SAMN10864255"^^xsd:anyURI ;
    nmdc:location "The East River watershed near Crested Butte, Colorado, USA" ;
    nmdc:mod_date "2021-06-15" ;
    nmdc:name "Bulk soil microbial communities from the East River watershed near Crested Butte, Colorado, United States - ER_198" ;
    nmdc:ncbi_taxonomy_name "soil metagenome" ;
    nmdc:sample_collection_site "soil" ;
    nmdc:sample_link "gold:Gs0135149" ;
    nmdc:specific_ecosystem "Bulk soil" ;
    nmdc:type "nmdc:Biosample" .

[turbomam]

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