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Revision 1053

VegBIEN: Renamed specimenreplicate.reference_id to datasource_id and pointed it to party instead of reference, since party is better optimized for storing names

View differences:

inputs/NYBG/test/import.specimens.out.ref
1
Inserted 80 new rows into database
1
Inserted 79 new rows into database
inputs/NYBG/test/VegBIEN.specimens.xml.ref
129 129
        <description>plant fungus: with rough brown bark, almost no buttressing, 1 m diam; fallen fruit and leaves</description>
130 130
        <museum_id><party><organizationname>NY Herbarium</organizationname></party></museum_id>
131 131
        <collectioncode_dwc>Herbarium</collectioncode_dwc>
132
        <reference_id><reference><shortname>NYBG</shortname></reference></reference_id>
132
        <datasource_id><party><organizationname>NYBG</organizationname></party></datasource_id>
133 133
        <catalognumber_dwc>00682023</catalognumber_dwc>
134 134
        <collectionnumber>9877</collectionnumber>
135 135
        <sourceaccessioncode>816590</sourceaccessioncode>
......
217 217
        </taxonoccurrence_id>
218 218
        <museum_id><party><organizationname>NY Herbarium</organizationname></party></museum_id>
219 219
        <collectioncode_dwc>Herbarium</collectioncode_dwc>
220
        <reference_id><reference><shortname>NYBG</shortname></reference></reference_id>
220
        <datasource_id><party><organizationname>NYBG</organizationname></party></datasource_id>
221 221
        <catalognumber_dwc>200996</catalognumber_dwc>
222 222
        <collectionnumber>545</collectionnumber>
223 223
        <sourceaccessioncode>220541</sourceaccessioncode>
inputs/NYBG/maps/VegBIEN.specimens.csv
39 39
PlantFungusDescription,"/description/_merge/2/_label[label=""plant fungus""]/value",,
40 40
InstitutionCode,/{museum_id/party/organizationname/_name/first},,11
41 41
CollectionCode,"/{museum_id/party/organizationname/_name/last,collectioncode_dwc}",Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
42
CatalogNumber,:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,"Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
43
CollectorNumber,:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1,,22
44
FieldNumber,:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
45
UniqueNYInternalRecordNumber,:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
42
CatalogNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,"Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
43
CollectorNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1,,22
44
FieldNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
45
UniqueNYInternalRecordNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
46 46
BasisOfRecord,,Brad: OMIT? See http://rs.tdwg.org/dwc/terms/index.htm#basisOfRecord for definition of this term.,15
47 47
ContinentOcean,,Brad: OMIT,59
48 48
DateLastModified,,"Brad: Mapping to VegX is incorrect. I think is this merely an internal timestamp indicated when record last modified, not necessarily when determination (taxon name) last modified. Probably we should omit this field, although might be useful for updating changed records from this source.",1
inputs/SALVIAS/maps/VegBIEN.organisms.csv
19 19
Habit,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=growthForm]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
20 20
Ind,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=individualCode]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."
21 21
DetType,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=voucherType]]:[@fkey=tableRecord_ID]/definedvalue","Brad: A SALVIAS value referring to the relationship between the voucher specimen and the observation. Affect how the identification of the specimen(latin name) is transferred to the observation. 'direct'=voucher specimen was collected from this same tree; they are one and the same individual. 'indirect'=voucher specimen was collected for a different individual, but the original data provider confirmed that this is the same species. 'default'=basically same as 'indirect'. 'uncollected'=no voucher specimen, data provider  asserted that this was the name but was unable to collect. The main different is that with 'direct', 'indirect', and 'default', the scientific name can be updated automatically based on the name attached to the specimen voucher (assuming you have a link to that data, presumably from a herbarium database. Whereas, if det_type='uncollected', the name can never change because there is no specimen."
22
coll_number,/specimenreplicate:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,Brad: Incorrect. Map instead as for voucher_string
23
census_date,/specimenreplicate:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/collectiondate/_*/date,
22
coll_number,/specimenreplicate:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,Brad: Incorrect. Map instead as for voucher_string
23
census_date,/specimenreplicate:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectiondate/_*/date,
24 24
auth,"/taxondetermination[*_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Authority]:[determinationtype=""Computer (automated)"",iscurrent=true]/*_id/plantconcept/*_id/*/plantname",Brad: Incorrect. This is the author of the scientificName. The should be a place for this in the taxonomic name elements of VegB and VegX. Let's discuss.
25 25
Family,"/taxondetermination[*_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=""Computer (automated)"",iscurrent=true]/*_id/plantconcept/*_id/*/plantname",
26 26
Genus,"/taxondetermination[*_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Genus]:[determinationtype=""Computer (automated)"",iscurrent=true]/*_id/plantconcept/*_id/*/plantname",
inputs/NYBG-CSV/test/import.specimens.out.ref
1
Inserted 80 new rows into database
1
Inserted 79 new rows into database
inputs/NYBG-CSV/test/VegBIEN.specimens.xml.ref
129 129
        <description>plant fungus: with rough brown bark, almost no buttressing, 1 m diam; fallen fruit and leaves</description>
130 130
        <museum_id><party><organizationname>NY Herbarium</organizationname></party></museum_id>
131 131
        <collectioncode_dwc>Herbarium</collectioncode_dwc>
132
        <reference_id><reference><shortname>NYBG</shortname></reference></reference_id>
132
        <datasource_id><party><organizationname>NYBG</organizationname></party></datasource_id>
133 133
        <catalognumber_dwc>00682023</catalognumber_dwc>
134 134
        <collectionnumber>9877</collectionnumber>
135 135
        <sourceaccessioncode>816590</sourceaccessioncode>
......
217 217
        </taxonoccurrence_id>
218 218
        <museum_id><party><organizationname>NY Herbarium</organizationname></party></museum_id>
219 219
        <collectioncode_dwc>Herbarium</collectioncode_dwc>
220
        <reference_id><reference><shortname>NYBG</shortname></reference></reference_id>
220
        <datasource_id><party><organizationname>NYBG</organizationname></party></datasource_id>
221 221
        <catalognumber_dwc>200996</catalognumber_dwc>
222 222
        <collectionnumber>545</collectionnumber>
223 223
        <sourceaccessioncode>220541</sourceaccessioncode>
inputs/NYBG-CSV/maps/VegBIEN.specimens.csv
37 37
PlantFungusDescription,"/description/_merge/2/_label[label=""plant fungus""]/value",,
38 38
InstitutionCode,/{museum_id/party/organizationname/_name/first},,11
39 39
CollectionCode,"/{museum_id/party/organizationname/_name/last,collectioncode_dwc}",Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
40
CatalogNumber,:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,"Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
41
CollectorNumber,:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1,,22
42
FieldNumber,:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
43
UniqueNYInternalRecordNumber,:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
40
CatalogNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,"Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
41
CollectorNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1,,22
42
FieldNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
43
UniqueNYInternalRecordNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
44 44
BasisOfRecord,,Brad: OMIT? See http://rs.tdwg.org/dwc/terms/index.htm#basisOfRecord for definition of this term.,15
45 45
ContinentOcean,,Brad: OMIT,59
46 46
DateLastModified,,"Brad: Mapping to VegX is incorrect. I think is this merely an internal timestamp indicated when record last modified, not necessarily when determination (taxon name) last modified. Probably we should omit this field, although might be useful for updating changed records from this source.",1
inputs/SALVIAS-CSV/test/VegBIEN.organisms.xml.ref
54 54
            <definedvalue>10</definedvalue>
55 55
        </definedvalue>
56 56
        <specimenreplicate>
57
            <reference_id><reference><shortname>SALVIAS</shortname></reference></reference_id>
57
            <datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id>
58 58
            <catalognumber_dwc>14598</catalognumber_dwc>
59 59
        </specimenreplicate>
60 60
        <taxondetermination>
......
170 170
            <definedvalue>100</definedvalue>
171 171
        </definedvalue>
172 172
        <specimenreplicate>
173
            <reference_id><reference><shortname>SALVIAS</shortname></reference></reference_id>
173
            <datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id>
174 174
            <catalognumber_dwc>14669</catalognumber_dwc>
175 175
        </specimenreplicate>
176 176
        <taxondetermination>
inputs/SALVIAS-CSV/test/import.organisms.out.ref
1
Inserted 82 new rows into database
1
Inserted 81 new rows into database
inputs/SALVIAS-CSV/maps/VegBIEN.organisms.csv
27 27
habit,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=growthForm]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
28 28
individual_code,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=individualCode]]:[@fkey=tableRecord_ID]/definedvalue","Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."
29 29
det_type,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=voucherType]]:[@fkey=tableRecord_ID]/definedvalue","Brad: A SALVIAS value referring to the relationship between the voucher specimen and the observation. Affect how the identification of the specimen(latin name) is transferred to the observation. 'direct'=voucher specimen was collected from this same tree; they are one and the same individual. 'indirect'=voucher specimen was collected for a different individual, but the original data provider confirmed that this is the same species. 'default'=basically same as 'indirect'. 'uncollected'=no voucher specimen, data provider  asserted that this was the name but was unable to collect. The main different is that with 'direct', 'indirect', and 'default', the scientific name can be updated automatically based on the name attached to the specimen voucher (assuming you have a link to that data, presumably from a herbarium database. Whereas, if det_type='uncollected', the name can never change because there is no specimen."
30
coll_number,/specimenreplicate:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,Brad: Incorrect. Map instead as for voucher_string
30
coll_number,/specimenreplicate:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,Brad: Incorrect. Map instead as for voucher_string
31 31
specific_authority,"/taxondetermination[*_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Authority]:[determinationtype=""Computer (automated)"",iscurrent=true]/*_id/plantconcept/*_id/*/plantname",Brad: Incorrect. This is the author of the scientificName. The should be a place for this in the taxonomic name elements of VegB and VegX. Let's discuss.
32 32
family,"/taxondetermination[*_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=""Computer (automated)"",iscurrent=true]/*_id/plantconcept/*_id/*/plantname",
33 33
genus,"/taxondetermination[*_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Genus]:[determinationtype=""Computer (automated)"",iscurrent=true]/*_id/plantconcept/*_id/*/plantname",
schemas/vegbien.my.sql
2257 2257

  
2258 2258
CREATE TABLE specimenreplicate (
2259 2259
    specimenreplicate_id int(11) NOT NULL,
2260
    reference_id int(11) NOT NULL,
2260
    datasource_id int(11) NOT NULL,
2261 2261
    collectioncode_dwc text,
2262 2262
    catalognumber_dwc text,
2263 2263
    collectiondate timestamp NULL,
......
4212 4212
--
4213 4213

  
4214 4214
ALTER TABLE specimenreplicate
4215
    ADD CONSTRAINT specimenreplicate_keys_accessioncode UNIQUE (reference_id, collectioncode_dwc, sourceaccessioncode);
4215
    ADD CONSTRAINT specimenreplicate_keys_accessioncode UNIQUE (datasource_id, collectioncode_dwc, sourceaccessioncode);
4216 4216

  
4217 4217

  
4218 4218
--
......
4220 4220
--
4221 4221

  
4222 4222
ALTER TABLE specimenreplicate
4223
    ADD CONSTRAINT specimenreplicate_keys_catalognumber UNIQUE (reference_id, collectioncode_dwc, catalognumber_dwc);
4223
    ADD CONSTRAINT specimenreplicate_keys_catalognumber UNIQUE (datasource_id, collectioncode_dwc, catalognumber_dwc);
4224 4224

  
4225 4225

  
4226 4226
--
......
4228 4228
--
4229 4229

  
4230 4230
ALTER TABLE specimenreplicate
4231
    ADD CONSTRAINT specimenreplicate_keys_collectionnumber UNIQUE (reference_id, collectioncode_dwc, collectionnumber);
4231
    ADD CONSTRAINT specimenreplicate_keys_collectionnumber UNIQUE (datasource_id, collectioncode_dwc, collectionnumber);
4232 4232

  
4233 4233

  
4234 4234
--
......
4909 4909

  
4910 4910

  
4911 4911
--
4912
-- Name: fki_specimenreplicate_datasource_id; Type: INDEX; Schema: public; Owner: -; Tablespace: 
4913
--
4914

  
4915
CREATE INDEX fki_specimenreplicate_datasource_id ON specimenreplicate  (datasource_id);
4916

  
4917

  
4918
--
4912 4919
-- Name: fki_specimenreplicate_museum_id; Type: INDEX; Schema: public; Owner: -; Tablespace: 
4913 4920
--
4914 4921

  
......
4919 4926
-- Name: fki_specimenreplicate_reference_id_fkey; Type: INDEX; Schema: public; Owner: -; Tablespace: 
4920 4927
--
4921 4928

  
4922
CREATE INDEX fki_specimenreplicate_reference_id_fkey ON specimenreplicate  (reference_id);
4929
CREATE INDEX fki_specimenreplicate_reference_id_fkey ON specimenreplicate  (datasource_id);
4923 4930

  
4924 4931

  
4925 4932
--
......
6497 6504

  
6498 6505

  
6499 6506
--
6500
-- Name: specimenreplicate_museum_id; Type: FK CONSTRAINT; Schema: public; Owner: -
6507
-- Name: specimenreplicate_datasource_id; Type: FK CONSTRAINT; Schema: public; Owner: -
6501 6508
--
6502 6509

  
6503 6510

  
6504 6511

  
6505 6512

  
6506 6513
--
6507
-- Name: specimenreplicate_reference_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: -
6514
-- Name: specimenreplicate_museum_id; Type: FK CONSTRAINT; Schema: public; Owner: -
6508 6515
--
6509 6516

  
6510 6517

  
schemas/vegbien.sql
2593 2593

  
2594 2594
CREATE TABLE specimenreplicate (
2595 2595
    specimenreplicate_id integer NOT NULL,
2596
    reference_id integer NOT NULL,
2596
    datasource_id integer NOT NULL,
2597 2597
    collectioncode_dwc text,
2598 2598
    catalognumber_dwc text,
2599 2599
    collectiondate timestamp with time zone,
......
4658 4658
--
4659 4659

  
4660 4660
ALTER TABLE ONLY specimenreplicate
4661
    ADD CONSTRAINT specimenreplicate_keys_accessioncode UNIQUE (reference_id, collectioncode_dwc, sourceaccessioncode);
4661
    ADD CONSTRAINT specimenreplicate_keys_accessioncode UNIQUE (datasource_id, collectioncode_dwc, sourceaccessioncode);
4662 4662

  
4663 4663

  
4664 4664
--
......
4666 4666
--
4667 4667

  
4668 4668
ALTER TABLE ONLY specimenreplicate
4669
    ADD CONSTRAINT specimenreplicate_keys_catalognumber UNIQUE (reference_id, collectioncode_dwc, catalognumber_dwc);
4669
    ADD CONSTRAINT specimenreplicate_keys_catalognumber UNIQUE (datasource_id, collectioncode_dwc, catalognumber_dwc);
4670 4670

  
4671 4671

  
4672 4672
--
......
4674 4674
--
4675 4675

  
4676 4676
ALTER TABLE ONLY specimenreplicate
4677
    ADD CONSTRAINT specimenreplicate_keys_collectionnumber UNIQUE (reference_id, collectioncode_dwc, collectionnumber);
4677
    ADD CONSTRAINT specimenreplicate_keys_collectionnumber UNIQUE (datasource_id, collectioncode_dwc, collectionnumber);
4678 4678

  
4679 4679

  
4680 4680
--
......
5355 5355

  
5356 5356

  
5357 5357
--
5358
-- Name: fki_specimenreplicate_datasource_id; Type: INDEX; Schema: public; Owner: -; Tablespace: 
5359
--
5360

  
5361
CREATE INDEX fki_specimenreplicate_datasource_id ON specimenreplicate USING btree (datasource_id);
5362

  
5363

  
5364
--
5358 5365
-- Name: fki_specimenreplicate_museum_id; Type: INDEX; Schema: public; Owner: -; Tablespace: 
5359 5366
--
5360 5367

  
......
5365 5372
-- Name: fki_specimenreplicate_reference_id_fkey; Type: INDEX; Schema: public; Owner: -; Tablespace: 
5366 5373
--
5367 5374

  
5368
CREATE INDEX fki_specimenreplicate_reference_id_fkey ON specimenreplicate USING btree (reference_id);
5375
CREATE INDEX fki_specimenreplicate_reference_id_fkey ON specimenreplicate USING btree (datasource_id);
5369 5376

  
5370 5377

  
5371 5378
--
......
6967 6974

  
6968 6975

  
6969 6976
--
6970
-- Name: specimenreplicate_museum_id; Type: FK CONSTRAINT; Schema: public; Owner: -
6977
-- Name: specimenreplicate_datasource_id; Type: FK CONSTRAINT; Schema: public; Owner: -
6971 6978
--
6972 6979

  
6973 6980
ALTER TABLE ONLY specimenreplicate
6974
    ADD CONSTRAINT specimenreplicate_museum_id FOREIGN KEY (museum_id) REFERENCES party(party_id) ON UPDATE CASCADE ON DELETE CASCADE;
6981
    ADD CONSTRAINT specimenreplicate_datasource_id FOREIGN KEY (datasource_id) REFERENCES party(party_id) ON UPDATE CASCADE ON DELETE CASCADE;
6975 6982

  
6976 6983

  
6977 6984
--
6978
-- Name: specimenreplicate_reference_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: -
6985
-- Name: specimenreplicate_museum_id; Type: FK CONSTRAINT; Schema: public; Owner: -
6979 6986
--
6980 6987

  
6981 6988
ALTER TABLE ONLY specimenreplicate
6982
    ADD CONSTRAINT specimenreplicate_reference_id_fkey FOREIGN KEY (reference_id) REFERENCES reference(reference_id) ON UPDATE CASCADE ON DELETE CASCADE;
6989
    ADD CONSTRAINT specimenreplicate_museum_id FOREIGN KEY (museum_id) REFERENCES party(party_id) ON UPDATE CASCADE ON DELETE CASCADE;
6983 6990

  
6984 6991

  
6985 6992
--
mappings/VegX-VegBIEN.organisms.csv
90 90
/simpleUserdefined[name=growthForm]/value,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=growthForm]]:[@fkey=tableRecord_ID]/definedvalue",
91 91
/simpleUserdefined[name=individualCode]/value,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=individualCode]]:[@fkey=tableRecord_ID]/definedvalue",
92 92
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=collector]/groupType","/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=voucherType]]:[@fkey=tableRecord_ID]/definedvalue",
93
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName,/specimenreplicate:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/*_id/reference/shortname/_alt/1,
94
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/authorCode,/specimenreplicate:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,
95
/simpleUserdefined[name=collectionDate]/value,/specimenreplicate:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/collectiondate,
96
/simpleUserdefined[name=collectionDate]/value/_*/date,/specimenreplicate:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/collectiondate/_*/date,
93
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/authorCode,/specimenreplicate:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,
94
/simpleUserdefined[name=collectionDate]/value,/specimenreplicate:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectiondate,
95
/simpleUserdefined[name=collectionDate]/value/_*/date,/specimenreplicate:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectiondate/_*/date,
96
/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName,/specimenreplicate:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1,
97 97
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=auth])/Name","/taxondetermination[*_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Authority]:[determinationtype=""Computer (automated)"",iscurrent=true]/*_id/plantconcept/*_id/*/plantname",
98 98
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=fam])/Name","/taxondetermination[*_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Family]:[determinationtype=""Computer (automated)"",iscurrent=true]/*_id/plantconcept/*_id/*/plantname",
99 99
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=gen])/Name","/taxondetermination[*_id/role/rolecode=computer,*_id/plantconcept/plantstatus/plantlevel=Genus]:[determinationtype=""Computer (automated)"",iscurrent=true]/*_id/plantconcept/*_id/*/plantname",
mappings/for_review/VegX-VegBIEN.organisms.csv
90 90
/simpleUserdefined[name=growthForm]/value,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=growthForm]]/definedvalue",
91 91
/simpleUserdefined[name=individualCode]/value,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=individualCode]]/definedvalue",
92 92
//*s/taxonDetermination[role=collector]/groupType,"/definedvalue[*_id/userdefined[tablename=taxonoccurrence,userdefinedname=voucherType]]/definedvalue",
93
//party/organizationName,//reference/shortname/_alt/1,
94 93
//taxonNameUsageConcept/authorCode,//specimenreplicate/catalognumber_dwc,
95 94
/simpleUserdefined[name=collectionDate]/value,//specimenreplicate/collectiondate,
96 95
/simpleUserdefined[name=collectionDate]/value/_*/date,//specimenreplicate/collectiondate/_*/date,
96
//party/organizationName,//party/organizationname/_alt/1,
97 97
//*s/taxonConcept[@code=auth]/Name,"/taxondetermination[rolecode=computer,plantlevel=Authority]/*_id/plantconcept/*_id/*/plantname",
98 98
//*s/taxonConcept[@code=fam]/Name,"/taxondetermination[rolecode=computer,plantlevel=Family]/*_id/plantconcept/*_id/*/plantname",
99 99
//*s/taxonConcept[@code=gen]/Name,"/taxondetermination[rolecode=computer,plantlevel=Genus]/*_id/plantconcept/*_id/*/plantname",
mappings/for_review/DwC-VegBIEN.specimens.csv
47 47
"fieldNotes/_merge/2/_label[label=""plant fungus""]/value","/description/_merge/2/_label[label=""plant fungus""]/value",,
48 48
institutionCode,/{museum_id/party/organizationname/_name/first},,11
49 49
collectionCode,"/{museum_id/party/organizationname/_name/last,collectioncode_dwc}",Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
50
bien.datasource,//reference/shortname/_alt/1,,
51 50
catalogNumber,/catalognumber_dwc,"Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
52 51
recordNumber,/collectionnumber/_alt/1,,22
53 52
collectionID,/collectionnumber/_alt/2,,9
54 53
fieldNumber,/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
54
bien.datasource,//party/organizationname/_alt/1,,
55 55
occurrenceID,/sourceaccessioncode,"Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
56 56
acceptedNameUsage,,,135
57 57
acceptedNameUsageID,,,128
mappings/DwC-VegBIEN.specimens.csv
47 47
"fieldNotes/_merge/2/_label[label=""plant fungus""]/value","/description/_merge/2/_label[label=""plant fungus""]/value",,
48 48
institutionCode,/{museum_id/party/organizationname/_name/first},,11
49 49
collectionCode,"/{museum_id/party/organizationname/_name/last,collectioncode_dwc}",Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
50
bien.datasource,:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/*_id/reference/shortname/_alt/1,,
51
catalogNumber,:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,"Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
52
recordNumber,:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1,,22
53
collectionID,:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/2,,9
54
fieldNumber,:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
55
occurrenceID,:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
50
catalogNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,"Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
51
recordNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1,,22
52
collectionID,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/2,,9
53
fieldNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
54
bien.datasource,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1,,
55
occurrenceID,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
56 56
acceptedNameUsage,,,135
57 57
acceptedNameUsageID,,,128
58 58
associatedMedia,,,36

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