Revision 6035
Added by Aaron Marcuse-Kubitza about 12 years ago
| inputs/.geoscrub/geoscrub_cleaned_unique/new_terms.csv | ||
|---|---|---|
| 30 | 30 |
isCultivatedReason,OMIT,,Not geoscrub-related |
| 31 | 31 |
countryStd,acceptedCountry,, |
| 32 | 32 |
stateProvinceStd,acceptedStateProvince,, |
| 33 |
isNewWorld,OMIT,,Not geoscrub-related |
|
| 34 | 33 |
geoscrubID_idx_index,OMIT,,Placeholder column created by MySQL to PostgreSQL translation |
| 35 | 34 |
sourceTable_idx_index,OMIT,,Placeholder column created by MySQL to PostgreSQL translation |
| 36 | 35 |
sourceID_idx_index,OMIT,,Placeholder column created by MySQL to PostgreSQL translation |
| inputs/ACAD/Specimen/VegBIEN.csv | ||
|---|---|---|
| 52 | 52 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
| 53 | 53 |
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2, |
| 54 | 54 |
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/2, |
| 55 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/3/_if[@name=""if has taxonomic name""]/cond/_has_taxonomic_name/rank", |
|
| 56 | 55 |
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author, |
| 57 | 56 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
| 58 | 57 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
| inputs/.NCBI/nodes/VegBIEN.csv | ||
|---|---|---|
| 10 | 10 |
rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank", |
| 11 | 11 |
name_txt,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/then", |
| 12 | 12 |
rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
| 13 |
rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/3/_if[@name=""if has taxonomic name""]/cond/_has_taxonomic_name/rank", |
|
| 14 |
name_txt,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/3/_if[@name=""if has taxonomic name""]/then", |
|
| 13 |
name_txt,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/3, |
|
| 15 | 14 |
rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank, |
| 16 | 15 |
4,,** No join mapping for *4 ** |
| 17 | 16 |
5,,** No join mapping for *5 ** |
| inputs/.NCBI/nodes/test.xml.ref | ||
|---|---|---|
| 25 | 25 |
<then>$name_txt</then> |
| 26 | 26 |
</_if> |
| 27 | 27 |
</taxonepithet> |
| 28 |
<taxonomicname> |
|
| 29 |
<_if name="if has taxonomic name"> |
|
| 30 |
<cond><_has_taxonomic_name><rank>$rank</rank></_has_taxonomic_name></cond> |
|
| 31 |
<then>$name_txt</then> |
|
| 32 |
</_if> |
|
| 33 |
</taxonomicname> |
|
| 28 |
<taxonomicname>$name_txt</taxonomicname> |
|
| 34 | 29 |
</taxonlabel> |
| 35 | 30 |
</taxonlabel_id> |
| 36 | 31 |
<verbatimrank>$rank</verbatimrank> |
| inputs/SALVIAS/plotObservations/VegBIEN.csv | ||
|---|---|---|
| 107 | 107 |
infra_rank_1,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
| 108 | 108 |
infra_ep_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2, |
| 109 | 109 |
auth,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/2,Brad: This is the author of the scientificName. |
| 110 |
infra_rank_1,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/3/_if[@name=""if has taxonomic name""]/cond/_has_taxonomic_name/rank", |
|
| 111 | 110 |
auth,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author,Brad: This is the author of the scientificName. |
| 112 | 111 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
| 113 | 112 |
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
| inputs/UNCC/Specimen/VegBIEN.csv | ||
|---|---|---|
| 74 | 74 |
infrarank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then/_alt/2", |
| 75 | 75 |
infraname,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2, |
| 76 | 76 |
authors,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/2, |
| 77 |
usdaRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/3/_if[@name=""if has taxonomic name""]/cond/_has_taxonomic_name/rank/_alt/1", |
|
| 78 |
infrarank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/3/_if[@name=""if has taxonomic name""]/cond/_has_taxonomic_name/rank/_alt/2", |
|
| 79 | 77 |
authors,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author, |
| 80 | 78 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
| 81 | 79 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
| inputs/SALVIAS-CSV/Organism/VegBIEN.csv | ||
|---|---|---|
| 114 | 114 |
infra_rank_1,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
| 115 | 115 |
infra_ep_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2, |
| 116 | 116 |
specific_authority,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/2,Brad: This is the author of the scientificName. |
| 117 |
infra_rank_1,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/3/_if[@name=""if has taxonomic name""]/cond/_has_taxonomic_name/rank", |
|
| 118 | 117 |
specific_authority,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author,Brad: This is the author of the scientificName. |
| 119 | 118 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
| 120 | 119 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
| inputs/.TNRS/tnrs_other/VegBIEN.csv | ||
|---|---|---|
| 54 | 54 |
Name_matched_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
| 55 | 55 |
Infraspecific_epithet_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2, |
| 56 | 56 |
Name_matched_author,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/2,Contains author based on matched name |
| 57 |
Name_matched_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/3/_if[@name=""if has taxonomic name""]/cond/_has_taxonomic_name/rank", |
|
| 58 | 57 |
Taxonomic_status,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonstatus, |
| 59 | 58 |
Name_matched_author,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author,Contains author based on matched name |
| 60 | 59 |
Name_matched_accepted_family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family,Contains family based on matched name |
| inputs/.TNRS/tnrs_accepted/VegBIEN.csv | ||
|---|---|---|
| 57 | 57 |
Name_matched_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
| 58 | 58 |
Infraspecific_epithet_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2, |
| 59 | 59 |
Name_matched_author,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/2,Contains author based on matched name |
| 60 |
Name_matched_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/3/_if[@name=""if has taxonomic name""]/cond/_has_taxonomic_name/rank", |
|
| 61 | 60 |
Taxonomic_status,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonstatus, |
| 62 | 61 |
Name_matched_author,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author,Contains author based on matched name |
| 63 | 62 |
Name_matched_accepted_family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family,Contains family based on matched name |
| inputs/QMOR/Specimen/VegBIEN.csv | ||
|---|---|---|
| 55 | 55 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
| 56 | 56 |
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2, |
| 57 | 57 |
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/2, |
| 58 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/3/_if[@name=""if has taxonomic name""]/cond/_has_taxonomic_name/rank", |
|
| 59 | 58 |
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author, |
| 60 | 59 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
| 61 | 60 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
| mappings/VegCore-VegBIEN.csv | ||
|---|---|---|
| 235 | 235 |
forma,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/7/_join_words:[1=""fm. ""]/2", |
| 236 | 236 |
cultivar,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/8/_join_words:[1=""cult. ""]/2", |
| 237 | 237 |
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/2, |
| 238 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/3/_if[@name=""if has taxonomic name""]/cond/_has_taxonomic_name/rank", |
|
| 239 |
taxonNameOrEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/3/_if[@name=""if has taxonomic name""]/then", |
|
| 238 |
taxonNameOrEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/3, |
|
| 240 | 239 |
taxonomicStatus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonstatus, |
| 241 | 240 |
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author, |
| 242 | 241 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
| mappings/for_review/VegCore-VegBIEN.csv | ||
|---|---|---|
| 235 | 235 |
forma,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname, |
| 236 | 236 |
cultivar,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname, |
| 237 | 237 |
scientificNameAuthorship,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname, |
| 238 |
taxonRank,"//taxonlabel/taxonomicname/_if[@name=""if has taxonomic name""]/cond", |
|
| 239 |
taxonNameOrEpithet,"//taxonlabel/taxonomicname/_if[@name=""if has taxonomic name""]/then", |
|
| 238 |
taxonNameOrEpithet,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname, |
|
| 240 | 239 |
taxonomicStatus,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/taxonstatus, |
| 241 | 240 |
scientificNameAuthorship,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/author, |
| 242 | 241 |
family,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/family, |
Also available in: Unified diff
mappings/VegCore-VegBIEN.csv: Always map taxonNameOrEpithet to taxonomicname, now that it's globally unique at all ranks in the datasource that provides it (NCBI)