Revision 4195
Added by Aaron Marcuse-Kubitza over 12 years ago
| inputs/SALVIAS-CSV/1.organisms/map.csv | ||
|---|---|---|
| 33 | 33 |
specific_authority,computer.scientificNameAuthorship,Brad: This is the author of the scientificName. |
| 34 | 34 |
infra_rank_1,computer.taxonRank, |
| 35 | 35 |
infra_ep_1,computer.infraspecificEpithet, |
| 36 |
cf_aff,identificationQualifier,"Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank."
|
|
| 36 |
cf_aff,verbatimIdentificationQualifier,"Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank."
|
|
| 37 | 37 |
comments,,Brad: OMIT |
| 38 | 38 |
habit,habit,"Brad: This is growth form (tree, shrub, herb, etc.). It is an observation of a trait." |
| 39 | 39 |
no_of_individuals,individualCount,"Brad: This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this." |
| ... | ... | |
| 51 | 51 |
stem_canopy_position,canopyPosition, |
| 52 | 52 |
stem_liana_infestation,lianaInfestation, |
| 53 | 53 |
notes,stemNotes, |
| 54 |
orig_family,family,Brad: OMIT |
|
| 55 |
orig_species,scientificName/_name/last,Brad: OMIT |
|
| 54 |
orig_family,verbatimFamily,Brad: OMIT |
|
| 55 |
orig_species,verbatimSpecificEpithet,Brad: OMIT |
|
| inputs/SALVIAS-CSV/1.organisms/map.full.csv | ||
|---|---|---|
| 13 | 13 |
infra_rank_1,computer.taxonRank, |
| 14 | 14 |
cover_percent,coverPercent, |
| 15 | 15 |
stem_dbh,diameterBreastHeight, |
| 16 |
orig_family,family,Brad: OMIT |
|
| 17 | 16 |
habit,habit,"Brad: This is growth form (tree, shrub, herb, etc.). It is an observation of a trait." |
| 18 | 17 |
stem_height_m,height/_alt/1,"Brad: Same as for height, but applies to individuals stems, not trees. Rare." |
| 19 | 18 |
height_m,height/_alt/2, |
| 20 | 19 |
ht_first_branch_m,heightFirstBranch, |
| 21 | 20 |
stem_height_first_branch_m,heightFirstBranch,"Brad: Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare." |
| 22 |
cf_aff,identificationQualifier,"Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank." |
|
| 23 | 21 |
no_of_individuals,individualCount,"Brad: This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this." |
| 24 | 22 |
OBSERVATION_ID,individualID,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later." |
| 25 | 23 |
stem_liana_infestation,lianaInfestation, |
| ... | ... | |
| 41 | 39 |
coll_lastname,recordedBy.surName,"Brad: This is the collector of a separate specimen which vouchers this tree or species. I worry that vouchers are not properly accommodated in VegX. Again, we need to check with Nick." |
| 42 | 40 |
x_position,relativePlotX,"Brad: These are important, fundamental values of many tree plots" |
| 43 | 41 |
y_position,relativePlotY,Brad: See comment above for x_position |
| 44 |
orig_species,scientificName/_name/last,Brad: OMIT |
|
| 45 | 42 |
notes,stemNotes, |
| 46 | 43 |
tag1,tag/_alt/1,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once." |
| 47 | 44 |
stem_tag1,tag/_alt/2,"Brad: Same as tag1 & tag2, but applied to individual stems. I'm still not clear how to distinguish between methods which tag only individuals trees, and those which tag individual stems." |
| 45 |
orig_family,verbatimFamily,Brad: OMIT |
|
| 46 |
cf_aff,verbatimIdentificationQualifier,"Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank." |
|
| 47 |
orig_species,verbatimSpecificEpithet,Brad: OMIT |
|
| 48 | 48 |
intercept_cm,volumeCanopy,"Brad: This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance." |
| 49 | 49 |
det_type,voucherType,"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." |
| inputs/SALVIAS-CSV/1.organisms/VegBIEN.csv | ||
|---|---|---|
| 37 | 37 |
x_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition,"Brad: These are important, fundamental values of many tree plots" |
| 38 | 38 |
y_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition,Brad: See comment above for x_position |
| 39 | 39 |
individual_code,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2,"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." |
| 40 |
orig_species,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2/_name/last,Brad: OMIT |
|
| 41 | 40 |
habit,"/location/locationevent/taxonoccurrence/growthform/_map:[./{T,Arbol,palm}=tree,./{H,""Hemiepífito""}=hemiepiphyte,./{L,l,""L?"",Liana}=liana,E=epiphyte,S=shrub,Hb=herb,""vine-herbaceous""=vine,graminoid=grass,rosette=forb,*=*]/value","Brad: This is growth form (tree, shrub, herb, etc.). It is an observation of a trait.; According to <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.habit>, <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/SALVIAS#Habit>"
|
| 42 | 41 |
OBSERVATION_ID,/location/locationevent/taxonoccurrence/sourceaccessioncode,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later." |
| 42 |
orig_species,"/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=species]/plantname",Brad: OMIT |
|
| 43 |
orig_family,"/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=family]/plantname",Brad: OMIT |
|
| 44 |
cf_aff,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/taxonfit,"Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank." |
|
| 43 | 45 |
specific_authority,"/location/locationevent/taxonoccurrence/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=authority]/plantname",Brad: This is the author of the scientificName. |
| 44 | 46 |
infra_rank_1,"/location/locationevent/taxonoccurrence/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=subspecies]/plantname/_name/first", |
| 45 | 47 |
infra_ep_1,"/location/locationevent/taxonoccurrence/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=subspecies]/plantname/_name/last", |
| 46 | 48 |
specific_epithet,"/location/locationevent/taxonoccurrence/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=species]/plantname", |
| 47 | 49 |
genus,"/location/locationevent/taxonoccurrence/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=genus]/plantname", |
| 48 | 50 |
family,"/location/locationevent/taxonoccurrence/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=family]/plantname", |
| 49 |
orig_species,"/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[],do=""plantname[rank=_val]/parent_id""]/plantname[rank=binomial]/plantname/_name/last",Brad: OMIT |
|
| 50 |
orig_family,"/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=family]/plantname",Brad: OMIT |
|
| 51 |
cf_aff,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/taxonfit,"Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank." |
|
| 52 | 51 |
coll_firstname,/location/locationevent/taxonoccurrence/verbatimcollectorname/_name/first,Brad: See comment above |
| 53 | 52 |
coll_lastname,/location/locationevent/taxonoccurrence/verbatimcollectorname/_name/last,"Brad: This is the collector of a separate specimen which vouchers this tree or species. I worry that vouchers are not properly accommodated in VegX. Again, we need to check with Nick." |
| 54 | 53 |
det_type,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/cond/_eq:[right=indirect]/left","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." |
| inputs/SALVIAS-CSV/1.organisms/test.xml.ref | ||
|---|---|---|
| 138 | 138 |
</stemobservation> |
| 139 | 139 |
</plantobservation> |
| 140 | 140 |
</aggregateoccurrence> |
| 141 |
<authortaxoncode> |
|
| 142 |
<_alt> |
|
| 143 |
<1>$individual_code</1> |
|
| 144 |
<2><_name><last>$orig_species</last></_name></2> |
|
| 145 |
</_alt> |
|
| 146 |
</authortaxoncode> |
|
| 141 |
<authortaxoncode>$individual_code</authortaxoncode> |
|
| 147 | 142 |
<growthform> |
| 148 | 143 |
<_map> |
| 149 | 144 |
<T>tree</T> |
| ... | ... | |
| 167 | 162 |
</growthform> |
| 168 | 163 |
<sourceaccessioncode>$OBSERVATION_ID</sourceaccessioncode> |
| 169 | 164 |
<taxondetermination> |
| 170 |
<role>computer</role>
|
|
| 165 |
<isoriginal>true</isoriginal>
|
|
| 171 | 166 |
<plantconcept_id> |
| 172 | 167 |
<plantconcept> |
| 173 | 168 |
<plantname_id> |
| ... | ... | |
| 180 | 175 |
<parent_id> |
| 181 | 176 |
<plantname> |
| 182 | 177 |
<rank>authority</rank> |
| 183 |
<plantname>$specific_authority</plantname> |
|
| 184 | 178 |
<parent_id> |
| 185 | 179 |
<plantname> |
| 186 | 180 |
<rank>subspecies</rank> |
| 187 |
<plantname> |
|
| 188 |
<_name> |
|
| 189 |
<first>$infra_rank_1</first> |
|
| 190 |
<last>$infra_ep_1</last> |
|
| 191 |
</_name> |
|
| 192 |
</plantname> |
|
| 193 | 181 |
<parent_id> |
| 194 | 182 |
<plantname> |
| 195 | 183 |
<rank>species</rank> |
| 196 |
<plantname>$specific_epithet</plantname>
|
|
| 184 |
<plantname>$orig_species</plantname>
|
|
| 197 | 185 |
<parent_id> |
| 198 | 186 |
<plantname> |
| 199 | 187 |
<rank>genus</rank> |
| 200 |
<plantname>$genus</plantname> |
|
| 201 | 188 |
<parent_id> |
| 202 | 189 |
<plantname> |
| 203 | 190 |
<rank>family</rank> |
| 204 |
<plantname>$family</plantname> |
|
| 191 |
<plantname>$orig_family</plantname>
|
|
| 205 | 192 |
</plantname> |
| 206 | 193 |
</parent_id> |
| 207 | 194 |
</plantname> |
| ... | ... | |
| 218 | 205 |
</plantname_id> |
| 219 | 206 |
</plantconcept> |
| 220 | 207 |
</plantconcept_id> |
| 208 |
<taxonfit>$cf_aff</taxonfit> |
|
| 221 | 209 |
</taxondetermination> |
| 222 | 210 |
<taxondetermination> |
| 223 |
<role>identifier</role>
|
|
| 211 |
<role>computer</role>
|
|
| 224 | 212 |
<plantconcept_id> |
| 225 | 213 |
<plantconcept> |
| 226 | 214 |
<plantname_id> |
| ... | ... | |
| 230 | 218 |
<path> |
| 231 | 219 |
<plantname> |
| 232 | 220 |
<rank>binomial</rank> |
| 233 |
<plantname><_name><last>$orig_species</last></_name></plantname> |
|
| 234 | 221 |
<parent_id> |
| 235 | 222 |
<plantname> |
| 236 | 223 |
<rank>authority</rank> |
| 224 |
<plantname>$specific_authority</plantname> |
|
| 237 | 225 |
<parent_id> |
| 238 | 226 |
<plantname> |
| 239 | 227 |
<rank>subspecies</rank> |
| 228 |
<plantname> |
|
| 229 |
<_name> |
|
| 230 |
<first>$infra_rank_1</first> |
|
| 231 |
<last>$infra_ep_1</last> |
|
| 232 |
</_name> |
|
| 233 |
</plantname> |
|
| 240 | 234 |
<parent_id> |
| 241 | 235 |
<plantname> |
| 242 | 236 |
<rank>species</rank> |
| 237 |
<plantname>$specific_epithet</plantname> |
|
| 243 | 238 |
<parent_id> |
| 244 | 239 |
<plantname> |
| 245 | 240 |
<rank>genus</rank> |
| 241 |
<plantname>$genus</plantname> |
|
| 246 | 242 |
<parent_id> |
| 247 | 243 |
<plantname> |
| 248 | 244 |
<rank>family</rank> |
| 249 |
<plantname>$orig_family</plantname>
|
|
| 245 |
<plantname>$family</plantname> |
|
| 250 | 246 |
</plantname> |
| 251 | 247 |
</parent_id> |
| 252 | 248 |
</plantname> |
| ... | ... | |
| 263 | 259 |
</plantname_id> |
| 264 | 260 |
</plantconcept> |
| 265 | 261 |
</plantconcept_id> |
| 266 |
<taxonfit>$cf_aff</taxonfit> |
|
| 267 | 262 |
</taxondetermination> |
| 268 | 263 |
<verbatimcollectorname> |
| 269 | 264 |
<_name> |
| inputs/SALVIAS/1.organisms/map.csv | ||
|---|---|---|
| 52 | 52 |
NoInd,individualCount,"Brad: This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this." |
| 53 | 53 |
cover_percent,coverPercent, |
| 54 | 54 |
intercept_cm,volumeCanopy,"Brad: This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance." |
| 55 |
cfaff,identificationQualifier,"Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank."
|
|
| 55 |
cfaff,verbatimIdentificationQualifier,"Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank."
|
|
| 56 | 56 |
other_annotations,, |
| 57 | 57 |
morphocf,, |
| 58 | 58 |
IsMorpho,, |
| 59 |
OrigFamily,family,Brad: OMIT
|
|
| 60 |
OrigGenus,scientificName/_name/first,
|
|
| 61 |
OrigSpecies,scientificName/_name/last,Brad: OMIT
|
|
| 59 |
OrigFamily,verbatimFamily,Brad: OMIT
|
|
| 60 |
OrigGenus,verbatimGenus,
|
|
| 61 |
OrigSpecies,verbatimSpecificEpithet,Brad: OMIT
|
|
| 62 | 62 |
OrigAuth,, |
| 63 | 63 |
phenology,, |
| 64 | 64 |
canopy_position,canopyPosition, |
| inputs/SALVIAS/1.organisms/map.full.csv | ||
|---|---|---|
| 21 | 21 |
GROUP BY ""PlotID"", ""Line"" |
| 22 | 22 |
HAVING count(DISTINCT census_date) > 1 |
| 23 | 23 |
-----" |
| 24 |
OrigFamily,family,Brad: OMIT |
|
| 25 | 24 |
Notes,fieldNotes, |
| 26 | 25 |
height_m,height, |
| 27 | 26 |
ht_first_branch_m,heightFirstBranch, |
| 28 |
cfaff,identificationQualifier,"Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank." |
|
| 29 | 27 |
NoInd,individualCount,"Brad: This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this." |
| 30 | 28 |
PlotObsID,individualID,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later." |
| 31 | 29 |
liana_infestation,lianaInfestation, |
| ... | ... | |
| 38 | 36 |
coll_lastname,recordedBy.surName,"Brad: This is the collector of a separate specimen which vouchers this tree or species. I worry that vouchers are not properly accommodated in VegX. Again, we need to check with Nick." |
| 39 | 37 |
x_position,relativePlotX,"Brad: These are important, fundamental values of many tree plots" |
| 40 | 38 |
y_position,relativePlotY,Brad: See comment above for x_position |
| 41 |
OrigGenus,scientificName/_name/first, |
|
| 42 |
OrigSpecies,scientificName/_name/last,Brad: OMIT |
|
| 43 | 39 |
tag1,tag,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once." |
| 40 |
OrigFamily,verbatimFamily,Brad: OMIT |
|
| 41 |
OrigGenus,verbatimGenus, |
|
| 42 |
cfaff,verbatimIdentificationQualifier,"Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank." |
|
| 43 |
OrigSpecies,verbatimSpecificEpithet,Brad: OMIT |
|
| 44 | 44 |
intercept_cm,volumeCanopy,"Brad: This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance." |
| 45 | 45 |
DetType,voucherType,"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." |
| inputs/SALVIAS/1.organisms/VegBIEN.csv | ||
|---|---|---|
| 40 | 40 |
x_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition,"Brad: These are important, fundamental values of many tree plots" |
| 41 | 41 |
y_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition,Brad: See comment above for x_position |
| 42 | 42 |
Ind,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2,"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." |
| 43 |
OrigGenus,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2/_name/first, |
|
| 44 |
OrigSpecies,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2/_name/last,Brad: OMIT |
|
| 45 | 43 |
Habit,"/location/locationevent/taxonoccurrence/growthform/_map:[./{T,Arbol,palm}=tree,./{H,""Hemiepífito""}=hemiepiphyte,./{L,l,""L?"",Liana}=liana,E=epiphyte,S=shrub,Hb=herb,""vine-herbaceous""=vine,graminoid=grass,rosette=forb,*=*]/value","Brad: This is growth form (tree, shrub, herb, etc.). It is an observation of a trait.; According to <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.habit>, <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/SALVIAS#Habit>"
|
| 46 | 44 |
PlotObsID,/location/locationevent/taxonoccurrence/sourceaccessioncode,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later." |
| 45 |
OrigSpecies,"/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=species]/plantname",Brad: OMIT |
|
| 46 |
OrigGenus,"/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=genus]/plantname", |
|
| 47 |
OrigFamily,"/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=family]/plantname",Brad: OMIT |
|
| 48 |
cfaff,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/taxonfit,"Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank." |
|
| 47 | 49 |
auth,"/location/locationevent/taxonoccurrence/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=authority]/plantname",Brad: This is the author of the scientificName. |
| 48 | 50 |
infra_rank_1,"/location/locationevent/taxonoccurrence/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=subspecies]/plantname/_name/first", |
| 49 | 51 |
infra_ep_1,"/location/locationevent/taxonoccurrence/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=subspecies]/plantname/_name/last", |
| 50 | 52 |
Species,"/location/locationevent/taxonoccurrence/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=species]/plantname", |
| 51 | 53 |
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=genus]/plantname", |
| 52 | 54 |
Family,"/location/locationevent/taxonoccurrence/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=family]/plantname", |
| 53 |
OrigGenus,"/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[],do=""plantname[rank=_val]/parent_id""]/plantname[rank=binomial]/plantname/_name/first", |
|
| 54 |
OrigSpecies,"/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[],do=""plantname[rank=_val]/parent_id""]/plantname[rank=binomial]/plantname/_name/last",Brad: OMIT |
|
| 55 |
OrigFamily,"/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=family]/plantname",Brad: OMIT |
|
| 56 |
cfaff,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/taxonfit,"Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank." |
|
| 57 | 55 |
coll_firstname,/location/locationevent/taxonoccurrence/verbatimcollectorname/_name/first,Brad: See comment above |
| 58 | 56 |
coll_lastname,/location/locationevent/taxonoccurrence/verbatimcollectorname/_name/last,"Brad: This is the collector of a separate specimen which vouchers this tree or species. I worry that vouchers are not properly accommodated in VegX. Again, we need to check with Nick." |
| 59 | 57 |
DetType,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/cond/_eq:[right=indirect]/left","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." |
| inputs/SALVIAS/1.organisms/test.xml.ref | ||
|---|---|---|
| 110 | 110 |
</stemobservation> |
| 111 | 111 |
</plantobservation> |
| 112 | 112 |
</aggregateoccurrence> |
| 113 |
<authortaxoncode> |
|
| 114 |
<_alt> |
|
| 115 |
<1>$Ind</1> |
|
| 116 |
<2> |
|
| 117 |
<_name> |
|
| 118 |
<first>$OrigGenus</first> |
|
| 119 |
<last>$OrigSpecies</last> |
|
| 120 |
</_name> |
|
| 121 |
</2> |
|
| 122 |
</_alt> |
|
| 123 |
</authortaxoncode> |
|
| 113 |
<authortaxoncode>$Ind</authortaxoncode> |
|
| 124 | 114 |
<growthform> |
| 125 | 115 |
<_map> |
| 126 | 116 |
<T>tree</T> |
| ... | ... | |
| 144 | 134 |
</growthform> |
| 145 | 135 |
<sourceaccessioncode>$PlotObsID</sourceaccessioncode> |
| 146 | 136 |
<taxondetermination> |
| 147 |
<role>computer</role>
|
|
| 137 |
<isoriginal>true</isoriginal>
|
|
| 148 | 138 |
<plantconcept_id> |
| 149 | 139 |
<plantconcept> |
| 150 | 140 |
<plantname_id> |
| ... | ... | |
| 157 | 147 |
<parent_id> |
| 158 | 148 |
<plantname> |
| 159 | 149 |
<rank>authority</rank> |
| 160 |
<plantname>$auth</plantname> |
|
| 161 | 150 |
<parent_id> |
| 162 | 151 |
<plantname> |
| 163 | 152 |
<rank>subspecies</rank> |
| 164 |
<plantname> |
|
| 165 |
<_name> |
|
| 166 |
<first>$infra_rank_1</first> |
|
| 167 |
<last>$infra_ep_1</last> |
|
| 168 |
</_name> |
|
| 169 |
</plantname> |
|
| 170 | 153 |
<parent_id> |
| 171 | 154 |
<plantname> |
| 172 | 155 |
<rank>species</rank> |
| 173 |
<plantname>$Species</plantname> |
|
| 156 |
<plantname>$OrigSpecies</plantname>
|
|
| 174 | 157 |
<parent_id> |
| 175 | 158 |
<plantname> |
| 176 | 159 |
<rank>genus</rank> |
| 177 |
<plantname>$Genus</plantname> |
|
| 160 |
<plantname>$OrigGenus</plantname>
|
|
| 178 | 161 |
<parent_id> |
| 179 | 162 |
<plantname> |
| 180 | 163 |
<rank>family</rank> |
| 181 |
<plantname>$Family</plantname> |
|
| 164 |
<plantname>$OrigFamily</plantname>
|
|
| 182 | 165 |
</plantname> |
| 183 | 166 |
</parent_id> |
| 184 | 167 |
</plantname> |
| ... | ... | |
| 195 | 178 |
</plantname_id> |
| 196 | 179 |
</plantconcept> |
| 197 | 180 |
</plantconcept_id> |
| 181 |
<taxonfit>$cfaff</taxonfit> |
|
| 198 | 182 |
</taxondetermination> |
| 199 | 183 |
<taxondetermination> |
| 200 |
<role>identifier</role>
|
|
| 184 |
<role>computer</role>
|
|
| 201 | 185 |
<plantconcept_id> |
| 202 | 186 |
<plantconcept> |
| 203 | 187 |
<plantname_id> |
| ... | ... | |
| 207 | 191 |
<path> |
| 208 | 192 |
<plantname> |
| 209 | 193 |
<rank>binomial</rank> |
| 210 |
<plantname> |
|
| 211 |
<_name> |
|
| 212 |
<first>$OrigGenus</first> |
|
| 213 |
<last>$OrigSpecies</last> |
|
| 214 |
</_name> |
|
| 215 |
</plantname> |
|
| 216 | 194 |
<parent_id> |
| 217 | 195 |
<plantname> |
| 218 | 196 |
<rank>authority</rank> |
| 197 |
<plantname>$auth</plantname> |
|
| 219 | 198 |
<parent_id> |
| 220 | 199 |
<plantname> |
| 221 | 200 |
<rank>subspecies</rank> |
| 201 |
<plantname> |
|
| 202 |
<_name> |
|
| 203 |
<first>$infra_rank_1</first> |
|
| 204 |
<last>$infra_ep_1</last> |
|
| 205 |
</_name> |
|
| 206 |
</plantname> |
|
| 222 | 207 |
<parent_id> |
| 223 | 208 |
<plantname> |
| 224 | 209 |
<rank>species</rank> |
| 210 |
<plantname>$Species</plantname> |
|
| 225 | 211 |
<parent_id> |
| 226 | 212 |
<plantname> |
| 227 | 213 |
<rank>genus</rank> |
| 214 |
<plantname>$Genus</plantname> |
|
| 228 | 215 |
<parent_id> |
| 229 | 216 |
<plantname> |
| 230 | 217 |
<rank>family</rank> |
| 231 |
<plantname>$OrigFamily</plantname>
|
|
| 218 |
<plantname>$Family</plantname> |
|
| 232 | 219 |
</plantname> |
| 233 | 220 |
</parent_id> |
| 234 | 221 |
</plantname> |
| ... | ... | |
| 245 | 232 |
</plantname_id> |
| 246 | 233 |
</plantconcept> |
| 247 | 234 |
</plantconcept_id> |
| 248 |
<taxonfit>$cfaff</taxonfit> |
|
| 249 | 235 |
</taxondetermination> |
| 250 | 236 |
<verbatimcollectorname> |
| 251 | 237 |
<_name> |
| ... | ... | |
| 285 | 271 |
</parent_id> |
| 286 | 272 |
</location> |
| 287 | 273 |
</VegBIEN> |
| 288 |
Inserted 44 new rows into database |
|
| 274 |
Inserted 42 new rows into database |
|
Also available in: Unified diff
inputs/SALVIAS*/1.organisms/map.csv: Remapped OrigFamily/OrigGenus/OrigSpecies to new verbatim* taxonomic names. Also remapped cfaff to verbatimIdentificationQualifier, because it was previously mapped to the same taxondetermination as the Orig* terms, but this will later need to be remapped to identificationQualifier (not in this commit because that is a separate change). Note that the switch to the verbatim* taxonomic names removes a concatenated binomial that was part of the previous mappings, which put OrigGenus and OrigSpecies together into one scientificName.