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File formats for uploading data
Taxonomy is uploaded from a tab-separated CSV table with as many columns as needed. First line is the header. The first N columns must be the taxonomic ranks in hierarchical order from left to right, up to species. In the species column, the taxon name must be fully qualified (including all infraranks and respective authors).
After taxonomic columns, any number of columns specifying the native status of the species in each territory of interest may be appended. The headers of these are of the form territory:lu, territory:hs, etc. The acronym following the : will be the short name of each territory. Territories need not have been created before. These columns may be filled with any one of NATIVE, ENDEMIC, EXOTIC, NEAR_ENDEMIC, ASSUMED_NATIVE, DOUBTFULLY_NATIVE, NATIVE_REINTRODUCED, CRYPTOGENIC, DOUBTFULLY_EXOTIC, ASSUMED_EXOTIC, EXOTIC_REINTRODUCED, EXISTS, or may be left blank, in case the species does not occur in the given territory. Note: ENDEMIC is not a native status, it is accepted here just for convenience. Check the explanation of the native status.
Example table:
| order | family | species | territory:lu | territory:az | territory:ma | territory:ib |
|---|---|---|---|---|---|---|
| Alismatales | Alismataceae | Baldellia repens (Lam.) Ooststr. ex Lawalr subsp. baetica Talavera & Casimiro-Soriguer | NATIVE | NATIVE | ||
| Dipsacales | Valerianaceae | Valerianella dentata (L.) Pollich f. dentata | NATIVE | NATIVE | NATIVE | |
| Dipsacales | Valerianaceae | Valerianella multidentata Loscos & J.Pardo | NATIVE | ENDEMIC |
Occurrence records are uploaded from a tab-separated CSV table with as many columns as needed. First line is the header. All columns are optional.
These pertain to the inventory, i.e. a list of taxon observations. Taxon observations are grouped in the same inventory if they have the same code OR, if code is missing, if they have the same coordinates, same date and same observers.
| Field name | Description | ||
|---|---|---|---|
| only one of | ⁕ | latitude | The latitude of the inventory, in decimal degrees (e.g. 37.54778) or DMS (e.g. 37º26'13.4'' N) |
| longitude | The longitude of the inventory, in decimal degrees (e.g. 37.54778 -8.34667) or DMS (e.g. 7º12'56.3'' W) |
||
| ⁕ | coordinates | The complete coordinates of the inventory in the form latitude, longitude. e.g. 37.54778 -8.34667
|
|
| ⁕ | wkt_geom | The geographical expression of the inventory, in WKT format. Currently only pointz is supported. | |
| ⁕ | x | The X coordinate (easting), in UTM WGS84. This assumes the UTM zone 29 | |
| y | The Y coordinate (northing), in UTM WGS84. This assumes the UTM zone 29 | ||
| ⁕ | mgrs | The UTM square in [MGRS format](https://en.wikipedia.org/wiki/Military_Grid_Reference_System), e.g. 29T NG3486
|
|
| elevation | The altitude | ||
| taxa | The list of taxa observed in this inventory. This can be a single taxon or a list of taxa separated by +. e.g. cistus ladanifer+cistus crispus. If a list of taxa is used, taxa with doubtful identification can be suffixed with ? and those in flower suffixed by #, e.g. lavandula multifida#+sideritis hirsuta?. If, otherwise, taxon-level fields are to be used, then specify one taxon per line. |
||
| only one of | ⁕ | date | The date of the inventory. This can be a precise date e.g. 12-9-2007 or a vague date using question marks e.g. 23-5-?
|
| ⁕ | year ano | The year. | |
| month | The month. | ||
| day | The day. | ||
| precision | The precision of the coordinates. This can be a single number (e.g. 1km), which denotes a radius around the given coordinate, or a square (e.g. 500x500m), which denotes the size of the UTM square where the point is located. |
||
| locality | The description of the locality. | ||
| municipality | The municipality of the locality. | ||
| province | The province of the locality. | ||
| county | The county of the locality. | ||
| project | The acronym of the project where this inventory was conducted. | ||
| code código inventário | The short code of the inventory. All records with the same value in this field will be merged in the same inventory. | ||
| habitat | The habitat applicable to all taxa in this inventory. | ||
| threats | The threats applicable to all taxa in this inventory. | ||
| observers | The observers, as a comma-separated list of person names. | ||
| collectors | The collectors, as a comma-separated list of person names. | ||
| determiners | The determiners, as a comma-separated list of person names. | ||
These pertain to each of the observations within an inventory. Note that each observation may have its own geographical coordinates. If these are left blank, the inventory coordinated will be used.
| gpscode | The short code of the GPS point of the occurrence. | ||
| abundance | The estimation of the number of individuals present of this taxon. Can be a number or an interval (e.g.1200-1600). Not to be confused with coverIndex. |
||
| coverIndex | The cover of this taxon, as text. Can be written in any user-defined scale. | ||
| typeofestimate | The type of estimation for the number of individuals. One of: e Numerical estimate c Exact count g Rough estimate |
||
| comment | Public notes about this occurrence. | ||
| privatenote privateComment | Private notes about this occurrence. | ||
| phenostate | The phenological state of this taxon. One of: f Flower d Dispersion fd Flower+Dispersion v Vegetative r Resting c Immature fruit fc Flower+Immature fruit |
||
| confidence | The confidence in the identification by the observers. One of: c Quite certain a Almost sure d Doubtful |
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| naturalization | If this specimen is wild, cultivated or escaped from culture. One of: w Wild e Escaped c Cultivated |
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| excludeReason | If this occurrence is to be excluded from analyses, for what reason. One of: d Destroyed m Probably misidentified w Wrong coordinates e Escaped from cultivation i Introduced o Other reason |
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| hasphoto | Whether and which photos were taken. One of: s Specimen photo a Threat photo sa Specimen+Threat photo |
||
| hasspecimen | How many specimens were collected, if any. | ||
| only one of | ⁕ | observationlatitude | The latitude of this occurrence, which can be different from the Inventory. In decimal degrees or DMS. |
| observationlongitude | The longitude of this occurrence, which can be different from the Inventory. In decimal degrees or DMS. | ||
| ⁕ | observationcoordinates | The complete coordinates of this occurrence, which can be different from the Inventory. | |
| labeldata | The data written in the label of the herbarium voucher. | ||
| accession codHerbario | The accession code of the herbarium voucher. | ||
| specificthreats | The threats applicable to this taxon only. |