Difference between revisions of "App/specimen/batch load"
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|The verbatim text of the label(s) of the specimen or lot. Identical ''verbatim_labels'' are tied to a single collecting event in mx. Individual lines can be separated with "||", individual labels can be separated with "++". "||" and '++' will be replaced with one and two new lines respectively. | |The verbatim text of the label(s) of the specimen or lot. Identical ''verbatim_labels'' are tied to a single collecting event in mx. Individual lines can be separated with "||", individual labels can be separated with "++". "||" and '++' will be replaced with one and two new lines respectively. | ||
|Must be empty if ce_id is provided. | |Must be empty if ce_id is provided. | ||
+ | |- | ||
+ | |latitude | ||
+ | |A real number in decimal degrees format. | ||
+ | |Must be empty if ce_id is provided. | ||
+ | |- | ||
+ | |longitude | ||
+ | |A real number in decimal degrees format. | ||
+ | |Must be empty if ce_id is provided. | ||
+ | |- | ||
+ | |elev_min | ||
+ | |A real number indicating the minimum elevation of the elevation range. | ||
+ | |Must be empty if ce_id is provided. | ||
+ | |- | ||
+ | |elev_max | ||
+ | |A real number indicating the maximum elevation of the elevation range. | ||
+ | |Must be empty if ce_id is provided. | ||
+ | |- | ||
+ | |geog_id | ||
+ | |An mx id for a geographic unit that indicates the finest geographic unit for the collecting event. | ||
+ | |Must be empty if ce_id is provided. | ||
+ | |- | ||
+ | |method | ||
+ | |Interpreted version of the method given on the label (not verbatim). | ||
+ | |Must be empty if ce_id is provided. | ||
+ | |- | ||
+ | |locality | ||
+ | |Free text description of the locality, e.g. "1.5 km N Calgary" | ||
+ | |Must be empty if ce_id is provided. | ||
+ | |- | ||
+ | |sd_d | ||
+ | |Verbatim, max 2 character field in roman numeral or integer. | ||
+ | |Must be empty if ce_id is provided. | ||
+ | |- | ||
+ | |sd_m | ||
+ | |Verbatim, max 2 character field in roman numeral or integer. | ||
+ | |Must be empty if ce_id is provided. | ||
+ | |- | ||
+ | |sd_y | ||
+ | |Verbatim, max 4 character integer. | ||
+ | |Must be empty if ce_id is provided. | ||
+ | |- | ||
+ | |ed_m | ||
+ | |Verbatim, max 2 character field in roman numeral or integer. | ||
+ | |Must be empty if ce_id is provided. | ||
+ | |- | ||
+ | |ed_y | ||
+ | |Verbatim, max 4 character integer. | ||
+ | |Must be empty if ce_id is provided. | ||
|} | |} |
Revision as of 14:53, 7 June 2010
Contents |
Saving from Excel
If you work in Excel to capture your data you'll be exporting it prior to loading it. Your data should be saved in one of the following formats, (topmost preferred).
File format | Character Encoding |
---|---|
Tab Delimited Text (.txt) | MACINTOSH or ISO-8859-1 |
Windows Formatted Text (.txt) | ISO-8859-1 |
UTF-16 Unicode Text (.txt) | UTF-16LE |
Columns
Required for both lots and specimens
otu_id
or (both allowed if they match)
otu_name
OR
taxon_name_id
or (both allowed if they match)
taxon_name_string
Required for Lots
count
Required for Specimens
identifier
Optional for Specimens and Lots
One of
ce_id verbatim_label
One of
repository_id repository_coden
Any of
sex stage notes data_entry_by
Optional for lots
identifier
Optional for specimens
An additional determination
One of
det_name det_otu_id
and any of
determiner det_year det_basis
A type designation
both of
type type_of_taxon_name_id
Valid column heads on batch files
column headers | description | restrictions |
---|---|---|
ce_id | A mx collecting event id. | If present in a row then verbatim_label must be empty. |
count | Total specimens in a lot. | If present in a row then identifier must be empty. |
data_entry_by | A mx uses login. If supplied then all creator/updator fields are set to this person. If not supplied the creator is the person logged in. | None. |
det_basis | Free text describing how the specimen. determination was made. | Requires det_name or 'det_otu_id' to be included. Not applicable to lots. |
det_name | Free text determination of specimen. | If present in a row then det_otu_id must be empty. Not applicable to lots. |
det_otu_id | An id of an mx OTU that the specimen is determined as. | If present in a row then det_name must be empty. Not applicable to lots. |
det_year | A year in which a determination is made. | Requires det_otu_id or det_name to be present. Not applicable to lots. |
determiner | Free text indicator of determiner. | Requires det_otu_id or det_name to be present. Not applicable to lots. |
identifier | An identifier in the form of "namespace identifier", like "NCSU 1234". | The namespace must be present in mx. Applicable to lots or specimens. Must be unique within given category (lots/specimens). |
notes | Free text notes. | None. |
otu_id | A mx OTU id to which a specimen or lot is primarily attached. | Must match an OTU found by otu_name if otu_name is also provided. |
otu_name | A mx OTU name (not associated taxon name, manuscript name, nor matrix name) which identifies the specimen. | The named OTU must exist in the database. Must match the OTU indicated by otu_id if otu_id is also provide. If otu_id is not provided must be unique for the given project. |
repository_coden | A mx repository coden, like "NCSU". | Must match a coden in repositories. If provided repository_id must be empty. |
repository_id | A mx id matching a respository. | Must match a coden in repositories. If provided repository_coden must be empty. |
sex | Free text determination of sex, standard use is "male" or "female". Applicable to lots or specimens. | None. |
stage | Free text determination of stage. Applicable to lots or specimens. | None. |
taxon_name_id | Mx taxon name id which identifiers a specimen. | Must be tied to a single OTU. Applicable to specimens only. Must be empty if otu_id or otu_name is provided. Must match taxon_name_string if taxon_name_string is provided. |
taxon_name_string | Mx taxon name which identifiers a specimen. | Name in mx must be unique, and associated id must be tied to a single OTU. Applicable to specimens only. Must be empty if otu_id or otu_name is provided. Must match taxon_name_id if taxon_name_string is provided. At present matches only single word string. |
type | The code recognized type status of the specimen. Like "holotype", "paratype", "syntype", "neotype", or "paralectotype". Not for non governed things like "allotype". | Applicable to specimens only. Must be used in combination with type_of_taxon_name_id. |
type_of_taxon_name_id | The mx taxon name id that the type refers to. | Applicable to specimens only. Must be used in combination with type. |
verbatim_label | The verbatim text of the label(s) of the specimen or lot. Identical verbatim_labels are tied to a single collecting event in mx. Individual lines can be separated with "||", individual labels can be separated with "++". "||" and '++' will be replaced with one and two new lines respectively. | Must be empty if ce_id is provided. |
latitude | A real number in decimal degrees format. | Must be empty if ce_id is provided. |
longitude | A real number in decimal degrees format. | Must be empty if ce_id is provided. |
elev_min | A real number indicating the minimum elevation of the elevation range. | Must be empty if ce_id is provided. |
elev_max | A real number indicating the maximum elevation of the elevation range. | Must be empty if ce_id is provided. |
geog_id | An mx id for a geographic unit that indicates the finest geographic unit for the collecting event. | Must be empty if ce_id is provided. |
method | Interpreted version of the method given on the label (not verbatim). | Must be empty if ce_id is provided. |
locality | Free text description of the locality, e.g. "1.5 km N Calgary" | Must be empty if ce_id is provided. |
sd_d | Verbatim, max 2 character field in roman numeral or integer. | Must be empty if ce_id is provided. |
sd_m | Verbatim, max 2 character field in roman numeral or integer. | Must be empty if ce_id is provided. |
sd_y | Verbatim, max 4 character integer. | Must be empty if ce_id is provided. |
ed_m | Verbatim, max 2 character field in roman numeral or integer. | Must be empty if ce_id is provided. |
ed_y | Verbatim, max 4 character integer. | Must be empty if ce_id is provided. |