App/specimen/batch load
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Contents |
Batch importing
Required for both
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. | 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. ALSO must already be created, in database. |
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. |