|
|
| (10 intermediate revisions by one user not shown) |
| Line 1: |
Line 1: |
| − | == Batch importing == | + | == Overview == |
| | | | |
| − | === Required for both ===
| + | Specimens records can be generated in mx in a number of different manners. The entry points for doing this are: |
| | | | |
| − | otu_id
| + | # The specimen tab (click "new") |
| | + | # When [[App/otu/show|showing an OTU]], click "material" on the leftmost navigation links to get [[App/otu/show material|here]] |
| | + | # When [[App/ce/show|showing a collecting event]], click "material" on the leftmost navigation links to get [[App/ce/show_material|here]] |
| | + | # When [[App/lot/show|showing a lot]], click "create (extract from value)" or "create (clone, no extraction)" on the leftmost navigation links |
| | + | # In batches, see [[App/specimen/batch_load|here for information on batch loading]], on the Specimen tab click "more options" then "batch load" |
| | | | |
| − | ''or (both allowed if they match)''
| + | == Specimen help pages == |
| − | otu_name
| + | |
| | | | |
| − | '''OR'''
| + | {{Special:Prefixindex/App/specimen/}} |
| − | | + | |
| − | 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. Not applicable to lots. Must be unique.
| + | |
| − | |-
| + | |
| − | |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.
| + | |
| − | |-
| + | |
| − | |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 new lines respectively.
| + | |
| − | |Must be empty if ce_id is provided.
| + | |
| − | |}
| + | |
Specimens records can be generated in mx in a number of different manners. The entry points for doing this are:
