Difference between revisions of "App/specimen"
From mx Help Wiki
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'''A type designation''' | '''A type designation''' | ||
type | type | ||
+ | |||
+ | == 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. | ||
+ | |} | ||
+ | |||
+ | |||
+ | == Batch file example == |
Revision as of 09:23, 15 September 2009
Contents |
Batch importing
Required for Lots
count
Required for Specimens
identifier
Required for both
otu_id otu_name
OR
taxon_name_id taxon_name_string
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 specimens
An additional determination
One of
det_name det_otu_id
and any of
determiner det_year det_basis
A type designation
type
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. |