Data Entry Assistant (DEA) 2.0 Procedures - Revision history

Hemly.1 at 20:31, 3 February 2016

2016-02-03T20:31:10Z

Hemly.1 at 20:26, 3 February 2016

2016-02-03T20:26:08Z

Jcora at 21:54, 19 November 2014

2014-11-19T21:54:38Z

Jcora: /* Entering New Specimen Records */

2014-11-19T21:49:34Z

‎Entering New Specimen Records

Jcora at 21:46, 19 November 2014

2014-11-19T21:46:54Z

Jcora: /* Setting Habitats */

2014-11-19T20:50:43Z

‎Setting Habitats

Jcora: /* Setting Habitats */

2014-11-19T20:41:35Z

‎Setting Habitats

Jcora at 20:40, 19 November 2014

2014-11-19T20:40:21Z

Jcora at 18:20, 19 November 2014

2014-11-19T18:20:49Z

Jcora at 17:57, 19 November 2014

2014-11-19T17:57:14Z

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 '''Introduction'''
-This section contains information on the practices for preparing occurrence records for entry into the xBio:D database using the [http://osuc.osu.edu/DEA2 Data Entry Assistant (DEA) 2.0]. The DEA2 web application requires that occurrence records be present in a properly formatted data entry template ([[File:Data_Entry_Template_31-Oct-2014.xls]]) file according to the [[Data Transcription Procedures]] protocol or a properly pre-formatted data entry template [[File:DEA data entry template-full 28-Aug-2014.xls]].
+This section contains information on the practices for preparing occurrence records for entry into the xBio:D database using the [http://osuc.osu.edu/DEA2 Data Entry Assistant (DEA) 2.0]. The DEA2 web application requires that occurrence records be present in a properly formatted data entry template ([[File:Data_Entry_Template_31-Oct-2014.xls]]) file according to the [[Data Transcription Procedures]] protocol or a properly pre-formatted data entry template [[File:DEA_data_entry_template-full 31-Oct-2014.xls]].
 The [[#DEA Processing|DEA Processing]] steps do not need to be followed in the order defined in this document, but all of the parts specified do need to be completed when starting from verbatim label data. If pre-formatted specimen data is used, DEA2 will check to see if the specified values are valid according to [[xBio:D Controlled Vocabularies]]. Please refer to this Excel file ([[File:DEA2-example-processed_19-Nov-2014.xls]]) for a real-world example of a file that has already been processed within DEA2.

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 '''Introduction'''
-This section contains information on the practices for preparing occurrence records for entry into the xBio:D database using the [http://osuc.osu.edu/DEA2 Data Entry Assistant (DEA) 2.0]. The DEA2 web application requires that occurrence records be present in a properly formatted data entry template ([[File:Data_Entry_Template_28-Aug-2014.xls]]) file according to the [[Data Transcription Procedures]] protocol or a properly pre-formatted data entry template [[File:DEA data entry template-full 28-Aug-2014.xls]].
+This section contains information on the practices for preparing occurrence records for entry into the xBio:D database using the [http://osuc.osu.edu/DEA2 Data Entry Assistant (DEA) 2.0]. The DEA2 web application requires that occurrence records be present in a properly formatted data entry template ([[File:Data_Entry_Template_31-Oct-2014.xls]]) file according to the [[Data Transcription Procedures]] protocol or a properly pre-formatted data entry template [[File:DEA data entry template-full 28-Aug-2014.xls]].
 The [[#DEA Processing|DEA Processing]] steps do not need to be followed in the order defined in this document, but all of the parts specified do need to be completed when starting from verbatim label data. If pre-formatted specimen data is used, DEA2 will check to see if the specified values are valid according to [[xBio:D Controlled Vocabularies]]. Please refer to this Excel file ([[File:DEA2-example-processed_19-Nov-2014.xls]]) for a real-world example of a file that has already been processed within DEA2.

← Older revision		Revision as of 21:54, 19 November 2014
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	This section contains information on the practices for preparing occurrence records for entry into the xBio:D database using the [http://osuc.osu.edu/DEA2 Data Entry Assistant (DEA) 2.0]. The DEA2 web application requires that occurrence records be present in a properly formatted data entry template ([[File:Data_Entry_Template_28-Aug-2014.xls]]) file according to the [[Data Transcription Procedures]] protocol or a properly pre-formatted data entry template [[File:DEA data entry template-full 28-Aug-2014.xls]].		This section contains information on the practices for preparing occurrence records for entry into the xBio:D database using the [http://osuc.osu.edu/DEA2 Data Entry Assistant (DEA) 2.0]. The DEA2 web application requires that occurrence records be present in a properly formatted data entry template ([[File:Data_Entry_Template_28-Aug-2014.xls]]) file according to the [[Data Transcription Procedures]] protocol or a properly pre-formatted data entry template [[File:DEA data entry template-full 28-Aug-2014.xls]].

−	The [[#DEA Processing\|DEA Processing]] steps do not need to be followed in the order defined in this document, but all of the parts specified do need to be completed when starting from verbatim label data. If pre-formatted specimen data is used, DEA2 will check to see if the specified values are valid according to [[xBio:D Controlled Vocabularies]].	+	The [[#DEA Processing\|DEA Processing]] steps do not need to be followed in the order defined in this document, but all of the parts specified do need to be completed when starting from verbatim label data. If pre-formatted specimen data is used, DEA2 will check to see if the specified values are valid according to [[xBio:D Controlled Vocabularies]]. Please refer to this Excel file ([[File:DEA2-example-processed_19-Nov-2014.xls]]) for a real-world example of a file that has already been processed within DEA2.

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 === Entering New Specimen Records ===
-The final step in the data entry protocol is enter the specimen record itself. Specimen records may be vouchered or unvouchered, but both must have a unique identifier for the specimen record and a depository. In xBio:D, a depository may be an unvouchered collection of records, but an xBio:D collection ID must still be used to define the unvouchered depository. A privileged user can entering specimen records into xBio:D using DEA2 by going to ''Batch -> Enter Specimens'' from the DEA2 menu to go to the ''Enter Specimens'' page. Press the ''YES'' button next to ''Begin processing?'' to initiate specimen record entry. DEA2 will take the specimen information for each record present within the "Main" worksheet, compare the ''cuid'' to existing specimen records within xBio:D, then enter the new specimen record if necessary.
+The final step in the data entry protocol is enter the specimen record itself. Specimen records may be vouchered or unvouchered, but both must have a unique identifier for the specimen record and a depository. In xBio:D, a depository may be an unvouchered collection of records, but an xBio:D collection ID must still be used to define the unvouchered depository. A privileged user can entering specimen records into xBio:D using DEA2 by going to ''Batch -> Enter Specimens'' from the DEA2 menu to go to the ''Enter Specimens'' page. Press the ''YES'' button next to ''Begin processing?'' to initiate specimen record entry. DEA2 will take the specimen information for each record present within the "Main" worksheet, compare the ''cuid'' to existing specimen records within xBio:D, then enter the new specimen record if necessary. Upon successful entry of a specimen record, that label information and the comments are stored along with the collecting event information for the entered specimen to facilitate rapid processing of subsequent specimen records that contain the same information within DEA2.
 If an error occurs while entering a specimen record, DEA2 will display a form with all of the specimen information for the new specimen record and highlight the problem field. In the case of a controlled vocabulary term, i.e., life status, specimen sex, type status, etc., not being present in the xBio:D database, please contact [mailto:cora.1@osu.edu Joe Cora] and request the vocabulary term to be added right away. Most of the controlled vocabulary terms within the specimen info form will present available values that are dynamically generated from the xBio:D database to aid in the proper specification of terms. Authorized users may enter [http://osuc-mgr.osu.edu/addPerson.html new people] or a [http://osuc-mgr.osu.edu/addParty.html new party] from the Database Manager.
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 When all of the specimen records have been entered, the DEA2 process will be completed. Before moving onto a new file, unload the current file to remove unnecessary replicate of specimen data from the local DEA2 database. To unload a file, click on the working filename next to the username in the menu at the top right of a page and select the ''Unload'' action. A prompt confirming that the current file should be unloaded will display, and after confirmation, the file will be unloaded.
 == Changes from DEA to DEA2 ==

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 === Entering New Localities ===
-Localities represent the geospatial location in which a specimen was collected and is rooted to a geopolitical hierarchy, and each specimen record within xBio:D is required to be linked to a locality. Roughly following the guidelines presented within the [[Locality Georeferencing and Generation]] page, a privileged user can enter additional localities in xBio:D using DEA2. Begin by going to ''Batch -> Enter Localities'' from the DEA2 menu to go to the ''Enter Localities'' page. DEA2 will take the locality information for each record present within the "localities" worksheet, compare the locality name to existing locality names within xBio:D, then enter the new locality name if necessary. After a locality is entered, DEA2 will take the locality name associated with the specimen record within the "localities" sheet and set the ''loc_name'' field within the "Main" worksheet for the corresponding specimen record. If a corresponding specimen record is not found, i.e., the matching ''cuid'' is not located within the "Main" sheet, then DEA2 will not copy the locality name. The locality name will still be entered regardless. If a locality name is already present within the xBio:D database, then DEA2 will nevertheless attempt to match the locality name for a specimen record in "localities" to its corresponding record in "Main".
+Localities represent the geospatial location in which a specimen was collected and is rooted to a geopolitical hierarchy, and each specimen record within xBio:D is required to be linked to a locality. Roughly following the guidelines presented within the [[Locality Georeferencing and Generation]] page, a privileged user can enter additional localities in xBio:D using DEA2. Begin by going to ''Batch -> Enter Localities'' from the DEA2 menu to go to the ''Enter Localities'' page. Press the ''YES'' button next to ''Begin processing?'' to initiate locality entry. DEA2 will take the locality information for each record present within the "Localities" worksheet, compare the locality name to existing locality names within xBio:D, then enter the new locality name if necessary. After a locality is entered, DEA2 will take the locality name associated with the specimen record within the "Localities" sheet and set the ''loc_name'' field within the "Main" worksheet for the corresponding specimen record. If a corresponding specimen record is not found, i.e., the matching ''cuid'' is not located within the "Main" sheet, then DEA2 will not copy the locality name. The locality name will still be entered regardless. If a locality name is already present within the xBio:D database, then DEA2 will nevertheless attempt to match the locality name for a specimen record in "Localities" to its corresponding record in "Main".
 [[File:enter_localities_start-dea2.png|none|frame|Begin entering localities]]
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 === Entering New Specimen Records ===
-''TODO''
+The final step in the data entry protocol is enter the specimen record itself. Specimen records may be vouchered or unvouchered, but both must have a unique identifier for the specimen record and a depository. In xBio:D, a depository may be an unvouchered collection of records, but an xBio:D collection ID must still be used to define the unvouchered depository. A privileged user can entering specimen records into xBio:D using DEA2 by going to ''Batch -> Enter Specimens'' from the DEA2 menu to go to the ''Enter Specimens'' page. Press the ''YES'' button next to ''Begin processing?'' to initiate specimen record entry. DEA2 will take the specimen information for each record present within the "Main" worksheet, compare the ''cuid'' to existing specimen records within xBio:D, then enter the new specimen record if necessary.

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 === Setting Habitats ===
-Habitats define a type of environment or biological community in either broad or specific terms in which a specimen was collected. Begin by going to ''Set -> Set Habitats'' within the DEA2 menu to load the ''Set Habitats'' page. DEA2 provides for two separate manners of processing habitats depending on the data processing protocol used. The behavior for dealing with records is the same as field codes, so see the [[#Setting Field Codes]] section for more information. The habitats do not follow a controlled vocabulary and a not limited to certain standardized text strings. However, multiple, distinct habitats should be separated by a semicolon (;) then a space and will automatically be translated when a slash (/) is found, e.g., ''forest / by stream'' -> ''forest; by stream''.
+Habitats define a type of environment or biological community in either broad or specific terms in which a specimen was collected. Begin by going to ''Set -> Set Habitats'' within the DEA2 menu to load the ''Set Habitats'' page. DEA2 provides for two separate manners of processing habitats depending on the data processing protocol used. The behavior for dealing with records is the same as field codes. See the [[#Setting Field Codes]] section for more information. The habitats do not follow a controlled vocabulary and a not limited to certain standardized text strings. However, multiple, distinct habitats should be separated by a semicolon (;) then a space and will automatically be translated when a slash (/) is found, e.g., ''forest / by stream'' -> ''forest; by stream''.
 Copy the interpreted habitat into the habitat box, then press the ''Set Habitat'' button to assign the habitat to all of the records in which the ''loc_name'' or ''new_comments'' column matches the current record depending on the record selection method. If a habitat is not specified, press the ''No Habitat Specified'' button to skip the current record and all matching records until the next distinct specimen record is found. If the ''loc_name'' or ''new_comments'' columns match a specimen record that had already been entered into the xBio:D database, DEA2 will automatically assign that habitat to the matching record.

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 === Setting Habitats ===
-''TODO''
+Habitats define a type of biological community in either broad or specific terms in which a specimen was collected. Begin by going to ''Set -> Set Habitats'' within the DEA2 menu to load the ''Set Habitats'' page. DEA2 provides for two separate manners of processing habitats depending on the data processing protocol used. The behavior for dealing with records is the same as field codes, so see the [[#Setting Field Codes]] section for more information. The habitats do not follow a controlled vocabulary and a not limited to certain standardized text strings. However, multiple, distinct habitats should be separated by a semicolon (;) then a space and will automatically be translated when a slash (/) is found, e.g., ''forest / by stream'' -> ''forest; by stream''.
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 [[File:specify_assoc_new_comments-dea2.png|none|frame|Specimen data from ''new_comments'' (left side)]]
 [[File:specify_assoc_assocs-dea2.png|none|frame|Biological associate and relationship (right side)]]

← Older revision		Revision as of 18:20, 19 November 2014
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	Copy the interpreted field code into the field code box, then press the ''Set Field Code'' button to assign the field code to all of the records in which the ''loc_name'' or ''new_comments'' column matches the current record depending on the record selection method. If a field code is not specified, press the ''No Field Code Specified'' button to skip the current record and all matching records until the next distinct specimen record is found. If the ''loc_name'' or ''new_comments'' columns match a specimen record that had already been entered into the xBio:D database, DEA2 will automatically assign that field code to the matching record.		Copy the interpreted field code into the field code box, then press the ''Set Field Code'' button to assign the field code to all of the records in which the ''loc_name'' or ''new_comments'' column matches the current record depending on the record selection method. If a field code is not specified, press the ''No Field Code Specified'' button to skip the current record and all matching records until the next distinct specimen record is found. If the ''loc_name'' or ''new_comments'' columns match a specimen record that had already been entered into the xBio:D database, DEA2 will automatically assign that field code to the matching record.
		+	[[File:set_field_codes_match-dea2.png\|none\|frame\|Set field code]]

	Under ''Page Options'' on the left menu, users can select ''Review set field codes'' to review which specimens records have been processed and the current field code for the records. If a field code was incorrectly set, press the ''Remove'' button next to the record which contains the improper code to remove the action and allow the user to process the record again. DEA2 will remove the ''set collecting method'' action for all of the records in which the ''loc_name'' or ''new_comments'' column matches the selected record depending on the record selector described above.		Under ''Page Options'' on the left menu, users can select ''Review set field codes'' to review which specimens records have been processed and the current field code for the records. If a field code was incorrectly set, press the ''Remove'' button next to the record which contains the improper code to remove the action and allow the user to process the record again. DEA2 will remove the ''set collecting method'' action for all of the records in which the ''loc_name'' or ''new_comments'' column matches the selected record depending on the record selector described above.

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 After the collecting method has been determined, press the ''Set Collecting Method'' button to assign the collecting method to all of the records in which the ''new_comments'' column matches the current record. If a collecting method is not specified, press the ''No Collecting Method Specified'' button to skip the current record and all matching records until the next distinct specimen record is found. If the ''new_comments'' match a specimen record that had already been entered into the xBio:D database, DEA2 will automatically assign that collecting method to the matching record.
-Under ''Page Options'' on the left menu, users can select ''Review set collecting methods'' to review which specimens records have been processed and the current collecting collecting method for the records. If a collecting method was incorrectly set, press the ''Remove'' button next to the record which contains the improper method to remove the action and allow the user to process the record again. DEA2 will remove the ''set collecting method'' action for all of the records in which the ''new_comments'' column matches the selected record.
+Under ''Page Options'' on the left menu, users can select ''Review set collecting methods'' to review which specimens records have been processed and the current collecting method for the records. If a collecting method was incorrectly set, press the ''Remove'' button next to the record which contains the improper method to remove the action and allow the user to process the record again. DEA2 will remove the ''set collecting method'' action for all of the records in which the ''new_comments'' column matches the selected record.
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 === Setting Field Codes ===
-''TODO''
+Field codes are a means for collectors to identify a particular sample or collecting event from the field and easily associate the material with detailed information in his/her field notes. In xBio:D, field codes are linked to a specific collecting event, and depending on the preference of the user, may also be a collecting event code applied ''post hoc''. Begin by going to ''Set -> Set Field Codes'' within the DEA2 menu to load the ''Set Field Codes'' page. DEA2 provides for two separate manners of processing field codes depending on the data processing protocol used: one is setting by locality name, which is the default; and the other is setting by the labels and comments. The OSUC data entry protocol involves placing both field code and habitat, if specified, within the locality name, which typically requires far less effort than processing on the labels and comments alone. The field codes do not follow a controlled vocabulary and a not limited to certain standardized text strings. However, multiple, distinct field codes should be separated by a semicolon (;) then a space, e.g., ''ROM_OSU 308469; AL22512''.