About - Manual
User: Guest  [click to login]  [register]

Morphbank Custom Worksheet Instructions

To use this workbook for upload to Morphbank, a user must have unique identifiers for their Specimens and Images. Unique identifiers are optional for Views and just what a unique identifier is and how to construct one is included in these instructions. If the data to be uploaded does not have unique identifiers, use our options Data Entry Workbook - Animalia or Data Entry Workbook - Plantae. Note that these workbooks are located for easy download from Documents and are easily modified to suit other kingdoms.

HINT: Before using this, or any mass upload method, please take the time to upload 2 or 3 images via the web-interface at http://www.morphbank.net. Familiarity results in a much faster learning curve and less confusion when it comes to filling out the various forms found in a workbook or in getting the data mapped to Morphbank's XML schema.
Custom Workbook - SAMPLE DATA SETS
  • SCAMIT: A data set from an invertebrate taxonomy group in Southern California. Note only fields they use are present. Also, drop-downs are customized for the taxonomic group of interest as needed for different labs.
  • USMS: From the herbarium at the University of Southern Mississipi, this data set was generated by mapping an existing database to Morphbank fields. An SQL query on that database generated this dataset with column headers that match Morphbank fields. Again note minimal fields used to fit the needs / desires of this institution.
  • Tall Timbers: Similar to the above set, a research station interested in creating an image repostitory of the various specimen collections created and housed at their facility, used an abbreviated version of the custom workbook. Note their data entry form shown here is tailored to show only the fields they need to work with.

Custom Workbook Considerations

This Excel workbook contains 5 sheets: Data, UserProperties, ContributorInfo, Field Help and Drop Downs

Suggestion: download and open the Morphbank Custom Workbook to look at while reading this documentation.
  1. Before filling out and submitting this workbook to Morphbank, check all the needed taxon names with names in the Morphbank database. There are two ways to do this.
    1. Login to Morphbank, go to HeaderMenu > Tools > Submit > Taxon Name. Here a user can access the Taxon Name Search to see if a name is in Morphbank or not, or is in Morphbank in > 1 location. Any names not in Morphbank need adding before the upload using the custom workbook.

      1. Names can be added via the web-interface from Sub-Order and lower ranks. Go to HeaderMenu > Tools > Submit > Taxon Name to start. Try the Online User Manual - Add Taxon Name for help with this process.
      2. If many names need adding or if many names need adding at the rank of Order or higher, contact Morphbank mbadmin at scs dot fsu dot edu as we have another strategy for this situation.
      3. If a taxon name is in Morphbank more than one time, each occurrence has a unique taxonomic serial number (tsn). The user will need to make a note of the tsn that represents the taxon name placement preferred and put that tsn in the custom workbook Determination TSN column on the Data sheet.

    2. Using Name Query, a list of taxon names can be searched all-at-once and a list of tsns returned. This list can be pasted directly into the Data sheet Determination TSN column.


    Mapping and User Properties

  2. Next, review the fields present in the workbook. Most of them are from the DarwinCore2 Schema (v1.2). Each Contributor will need to map their data to these fields to see what matches and what does not. Then, decide which fields must go into Morphbank and which really do not need to be stored here. If extra fields, that Morphbank does not have, must go into Morphbank, they must be defined by the user. These are User Properties. If at all possible, try to find a field in one of the following Schemas that fits the dataset in question. Someone at Morphbank can help with this, just ask.
  3. Entering a User Property in the Workbook - an example

    • Let's say the userProperty = Size. The Contributor has specific size information.
    • To what object in Morphbank (image, specimen, locality, view) does the size information relate? For the sake of this example, the Contributor obtained the size measurement by directly measuring the specimen.
    • In the Workbook in the Data sheet, find the Specimen section and the userProperty column in that section.
    • In the column heading row, replace the <userProperty> text with new column header Size.
    • Under this new column heading, place the Size values for each Specimen.
    • Next, go to Sheet 2. Enter the name of the userProperty in the first column (in this case Size), under the column heading <userProperty>. In the next column (Associated MB Object), choose Specimen from the drop-down.
      • Now, the <userProperty> is defined as Size and this data will appear in Morphbank with the Specimen object..
    • If another <userProperty> is needed for Specimen, insert another column next to the Size column on Sheet 1, and repeat the above steps.
  4. Now, every item to go into Morphbank fits into one of the columns in the workbook. The columns labeled are for the data items where the Contributor finds a suitable datafield in one of the above Schemas, or comes up with a unique one. It is srongly suggested that users attempt to find a field that matches in one of the above defined Schema. It greatly facilitates sharing data between databases stored on different computers, aka interoperability.

  5. In addition to the Field Help sheet, see the Morphbank Online User Manual for Morphbank Field descriptions for more about what type of data goes into which field and what the format of the data needs to be for each of those fields.


  6. External Unique Identifiers (uid): What they are and how to fill out the columns in the workbook.

    Morphbank encourages UIDs


    If the provider (Contributor to Morphbank) maintains their own unique identifiers for their objects, these can be stored in Morphbank. With this identifier, the object is easily shared between systems. They also make it possible in the future for users to update their own data in Morphbank utilizing their own unique identifiers. In this workbook, a provider may supply Morphbank with unique ids for 3 Morphbank objects, image, specimen & view. A unique identifier must be unique within Morphbank itself. An example of a unique identifier might be to concatenate an organization name + an image file name. For this to work, the provider must control the naming conventions for images they supply to Morphbank so that no images will have the same combination.

    • In the workbook, the user is asked to populate two columns for any given uid. Provide the identifer in the External id column, example:0001568. In the Prefix column, provide what is to be concatenated with the id to make it unique. Example:CToL-I: Now the uid in Morphbank will appear as CToL-I:0001568.

    • It can be very simple to create these. Here are some ideas and guidelines.

      • Usually, an acronym for the institution/collection or person is suitable for the Prefix.
      • The identifier for the image can be the name of the image, or a unique number given to that image.
        • note the Contributor must keep track of these on their end.
      • The identifier for a specimen is usually the catalognumber or it might be the collector's identifier (the number given to that item when it was collected by a particular individual).
      • Keep in mind that Darwin Core has a simple strategy for creating unique identifiers that consists of concatenating the institution code + collectioncode + catalognumber. So, if the data is coming from a formal collection, this can be used. In Morphbank, the institution code + collection code would make up the Prefix. The catalognumber goes in the External id column.
        • An example:
          • prefix FSU:FSU + External id 000126543
          • concatenated in Morphbank, the uid = FSU:FSU:000126543
          • it could be read as Florida State University, FSU = Herbarium Acronym from Index Herbariorum, 000126543 is the catalog number of a given specimen in that collection.

  7. Fields not needed in the Workbook can be deleted -- for clarity and ease of use of the workbook.

  8. For any columns that a User decides to populate - Do Not Change the column headings (except for userProperty).

  9. In addition to the Field Help sheet, see the MB Table Descriptions for even more about Morphbank database tables and field types (varchar, text, field length restrictions).

  10. Send the completed workbook to Morphbank along with the images. The workbook can be sent via e-mail, cd/dvd, or ftp. Send images via cd/dvd, ftp or mail a hard drive with the images.

  11. The file will be validated to check the contents. This validation looks at field content match (text fields contain text, numeric fields contain numerics) and overall data. Morphbank will return the file to the sender with questions if need be, otherwise it will be uploaded. Always keep a copy of the workbook.
Next
Contents