Manual - Morphbank
Contents
1. do not chang 2 ill Hil 1 Figure 5 Specimen Worksheet Columns A X Specimen Sequence Number This column is auto generated Itis a number that corresponds to the order of input made in the Specimen worksheet Do not change it This number will be used to make a relation in the workbook between the data for a given specimen and the images associated with that specimen Scientific Name required Choose the taxon name for your specimen from the drop down The taxon names in this drop down come from the SpecimenTaxonData worksheet Basis of Record required dwc Choose one of the options from the drop down list Current choices are Observation Living Organism Specimen Germplasm Seed f additional options are needed please contact Morphbank at mbadmin scs fsu edu The list of options is based on the Darwin Core standard Sex required dwc Choose one of the options from the drop down list The list contains a set of terms based on community consensus Male Female Hermaphrodite Indeterminate if the specimen was examined but the sex could not be determined Unknown if the specimen was not examined for its sex or if the sex is not applicable to a particular specimen Transitional if the specimen is 23 os PhS Zy x between sexes like sequential hermaphrodites If additional options are needed please contact Morphbank at mbadmin scs fsu edu The list of options is based on the Darwin Core2. Ph P lt owe q Contributors to the Morphbank Data Entry Workbook User Manual Wilfredo Blanco Robert Bruhn Matt Buffington Cynthia Gaitros David Gaitros Neelima Jammigumpula Karolina Maneva Jakimoska Austin Mast Debbie Paul Greg Riccardi Fredrik Ronquist Katja Seltmann Steve Winner mph Sas 2 gt wW Last Updated 10 10 2010 Morphbank offers a service using this prepared data entry workbook Submitters fill out and deliver the Excel workbook to Morphbank os PhS SAS p x Hy w circumstances users enter text in the Information Withheld column of the Locality sheet to tell users how to obtain the withheld data if needed Before entering data into the workbook please gather the following information e A Morphbank Account Please acquire a Morphbank username and password prior to submitting the workbook via the login screen at www morphbank net gt Tools gt Login gt Request user account or by contacting Morphbank at mbadmin scs fsu edu If the user does not have an account before submitting the workbook one will be generated at that time e General information about your image collection including the Morphbank contributor person with authority to release the images to the public release date Morphbank group to which the images should be attributed and a project link if one exists to which the images are related e Locality details including continent ocean countr
3. 3 3 Institution name Figure 2 Image Collection Worksheet Contributor Full Name required Enter the first name and last name only of the contributor of the images In Morphbank the contributor is a person with a Morphbank account who possesses the authority to release the images to the public Obtain an account at www morphbank net click Tools gt Login gt Request new account Contributor Username required The contributor must be a Morphbank account holder Once the account is set up the user has a Morphbank Username and password Submitter Full Name required Enter the first name and last name only of the person who prepared this workbook and submitted it to Morphbank for upload A Submitter must be a Morphbank user The Submitter may or may not be the same as the Contributor Obtain an account at www morphbank net click Tools gt Login gt Request new account os PhS SAS p x Hy w Release Date required yyyy mm dd Enter the release date for the images if the images are not for immediate release to the public The release date can be at most five years from the date of inclusion of the images in Morphbank If you have different sets of images with different release dates please create a separate Excel file for each image set Group required Enter the Morphbank Group name to which the images should be attributed If the images are not for immediate release they can still be viewed and modified
4. automatically populated based on the previous choice Do not change them If the needed view is not provided in the MyView Name list proceed to the second part of this sheet and create the needed views by populating each of the column cells C J required HINT Choosing or creating views with this worksheet creates a drop down of views for use AO omen Dorsolateral I ed EA pene donot Specimen to Taxon enTaxonData Loc Mia Use the bottom half of the worksheet Columns C J required to create any needed views not found in the top half of the worksheet Select the desired Specimen Part View Angle etc from the drop down lists to create a new view Use the Supporting Data sheet to add needed items to a particular drop down list Column J is a text field Figure 4 MyView Worksheet Columns A J View sequence number A number that corresponds to the order of input made in the MyView worksheet This column is auto generated Do not change it My View Name required Column B in the top half of this worksheet has a drop down with existing views in Morphbank Select the desired view from Column B and do not alter columns C J on the top half of the worksheet If views needed are not there create new views on the bottom half of the workbook using columns C J as described next Specimen Part required Enter choose from the drop down list the name of the specimen part presented by the view i e what s
5. etc Inside each folder place the excel sheet named mb3_yourfilename xls and all associated images Be sure to have the correct image file names as they appear in mb3_yourfilename xls You can deliver your data to Morphbank three ways 1 Save all image collection files on a CD and send to Morphbank by land mail See contacts section of this manual next Make sure to keep a backup copy for yourself and send with proper postage and protection Please include a business phone number and contact information so you can be contacted by Morphbank 2 Provide the name of your directory repository from where we can directly download mb3_yourfilename xls and the corresponding images You should also set a time slot of when we can do the file transfer Be aware that during this time slot your data will be publicly accessible 3 Morphbank provides an ftp upload service as an alternative to mailing CDs DVDs Registered Morphbank users may email mbadmin scs fsu edu for an ftp upload username password and server hostname Although you should be familiar with ftp only minimal experience is necessary to use this service The Morphbank server may be accessed by using secure shell terminal command line or any graphic ftp program Once a Morphbank administrator has sent account information users may begin uploading Be sure to use ftp file transfer protocol or sftp as instructed by someone from mbadmin scs fsu edu There is no limit on the number of
6. by the members of this Morphbank Group If you are Group Coordinator of this group you can add any Morphbank user to this group Contact Morphbank at mbadmin scs fsu edu if you need a new Morphbank group If you have different sets of images you want to associate with other Morphbank groups create a separate Excel file for each image set Institution Name Provide an institution name if applicable for an institution associated with the data in the workbook This field provides the label for an external link given in the next field Institution Link Provide a link in http format to the above named institution This link to the institution will be added as an external link to all the image and specimen records created as a result of the provided data for upload Project Name Provide a project name if applicable associated with the data in the workbook This field provides the label for an external link given in the next field Project Link Provide a link in http format to the above named project This link will be added as an external link to all the image and specimen records created as a result of the provided data for upload Project Name Provide a second project name if applicable desired associated with the data in the workbook This field provides the label for an external link given in the next field Project Link Provide a link in http format to the second project named above This link will be added as an external li
7. files uploaded at one time Once the images are on the server notify mbadmin scs fsu edu of the completion include a message requesting that the account remain open if needed If the account is not requested to remain open Morphbank will delete the files off the server once they have been received and the account password changed This service may be used once or many times depending on the users specific needs 4 Morphbank is currently working on designing a web interface for users to upload their data and images directly from these forms When this option is online data is uploaded first to a test server and any errors reported Once the data enters correctly it is uploaded to the production server 42 ph Sx oe q X Note If errors are found within your Excel workbook they will be commented and the workbook will be returned for corrections Please include a business hours phone number so one of the Morphbank team can contact you Contact Information Questions or Comments Morphbank Administration mbadmin scs fsu edu Deborah Paul dpaul scs fsu edu Contacts Morphbank Administration mbadmin scs fsu edu Land Mail Address Morphbank Group c o Deborah Paul Mail Code 4120 Florida State University Tallahassee FL 32306 4120 43
8. images organized efficiently beforehand e g images relating to the same taxon or the same body structure etc simplifies data entry Many columns have from the choices to fill the cell Additional items can be added to most drop downs Select basis of record from_ drop down To add anew entry you reed to contact Morphbank BasisOfRecord is a Darwin Core field cmenTaxonData feocain Columns highlighted in blue are required fields Tan columns are suggested amp white columns are optional Select tabs to jump to a different worksheet o scroll the tab bar use the arrows at the fa eft The active worksheet is highlighted white Figure 1 Anatomy of a Workbook Page e Order of data entry Once taxon names are checked and all other data is located and ready for entry open the Excel file and click on the Excel spreadsheet tab that corresponds to the area of the workbook you would like to propagate see Fig 1 The preferred order for entering data into the Morphbank workbook is ImageCollection Locality SpecimenTaxonData Specimen MyView Images ExternalLinks and the Supporting Data page as needed e Entering image collection data Select the ImageCollection tab first to enter general information about the collection of images os PhS Se fal Ky w Entering locality data After entering ImageCollection data proceed to the Locality tab and fill in all applicable fields These fields are lin
9. is withheld You may provide a reason for withholding information example endangered species and a contact person who has the authority to release this information to a given group of users Note This worksheet has 250 initialized rows for data If more rows are needed see the Additional Notes section of this manual for instructions on inserting additional rows 29 mph 9 lt 2 Oe External Links The External links worksheet is optional and populated last Use this option to link the deposited images to any external link like other databases NCBI accession numbers location maps etc Links may be associated with any Morphbank table so they can appear in the SpecimenRecord ImageRecord LocationRecord or ViewRecord tables This worksheet has 6 columns 1 _ObiectT ld Image Specimen cE To associate a URL with an Localit object in this workbook first Cn Go s choose the object type here 8 HINT This is an Optional sheet 9 for adding External Links to any 10 object in the workbook in 11 addition to those URLs given on 12 the ImageCollection sheet feeder or tint S ExternalLinks Supportin Figure 8 External Links Object Type required only if this sheet is used Choose from the drop down list the Object Type for which you want to create a link The choices are Specimen View Image and Locality Note well if the same institution and or project link is to be added to all the Specimens
10. its own for the purpose of only adding names to Morphbank To add 30 names or less at the rank suborder or lower it may be more efficient to use the Morphbank web interface to add the needed taxon names If names need to be added above the suborder rank contact mdadmin scs fsu edu 17 2 ws Y A 8 c 0 E F G M K L Ww Q Taxon Sciontifichame use if not in Morphbank Publication tame String norphban lication Id Pages Tradedej cote ure Family required Enter the family to which the taxon name in column H belongs HINT All names entered from column A through column G are for parents of the taxon name in pocmen TaxonDate toc Scemelses pporenga column H Figure S Specimen Taxon Data Worksheet Columns A O Parentage must be indicated at each rank where the child is new to Morphbank The parents must already be in Morphbank When adding a child to parents already in Morphbank one row entry for that name is sufficient Columns A G indicate parentage for the Scientific Name given in column H Example 1 Beauprea gracilis is not in Morphbank the genus Beauprea is in Morphbank To add the child gracilis to the Genus Beauprea fill out the Excel Spreadsheet as follows 15 Proteaceae Beauprea Beauprea gracilis Brongn and Gris 1871 i 16 4 17 E M 4 gt gt ImageCollection Z Images MyView Specimen SpecimenTaxonData nu m olumns A G are parents of child in Column H In this example
11. ContinentOcean Country and Locality Description all read Unknown Notes dwc occurrenceRemarks A free text field to enter additional notes related to the specimen record Specimen notes might include voucher label information i e DNA anatomical etc about a specimen or other information such as the duration of the collection trapping sessions noting a range of dates the process took place Specimen Description This column is auto generated Do not change it It provides the drop down list in the Image worksheet and so it makes the link between images and associated specimens The field is a concatenation of specimen sequence number genus species sex date collected locality Note This worksheet has 250 initialized rows for data If more rows are needed see the Additional Notes section of this manual for instructions on inserting additional rows 26 ph Sas owe Y Locality After completing the Image Collection worksheet proceed to the Locality tab These fields are linked to fields in other tabs so you will only have to enter unique locality data once Make sure data for locality coordinates are in the decimal form given in the examples for Latitude and Longitude in this section The Locality worksheet should contain detailed information about the localities where the specimens were collected The information entered in this worksheet provides the drop down list in the Specimen worksheet Explanation of how
12. a column Before altering the string SupportingData A 2 A 101 After altering the string SupportingData l A 2 A 111 Fig 13 Once the number string has been changed to reflect the newly generated rows select the OK button and close Ten more specimen parts may now be added to the list Detine Name Names in workbook SpecimenPart Country DevelopmentalStage Form ImagingTechnique LocalityName PreparationTechnique Sex SpecimenDescription SpecimenPart TypeStatus Refers to SupportingData 42 Figure 13 Alter Number String to Reflect New Rows 34 Hint Excel 2007 The same task of updating the drop down definitions is done by going to Formulas Defined Names Section Name Manager Click to open Name Manager reveals Name Manager Name A SpecimenDescription zW kj SpecimenPart Refers to X v 5upportingData A 2 A 75 Figure 14 Name Manager Excel 2007 Change the column number in the Refers to field see above or click the Edit button and update the column number there The result is the same 35 Ph x q Ou Additional Notes Inserting new rows into the worksheets The Specimen Locality and Image worksheets have 250 initialized rows while MyView has 30 rows to be populated from a drop down list and 200 rows for creating new views If you need to add more entries for auto generated columns columns that reference columns from other sheets and displ
13. and Images this is done easily with the first worksheet Image Collection This External Links worksheet allows unique links to specific objects Type Description for External Link required only if this sheet is used Choose from the drop down list the Type Description for External Link The choices in this column will change to match the Object type selected For example If an Object Type of Specimen View or Locality is selected the Type Description choices will contain the description field from that associated worksheet Specimen will contain the description field from the Specimen Worksheet View will contain the description field from the View Worksheet etc If an Object Type of Image is selected the Type Description choice will be the image_file name os PhS Se A y w Type of External Link required only if this sheet is used Choose the Type of External Link from the drop down list The choices are Google map for Locality object and GenBank for Specimen object For adding new types of external links like University collections refer to the Supporting Data worksheet and add the desired entry Label for External Link required only if this sheet is used Type a short descriptive label The label is the name of the link that appears on the Morphbank page Appropriate labels would include the name of the institution that the link is going back to or the name of the gene region that is linking to an accession number Examples Goo
14. ank and go to gt help gt namequery With this search feature copy and paste in a list of names to be searched The output is divided into names found names not found and is available for download in csv format Use this information to construct a list of names to fill out this worksheet 1 If ataxon name is a already in Morphbank and b only in Morphbank one time then e The only columns necessary to fill in for that name are Family column A and Scientific Name String column H which is the taxon name exactly as it appears in Morphbank without the author year e Note the Family column helps to resolve parentage in cases where a genus name exists in more than one Kingdom 2 Ifa taxon name is not in Morphbank check the parents of that taxon name to see if the higher rank names are in the database e For example if the species taxon name desired is not in Morphbank but the Genus is the worksheet needs only one line of data to add that name see examples e Ifthe Genus and species are not in Morphbank then one row of the worksheet adds the Genus the next row the child Species and so on 3 Parentage for a new taxon name to be added to Morphbank is given in columns A G To add large numbers of names at the rank of Genus or lower the SpecimenTaxonData sheet is efficient Ideally the Specimen TaxonData worksheet needs to be completed after the ImageCollection and Locality worksheets This worksheet can also be used on
15. any newly generated rows accessible so the values show up as drop down selection options on the appropriate worksheet In this example new rows were added to the MyView worksheet See section above titled Additional Notes to learn how to add additional rows To make these new Views appear in the drop down list of Column C in the Image worksheet follow these steps 38 Ph x y e From the top menu choose Insert gt Name gt Define Fig 18 Insert Format Tools De Rows Columns Worksheet il Chart Fle Function X Picture gt Paste Q Hyperlink Ctri K Create v S Apply Label Figure 18 Top of Page Menu Insert gt Name gt Define e Inthe Define Name window select the auto generated column name from the worksheet where the new rows where generated If new rows were added to the Specimen worksheet select SpecimenDescription f new rows were added to the Locality worksheet select LocalityName If new rows were added to the MyView worksheet select ViewName Fig 19 Detine Name Names in workbook ViewName Form ImagingTechnique SA PreparationTechnique Sex SpecimenDescription SpecimenPart TypeStatus Refers to MyView J 2 3 301 Figure 19 Define Name Menu 39 e At the bottom of the Define Name window there is a field called Refers to There will be a string of characters that look something like View 2 J 301 This indi
16. ay drop down list follow this procedure Images Worksheet If more than 250 images are to be entered the user will need to add more initialized rows to the images worksheet Add the new rows using row 250 as shown before putting any data in row 250 To Add new rows e Select all of the cells in the last auto generated row last row that can contain data by clicking on the cell in column A of the last initialized row and dragging to column F of that row The row will now be highlighted Fig 15 Figure 15 Highlight the Last Row of Cells e Move the mouse to the right lower corner of that last cell of the row you just selected where the dot is The cursor will be shaped like a Plus sign 36 Click on the dot and drag the cursor down the number of rows you wish to add Select Copy Cells option from the drop down menu Fig 16 Figure 14 Click on indicated symbol to reveal drop down list If there was information in the last auto generated row that information has been copied to the new rows You can write over the information or remove it using clear contents To remove data select and drag over all the rows and columns with the unwanted information to highlight them Do not highlight and delete column A Image Sequence Number and then right click or apple click and select clear contents from the pop up menu Clear contents removes data but not the und
17. cates that the name ViewName is associated with column J row 2 through column J row 301 of the MyView worksheet Alter the last number in this string to reflect the value of the last row that was added For example if you added 10 new rows the string would look like View 2 J 311 Fig 20 e Once the number string has been changed to reflect the newly generated rows select the OK button and close Denne Name Names in workbook ViewName Form ImagingTechnique LocalityName PreparationTechnique Sex SpecimenDescription SpecimenPart TypeStatus Refers to MyView J 2 J 811 Figure 17 Definition Changed to Reflect the 10 New Rows 40 Ph Se ry y Hint Excel 2007 In Excel 2007 the same task of updating the drop down definitions is done by going to Formulas Defined Names Section Name Manager Click to open Name Manager reveals Name Manager Name A E ObjectType Wa z Vu oe SpecimenPart lt Refers to X ov Myview B 2 B 253 Figure 21 Definition Changed to Reflect the 10 New Rows Change the column number in the Refers to field see above or click the Edit button and update the column number there The result is the same 41 os PhS SAS p x Hy w How to Save and Deliver the Files For each image set with different release dates create separate folders Name each folder as desired for example ImageCollection1 ImageCollection2
18. cified file names must exactly match the file names for the images delivered with the Excel workbook Do not leave blanks in the image file name use_underscores to name the images with more intuitive names Please put all images in the same folder Note that if the images are tiff it is best is if the colorspace is RGB and not CMYK or grayscale Photographer Column G Free text field to enter the name s of any photographer s Please separate multiple names by commas This is a new field in v 3 of Morphbank eol set to 1 or 0 Column H Morphbank is an eol collaborator and by default images in Morphbank are harvested for display at eol Note well images only go to eol after they become public in Morphbank Sometimes a Contributor s images may already be at eol or a given set of images may not be suitable for eol In this case enter a 0 zero in this field Enter 1 for images to go to eol as soon as they are public Note This worksheet has 250 initialized rows for data If more rows are needed see the Additional Notes section of this manual for instruction on inserting additional rows If more than 300 rows are needed split the data set into a separate workbook 13 eres 0 MyView The MyView worksheet has 10 columns and consists of two parts In the first section the submitter can choose an existing Morphbank view from the drop down list located in the first column MyView Name the rest of the columns will be
19. cimen belongs Make sure that all codes used in this column are also given on the Image Collection worksheet together with the full name and address of the collections Catalog Number suggested dwc catalogNumber Enter a unique alphanumeric value which identifies the specimen record within the collection It is recommended that this value provides a key by which the actual specimen can be identified If a biological specimen individual organism is represented by several collection items for instance representing various types of preparation this value should identify the individual collection item Previous Catalog Number dwc otherCatalogNumbers Enter a previous catalogue number if the specimen was earlier identified by another catalog number in the current catalog or atin another institution catalog A fully qualified catalog number is preceded by Institution Code and Collection Code with a space separating each sub element Referencing a previous catalog number does not imply that a record for the referenced item is or is not present in the corresponding catalog or even that the referenced catalog still exists This category pertains mainly to museums or personal collections Related Catalog Item Enter a fully qualified identifier of a related catalog item a reference to another specimen A fully qualified identifier consists of Institution Code Collection Code and Catalog Number with a space separating each of the three sub ele
20. d from a Philips SEM system need to be modified to appear correctly in Morphbank See warning note below Photoshop psd images should be flattened and saved as one of the image file types above WARNING Philips SEM users Image Display Problem Philips SEM machines utilize non square shaped pixels so when the images are outside of Philips software they are distorted slightly To Fix The images need to be resized from 1424X968 to 1424X1064 for high resolution images and 712X484 to 712X532 for standard resolution Philips has a small conversion program called XL Sitretch or images can be resized manually with image manipulation software such as Photoshop Note We suggest all applicable data fields be completed This improves the reliability and accuracy of data searches within the Morphbank database Additionally great care should be taken to make sure all entries are as complete and precise as possible Inaccurate workbook pages require corrections which will mean delays in importing the data to the database Numerous inaccuracies in the submitted workbook may result in its return to the submitter for review and correction ph K Od Data Entry Strategies e Organization folder It is helpful to place all the images that will be uploaded to Morphbank together in a folder on your machine The organization of the images in this folder influences the order of the image data input into the Excel spreadsheet Having these
21. edu for help To make newly entered items in any Supporting Data column visible in a given drop down list you need to follow this procedure Making Supporting Data accessible Example 1 Excel 2003 e From the top menu choose Insert gt Name gt Define Fig 11 14 Insert Format Tools De Rows Columns Worksheet ill Chart Je Function Picture gt Paste N 2 Hyperlink Ctrl K Create v S Apply Label Figure 11 Adding extra cells e Inthe Define Name window select the column name from the worksheet where the extra data was will be entered If new rows are needed for Specimen Part select that name from the list Fig 12 e Atthe bottom of the Define Name window there is a field called Refers to There will be a string of characters that look something like SupportingData A 2 A 101 Define Name Names in workbook SpecimenPart Country DevelopmentalStage Form ImagingTechnique LocalityName PreparationTechnique Sex SpecimenDescription l TypeStatus hy Refers to SupportingData 4 2 4 101 Figure 12 Define Name 33 Ph Sp Ie q This indicates that the Specimen Part data is associated with column A row 2 through row 101 of the Supporting Data worksheet Alter the last number in this string to reflect the value of the last row that is needed for the extra data For example if 10 extra entries are needed for the Supporting Dat
22. erlying formatting that creates drop downs 247 246 1 T A T A T A 1 248 247 1 1 iit 1 H tilt 1 tiiit 248 1 H tii 1 H 1 H 1 H 249 1 iiiit KEA KEA KE tii SSS iE a E 4 gt i ImageCollection Images View Specimen Locality 7 SupportingData ProtectedData I lt Figure 15 Newly Generated Rows 251 255 y Specimen Locality and MyView Worksheets If adding more than 250 specimens or localities or more than 200 extra views the user will need to insert more initialized rows to the appropriate worksheet The process will include adding new rows and then making sure the new information in those rows is accessible by the other worksheets Add new rows Follow the instructions above for adding new rows to the images worksheet to add new rows to the MyView worksheet The results will look something like fig 17 It is important now to make any new rows appear in their respective drop downs gt NN Smagetdlecton Images Myview Spaceman Z Uocalty Z Exteraiiris Sunportngoata_ Figure 16 Ten New Rows Added to the MyView Worksheet Only Columns F J Showing Making Extra Rows accessible Example 2 Excel 2003 The drop down menus on other worksheets use the information in the auto generated column last column on the Specimen Specimen Description Locality Locality Name or MyView View Name worksheets to supply information to other worksheet drop down lists It is necessary to make
23. es is added Note that the specific epithet of the species is placed in column D specific epithet Columns A B and D here with Vespidae NewGenus newspeciesepithet indicate the parent of the new subspecies name in column H Rows 9 13 show how to add sp names temporary names 20 Ph si Fa Hibiscus newepithet ssp subspecies Hibiscus newepithet ssp subspecies var iota _ Hibiscus newepithet Hibiscus Hibiscus Heteropogon Dichanthelium Echinochloa NewGenus Subgenus NewGenus Subgenus speciesepithet Hibiscus newepithet Hibiscus newepithet ssp subspecies Hibiscus newepithet ssp subspecies var iota Hibiscus newepithet ssp subspecies var iota f delta Hibiscus newepithet newsubspecies _ Hibiscus sp alpha Hibiscus sp leon1 Circaea Cuttivar Spiraea betulifolia Cultivar Aira aff elegans Panicum cf alatum Heteropogon near contortus Dichanthelium boscii Echinochloa elliptica near gamma Echinochloa elliptica aff delta X Genus X Genus species Hibiscus x species i Hibiscus speciesa x speciesb Hibiscus speciesa x Hibiscus speg Figure S3 Sample Plantae Specimen Taxon Data Add children Figure S3 gives examples for how to add various types of names at various ranks The rows have been highlighted for clarity In row 2 a NewGenus is added under the family Malvaceae Row 3 shows a new Subgenus added under the NewGenus Notice the Subge
24. et must match EXACTLY with the image filename you upload to Morphbank to the website to the ftp site or via CD DVD For best practice the filename of the image must NOT contain spaces The filename may_contain_underscores If both uppercase and lowercase letters are used in a given filename these must be the same in the spreadsheet Entering link data This is the final step in the population of the Morphbank workbook This worksheet is optional and is for those users who want to cite more links to the entered data Specimen Image Locality or View Note that the mageCollection worksheet has 3 possible URLs 1 institution link and 2 project links that are associated with all images and specimens in the workbook if the fields are used Note If changes are made to the location information you must manually update the changes to the specimen and image information If changes are made to the MyView sheet the My View choices on the Image worksheet have to be reselected from the drop down Changes made in one area of the workbook are not automatically reflected in other areas in the workbook Ph Sak oe q Image Collection The mageCollection worksheet allows you to provide general information about your collection of images Fill out this worksheet first 4 a Cc 1 2 orphbank Data try Workbook Contributor frst namelast name ony _ 6 Submitter first_name last_name only 7 Release date yyyy mm dd
25. gle Map CO1 AMNH External Link required only if this sheet is used Provide the exact name of the external link URL The accuracy of the provided data will be crucial for a proper linking from to Morphbank Users are responsible for maintaining their own links i e replacing updating or correcting outdated incorrect or otherwise broken links This can be done through the Morphbank web interface Edit External Links after the images are uploaded to Morphbank External Link Notes optional This is a free text entry to further describe the usage of the link An example would be to make a comment about an institution that is being linked to NOTE Be sure to have an object created before adding an external link If any changes are made to the spread sheet it is necessary to re choose the description to which the external link is associated with 31 W gt Zy S Supporting Data The Supporting Data worksheet provides the data for the dropdown lists that can be updated Specimen Part View Angle Preparation Technique Imaging Technique Continent Ocean Developmental Stage Form Type Status and Type of External Link Each of the columns can be updated by just entering the desired value in the first empty cell of that column 10 Cercus and abdominal tergum 9 11 Foreleg 12 Forelegs 13 Forewings 14 Gula 17 Herbarium specimen 18 Hind fernur 19 Hind leg Dorsolateral from left Lateral Lateral from left Latera
26. ked to fields in other tabs so you will only have to enter unique Locality data once Make sure any data for Locality coordinates are in the degrees decimalized format given in the examples in the Locality section of this manual There are many online resources for translating degrees to decimal One example is http www jeeep com details coord Entering specimen taxon data After entering the Locality data enter all taxon names associated with the specimens and images to be uploaded Each distinct taxon name only needs to be entered once If names at rank higher than genus need adding to Morphbank there are options other than the spreadsheet Names at rank of Suborder or lower can be added via the web interface In the event names of rank higher than suborder need adding contact mbadmin scs fsu edu Entering specimen data After entering the Specimen Taxon Daita proceed to the Specimen tab As in Locality fields in this worksheet are linked to drop down menus in other tabs Drop down menus are provided for many of the specimen fields If an option you would like to input is not provided in the drop down menu proceed to Supporting Data tab and modify the contents of the category as necessary o Notice that Locality is a field here this field links to the data entered in the Locality worksheet Choose the locality that suits the particular specimen you are working with this is the reason why you filled in the locality data first If y
27. l from right Left anterior right posterior Left dorsal Lef dorsal right ventral Left posterior right anterior Left ventral right dorsal Posterior Posterodorsal Posteroventral Right dorsal left ventral Ventral ir dried gold coated Cleaned in absolute ethanol Cleaned in absolute ethanol air dred mounted in Euparal Cleaned in ammonia air dried gold coated Cleaned in ammonia mounted in Euparal Cleared in KOH mounted in Euparal No preparation UNKNOWN Reflected light macrophotography Reflected light sean SEM Transmitted light brightfield 20 Hind legs Figure 9 Supporting Data Worksheet Columns A D 2 Auto Montage eee 3 Reflected light macrophotography 4 Reflected light scan 5 SEM 6 Transmitted light brightfield Holotype Paratype Final instar larva Figure 10 Supporting Data Worksheet Columns D H In this worksheet only a limited number of extra entries can be made in any particular column because some extra cells have been preformatted to be included in the resulting drop down For Specimen Part there are 100 initialized cells for extra entries for all other columns there are 20 cells for extra entries If you need to add more than the pre formatted number of extra cells it is necessary to update the drop down definitions so new values show up as drop down selection options on the appropriate worksheet Please feel free to contact 32 ges S 5 CA q mbadmin scs fsu
28. ld decide the highest possible applicable taxon in which they have confidence that the terminology for that view is relevant In this case lateral habitus may be useful as a view name through Hexapoda but may not necessarily apply to images of the side view of all animals This information is required Note This worksheet has 30 rows for existing views to be chosen and 200 more for new views to be created If more rows are needed see the Additional Notes section of this manual for instructions on inserting additional rows Be sure not to use the same view twice by only applying a slight change If almost the same view is needed even if only one field is different create a separate view On the Image sheet never change the existing view which was chosen for some other image The result will affect the upload by omitting some of the images that will now appear with invalid views 16 orPhe SpecimenT axonData All taxonomic names used in this upload need to be entered in this sheet Check the database for names before filling in the SpecimenTaxonData worksheet To check just a few names login to the website at http www morphbank net gt header menu gt tools gt submit gt taxon name This opens Taxon Search Enter the taxon name and click to search and if not found be sure to check if the parent is in Morphbank or not If more than 20 or so names need checking use the Name Query feature instead Login to Morphb
29. ments Relationship Type Enter a string named value that specifies the relationship between the specimen and the related catalog item Example of possible values include parasite of epiphyte on progeny of etc 25 os PhS Se el By w Collection Number suggested dwc recordNumber Enter an identifying number a string which was applied to the specimen at the time of collection observation by the collector This number links different parts preparations of a single specimen and field notes with the specimen Collector s Name suggested dwc recordedBy If Known enter the name s of the collector s responsible for collection of the specimen or taking the observation Separate each collectors name with a comma Example John Smith Jane Doe Date Collected Enter the date when the specimen was collected The date format should be yyyy mm dd If the day is unknown enter yyyy mm 00 or if the month is unknown enter yyyy 00 00 Locality required Enter the locality from which the specimen was collected This column is a drop down list that comes from data entered in the Locality worksheet Each item in the drop down list contains the locality sequence number followed by the locality description To populate this column first enter the data in the Locality worksheet and then choose the appropriate option from the drop down list If the locality is Unknown create a locality on the Locality worksheet where
30. mine Locality Description required Enter the name of the Region Province County Place and displacement from this name if applicable from which the specimen was collected Examples FL Tallahassee Apalachicola National Forest FL St George Island The locality description should correspond to label data where possible Latitude dwc decimalLatitude Enter the latitude of the locality in degrees decimal format for example 40 446195 79 948862 Note that is understood Convert minutes and seconds to a decimal part if applicable The number entered should be between 0 0000 and 90 0000 Conversion websites exist that convert degrees to decimal One example site is http Awww jeeep com details coord Longitude dwc decimalLongitude Enter the longitude of the locality in degrees decimal format for example 40 446195 79 948862 Note that is understood Convert minutes and seconds to a decimal part if applicable The number entered should be between 0 0000 and 180 0000 Conversion websites exist that convert degrees to decimal One such site is http www jeeep com details coord Locality Name Auto ted Do not ch qeil M Information Withheld 4 4Locali ExternalLinks SupportingData 7 lil Figure 7 Locality Worksheet Columns G M Coordinate Precision dwc coordinatePrecision Enter an estimate of how tightly the longitude and latitude of the collecting locality was specified Express the p
31. n the images to which you plan to apply this view Example If you enter adult as the developmental stage for the view you cannot apply this view to an image of a larva if you need to apply a similar view to a larva you need to create a new view entry 15 Sex required dwc Choose one option from the drop down list The option you choose may or may not be one you entered in the Sex column in the Specimen worksheet for the specimens in the images to which you plan to apply this view For example if a Specimen is a hermaphrodite a given image of that specimen may show the male or female part of the organism Form required Choose one option from the drop down list The option you choose should be the same as the one you enter in the Form column in the Specimen worksheet for the specimens in the images to which you plan to apply this view Examples queen worker exposed You may choose indeterminate if the view does not apply to a specific morphological form in which case you can apply the view to images of specimens of any morphological form View Applicable to Taxon required Enter the name of the highest taxon to which this view is applicable It is possible for a view to be applicable outside of the user s immediate taxon of interest For example the view name of lateral habitus when photographing a wasp is relevant for Insecta but it can also be applied to Arthropoda Hexapoda and perhaps Animalia The user shou
32. nk to all the image and specimen records created as a result of the provided data for upload 10 Ph Sen s owe 4 Images The mages worksheet should be the last worksheet filled out This is the heart of the data entry process and may take the most time The Images worksheet records information about the images in the collection This worksheet has five columns B F to populate and 2 new optional columns G H The explanation of how to populate them is given below spor 1 Number Description Name _ Magnification Info Image file name Fill out this Image worksheet last If more rows are needed see the Addition Notes section of this manual If more than 300 rows are needed divide the upload into another workbook Figure 3 Images Worksheet Image Sequence Number A number that corresponds to the order of input made in the Images worksheet This column is auto generated Do not change it Specimen Description required Choose a specimen description from the drop down list which is auto generated from the Specimen worksheet If necessary go to the Specimen worksheet to add new specimen entries If there is more than one image for a given specimen we recommend that you enter these images sequentially so they can easily be linked to the same specimen record However this is not strictly necessary as long as you link all of the images to the correct specimen record Note that
33. nus must be in parentheses 21 gt q X A new species is added in row 4 under the Subgenus Note for these rows how the columns A B and C are the parents of the children in column H In rows 5 8 a new species subspecies variety and form are added The rank indicators must be ssp var f if you wish to nest them as they are here in order for them to insert correctly Again note how the parentage is indicated parsed in columns A F for rows 5 8 Subspecies can be added without indicators as in row 9 but no lower rank names can be added under it Temporary names using sp or sp may be added as shown in rows 10 and 11 Adding cultivar names is illustrated in rows 12 and 13 ICNCP must appear in column M for these names to insert as cultivars Rows 14 19 show how names are added that have rank qualifiers In these examples the rank qualifier prefixes are aff cf near and Notice they have no dots after them In row 24 a rank qualifier suffix sensu lato appears Hybrid names are shown in rows 20 24 22 Specimen The Specimen worksheet is associated with the Specimen table in the Morphbank database The data entered here should provide information about the specimen and the parties involved in the collection of it This worksheet has 24 columns Below is an explanation of how to populate each one of them Specimen Sequence Number do not alter T 2 M 4 gt h ImageCollection
34. om version of the workbook with a given set of views contact mbadmin scs fsu edu Magnification Enter a positive decimal number that corresponds to the magnification of the image The magnification is calculated by dividing the size of an object as it appears on the image when the image is rendered at normal or native size 100 by the actual size of the object Example if the leg of the specimen is 0 5 mm long and on the image it appears to be 20 mm long the magnification is 20 0 5 40 If possible specify the magnification for all images particularly if you do not have a scale bar in them This is a numeric field no text characters Example 20 is permitted not 20x Copyright Info required Enter the name s of the person s organization who owns the copyright of the image or who could give a user of the Morphbank system information about the image copyright Include the person s Morphbank username and or email if possible This information makes it easier for anyone interested in contacting someone regarding copyright Example Janice Doe jdoe scs fsu edu Image File Name required Enter the exact name of the image file corresponding to this entry in the worksheet If data entered here is incorrect it will be impossible for Morphbank to link the metadata specimen locality etc with an image The 12 os PhS Se ral Zy w format should be image_name image_type Image type can be jpeg gif tif bmp etc The spe
35. orphbank Check the Publications in Morphbank before filling out the worksheet If it s already there note the id and enter it in the workbook Publication Pages optional If known enter the page number s where the name appears in the publication Names may be added to Morphbank without complete publication data Trade Designation Names optional For cultivar purposes use this field to enter a cultivar s Trade Name Nomenclatural Code required only if a cultivar name is added If known enter the nomenclatural code the taxon name follows such as ICBN ICZN ICNCP or other appropriate code If name to be added is a cultivar this field must read ICNCP Name Source optional If taxon name data is gathered from another taxonomic name server database enter that information here such as TROPICOS IPNI uBio World Spider Catalog etc Note well for Morphbank Publication Id If using this field it greatly assists the workflow if one adds all the needed publications to Morphbank before filling out the worksheet Names may be added to Morphbank without complete publication data Fields lettered O are optional with one exception If adding a cultivar name column M Nomenclatural Code must read ICNCP 19 Ph SA F N q Example 2 adding typical names in kingdom Animalia pecific epithet _ ssp var forma ScientificName Stri NewGenus NewGenus Subgenus 1 E Genus Vespidae Ves
36. ou have a lot of different taxa which you may this tab is eventually going to have a great deal of data associated with it Entering view data Next visit the My View tab This worksheet is split into two parts In the top part users can choose a view from a drop down list of existing views in Morphbank Check to see that the views needed are listed If the views currently in the spreadsheet are not suitable add new views using the second part bottom half of this worksheet Entering image data Next proceed to the Images worksheet This is the heart of the whole process and quite possibly may be the place you spend the most time Under Specimen Description choose from the drop down menu the specimen descriptor of the images you are going to input This links to the data in the Specimen worksheet and that is why the Specimen data is populated first Magnification Copyright Information and Image File Name all have to be manually entered My View Name is a drop down field and is linked to the MyView worksheet Make sure that the views needed in the drop down list If view data was entered in os PhS Se x y W the previous step and it is not on the list a mistake was made on the MyView Worksheet A final suggestion for this tab is in regards to the Image File Name if data entered here is incorrect it is impossible for Morphbank to link the metadata specimen locality etc with an image The image filename given in the spreadshe
37. pecimen part is featured in the image If the specimen part is not in the drop down list you can add it through the Supporting Data worksheet by adding a new entry to the Specimen Part column there View Angle required Enter choose from the drop down list a description of the view angle that corresponds to the view View Angle is from the viewpoint of the camera with respect to the object being imaged You can add new values to the drop down list by adding a new entry to the View Angle column in the Supporting Data worksheet Imaging Technique required Enter choose from the drop down list the imaging technique used for this view If the imaging technique used is not in the list you can add the value by adding a new entry to the Imaging Technique column in the Supporting Data worksheet Preparation Technique required Enter choose from the drop down list the imaging preparation technique used for the view This field captures data about the preparation done to the specimen if any in order capture the image s If the image preparation technique used is not in the list you can add the value by adding a new entry to the Imaging Preparation Technique column in the Supporting Data worksheet Developmental Stage required dw lifeStage Enter choose from the drop down list the developmental stage of the specimen presented in the view The stage you select should be the same as the stage entered in the Specimen worksheet for the specimens i
38. pidae NewGenus 4 Vespidae NewGenus Subgenus NewGenus Subgenus speciesepithet 5 Vespidae NewGenus NewGenus newspeciesepithet 6 Vespidae NewGenus newspeciesepithet NewGenus newspeciesepithet subspecies 7 Vespidae AnotherGenus 8 Vespidae AnotherGenus AnotherGenus speciesepithet 9 Vespidae AnotherGenus AnotherGenus sp 12345 10 Vespidae AnotherGenus AnotherGenus sp beta Gasteruption sp 1 Gelis sp A Gelis sp A subspecies 11 Gasteruptiidae Gasteruption 12 Ichneumonidae Gelis Ichneumonidae Gelis spA Images MyView Specimen SpecimenTaxonData L J K L M N 6 Examples to show how to add names at various ranks tName 1989 World Spider Catalog 2 7 genus Species2000 3 subgenus 4 5 8 species j 6 13 subspecies j 9 10 11 12 sp names 1 Jones 2009 M SupportingD Figure S2 Sample Animalia Specimen Taxon Data In the screen shot above a user wants to add a genus under the Vespidae family A search of Morphbank reveals this genus name is not in the database By placing Vespidae in the Family column NewGenus in column H is added to Morphbank as a child of Vespidae Next a subgenus is added under the NewGenus Note that in order for the software to understand the name is a subgenus it must be in parentheses In row 4 the species is added A different species is added in row 5 same genus And in row 6 the first subspeci
39. recision as a distance in meters that corresponds to a radius around the latitude longitude coordinates Leave the field blank if the precision is unknown cannot be established or is not applicable Minimum Elevation dwc minimumElevationInMeters Enter the minimum elevation of the locality in meters above positive or below negative sea level 28 os PhS lt ws Maximum Elevation dwc maximumElevationInMeters Enter the maximum elevation of the locality in meters above positive or below negative sea level Minimum Depth dwc minimumDepthInMeters Enter the minimum depth of the locality in meters below the surface of the water where the collection was made All material collected for this specimen record should be at least this deep Use positive number for below the surface and negative for above Maximum Depth dwc maximumDepthInMeters Enter the maximum depth of the locality in meters below the surface of the water where the collection was made All material collected for this specimen record should be at most this deep Use positive number for below the surface and negative for above Locality Name This column is auto generated Do not change it The content of it is a concatenation of locality sequence number and locality description This column is made for easy look up of localities in the Specimen worksheet Information Withheld dwc informationWithheld This column needs to be populated only when locality data
40. se the type status of the specimen If the Type Status you need to specify is not on the list you can update the list by making a new entry in the Type Status column in the Supporting Data worksheet After that the new type status should appear at the end of the list The type status indicates the kind of nomenclatural type that a specimen represents The type status should refer to the name given to the specimen in the next few columns The Morphbank system can store any number of determinations and type designations for a specimen contact Morphbank at mbadmin scs fsu edu _ if some of your specimens require more than a single type designation or determination Determined By dwc identifiedBy Enter the name s of person s who determined the taxonomic category of the specimen Add the names separated by a comma 24 S 5 F y w Date Determined dwc dateldentified Enter the date when the specimen was determined Use the format yyyy mm dd If the day is unknown enter yyyy mm 00 or if the month is unknown enter yyyy 00 00 Make sure the date is current or a past date Determination Notes dwc identificationRemarks Enter any notes related to the determination of the specimen Institution Code suggested dwc institutionCode Enter the code for the institution to which the collection belongs Collection Code suggested dwc collectionCode Enter a unique alphanumeric value which identifies the collection to which the spe
41. standard Developmental Stage required dwc lifeStage Enter choose from the drop down list the developmental stage of the specimen If the stage that you need to specify is not on the list you can update the list by making a new entry in the Developmental Stage column in the Supporting Data worksheet After that the new stage will appear at the end of the drop down list for Developmental Stage Form required Enter choose a description of the morphotype of the specimen Examples queen worker exposed Use Indeterminate if you do not wish to apply a specific morphotype designation to the specimen If your specimen is of a morphotype that is not part of the drop down list you can update the list by making a new entry in the Form column in the Supporting Data worksheet After that the new form will appear at the end of the drop down list Information about the Supporting Data worksheet is provided at the end of this manual Preparation Type dwc preparations Enter the type of specimen preparation if applicable This is the preparation of the whole specimen before incorporation into the collection Examples include Pressed and Dried and 70 ethanol Number of Individuals dwc individualCount Enter the number of individuals that were collected observed This is the number of individuals in the lot or container representing the specimen record Type Status required dwc typeStatus From the drop down list choo
42. the Specimen Description drop down list only contains an abbreviated description of each specimen If you have similar entries in the Specimen worksheet make sure that you link each image to the right specimen entry The easiest way to do this is to make sure that the first 11 os PhS SAS 2 x Zy y number in the Specimen Description the specimen sequence number in the Specimen worksheet is correct My View Name required Select the View describing the image from the drop down list The content of the drop down list is taken from the View worksheet The pre specified views in the View worksheet are those contained in the Morphbank system when the workbook was last updated by the Morphbank group One workbook features views pertinent to Animalia the other has Plantae views If you need to add one or more new views to describe your images simply add rows to the bottom half of the View worksheet Your new view will be available to all users of Morphbank after your data have been uploaded to the system When choosing a view name from the drop down list please note that the list is sorted alphabetically on specimen part so match this first before looking at the other data defining the view If the view data was entered in the previous step and it is not on the list a mistake was made on the View worksheet Care needs to be taken to ensure any new View options are properly linked to the Images tab If you would like help to create a cust
43. the species Beauprea gracilis Brongn and Gris 1871 is added to Morphbbank The parents Beauprea and Proteaceae are already in Morphbank Figure S1 Specimen Taxon Data Add a child Family required Enter the Family name here as it appears in the database Genus Subgenus Specific epithet ssp var forma required if Use these columns when needed to indicate parent of taxon name in column H If the taxon rank of name in column H is a subspecies then at least columns A B and D Family Genus and Specific epithet are filled out as parents of name in column H 18 Scientific Name String required Enter the scientific name here as it is to appear in the database Taxon Author Year optional Enter this information if known as it is to appear in the database No need to add it at all if taxon name is already in Morphbank as desired The software finds the only possible match via the string of text in column H ScientificNameString f the author year is entered for a name existing in Morphbank it too must match exactly as it appears in Morphbank or the name with author year goes into the database again Morphbank Publication Id optional In Morphbank log in gt select group gt submit gt publication Enter the publication data if Known for the taxon name click submit note the publication id and enter it in the spreadsheet Note for any given taxon name the journal it was published in may already be in M
44. to populate each of its 14 columns is provided below Locality Sequence Number cannot be altered equired ContinentOcean r Select continent o drop down list If ContinentOcean v cean from the a alue needed is S oon aa mwn alt if lorphbank missing contact M VN or Not HINT use UNKNO ied for 11 10 Applicable as neec 12 11 specimens w o loc ality data Figure 6 Locality Worksheet Columns A F Locality sequence number A number that corresponds to the order of input made in the Locality worksheet This column is auto generated Do not change it Continent Ocean required Choose the continent or ocean where the specimen was collected from the drop down list If you need to enter a continent ocean not provided in the list you can make a new entry in the ContinentOcean column in the Supporting Data worksheet After this the new entry should appear at the end of the list Country required Choose one country political unit from where the specimen was collected The drop down list contains names of currently recognized countries If you need to add new entries to this list please contact Morphbank at 27 PhS SAL p x Oe mbadmin scs fsu edu For old specimens we recommend that the original country of collection if applicable is added to the Locality Description column and that the Country column is used to provide the current political unit for the locality if this is possible to deter
45. y locality description region province county and place and latitude longitude data if available e Information about the specimen and the parties involved in the collection of it including basis of record sex developmental stage form preparation type number of individuals collected or observed type status family collector s name date collected locality e Taxonomic name data for the specimens needs to be checked in the Morphbank database and names not in the Morphbank system will need to be added via the web this spreadsheet or a name upload sheet if many names need adding Contact mbadmin scs fsu edu o Use NameQuery to check taxon names extant in the database http www morphbank net Help nameMatch e Information about the view of the specimen in an image including specimen part view angle imaging technique preparation technique developmental stage sex form and name of the highest taxon to which this view is applicable e Images in the collection and information pertaining to them including specimen description view name copyright contact photographer and image file name to be uploaded The images sent to Morphbank must be one of the following image types 1 Bitmap bmp 2 Joint photographic experts group jpeg jpg 3 Tag information file format tiff ph Son s Y X tiff images are best saved as RGB color and NOT indexed color or CMYK color mode or grayscale tiff images generate
Download Pdf Manuals
Related Search