This guide shows how to enter data directly into SCAN/LepNet portal for your collection and how to edit existing records. The YouTube video below illustrates the steps used in SCAN, complemented by a step-by-step written guide. Additionally, there is  Data Entry Guide written for the OpenHerbarium portal, although the dialog boxes look a little different than SCAN dialog boxes. Some people prefer to enter data into Excel and upload a csv version.  The issues with using Excel is because it is easy to make mistakes as well as Excel inserts code that can corrupt some fields when transferring to the SCAN database, and there is no controlled vocabulary (e.g. taxonomic names). It is easy to annotate records, but one should only delete records as a last resort. You should only enter records from individual specimens or lots where all the individuals are likely the same species.  Specimen labels should include the catalogNumber or a barcode that includes the catalogNumber.  If you delete a record the catalogNumber should not be used again. 

Entering and Editing Data

Data Entry Terms

Adding new record

Start by clicking on the field Catalog number and type the catalog number of the specimen. If the auto-search box is checked, a warning for catalog number duplicates will pop up. The next fieldAccession # is for cases in which a specimen has multiple cataloging numbers.

Collector Information   Collector info includes who collected and when a specimen was collected. In this section of the data entry form the fields that are recorded are: Catalog Number, Accession #, collector, number, date (of the collection event) and associate collectors.

In the field Collector type the collector(s) name with the following format:

Firstname Lastname = (Neil Cobb)   OR   Initial. Lastname = (N. Cobb)    OR   Initial.Initial. Lastname = (N.S. Cobb)

Capitalize first and last names. If there is an initial, make it capital and add a period. Add a space before the last name but NOT between initials.

• If you get a name that is only a last name, it needs to be entered as a new collector. This is because many last names are shared. Example: There is a J. T. Polhemus and a D. A. Polhemus, so if only “Polhemus” is on the specimen tag you don’t know which one the name refers to. Enter only ‘Polhemus”.
• If there is no information for collector on the label, enter “Collector unknown.”
• If there are two collectors, enter the first one on the collector field and the second/other authors in the associated collectors field.
• Associated Collectors field is for all other collectors on the label after the first.
  • Example: J. Blackaller, A. Perez, A. Sonia
• Under “Collector” = J. Blackaller
  • Under “Associated Collector” = A. Perez, and A. Sonia

Number: In this field type any other legacy number, besides catalog numbers, associated with the specimen.

Date: The date on the specimen (collection date). This field is used for the earliest date of collection only (=start date). If the collection date on a specimen is a range, then click on the little pencil figure next to associated collectors.

Enter range in verbatim date field, with two values separated by “to.” If dates are valid full dates, start and end day should be automatically calculated and the start date will also be placed in the date field.

Example
Specimen label = 25-29 X 12 or Oct. 25-29 2012 etc…

Enter as the following:
Date (start): 2012-10-25
Verbatim Date: 2012-10-25 to 2012-10-29

If the collection date does not include day or month, replace that space with 00.

Example:

Specimen label= December, 1993

Enter as:

1993-12-00

Latest Identification

Scientific name: This field requires at least genus identification. Once the genus is typed, this field will show a scroll down menu with species names. Select the species name from this menu. If the species genus name is not included in the scroll down menu, verify the species/genus name. If the species name is verified and still not found contact your museums SCAN Symbiota administrator to add a species/genus to the menu.

Author: This name section should contain the sanctioning author of the taxon. This should be linked to the appropriate Author Name article. This field will auto fill if the species name has been recorded. Usually no author is linked if there is only genus level identification or the species was misspelled.

ID Qualifier: A brief phrase or a standard term (“cf.”, “aff.”) to express the determiner’s degree of uncertainanty about the Identification.

Family: If specimen is not identified to species, this field is available for family of specimen. This field will auto fill if the species name has been recorded.

Identified by: Name of person who identified the specimen. Same rules as collector names, First Last (N. Cobb). For NAU specifically:

CPMAB is only entered for “Determined by” when there is no determination label giving credit to someone else

OR

When there is not a determination label on subsequent specimens but there is on the first insect in the unit tray (i.e. Determined by: V. Narakol, CPMAB).

Date Identified: If specified on specimen, date the specimen was identified. If date was not on the label then enter “No record”.

ID References: A list (concatenated and separated) of references (publication, global unique identifier, URI) used in the identification of the specimen.

ID Remarks: Any comments/remarks on the identification of the specimen.

Locality

This field is for any locality information found on the specimen labels. The initial fields are very self-explanatory: Country, state/province, county and municipality. The field locality is for the specific description of the place including: higher geography,  water body, island, island group, town, region, trap or site (ex. Pitfall trap #13).

Check box of Locality Security: Check this if the specimen is of special concern such that the location from which it was collected needs to be hidden.

Latitude/Longitude: The geographic latitude (in decimal degrees) of the geographic center of a location. Positive values are north of the Equator; negative values are south of it. Legal values lie between -90 and 90, inclusive. The geographic longitude (in decimal degrees) of the geographic center of a Location. Positive values are east of the Greenwich Meridian; negative values are west of it. Legal values lie between -180 and 180, inclusive. If the label has GPS coordinates then write them as verbatim in the “Verbatim Coordinates” section (ex. 42.5555, 108.5555). If these coordinates are given as a degree (with a ° symbol), then use the “Tools” button to calculate these values automatically.

Geolocate locality symbol: Launches geolocate. GeoLocate is a georeferencing tool that will generate coordinates from a text description of a locality. Clicking on the GeoLocate symbol will submit the country, state, county, locality, and verbatim coordinates to the GeoLocate web tool. GeoLocate will use this information to generate coordinates and error accuracy that best represents the locality. While specific knowledge of an area will often generate a more precise georeferencing, GeoLocate can still be useful for getting you into the general area which then can be fine tuned.

If no coordinates are given then you should Georeference (the process of finding coordinates to the best of your ability by using a map, “reference the geography”). It is acceptable to provide an initial set of lat-long coordinates and then have someone with extensive regional geographic knowledge with georeferencing expertise provide more accurate estimates for a batch of records.  Georeferencing can be a huge time sink especially if someone is not trained in georeferencing and has little knowledge of regional geography. If you decide to georeference each record that only has locality information then use the following protocol.

1. Make sure all of the locality data is typed correctly into each field: country, state, town and any higher degree of specificity.
2. Click on the GEOLocate symbol (swirly icon below) and a map will pop up to help you automatically find the coordinates.
   
3. Find the point on the map that best corresponds to the locality information. This may require re-typing the “locality string” or searching the map for the most accurate location. If need be, type in the closest major town in the “locality string” and hit enter. At the upper right corner of the map (white plus on a blue square) you can select between Google and Bing mapping options, some may offer a higher degree of topographic data depending on the locality.GEOLocate does not recognize street addresses – so Google Earth needs to be used for these.
4. Click on the “Place marker” button, then click the map to pin your locality. The green point is the one that will be read by the database, the red points are secondary possible points and do not affect your results. You can select a red point by clicking on it and it will turn green. The grey circle around the map is the zone of uncertainty.
5. Once you are confident that you have found the correct area you need to guess on the level of uncertainty. Click on the green point and a menu will pop-up, click  on thety”
6. Once you click, a grey arrow will appear above the circle – click and drag that arrow to an approximate area around the point. Collecting localities are very often on or near a road – approximate a few hundred meters around that road or area to give an idea of where the collecting may have happened.
7. Often a label only says “9 mi N…”, but there is no direct road north of that town. Take two measurements using the “measurement” button, one for the road and one for a direct path “as a crow flies”. The road measurement will be a minimum point, and the direct flight will bemaximum. Make sure your zone of uncertainty roughly encompasses both points.
8. Click on “Save To Your Application” at the very bottom of the page. All of your values will automatically be entered into the database.
9. Type your name in the “Georeferenced by” field.
10. Add a note in “Georeference Remarks” if the following apply.

• If only coordinates are on label but you looked up altitude write:
  1. “Coordinates on label”
• If only elevation is on label but you looked up coordinates:
  1. “Elevation on label”
• If both coordinates and altitude were on label (and you did not georeference): In “Georeference Sources” write “Label”.

Uncertainty (meters): The horizontal distance (in meters) from the given decimal latitude and decimal longitude describing the smallest circle containing the whole of the Location. Leave the value empty if the uncertainty is unknown, cannot be estimated, or is not applicable (because there are no coordinates). Zero is not a valid value for this term.

Google Maps symbol: Launches google maps. Click on the globe symbol located to the right of the longitude field to open an interactive map to aid georeferencing. This Google Maps interface has the standard control features that allows one to zoom, pan, and change map backgrounds. Clicking on the map will add a marker and place the decimal coordinates to the upper left of the map. Click the “Submit Coordinates” button to transfer the new coordinates to the data entry form. If coordinates already exist in the decimal lat/long fields when the map is opened, the map will focus and zoom into these coordinates. Clicking on another location on the map will move the marker.

Tools:  Option for entering GPS coordinates in different values other than decimal degrees. Enter in appropriate section and click the button to auto-populate the above long/lat fields.

Datum: The ellipsoid, geodetic datum, or spatial reference system (SRS) upon which the geographic coordinates given in decimal latitude and decimal longitude as based. Usually comes from GPS.

Elevation in Meters: Meters above sea level of the geographic location. Enter only meters if given, minimum elevation on left, maximum on right. If the elevation is in feet (Verbatim Elevation) use the option below. If there is no elevation you can try and approximate this value using Google Earth (GEOLocate does not include elevations so the standalone Google Earth software must be used for this). If you lookup only the elevation leave a note in Georeference Remarks.

Blue Arrows: For converting feet to meters – automatically populates corresponding fields, same minimum and maximum orientation as before. The number will only be converted if you add the prime dash symbol ‘ for feet after the #.

Verbatim Elevation: See above.

Verbatim Coordinates: The verbatim original spatial coordinates of the location.

Georeferenced By: A list (concatenated and separated) of names of people, groups, or organizations who determined the georeference (spatial representation) for the location.

Georeference Protocol: A description or reference to the methods used to determine the spatial footprint, coordinates, and uncertainties.

Georeference Sources: A list of maps, gazetteers, or other resources used to georeference the location, described specifically enough to allow anyone in the future to use the same resources. If you used the GEOLocate tool then this will automatically be populated and will read GEOLocate. If you use another method please indicate (Google Earth, Bing Maps, TopoZone, USGS, etc.). If the coordinates were on the label write Label.

Georeference Verification Status: A categorical description of the extent to which the georeference has been verified to represent the best possible spatial description.

Georeference Remarks: Notes or comments about the spatial description determination. This is where you must leave a remark commenting on where the coordinate data are from. See Georeference sources.

Miscellaneous

Habitat: A description of the habitat in which the collecting event occurred.

Substrate: A description of the surface or material on or from which the specimen was collected.

Associated Taxa: A list (concatenated and separated) of identifiers or names of taxa and their associations with the specimen.

Description: A physical description of the specimen at the time of collection. This often includes information that can be lost or difficult to observe after the collecting and preservation process.

Associated species entry aid: Symbol circled in red above. This is used to find any taxon ecologically/biologically associated to the specimen.

Notes: Any notes/comments regarding the specimen.

Life stage: The age class or life stage of the biological individual(s) at the time the specimen was recorded. Use terms such as immature or adults.

1. Single specimen or multiples of one sex. Enter “Adult” or “Immature”.
2. Multiple males/females/immatures of different sex or combination. Enter all of the data in the “Life Stage” field as follows: # Males, # Females, # Immature. Fully spell out these words, do not abbreviate. Add number BEFORE each gender and follow with a comma. For example:

6 Males, 3 Females, 3 Immature or

2 Males, 1 Female

Sex: The sex of the biological individual(s) represented in the specimen. Enter gender of the specimens ONLY if option #1 above was followed. If there are multiple genders in a vial leave this box blank.   EX. Use terms such as male, female, or hermaphrodite.

Individual count: The number of individuals represented. If this data is not written on the ID label, then you or an ID volunteer will have to count.

Sampling protocol: The name of, reference to, or description of the method or protocol used for collecting the specimen. Record the method that is on the label.  You can use this list of standardized terms to reference, do not abbreviate methods (and ask if you’re unsure what a label abbreviate means).

Preparations: A list (concatenated and separated) of preparations and preservation methods for a specimen.

Phenology: The reproductive condition of the specimen.

Establishment means: The process by which the specimen became established at the location.

Cultivated check box: Used for Plant databases, will be hidden in future versions of SCAN Symbiota.

Curation
This field is used for any known information on the preparation of the specimen.

Type Status: A list of nomenclatural types (type status, typified scientific name, publication) applied to the specimen. You will find this information on the ID label in the vial. E.g., “holotype” or “paratype” or “allotype” or just “type”.

Disposition: The current state of a specimen with respect to the identified collection.

Occurrence ID: An identifier for the specimen (as opposed to a particular digital record of the occurrence). In the absence of a persistent global unique identifier, construct one from a combination of identifiers in the record that will most closely make the occurrenceID globally unique.

Field number: An identifier given to the specimen in the field. Often serves as a link between field notes and the Event.

Owner Code: The name (or acronym) in use by the institution having ownership of the object(s) or information referred to in the record.

Basis of Record: The specific nature of the data record. Always will be “Preserved Specimen”

Language: Language in the specimen labels. Default is English.

Label Project: Used for printing labels. You can create a label project and print that set of labels after you’ve entered the data.

Duplicate Count: Only relevant to plant databases, will be hidden in future versions of SCAN Symbiota.

Processing Status: In this field there is a drop down menu with the following choices: No Set Status, Unprocessed, Unprocessed/OCR, Unprocessed/NLP, Stage 1, Stage 2, Stage 3, Pending, Duplicate, Pending Review, Expert Required, Reviewed and Closed. The collection manager or curator can use this field to review and accept/correct specimen records.

Follow-up Action

Go to New Record: To add a new record, select this option and click on add record.

Go to New Record and Carryover Locality Information: If several specimens have the same locality information, you may select this option and the locality information will carry to the next new record.

Remain on Editing Page (add images, determinations, etc): This option saves the information but it remains only on the editing page.