logo Calflora Observation Upload Help
Updated February 16, 2023
The Observation Upload Application is intended to provide a way to upload a dataset (e.g. a spreadsheet or another database) of plant observations into the the Calflora database.

    Note: If you would like to contribute a dataset to the Calflora Database, as a first step please describe the dataset using the Metadata Catalog / GIS Upload application. Then use this application (Observation Upload) to get the data into the database.

Each source dataset has a certain set of columns. The function of this application is to map the source dataset's column set into a form that can be stored in the Calflora database, filling all of the required fields for each record, and preserving as as many non-required fields from the source as possible.

The most interesting part of using the application is assigning input fields from the source dataset into their online database equivalents (Step 4). Below is an explanation of the various database fields.

Required Fields

    The following fields are required -- a record will not not go into the database if any of these are missing:
    Observer, Source, Observation Date, Taxon, and either Latitude, and Longitude, or UTM Easting, UTM Northing, and UTM Zone. Note that if some of these fields are not present in the input data, you can set a value that will apply to all records in the Constants section of the ASSIGN panel.

Important Fields

    The following fields are important for weed work, so please try to get them in if they are present in the input data in any form: Infested Area, Gross Area, Phenology, Cover (AKA Canopy Closure), and Distribution.

    For some database fields such as Infested Area, the application offers several methods for filling it. Choose the appropriate method depending on how infested area data is articulated in the input. For instance, there might be just one input field with a number in it representing square meters. Or, there might be an input field containing both count and units such as 0.25 hectares.

      1. If infested area data is separated in the input into a count field (15) and a units field (square meters), assign those fields to Infested Area Count and Infested Area Units.

      2. If the count is present in the input data, but units are constant throughout the dataset (square meters), then assign the input count field to Infested Area Count, and set the units in the Constants / Infested Area Units section of the ASSIGN panel.

      3. If count and units occur in the same input field (15 square meters), assign the input field to InfestedArea, which will split the input into count and units.


Size Constaints
    Very large uploads may time out before finishing successfully.
 

Using the Application in 8 Steps

    Step 1: Supply Input Data
      If you have data in spreadsheet, text file, or database, copy it from that application and then paste it into the big Input Data text area.

      If you have a shapefile, press UPLOAD FILES, and then browse for each of four component files: .dbf, .prj, .shp and .shx. Note that each of these component files is necessary. When you press UPLOAD NOW, the shapefile is uploaded to the server, taken apart, and the data is returned to the Input Data area of this application as Bar Delimited text. If the shapefile has lines or polygons in it, the line or polygon geometry will be saved on the server, and a pointer to it (geomid) will be included in the data. In this way, when you save the records (Step 6), each record will be associated with the appropriate original geometry.

      Note that for line and polygon records, the values of Latitude and Longitude that appear in the input data represent the centroid of the shape.

      Large Datasets: If you upload a large shapefile, the server will break it up into sections, and give it back to this application section-by-section. Note that field assignments, constant values and field value corrections that you make for the first section will continue to apply to the remaining sections. Go through the whole process (including saving the results) for each section.

    Step 2: Input Format
      Choose the appropriate format for the input data.
    Step 3: Parse Input Data
      Press the PARSE button. You will see if the data is being properly chopped up into fields. The assumption is that the first line of the input data contains the field names.
    Step 4: Assign Input Fields to Database Fields
      Press ASSIGN to open the assign panel. For each input field, select it by clicking on the name, then choose a database field to which it will be assigned. For instance, if there is an input field named PLANT containing scientific name, select it, and then select Taxon in the Database Fields list. Not all input fields need to be assigned to database fields.

      Press APPLY to close the assign panel. If all required database fields have not been assigned (or if you negelected to specify Gross Area Units, for instance), the application will display a warning. Proceed to Step 5 only when there is no warning.

      Referencing a Metadata Catalog Record:
      Enter a value into the Metadata Catalog # field to link the current dataset to a metadata catalog record. Metadata catalog record numbers begin with gmd.

      Press load constants to populate fields in the Constants section with values from the metadata catalog record. The following fields will be populated:

        Source Organization(s)
        Observation Date
        Location Description
        Accuracy: Meter Radius
    Step 5: Validate Plant Names
      When you press VALIDATE, the application will collect all values of Taxon (either present in the input data or set as a constant in the assign panel) and send them off to the server for validation. If there are any spelling errors, you will see a list of them, and have a chance to correct them in Step 6.

      Note that genus only names (Euphorbia) are acceptable. The word unknown is also acceptable. If you want to add the scientific name of a plant that is not currently in the database, put a star (*) in front of the name.

    Step 6: Convert Data
      Press CONVERT to convert the input data to a database compatible form. During the conversion process, you will see a warning if a particular record is missing any required field, or has an unacceptable value in any field. When this happens, you will have a chance to either delete that line of input, or correct the value.

       
      Field Value Correction: Suppose that the word Tamarisk occurs as the value of Taxon many times in the input data (and is flagged as invalid during Step 5). If you correct it to Tamarix the first time it comes up, then Tamarix will be the suggested correction every other time it comes up. Or, press the replace all button, and Tamarisk will be replaced by Tamarix wherever it occurs as the value of Taxon.

       
      At the end of this step, the results appear in a table at the bottom of the page. You can view the results through several different views, as a way of proofing the data before saving it. Use the Column Set selector to change view.

      Using Data Profiles: "Data Profile" means the set of field assignments, constant values and field value corrections you have made. Occasionally a source organization will produce more than one dataset with exactly the same field structure but different data. If this is the case, you can setup a data profile for the first dataset, save it, and then reuse it for the other datasets.

      The right time to save a data profile is after you have sucessfully made it through Step 6. To save a data profile, press Save Data Profile, enter a name, and press the SAVE button.

      The right time to restore a previously saved data profile is right when you reach Step 4. Press Restore Data Profile, choose a profile name from the drop down list, and press the RESTORE button. Then when you open the assign panel, you should see appropriate field assignments and constant values. (If you do not see any field assignments, then the data profile you chose is probably not appropriate for the data.)

    Step 7: Save Results
      Press the SAVE button. The records are written to the database as unpublished, so that no other users besides yourself can see them. When you press the Review and publish the saved records link, it will open the My Observations application, and show you the records you just saved in a table and on a map.
    Step 8: Edit and Publish Results
      From the My Observations application, you can publish all of the records, delete all of the records, or edit, publish or delete them individually.
FIELDS IN ALPHABETICAL ORDER

Comments
Anything of interest about the plant or site.

Common Name
The common name of the plant observed.

County
Full County name e.g. Riverside. This field is not necessary, as the server software will interpolate county from the point location.

Cover: If you drew an imaginary line around the outer boundary of the infestation, the amount of ground actually covered by the plant. AKA Percent Cover.


0absent
0 - 1trace
1 - 5
5 - 25
25 - 50
50 - 75
75 - 95
95 - 100

Cover Decimal
Use this field when the input has a number like 0.3 which should be interpreted as 30%. This field will convert 0.3 to 25 - 50.

Cover Percent
Use this field when the input has a number like 30 which should be interpreted as 30%. This field will convert 30 to 25 - 50.

Cover
Use this field if the input contains words like trace, low, moderate, or high instead of percent numbers.

Distribution Code
The distribution of the plant across the landscape.

CODEVALUE
1Single Plant
2Scattered Plants
MDense Monoculture
PScattered Dense Patches

Distribution
Use this field if the input contains words like single, individual, one, scattered, monoculture, or patch. The software will resolve it to the appropriate Distribution Code.

geomid
The geometry id # of an uploaded shapefile.
If you use UPLOAD FILES to upload a shapefile that contains lines or polygons, the geometry of each line or polygon is stored in the database during upload, and assigned an id #. The geometry id #s are returned to this application in the input data. geomid is a way of linking the record uploaded from this application with the geometry that came from the original shapefile. geomid numbers start with sg (shape geometry).

Gross Area Count
Gross Area: The area of ground covered by the plant, if you drew an imaginary line around the outer boundary of the infestation.

The number of units e.g. 15.

Gross Area Units
Acres
Hectares
Square Feet
Square Meters

GrossArea
Use this field if the gross area count and units are both present in a single input field e.g. 15 square meters.

Habitat
The primary habitat type at this location.

  • Forest: Tree-dominated, generally with a closed canopy (e.g., redwood forest, eucalyptus grove)
  • Open Woodland: Tree-dominated, but with open areas between the trees (e.g., oak woodland)
  • Scrub/Shrubland: Shrub-dominated, with few or no trees (e.g., coastal scrub, chaparral)
  • Grassland / Open Field: Grass-dominated, with few to no shrubs or trees
  • Stream bank / bed: The banks or dried bed of a stream, creek or river
  • Wetland: Herbaceous-plant-dominated, with standing water at least part of the year and wetland indicator plants (e.g., cattails, rushes, pickleweed marsh, vernal pool)
  • Open Water: Pond, lake, river, estuary, etc.
  • Beach / Dune: Generally some open sand, or there would be if not infested with iceplant or European beachgrass
  • Planted Area (Lawn, crop, etc.): An area purposely planted for agricultural, recreational or ornamental use.
  • Roadside: An area immediately adjacent to a road.

Integrator
An organization that collects records from other sources.

After a record leaves Calflora, Calflora is considered to be the integrator, or one of the integrators. Use this field to specify other organizations that acted in the capacity of integrator before the record reached Calflora, if any. Please use acronyms or short names. Examples: Cal-IPC; SFWMA

Infested Area Count
Infested Area: The area of ground covered by the plant if there were no spaces between the plants.

The number of units e.g. 15.

Infested Area Units

Acres
Hectares
Square Feet
Square Meters

InfestedArea
Use this field if the infested area count and units are both present in a single input field e.g. 15 square meters.

Latitude, Longitude
The center of the infestation, expressed in decimal latitude and longitude, WGS84 datum.

Location Description
A brief description of where the plant is.

Metadata Catalog #
The record # of an entry in the Metadata Catalog.
If the records uploaded from this application are described by a Metadata Catalog entry, please include the record number of the entry (top of the Constants section).

National Ownership Code
The land owner, manager, or steward.

CODEVALUE
OTH Other / Unknown
PVLT Private Land Trust
PVLA Private Landowner
PBLA Public Land
CGOV City or County Government
STAT State Government
USOT U.S. Government:
BLM * Bureau of Land Management
DOD * Department of Defense
NPS * National Park Service
USFS * USDA Forest Service

National Ownership
Use this field if the input contains words like private, trust, reserve, state, county, or national. The software will resolve it to the appropriate National Ownership Code.

Observation Date
Date the plant was observed. Dates are kept in the database in the form YYYY-MM-DD; for example, 2012-12-31. Note that this field accepts dates written in the database format, and also convert dates in any of the following formats to the database format:

    20121231
    12/31/2012
    31 Dec 2012

Observer
Name of the person who observed the infestation.

Phenology: The life stage of the plant(s) at time of observation.

Phenology Code

CODEVALUEEXPLANATION
S Seedling / rosette Young, non-reproductive growth
B Bolting When the flowering stalk begins to shoot up in plants with a basal rosette of leaves (thistles or mustards, for example)
F Flowering In bud or flower
R Fruiting Setting seed or fruit
D Dead / skeleton Dried/dead plant or dormant perennial
L Leafing out Producing new leaves (for deciduous perennial plants such as tree of heaven)
M Mature A perennial plant NOT in one of the above stages

Phenology
Use this field if the input contains words like mature, flower, bolt, seedling, fruit, dead, skeleton, or leaf. The software will resolve it to the appropriate Phenology Code.

Source
The organization(s) responsible for the record. This might include both the organization that paid for the survey and the organization that did the field work. The contributing organization is listed first. For instance

    SFPUC; Nomad Ecology

Taxon
The scientific name of the plant observed, without authors and with only the genus capitalized. For instance

    Acacia dealbata

Transcription Notes
A catch all database field for important fields in the input that do not fit anywhere else. More than one input field can be assigned to Transcription Notes.

UTM Easting, UTM Northing
The center of the infestation, expressed in UTM meters, WGS84 datum.

UTM Zone
10 or 11 for California.