Do-It-Yourself Data Entry

  • While we have awesome (paid) student interns that search the literature and standardize the entry of data into the FRED framework, we also encourage scientists to enter their own data and meta-data into FRED, both because you know your data best, and because you may have access to individual replicates or samples that may not have been included in a main publication that is publicly available. We have written a series of guidelines to help facilitate this below. 

    Note: The 'F000##' terminology used below refers to the unique IDs of associated columns. 

    1. Potentially helpful site metadata that do not fit into their own column go in Notes_Location (F01221).
    2. Other potentially helpful metadata that do not fit into their own column go in Notes_Miscellaneous notes (F00079).
    3. Aside from sentences and proper nouns, all text entries should be completely lowercase.
    4. The following columns should always be filled:

    F00003, F00004: Abbreviated article citation, Data source_Citation

    F00055: Belowground part
    Note: Write “CR + FR” if mean root diameter (F00679) is between 2.0 and 2.2.

    F00064: Root vitality_Roots living or dead

    F00071: Notes_Collection method

    F01185: Latitude_main

    F01186: Longitude_main

    1. The following columns are to be filled where possible based on outside sources:

      Fill the following columns in FRED based on The Plant List (www.theplantlist.org):

    F01286: Plant taxonomy_Accepted genus_TPL

    F01287: Plant taxonomy_Accepted species_TPL

    F01344: Plant taxonomy_Accepted subspecies_TPL

    F01289: Plant taxonomy_Accepted family_TPL
    Note: If family (F01289) is listed in the Plant List as Compositae, enter “Asteraceae” instead. If it is listed as Leguminosae, enter “Fabaceae” instead.

    F01291: Plant taxonomy_Accepted group_TPL

    F01413: Plant taxonomy_Species name unresolved
    Note: If the species name is not present in The Plant List, enter it in these columns anyway, but enter “absent” in the “Species name unresolved” column (F01413). If the species name is listed as unresolved, enter “unresolved” in the “Species name unresolved” column (F01413).

    Fill the following column based on the Angiosperm Phylogeny website (http://www.mobot.org/MOBOT/research/APweb/):

    F01290: Plant taxonomy_Accepted order_APW
    Note: If a species is listed as “Eulypod II” or “Polypodiales-Eulypod 1”, enter “Polypodiales” instead.

    Fill the following columns from the TRY categorical traits package, https://www.try-db.org/TryWeb/Data.php#3:
    Note: Use the read.CSV and write.CSV functions and the plyr package. If the species is not present in the TRY dataset, try searching for some of its synonyms that are listed on The Plant List. If you still cannot find it, make a note to this effect in Notes_Miscellaneous notes (F00079).

    F00042: Plant leaf habit_TRY

    F00041: Plant leaf type_TRY

    F00043: Plant photosynthetic pathway_TRY

    F00032: Plant growth form_TRY
    Note: If the “climber” column is marked in TRY, change the growth form to “climber”.
    Note: If the growth form column is empty in TRY, try searching for it in the Engelmann database, DOI: 10.1002/ecy.1569.

    F00044: Plant woodiness_TRY
    Note: If the “woodiness” column is empty in TRY, but the growth form is “tree”, “shrub”, or “climber”, enter, “woody”.

    Fill the following columns from the Taseski database, DOI: 10.1002/ecy.2614, https://esajournals.onlinelibrary.wiley.com/doi/full/10.1002/ecy.2614:

    F01456: Plant growth form_Taseski
    Note: The support column codes in Taseski are “F”, “C”, “P”, “E”, “H”, “M”, and “A.” In FRED, please list these codes as “free-standing”, “climber”, “parasite”, “epiphyte”, “hemi-epiphyte”, “holo-mycoheterotroph”, and “aquatic”, respectively.
    Note: If a species is not present in the Taseski database, list as “unspecified” in FRED.

    1. Refer to Root Trait List to see root traits and associated definitions to determine where your data best fit.
    2. If the units in your data differ from those in FRED, convert them, but only if there is a direct (i.e. mathematical) conversion; e.g., mm/cm2 to cm/m2. If the conversion requires making assumptions about the nature of the measurement (e.g., by assuming a soil bulk density), it may be necessary to discuss with CM Iversen (iversencm@ornl.gov) or ML McCormack (lmccormack@mortonarb.org). If assumptions are made, make a note about it in the notes column (F00079), or add a new column if necessary.
    3. Freely add new columns if needed to accommodate an associated statistical metric (e.g. n, SE, min, max, median) for an already-present trait.
    4. For new columns for traits that are not already present, defer to CM Iversen (iversencm@ornl.gov).

      Note: we will often use from a global synthesis to help us find appropriate papers; in this case we attribute that synthesis in a column made specially for that (‘Data set_Citation’, F00006). But we then go back to check each original paper (where we can find them, in English), and add those papers one by one to the database. These data are then attributed to the original work in column F00004 (‘Data source_Citation’). The reason we return to the original work is because we also want to harvest the ancillary data (soil characteristics, other root traits, etc.) and syntheses don’t often include everything from the original paper.