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\item Use the web interface
\begin{itemize}
\item to enter metadata pertaining to your data set (new sites,
species, cultivars, citations,
treatments, managements, or
cultivars); treatments);
\item to obtain a template appropriate for your data set.
\end{itemize}
\item Fill in the template with your data. There are four templates to choose from:
...
\textbf{This template must be modified before it can be used.} In particular, the column headings \verb|[trait variable 1]| \dots \verb|[trait variable n]| must be replaced by actual variable names that \textit{exactly} match names of variables in the database that have been marked to be recognized as trait variables. The number of these trait variable columns may need to be increased or decreased to accomodate the data set.
Some trait variables allow or even require corresponding covariate information to be included. Again, the column headings \verb|[covariate 1]| \dots \verb|[covariate n]| must be changed to actual covariate variable names, and the number of these columns may need to be increased or decreased to match the available information. As with the yield data templates, some columns may also need to be deleted. For a list of recognized trait variable names and their corresponding required and optional covariates, visit the trait
variable/covariated variable/covariates list at www.betydb.org. [TO-DO: Make this Web page.]
\item \href{https://docs.google.com/spreadsheets/d/1Bv4dAPKU6YDJ6yB0DC4bAmHoGxSLgKybMpTR7qBvCu0/export?format=csv&gid=0}{traits\_by\_doi.csv} --- As with the corresponding yield data template, use this template if you are uploading trait data and you wish to specify the citation in the file by doi or if you plan to specify the citation interactively (in which case delete the \verb|citation_doi| column). \textbf{Again, this template must be modified before it can be used.}
\end{itemize}
\item Use the web interface to upload your data set and insert it into the database.
\end{enumerate}
In \textit{In what follows, the term "field" always refers either to a column name used in the heading of the uploaded CSV file or to an entry in that column in some particular row of the file. On the other hand, and the term "column" may either refer to a column of data in the uploaded CSV file or to an attribute of a trait or yield datum in the traits or yields table of the
database. database.}
\subsection{Detailed CSV Data File Specifications}
\subsubsection{Required
fields}: fields}
\begin{enumerate}
\item For yields uploads, the only required field is a \verb|yield| column.
\item For trait uploads, there must be at least one column whose label exactly matches the variable name for the trait value being specified. (Leading and trailing spaces are permitted, but letter case must exactly match the name of the variable specified in the database.)
If this trait variable has any required covariates, columns for these covariates must be included.
\end{enumerate}
\subsubsection{Information that is required but that \textit{may} be specified interactively for the entire dataset.}
(Data \textit{Data values may be specified interactively only if there is a single value that pertains to the whole data
set.) set.}
\subsubsubsection{Information \textbf{\textit{Information that references existing database
entries} entries}}
\begin{enumerate}
...
\item If only one citation for the entire dataset exists, it may be specified
interactively by choosing a citation on the citations page instead of
including citation information in the CSV file.
\item Otherwise, specify the citation in the CSV
table, file, either by doi or by
author, year, and title.
\item If a DOI is available for all citations in the data set, the citation
corresponding to each row may be specified in a \verb|citation_doi| column. In
...
that is being used to determine how the data will associated with a
citation in the database.) Each value in the \verb|citation_doi| column must
exactly match the \verb|doi| attribute of some row in the \verb|citations| table except
that
letter case and leading and trailing spaces are ignored.
\item Conversely, if a DOI is not available for all citations in the data set,
or if it is preferred to specify the citation by author, year, and title,
then the \verb|citation_doi| column should \textit{not} be included and the columns
...
the data set, the treatment may be specified interactively provided that
the citation is specified interactively as well.
\item Otherwise, a \verb|treatment| column is required. The value must match an
existing \verb|name| column value in the \verb|treatments| table of the
database. database; moreover, this matching treatment must be consistent with the specified citation.
(Again, letter case, leading and trailing spaces, and extra internal
spaces are ignored when searching for a match.)
\end{itemize}
\end{enumerate}
\subsubsubsection{Other information} \textbf{\textit{Other information that may be specified interactively}}
\begin{enumerate}
\item Date
...
\end{enumerate}
\subsubsection{Other information that \subsubsection{Numerical Data (This is \textit{never} specified
interactively} interactively.)}
\subsubsubsection{Data \textbf{\textit{Data for
Yields} Yields}}
\begin{enumerate}
\item Yield
Every yield data upload file must have a \verb|yield| column. The data in
this column must always be a parsable non-negative number and must never
be blank. Scientific notation is not currently supported. As noted
above, the number given in the file is subject to rounding before being
inserted into the database.
\item Sample Size
An \verb|n| column is required if and only if an \verb|SE| column is included. The value must always be an integer greater than 1.
\item Standard Error
An \verb|SE| column is required if and only if an \verb|n| column is included;
this datum will be inserted into the
stat \verb|stat| column of the
yields \verb|yields| table,
and the
statname \verb|statname| column value will be set to "SE".
\end{enumerate}
\subsubsubsection{Data \textbf{\textit{Data for
Traits} Traits}}
\begin{enumerate}
...
unique entity id. Said another way, there is a one-to-one
correspondence between rows in the CSV file and resultant rows in the
\verb|entities| table, the table that keeps track of this grouping.) As with
yield numbers, the data in this column must always be a parsable
number, number
and is subject to rounding before being inserted into the database. In
addition, it must conform to any range restrictions on the value of the
variable.
...
\begin{itemize}
\item If any of the included trait variables has a required covariate, there
must be a column corresponding to that covariate.
\item For any of the included trait variables
that has an optional covariate, a
column corresponding to that covariate \textit{may} be included.
\item The template for traits uploads provides dummy column headings
\verb|[covariate 1]|, \verb|[covariate 2]|, etc., which must be changed to actual
...
\item Sample Size and Standard Error
To enter
n \verb|n| and
SE, \verb|SE|, add additional columns
\verb|[trait variable 1] n| and \verb|[trait variable 1] SE|, etc.
or
\verb|[covariate 1] n| and \verb|[covariate 1] SE|, etc. as needed.
Again,
values of \verb|n| must be at least 2, and columns for \verb|n| and \verb|SE|
must both be present or both be absent for any particular trait variable or
covariate.
\end{enumerate}
\subsubsection{Optional
data}: data}
\begin{enumerate}
\item Sample Size and Standard Error
As noted above, these are both optional, but if one of these is
included, the other must be included as well. In other words, the
column heading list must include both of \verb|n| and \verb|SE|
(or, in the case of traits, \verb|[trait or covariate variable k] n| and \verb|[trait or covariate variable k] SE|) or neither.
Note that if \verb|n| and \verb|SE| are not given fields of the uploaded CSV
file, the value of the \verb|n| column of the traits or yields table will
default to 1 and the \verb|stat| and \verb|statname| column values will default
...
\begin{itemize}
\item If a uniform value for the species is provided interactively when
uploading the data set, the cultivar may be specified this way as
well well, provided that it also has a uniform value for the whole data
set.
\item Otherwise, to include cultivar information in the upload file, both a
\verb|species| and a \verb|cultivar| column must be included. The values in
the \verb|cultivar| column are allowed to be blank (in which case a value
of NULL is inserted into the \verb|cultivar_id| column for the given row);
but if provided,
they the value must match the value of the \verb|name| column in
some row of the \verb|cultivars| table, and moreover, this row must be a
row associated with the species corresponding to the value given in
the \verb|species| column. Again, matching is case insensitive, and
