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## BETYdb: Entering new data through the web interface  Before entering data, it is first necessary to add and select the  citation that is the source of the data. It is also necessary for each  data point to be associated with a Site, Treatment, and Species.  Cultivar information is also required when available, but it is only  relevant for domesticated species. Fields with an asterisk (*) are  required.   ### Adding a Citation  Citation provides information regarding the source of the data. This  section should allow us to locate and access the paper of interest.  A PDF copy of each paper should be available through Mendeley.  1. Select one of the starred papers from your project's Mendeley folder.  2. The data to be entered should be specified in the notes associated  with the paper in Mendeley  3. Identify (highlight or underline) the data (means and statistics)  that you will enter  4. Enter citation information   * [Data entry form](https://www.betydb.org/citations/new) for a new  site: `BETYdb` → `Citations` → `new`  * **Author**: Input the first author’s last name only  * **Year**: Input the year the paper was published, not submitted, reviewed,  or anything else  * Fill out Title, Journal, Vol, & Pg. For unknown information, input 'NA'  * **DOI**: The 'digital object identifier'. If DOI is available, PDF and  URL are optional. This can be located in the article or in the  article website. Use Ctrl+F 'DOI' to find it. Some older  articles do not have a DOI.  * **URL**: Web address of the article, preferably from publisher's website  * **PDF**: URL of the PDF of the article   5. [Form for entering a new citation](https://www.betydb.org/citations/new)     ### Adding a Site  Each experiment is conducted at a unique site. In the context of BETY,  the term 'site' refers to a specific location and it is common for many  sites to be located within the same experimental station. By creating  distinct records for multiple sites, it is possible to differentiate  among independent studies.  1. Before adding a site, search to make sure that site is not already  entered in the database.  2. Search for the site given latitude and longitude  - If an institution name or city and state are given, try to  locate the site on Google Maps  - If a site name is given, try to locate the site using a  combination of Google and Google Maps  - If latitude and longitude are given in the paper, search by lat  and lon, which will return all sites within ± 1 degree lat and  long.  - If an existing site is plausibly the same site as the one  mentioned in the paper, it will be necessary to check other  papers linked to the existing site.  - Use the same site if the previous study uses the *exact same  location* and experimental setup.  - Create a new site if the study was conducted in a different  fields (i.e., not the exact same location).  - Create a new site if one study was conducted in a greenhouse  and another was conducted in a field.  - Do not use distinct sites for seed source in a common garden  experiment (see ’When not to enter a new site’ below)  3. To use an existing site, click `Edit` for the site, and then select  current citation under `Add Citation Relationships`  4. If site does not exist, add a new site.       | Descriptors | Additional Notes |   |:-----------------------------|:-------------------------  | Site Name |Site identifier, sufficient to uniquely identify the site within the paper |  | City | Nearest city |   | State | State, if in the US |  | Country | Country |   | Longitude | Decimal Form. For conversion see the equation in [Table 9](#Table 9) |  | Latitude | Decimal Form. For conversion see the equation in [Table 9](#Table 9) |  | Greenhouse | TRUE if plants were grown in a greenhouse, groth champer of post. FALSE if not used as control |  | Soil |By percent clay, sand, and silt if given |   | SOM |Soil organic matter (% by weight) |   | MAT | Mean Annual Temperature (°C) |  | MAP | Mean Annual Percipitation (mm) |  | MASL |Elevation (meters above sea level, m) |  | Notes | Site Details not included above |  | Soil Notes | Soil details not included above |  | Rooting Zone Depth | Measured in Meters (m) |  |Depth of Water Table| Measured in Meters (m) |  5. Do **not** enter a new site When plants (or seeds) are collected from multiple locations and then grown in the same location, this is called 'common garden experiment'. In this case, the location of the study is included as site information. Information about the seed source can be entered as a distinct cultivar.    ### Site Location   If latitude and longitude coordinates are not available, it is often  possible to determine the site location based on the site name, city,  and other information. One way to do this would be to look up a location  name in [Google Maps](http://maps.google.com) and then locate it on the  embedded map. Google Maps can provide decimal degrees if the LatLng  feature is enabled, which can be done  [here](http://maps.google.com/maps?showlabs=1). Google Earth can be  particularly useful in locating sites, along with their coordinates and  elevation. Alternatively, the site website or address might be found  through an internet search (e.g. Google).  Use Table 2 to determine the number of significant digits to indicate the level  of precision with which a study location is known.       | Location Detail | Degree Accuracy |  |:----------------|-------------------------:|  | City | 0.1 |  | Mile | 0.01 |  | Acre | 0.001 |  | 10 Meters | 0.0001 |      **Figure 3**: [Form for entering a new site](https://www.betydb.org/sites/new)  ### Adding a Treatment  Treatments provide a description of a study’s  treatments. Any specific information such as rate of fertilizer  application should be recorded in the managements table. In  general, managements are recorded when Yield data is collected, but not  when only Trait data is collected.  **When not to use treatment**: predictor variables that are not based on distinct managements, or that are distinguished by information already contained in the trait (e.g. site, cultivar, date fields) should not be given distinct treatments. For example, a study that compares two different species, cultivars or genotypes can be assigned the same control treatment; these categories will be distinguished by the species or cultivar field. Another example is when the observation is made at two sites: the site field will include this information.   * A treatment name is used as a categorical (rather than continuous)  variable: it should be easy to find the treatment in the paper based on  the name in the database. The treatment name does not have to indicate  the level of treatment used in a particular treatment - this information  will be included in the management table.  * It is essential that a control group is identified with each study. If  there is no experimental manipulation, then there is only one treatment. In  this case, the treatment should be named 'observational' and listed as  control. To determine the control when it is not explicitly stated, first  determine if one of the treatments is most like a background condition  or how a system would be in its non-experimental state. In the case of  crops, this could be how a farmer would be most likely to treat a crop.  **Name**: indicates type of treatment; it should be easy for anyone with the  original paper to be able to identify the treatment from its name.   **Control**: make sure to indicate if the treatment is the study 'control' by  selecting true or false   **Definition**: indicates the specifics of the treatment. It is useful for  identification purposes to use a quantified description of the  treatment even though this information can only be used for analysis  when entered as a management.       ### Adding a Management   Managements refers to something that occurs at a specific time and has a  quantity. Managements include actions that are done to a plant or  ecosystem, such as the planting density or rate of fertilization, for example.  Managements are distinct from treatments in that a treatment is used to  categorically identify an experimental treatment, whereas a management  is used to describe what has been done.  Managements are the way a treatment becomes quantified. Each treatment  is often associated with multiple managements. The combination of  managements associated with a particular treatment will distinguish it  from other treatments. The management types that can be entered into  BETY are described in [Table 3](#Table 3).  Each management may be associated with one or more treatments. For  example, in a fertilization experiment, planting, irrigation, and  herbicide managements would be applied to all plots but the  fertilization will be specific to a treatment. For a multi-year  experiment, there may be multiple entries for the same type of  management, reflecting, for example, repeated applications of herbicide  or fertilizer (for example, see [Figure 6](#Figure 6)).  *note:* At present, managements are recorded for Yields but not for  Traits, unless specifically required by the data or project manager.  To associate a management with multiple treatments, first create the  management, then edit the management and add treatment relationships.  **Dateloc**: date level of confidence, explained in [Adding a Trait](#Section_5.5) and defined in [Table 6](#Table 6)   **Mgmttype**: the name of the management being used. A list of standardized  management types can be found in [Table 3](#Table 3)   **Level**: a quantification of mgmttype   **Units**: refers to the units of the level. Units should be converted to those  in [Table 3](#Table 3)     **Figure 6**: [Form for entering and editing relationships between treatments and managements](https://www.betydb.org/treatments)    ### Adding a Trait  In general, a 'trait' is a phenotype (a characteristic that the plant  exhibits). The traits that we are primarily interested in collecting  data for are listed in [Table 6](#Table 6). Before adding trait data, it is necessary to have the citation, treatments, and site information already entered. If the correct  citation is not identified at the top of the page [Figure 8](#Figure 8). To add a new Trait,  go to the [new trait](http://www.betydb.org/traits/new)  page: `Trait` → `new`.  Presently, we are also using the Trait table to record ecosystem level  measurements other than Yield. Such ecosystem level measurements can  include leaf area index or net primary productivity, but are only  collected when required for a particular project. Most of the fields in the Traits table are also used in the Yields table. Here is a list of the fields with a brief description, followed  by more thorough explanations:  **Species**: Search for species in the database using the search box; if species  is not found   **Cultivar**: primarily used for crops; If the cultivar being used is not found in  drop-down box   **DateLOC**: Date Level of confidence. See for values.   **Mean**: mean is in units of tons per hectare per year (t/ha)   **Stat name**: is the name of the statistical method used (usually one of SE, SD, MSE,  CI, LSD, HSD, MSD). See for more details.   **Statistic**: is the value of the statistic associated with Stat name.   **N**: Always record N if provided. N is the number of experimental  replicates, often referred to as the sample size; N represents the  number of independent units within each treatment: in a field  setting, this is often the number of plots in each treatment, but in  a greenhouse, growth chamber, or pot-study this may be the number of  chambers, pots, or individual plants. Sometimes this value is not  clearly stated.   ### dateLOC  The date level of confidence (DateLOC) provides an indication of how accurately the date associated with the trait or yield observation is  known. It provides the values that should be entered in this field. If the  event occurred at a level of precision not defined by an integer in this  table, then use fractions. For example, we commonly use 5.5 to indicate a one week level of precision. If the exact year is not known, but the time of  year is, then use 91 to 97, with the second digit to indicate the information  known within the year.    **Figure 9**: [Form used to enter a new trait](https://www.betydb.org/traits/new)  #### Statistics  Our goal is to record statistics that can be used to estimate standard  deviation or standard error. Many different methods can be used to  summarize data, and this is reflected in the diversity of statistics  that are reported. An overview of these methods is given in a  description below.  Where available, direct estimates of variance are preferred, including  Standard Error (SE), sample Standard Deviation (SD), or Mean Squared  Error (MSE). SE is usually presented in the format of mean   (±SE). MSE is usually presented in a table. When  extracting SE or SD from a figure, measure from the mean to the upper or  lower bound. This is different than confidence intervals and range  statistics (described below), for which the entire range is collected.  If MSE, SD, or SE are not provided, it is possible that LSD, MSD, HSD,  or CI will be provided. These are range statistics and the most  frequently found range statistics include a Confidence Interval (95%CI),  Fisher’s Least Significant Difference (LSD), Tukey’s Honestly  Significant Difference (HSD), and Minimum Significant Difference (MSD).  Fundamentally, these methods calculate a range that indicates whether  two means are different or not, and this range uses different approaches  to penalize multiple comparisons. The important point is that these are  ranges and that we record the entire range.  Another type of statistic is a “test statistic”; most frequently there  will be an F-value that can be useful, but this should not be recorded  if MSE is available. Only if there is no other information available should you  record the P-value.  ### Adding a Yield and Covariate  The protocol for entering yield data is identical to entering data for a  trait, with a few exceptions:  1. There are no covariates associated with yield data  2. Yield data is always the dry harvestable biomass; if necessary,  moisture content can be added as a trait  Yield is equivalent to aboveground biomass on a per-area  basis, and has units of Mg ha^-1 y1   To add a new yield, go to the [new  yield](http://www.betydb.org/yields/new) page  Covariates are required for many of the traits. Covariates generally  indicate the environmental conditions under which a measurement was  made. Without covariate information, the trait data will have limited  value.  A complete list of required covariates can be found in . For all  respiration rates and photosynthetic parameters, temperature is recorded  as a covariate. Soil moisture, humidity, and other such variables that  were measured at the time of the measurement may be required in  order to standardize across studies.  When root data is recorded, the root size class needs to be entered as a  covariate. The term ’fine root’ often refers to the \(<\)2mm size class,  and in this case, the covariate `root_maximum_diameter` would be set to 2.   If the size class is a range, then the `root_minimum_diameter` can also be used.  To add a new covariate, go to the [new covariate](http:www.betydb.org/covariates/new) page  ### Adding a PFT, Species, and Cultivar  Plant functional types (PFTs) are used to group plants for statistical  modeling and analysis. PFTs are associated with both a specific set of  priors, and a subset species for which the traits and yields data  will be queried. In many cases, it is appropriate to use default PFTs  (e.g. `tempdecid` is temperate deciduous trees)  In other cases, it is necessary to define PFTs for a specific project.  For example, to query a specific set of priors or a subset of a species, a  new PFT may be defined. For example, Xiaohui Feng defined PFTs for the  species found at the EBI Farm prairie. Such project-specific PFTs can  be defined as `` `projectname`.`pft` `` (i.e. `ebifarm.c4grass` instead  of `c4grass`).  Species that are found or cultivated in the United States should be in  the Plants table. Look it up there first.  To add a new Cultivar, go to the [new  cultivar](https://www.betydb.org/cultivars/new) page: `Cultivar`  → `new`.   ## BETYdb: Bulk Data Upload  Currently the web interface does not support bulk data upload, although  this is a planned feature for BETY 2.0.  For bulk data upload, or for a complete view of the tables in BETY, a  blank spreadsheet can be found  [online](https://spreadsheets0.google.com/spreadsheet/pub?hl=en&hl=en&key=0Ai_PDCcY5g2JdFN1UDJJdjNsZk9RM0Z6bnFDdlQ0clE&output=html)  and can be downloaded in .xls format  [spreadsheet](https://spreadsheets0.google.com/spreadsheet/pub?hl=en&hl=en&key=0Ai_PDCcY5g2JdFN1UDJJdjNsZk9RM0Z6bnFDdlQ0clE&output=xls).  Contact [David LeBauer](mailto:[email protected]) or [Mike  Dietze](mailto:[email protected]) for more information about using  this method of data upload.